From 38b89e68b53a2f0b32122c4379d1748076335628 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Mon, 8 Nov 2021 17:42:44 +0100 Subject: [PATCH 01/58] DOCS: updating and improving the documentation on all functions. --- diaid_pasef/method_optimizer.py | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/diaid_pasef/method_optimizer.py b/diaid_pasef/method_optimizer.py index cea2211..b8d17f4 100644 --- a/diaid_pasef/method_optimizer.py +++ b/diaid_pasef/method_optimizer.py @@ -18,7 +18,7 @@ def optimization( zi: np.ndarray, method_conf: dict, optimizer_parameters: dict, -) -> 'optimize.OptimizeResult': +) -> 'scipy.optimize.optimize.OptimizeResult': """ Optimize dia-PASEF method parameters: Bayesian optimization using a Gaussian proces. The output values should follow a multivariate gaussian curve. @@ -101,10 +101,10 @@ def single_optimization_run( zi: np.ndarray, method_conf: dict, ) -> int: - """This function contains one method creation step. First a diaPASEF scheme + """This function contains one optimization step. First a dia-PASEF scheme is calculated based on the scan area coordinates, second the evaluation parameter is calculated to estimate the optimization potential, last - the diaPASEF method scheme is printed on top of the kernel density + the dia-PASEF method scheme is printed on top of the kernel density estimation of the used proteomics library to follow the optimization process visually. @@ -112,10 +112,7 @@ def single_optimization_run( library (pd.DataFrame): a pre-filtered data frame with unified column names containing all required precursor information. method_parameters (dict): dictionary, which includes all input parameters - for creating a diaPASEF method (e.g., m/z-range, ion mobility-range, - number of diaPASEF scans, number of ion mobility steps, the overlap of - the diaPASEF windows, a shift of the final window scheme in the ion - mobility axis to account for the blind spot of the + for creating a dia-PASEF method. evaluation_parameter (str): parameter, which was selected for optimization (e.g., all precursors, all doubly charged precursors). dim (list): y-coordinates of the scan area = A1, A2, B1, B2. x-coordinate @@ -164,13 +161,14 @@ def single_optimization_run( ) return result + def write_tested_parameters_into_csv( opt_result: pd.DataFrame, # scipy.optimize.optimize.OptimizeResult optimizer_parameters: str, method_conf: dict, ) -> None: - """This function writes all important parameters into a .csv that were used - during the method optimization step. + """This function writes all important parameters that were used during the + method optimization step into a .csv file. Parameters: opt_result (pd.DataFrame): a dictionary containing all input and output From 7b1457606490e3f9d7d3c031a296605086c90eb9 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 16 Nov 2021 08:50:13 +0100 Subject: [PATCH 02/58] FEAT: calculate time of functions with import time --- diaid_pasef/cli.py | 1 + 1 file changed, 1 insertion(+) diff --git a/diaid_pasef/cli.py b/diaid_pasef/cli.py index c35378d..2f01d96 100644 --- a/diaid_pasef/cli.py +++ b/diaid_pasef/cli.py @@ -3,6 +3,7 @@ # external import click +import time # local import diaid_pasef From ab012e9ea1fde53cb2b23505cf150adac1af0e49 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 16 Nov 2021 08:51:13 +0100 Subject: [PATCH 03/58] CHORE: do not display all precursors FEAT: histogram plot also for IM --- diaid_pasef/graphs.py | 71 +++++++++++++++++++++++++++++++++++++------ 1 file changed, 61 insertions(+), 10 deletions(-) diff --git a/diaid_pasef/graphs.py b/diaid_pasef/graphs.py index 4110b31..ec72515 100644 --- a/diaid_pasef/graphs.py +++ b/diaid_pasef/graphs.py @@ -101,14 +101,14 @@ def plot_precursor_distribution_as_histogram( """ colors = ['#7AC7C9', '#4EA7BB', '#267FA5'] - hist = sns.distplot( - library_subset['mz'], - hist=True, - kde=False, - rug=False, - color=colors[0], - label='all precursors' - ) +# hist = sns.distplot( +# library_subset['mz'], +# hist=True, +# kde=False, +# rug=False, +# color=colors[0], +# label='all precursors' +# ) hist = sns.distplot( library_subset['mz'][library_subset['Charge'] == 2], hist=True, @@ -135,6 +135,57 @@ def plot_precursor_distribution_as_histogram( hist.figure.savefig(file_name, bbox_inches='tight', pad_inches=0, dpi=300) plt.clf() +def plot_precursor_distribution_as_histogrami_IM( + library_subset: pd.DataFrame, + plot_parameters: dict, + file_name: str, +) -> None: + """Plot histogram with the precursor distribution in the m/z dimension + sorted by charge state. + + Parameters: + library_subset (pd.DataFrame): pre-filtered data frame with unified column + names. + plot_parameters (dict): dictionary, which contains all input parameters for + creating plots (e.g., displayed m/z-range, ion mobility-range) + file_name: file path and file name where the plot should be saved. + """ + + colors = ['#7AC7C9', '#4EA7BB', '#267FA5'] +# hist = sns.distplot( +# library_subset['mz'], +# hist=True, +# kde=False, +# rug=False, +# color=colors[0], +# label='all precursors' +# ) + hist = sns.distplot( + library_subset['IM'][library_subset['Charge'] == 2], + hist=True, + kde=False, + rug=False, + color=colors[1], + label='doubly charged precursors' + ) + hist = sns.distplot( + library_subset['IM'][library_subset['Charge'] == 3], + hist=True, + kde=False, + rug=False, + color=colors[2], + label='triply charged precursors' + ) + hist.set( + xlim=(plot_parameters["plot_IM"][0], + plot_parameters["plot_IM"][1]) + ) + plt.ylabel('No. of precursors') + plt.legend(bbox_to_anchor=(0.8, 1.42)) + plt.xlabel('$\mathregular{\it{IM}}$') + hist.figure.savefig(file_name, bbox_inches='tight', pad_inches=0, dpi=300) + plt.clf() + def plot_density_and_method( df: pd.DataFrame, @@ -164,7 +215,7 @@ def plot_density_and_method( plt.pcolormesh( xi, yi, zi.reshape(xi.shape), vmax=0.02, - cmap=plt.cm.viridis + cmap=plt.cm.Greys ) pc = PatchCollection( rect, @@ -176,7 +227,7 @@ def plot_density_and_method( ax.set_xlim(plot_parameters["plot_mz"][0], plot_parameters["plot_mz"][1]) ax.set_ylim(plot_parameters["plot_IM"][0], plot_parameters["plot_IM"][1]) - ax.set_facecolor('#440256') + ax.set_facecolor('white') plt.xlabel('$\mathregular{\it{m/z}}$') plt.ylabel('$\mathregular{1/K_0}$ [Vs $\mathregular{cm^{-2}}$]') plt.colorbar().set_label('Density', labelpad=-28, y=1.14, rotation=0) From a4949675ea6248f0f01f66ab128f76a55d29ed1f Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 16 Nov 2021 08:51:40 +0100 Subject: [PATCH 04/58] CHORE: no changes --- diaid_pasef/graphs_for_gui.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/diaid_pasef/graphs_for_gui.py b/diaid_pasef/graphs_for_gui.py index 6ce9cce..105a25a 100644 --- a/diaid_pasef/graphs_for_gui.py +++ b/diaid_pasef/graphs_for_gui.py @@ -19,7 +19,7 @@ ) -qmesh = desnity_plot_GUI(xi, yi, zi) +qmesh = density_plot_GUI(xi, yi, zi) plot_window_scheme_on_top_of_density(df_parameters_final, qmesh, plot_parameters) @@ -101,7 +101,7 @@ def boxes_GUI( return rect -def desnity_plot_GUI( +def density_plot_GUI( xi: np.ndarray, yi: np.ndarray, zi: np.ndarray From ad0181a1e1938e510be8c1f3dc4195d44f047b29 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 16 Nov 2021 08:52:43 +0100 Subject: [PATCH 05/58] CHORE: generalize default parameter file --- diaid_pasef/lib/default_parameters.json | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/diaid_pasef/lib/default_parameters.json b/diaid_pasef/lib/default_parameters.json index 57ed0c1..979ae46 100644 --- a/diaid_pasef/lib/default_parameters.json +++ b/diaid_pasef/lib/default_parameters.json @@ -1,6 +1,6 @@ { "input": { - "save_at" : "output_diaid_pasef_proteomics_diAID-PASEF_test", + "save_at" : "output", "PTM": "None", "library_name": "D:/diaid_pasef/diaid_pasef/static/AlphaPept_results.csv", "analysis_software": "AlphaPept", @@ -8,9 +8,9 @@ }, "method_parameters": { "mz": [300, 1200], - "ion_mobility": [0.6, 1.6], + "ion_mobility": [0.75, 1.3], "num_dia_pasef_scans": 5, - "im_steps": 3, + "im_steps": 2, "overlap": 0, "shift_of_final_method": 0.022, "scan_area_A1_A2_B1_B2_only_used_for_create": [0.68, 1.04, 0.9, 1.30] @@ -18,7 +18,7 @@ "graphs": { "plot_mz": [250, 1250], "plot_IM": [0.6, 1.6], - "numbins": 30, + "numbins": 20, "window_frame_color": "black", "window_color": "white", "window_transparency": 0.5 @@ -26,9 +26,9 @@ "optimizer": { "optimizer": "Gauss", "n_random_starts": null, - "n_calls": 5, - "n_start": 2, - "initial_points": 2, + "n_calls": 200, + "n_start": 20, + "initial_points": 20, "YA1": [0.5, 0.9], "YA2": [0.6, 1.0], "YB1": [0.9, 1.5], From b809870061278d6aac330d90eb7f82dc37f2df69 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 16 Nov 2021 08:55:44 +0100 Subject: [PATCH 06/58] CHORE: calculate timings --- diaid_pasef/main.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/diaid_pasef/main.py b/diaid_pasef/main.py index d04299f..50ca3b1 100644 --- a/diaid_pasef/main.py +++ b/diaid_pasef/main.py @@ -3,6 +3,17 @@ from diaid_pasef import method_evaluation from diaid_pasef import graphs +# import logging +# +# logger = logging.getLogger('root') +# formatter = logging.Formatter( +# '%(asctime)s> %(message)s', "%Y-%m-%d %H:%M:%S" +# ) +# logger.setLevel(logging.INFO) +# logger.setFormatter(formatter) + +import time + # for data manipulation: import pandas as pd @@ -68,6 +79,13 @@ def library_information( save_at + '/input_library/Histogram_precursor_distribution_in_library.pdf' ) + + #graphs.plot_precursor_distribution_as_histogrami_IM( + # library, method_conf["graphs"], + # save_at + + # '/input_library/Histogram_precursor_distribution_in_library_IM.pdf' + # ) + graphs.plot_density( xi, yi, @@ -113,6 +131,7 @@ def precursor_within_scan_area( method_parameters["mz"], method_parameters["ion_mobility"] ) + print(time.asctime()) print(dict_precursors_within_scan_area) pd.DataFrame({ From 7d2ef3ee273d34397f1122822230d791894ac045 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 15:17:08 +0100 Subject: [PATCH 07/58] FIX: rename diaid_pasef to py_diaid --- diaid_pasef/lib/default_parameters.json | 38 ----- py_diaid.egg-info/PKG-INFO | 190 ------------------------ py_diaid.egg-info/SOURCES.txt | 47 ------ py_diaid.egg-info/dependency_links.txt | 1 - py_diaid.egg-info/entry_points.txt | 2 - py_diaid.egg-info/requires.txt | 75 ---------- py_diaid.egg-info/top_level.txt | 1 - py_diaid/lib/default_parameters.json | 2 +- 8 files changed, 1 insertion(+), 355 deletions(-) delete mode 100644 diaid_pasef/lib/default_parameters.json delete mode 100644 py_diaid.egg-info/PKG-INFO delete mode 100644 py_diaid.egg-info/SOURCES.txt delete mode 100644 py_diaid.egg-info/dependency_links.txt delete mode 100644 py_diaid.egg-info/entry_points.txt delete mode 100644 py_diaid.egg-info/requires.txt delete mode 100644 py_diaid.egg-info/top_level.txt diff --git a/diaid_pasef/lib/default_parameters.json b/diaid_pasef/lib/default_parameters.json deleted file mode 100644 index 948e33d..0000000 --- a/diaid_pasef/lib/default_parameters.json +++ /dev/null @@ -1,38 +0,0 @@ -{ - "input": { - "save_at" : "output", - "PTM": "None", - "library_name": "D:/py_diaid/py_diaid/static/AlphaPept_results.csv", - "analysis_software": "AlphaPept", - "diaPASEF_method_only_used_for_evaluate": "D:/py_diaid/py_diaid/static/DIAParameterspy3TC.txt" - }, - "method_parameters": { - "mz": [300, 1200], - "ion_mobility": [0.75, 1.3], - "num_dia_pasef_scans": 5, - "im_steps": 2, - "overlap": 0, - "shift_of_final_method": 0.022, - "scan_area_A1_A2_B1_B2_only_used_for_create": [0.68, 1.04, 0.9, 1.30] - }, - "graphs": { - "plot_mz": [250, 1250], - "plot_IM": [0.6, 1.6], - "numbins": 20, - "window_frame_color": "black", - "window_color": "white", - "window_transparency": 0.5 - }, - "optimizer": { - "optimizer": "Gauss", - "n_random_starts": null, - "n_calls": 200, - "n_start": 20, - "initial_points": 20, - "YA1": [0.5, 0.9], - "YA2": [0.6, 1.0], - "YB1": [0.9, 1.5], - "YB2": [1.0, 1.8], - "evaluation_parameter": "No. of covered precursors" - } -} diff --git a/py_diaid.egg-info/PKG-INFO b/py_diaid.egg-info/PKG-INFO deleted file mode 100644 index 5526fa6..0000000 --- a/py_diaid.egg-info/PKG-INFO +++ /dev/null @@ -1,190 +0,0 @@ -Metadata-Version: 2.1 -Name: diaid-pasef -Version: 0.0.1 -Summary: An open-source Python package of the AlphaPept ecosystem -Home-page: https://github.com/MannLabs/py_diaid -Author: Patricia Skowronek, Sander Willems, Eugenia Voytik -Author-email: opensource@alphapept.com -License: Apache -Project-URL: Mann Labs at MPIB, https://www.biochem.mpg.de/mann -Project-URL: GitHub, https://github.com/MannLabs/py_diaid -Description: ![Pip installation](https://github.com/MannLabs/py_diaid/workflows/Default%20installation%20and%20tests/badge.svg) - ![GUI and PyPi releases](https://github.com/MannLabs/py_diaid/workflows/Publish%20on%20PyPi%20and%20release%20on%20GitHub/badge.svg) - - # diAID-PASEF - An open-source Python package of the AlphaPept ecosystem from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann). To enable all hyperlinks in this document, please view it at [GitHub](https://github.com/MannLabs/py_diaid). - - * [**About**](#about) - * [**License**](#license) - * [**Installation**](#installation) - * [**One-click GUI**](#one-click-gui) - * [**Pip installer**](#pip) - * [**Developer installer**](#developer) - * [**Usage**](#usage) - * [**GUI**](#gui) - * [**CLI**](#cli) - * [**Python and jupyter notebooks**](#python-and-jupyter-notebooks) - * [**Troubleshooting**](#troubleshooting) - * [**Citations**](#citations) - * [**How to contribute**](#how-to-contribute) - * [**Changelog**](#changelog) - - --- - ## About - - An open-source Python package of the AlphaPept ecosystem from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann). - - --- - ## License - - diAID-PASEF was developed by the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann) and is freely available with an [Apache License](LICENSE.txt). External Python packages (available in the [requirements](requirements) folder) have their own licenses, which can be consulted on their respective websites. - - --- - ## Installation - - diAID-PASEF can be installed and used on all major operating systems (Windows, macOS and Linux). - There are three different types of installation possible: - - * [**One-click GUI installer:**](#one-click-gui) Choose this installation if you only want the GUI and/or keep things as simple as possible. - * [**Pip installer:**](#pip) Choose this installation if you want to use diAID-PASEF as a Python package in an existing Python 3.8 environment (e.g. a Jupyter notebook). If needed, the GUI and CLI can be installed with pip as well. - * [**Developer installer:**](#developer) Choose this installation if you are familiar with CLI tools, [conda](https://docs.conda.io/en/latest/) and Python. This installation allows access to all available features of diAID-PASEF and even allows to modify its source code directly. Generally, the developer version of diAID-PASEF outperforms the precompiled versions which makes this the installation of choice for high-throughput experiments. - - ### One-click GUI - - The GUI of diAID-PASEF is a completely stand-alone tool that requires no knowledge of Python or CLI tools. Click on one of the links below to download the latest release for: - - * [**Windows**](https://github.com/MannLabs/py_diaid/releases/latest/download/py_diaid_gui_installer_windows.exe) - * [**macOS**](https://github.com/MannLabs/py_diaid/releases/latest/download/py_diaid_gui_installer_macos.pkg) - * [**Linux**](https://github.com/MannLabs/py_diaid/releases/latest/download/py_diaid_gui_installer_linux.deb) - - Older releases remain available on the [release page](https://github.com/MannLabs/py_diaid/releases), but no backwards compatibility is guaranteed. - - ### Pip - - diAID-PASEF can be installed in an existing Python 3.8 environment with a single `bash` command. *This `bash` command can also be run directly from within a Jupyter notebook by prepending it with a `!`*: - - ```bash - pip install py_diaid - ``` - - Installing diAID-PASEF like this avoids conflicts when integrating it in other tools, as this does not enforce strict versioning of dependancies. However, if new versions of dependancies are released, they are not guaranteed to be fully compatible with diAID-PASEF. While this should only occur in rare cases where dependencies are not backwards compatible, you can always force diAID-PASEF to use dependancy versions which are known to be compatible with: - - ```bash - pip install "py_diaid[stable]" - ``` - - NOTE: You might need to run `pip install pip==21.0` before installing diAID-PASEF like this. Also note the double quotes `"`. - - For those who are really adventurous, it is also possible to directly install any branch (e.g. `@development`) with any extras (e.g. `#egg=py_diaid[stable,development-stable]`) from GitHub with e.g. - - ```bash - pip install "git+https://github.com/MannLabs/py_diaid.git@development#egg=py_diaid[stable,development-stable]" - ``` - - ### Developer - - diAID-PASEF can also be installed in editable (i.e. developer) mode with a few `bash` commands. This allows to fully customize the software and even modify the source code to your specific needs. When an editable Python package is installed, its source code is stored in a transparent location of your choice. While optional, it is advised to first (create and) navigate to e.g. a general software folder: - - ```bash - mkdir ~/folder/where/to/install/software - cd ~/folder/where/to/install/software - ``` - - ***The following commands assume you do not perform any additional `cd` commands anymore***. - - Next, download the diAID-PASEF repository from GitHub either directly or with a `git` command. This creates a new diAID-PASEF subfolder in your current directory. - - ```bash - git clone https://github.com/MannLabs/py_diaid.git - ``` - - For any Python package, it is highly recommended to use a separate [conda virtual environment](https://docs.conda.io/en/latest/), as otherwise *dependancy conflicts can occur with already existing packages*. - - ```bash - conda create --name py_diaid python=3.8 -y - conda activate py_diaid - ``` - - Finally, diAID-PASEF and all its [dependancies](requirements) need to be installed. To take advantage of all features and allow development (with the `-e` flag), this is best done by also installing the [development dependencies](requirements/requirements_development.txt) instead of only the [core dependencies](requirements/requirements.txt): - - ```bash - pip install -e "./py_diaid[development]" - ``` - - By default this installs loose dependancies (no explicit versioning), although it is also possible to use stable dependencies (e.g. `pip install -e "./py_diaid[stable,development-stable]"`). - - ***By using the editable flag `-e`, all modifications to the [diAID-PASEF source code folder](py_diaid) are directly reflected when running diAID-PASEF. Note that the diAID-PASEF folder cannot be moved and/or renamed if an editable version is installed.*** - - --- - ## Usage - - There are three ways to use diAID-PASEF: - - * [**GUI**](#gui) - * [**CLI**](#cli) - * [**Python**](#python-and-jupyter-notebooks) - - NOTE: The first time you use a fresh installation of diAID-PASEF, it is often quite slow because some functions might still need compilation on your local operating system and architecture. Subsequent use should be a lot faster. - - ### GUI - - If the GUI was not installed through a one-click GUI installer, it can be activate with the following `bash` command: - - ```bash - py_diaid gui - ``` - - Note that this needs to be prepended with a `!` when you want to run this from within a Jupyter notebook. When the command is run directly from the command-line, make sure you use the right environment (activate it with e.g. `conda activate py_diaid` or set an alias to the binary executable (can be obtained with `where py_diaid` or `which py_diaid`)). - - ### CLI - - The CLI can be run with the following command (after activating the `conda` environment with `conda activate py_diaid` or if an alias was set to the py_diaid executable): - - ```bash - py_diaid -h - ``` - - It is possible to get help about each function and their (required) parameters by using the `-h` flag. - - ### Python and Jupyter notebooks - - diAID-PASEF can be imported as a Python package into any Python script or notebook with the command `import py_diaid`. - - A brief [Jupyter notebook tutorial](nbs/tutorial.ipynb) on how to use the API is also present in the [nbs folder](nbs). - - --- - ## Troubleshooting - - In case of issues, check out the following: - - * [Issues](https://github.com/MannLabs/py_diaid/issues): Try a few different search terms to find out if a similar problem has been encountered before - * [Discussions](https://github.com/MannLabs/py_diaid/discussions): Check if your problem or feature requests has been discussed before. - - --- - ## Citations - - There are currently no plans to draft a manuscript. - - --- - ## How to contribute - - If you like this software, you can give us a [star](https://github.com/MannLabs/py_diaid/stargazers) to boost our visibility! All direct contributions are also welcome. Feel free to post a new [issue](https://github.com/MannLabs/py_diaid/issues) or clone the repository and create a [pull request](https://github.com/MannLabs/py_diaid/pulls) with a new branch. For an even more interactive participation, check out the [discussions](https://github.com/MannLabs/py_diaid/discussions) and the [the Contributors License Agreement](misc/CLA.md). - - --- - ## Changelog - - See the [HISTORY.md](HISTORY.md) for a full overview of the changes made in each version. - -Keywords: bioinformatics,software,AlphaPept ecosystem,ms,mass spectrometry,bruker,timsTOF,proteomics,bioinformatics,diaPASEF -Platform: UNKNOWN -Classifier: Development Status :: 1 - Planning -Classifier: Intended Audience :: Science/Research -Classifier: License :: OSI Approved :: Apache Software License -Classifier: Operating System :: OS Independent -Classifier: Programming Language :: Python :: 3 -Classifier: Topic :: Scientific/Engineering :: Bio-Informatics -Requires-Python: >=3.8,<3.10 -Description-Content-Type: text/markdown -Provides-Extra: development-stable -Provides-Extra: development -Provides-Extra: stable diff --git a/py_diaid.egg-info/SOURCES.txt b/py_diaid.egg-info/SOURCES.txt deleted file mode 100644 index 48b62b2..0000000 --- a/py_diaid.egg-info/SOURCES.txt +++ /dev/null @@ -1,47 +0,0 @@ -LICENSE.txt -MANIFEST.in -README.md -setup.py -py_diaid/__init__.py -py_diaid/cli.py -py_diaid/graphs.py -py_diaid/graphs_for_gui.py -py_diaid/gui.py -py_diaid/loader.py -py_diaid/main.py -py_diaid/method_creator.py -py_diaid/method_evaluation.py -py_diaid/method_optimizer.py -py_diaid.egg-info/PKG-INFO -py_diaid.egg-info/SOURCES.txt -py_diaid.egg-info/dependency_links.txt -py_diaid.egg-info/entry_points.txt -py_diaid.egg-info/requires.txt -py_diaid.egg-info/top_level.txt -py_diaid/__pycache__/__init__.cpython-38.pyc -py_diaid/__pycache__/__init__.cpython-39.pyc -py_diaid/__pycache__/additions_to_main.cpython-38.pyc -py_diaid/__pycache__/cli.cpython-38.pyc -py_diaid/__pycache__/cli.cpython-39.pyc -py_diaid/__pycache__/graphs.cpython-38.pyc -py_diaid/__pycache__/graphs.cpython-39.pyc -py_diaid/__pycache__/gui.cpython-38.pyc -py_diaid/__pycache__/gui.cpython-39.pyc -py_diaid/__pycache__/loader.cpython-38.pyc -py_diaid/__pycache__/loader.cpython-39.pyc -py_diaid/__pycache__/main.cpython-38.pyc -py_diaid/__pycache__/main.cpython-39.pyc -py_diaid/__pycache__/method_creator.cpython-38.pyc -py_diaid/__pycache__/method_creator.cpython-39.pyc -py_diaid/__pycache__/method_evaluation.cpython-38.pyc -py_diaid/__pycache__/method_evaluation.cpython-39.pyc -py_diaid/__pycache__/method_optimizer.cpython-38.pyc -py_diaid/__pycache__/method_optimizer.cpython-39.pyc -py_diaid/docs/manual.pdf -py_diaid/img/github.png -py_diaid/img/max-planck-gesellschaft.jpg -py_diaid/img/mpi_logo.png -py_diaid/lib/default_parameters.json -py_diaid/static/AlphaPept_results.csv -py_diaid/static/DIAParameterspy3TC.txt -py_diaid/style/dashboard_style.css diff --git a/py_diaid.egg-info/dependency_links.txt b/py_diaid.egg-info/dependency_links.txt deleted file mode 100644 index 8b13789..0000000 --- a/py_diaid.egg-info/dependency_links.txt +++ /dev/null @@ -1 +0,0 @@ - diff --git a/py_diaid.egg-info/entry_points.txt b/py_diaid.egg-info/entry_points.txt deleted file mode 100644 index 181a68f..0000000 --- a/py_diaid.egg-info/entry_points.txt +++ /dev/null @@ -1,2 +0,0 @@ -[console_scripts] -py_diaid = py_diaid.cli:run diff --git a/py_diaid.egg-info/requires.txt b/py_diaid.egg-info/requires.txt deleted file mode 100644 index 6743729..0000000 --- a/py_diaid.egg-info/requires.txt +++ /dev/null @@ -1,75 +0,0 @@ -click -jupyter -jupyter_contrib_nbextensions -pyinstaller -autodocsumm -sphinx-rtd-theme -twine -bumpversion -pipdeptree -ipykernel -tqdm -psutil -panel -pandas -matplotlib -seaborn -scikit-optimize - -[:sys_platform == "win32"] -pywin32==225 - -[development] -jupyter -jupyter_contrib_nbextensions -pyinstaller -autodocsumm -sphinx-rtd-theme -twine -bumpversion -pipdeptree -ipykernel -tqdm -psutil -panel -pandas -matplotlib -seaborn -scikit-optimize - -[development-stable] -jupyter==1.0.0 -jupyter_contrib_nbextensions==0.5.1 -pyinstaller==4.2 -autodocsumm==0.2.6 -sphinx-rtd-theme==0.5.2 -twine==3.4.1 -bumpversion==0.6.0 -pipdeptree==2.1.0 -ipykernel==6.4.0 -tqdm==4.61.1 -psutil==5.8.0 -panel==0.12.4 -pandas==1.3.4 -matplotlib==3.4.3 -seaborn==0.11.2 -scikit-optimize==0.9.0 - -[stable] -click==8.0.1 -jupyter==1.0.0 -jupyter_contrib_nbextensions==0.5.1 -pyinstaller==4.2 -autodocsumm==0.2.6 -sphinx-rtd-theme==0.5.2 -twine==3.4.1 -bumpversion==0.6.0 -pipdeptree==2.1.0 -ipykernel==6.4.0 -tqdm==4.61.1 -psutil==5.8.0 -panel==0.12.4 -pandas==1.3.4 -matplotlib==3.4.3 -seaborn==0.11.2 -scikit-optimize==0.9.0 diff --git a/py_diaid.egg-info/top_level.txt b/py_diaid.egg-info/top_level.txt deleted file mode 100644 index 615c4d3..0000000 --- a/py_diaid.egg-info/top_level.txt +++ /dev/null @@ -1 +0,0 @@ -py_diaid diff --git a/py_diaid/lib/default_parameters.json b/py_diaid/lib/default_parameters.json index 55d6bb4..3e96f75 100644 --- a/py_diaid/lib/default_parameters.json +++ b/py_diaid/lib/default_parameters.json @@ -2,7 +2,7 @@ "input": { "save_at": "D:\\output_test2", "PTM": "None", - "library_name": "D:\\Input_for_diaid_pasef\\library21min24fractions.tsv", + "library_name": "D:\\Input_for_py_diaid\\library21min24fractions.tsv", "analysis_software": "MS_Fragger", "diaPASEF_method_only_used_for_evaluate": "D:/py_diaid/py_diaid/static/DIAParameterspy3TC.txt" }, From b9a1502d26d2b8275a205542a109c4fa14d59810 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 15:22:53 +0100 Subject: [PATCH 08/58] FIX: deleted unwanted changes --- py_diaid/cli.py | 1 - py_diaid/graphs.py | 53 ++-------------------------------------------- py_diaid/main.py | 18 ---------------- 3 files changed, 2 insertions(+), 70 deletions(-) diff --git a/py_diaid/cli.py b/py_diaid/cli.py index 46a97c0..ab90855 100644 --- a/py_diaid/cli.py +++ b/py_diaid/cli.py @@ -3,7 +3,6 @@ # external import click -import time # local import py_diaid diff --git a/py_diaid/graphs.py b/py_diaid/graphs.py index 0cd2de3..2c931d6 100644 --- a/py_diaid/graphs.py +++ b/py_diaid/graphs.py @@ -140,56 +140,7 @@ def plot_precursor_distribution_as_histogram( else: plt.clf() -def plot_precursor_distribution_as_histogrami_IM( - library_subset: pd.DataFrame, - plot_parameters: dict, - file_name: str, -) -> None: - """Plot histogram with the precursor distribution in the m/z dimension - sorted by charge state. - - Parameters: - library_subset (pd.DataFrame): pre-filtered data frame with unified column - names. - plot_parameters (dict): dictionary, which contains all input parameters for - creating plots (e.g., displayed m/z-range, ion mobility-range) - file_name: file path and file name where the plot should be saved. - """ - colors = ['#7AC7C9', '#4EA7BB', '#267FA5'] -# hist = sns.distplot( -# library_subset['mz'], -# hist=True, -# kde=False, -# rug=False, -# color=colors[0], -# label='all precursors' -# ) - hist = sns.distplot( - library_subset['IM'][library_subset['Charge'] == 2], - hist=True, - kde=False, - rug=False, - color=colors[1], - label='doubly charged precursors' - ) - hist = sns.distplot( - library_subset['IM'][library_subset['Charge'] == 3], - hist=True, - kde=False, - rug=False, - color=colors[2], - label='triply charged precursors' - ) - hist.set( - xlim=(plot_parameters["plot_IM"][0], - plot_parameters["plot_IM"][1]) - ) - plt.ylabel('No. of precursors') - plt.legend(bbox_to_anchor=(0.8, 1.42)) - plt.xlabel('$\mathregular{\it{IM}}$') - hist.figure.savefig(file_name, bbox_inches='tight', pad_inches=0, dpi=300) - plt.clf() def plot_density_and_method( @@ -220,7 +171,7 @@ def plot_density_and_method( plt.pcolormesh( xi, yi, zi.reshape(xi.shape), vmax=0.02, - cmap=plt.cm.Greys + cmap=plt.cm.viridis ) pc = PatchCollection( rect, @@ -232,7 +183,7 @@ def plot_density_and_method( ax.set_xlim(plot_parameters["plot_mz"][0], plot_parameters["plot_mz"][1]) ax.set_ylim(plot_parameters["plot_IM"][0], plot_parameters["plot_IM"][1]) - ax.set_facecolor('white') + ax.set_facecolor('#440256') plt.xlabel('$\mathregular{\it{m/z}}$') plt.ylabel('$\mathregular{1/K_0}$ [Vs $\mathregular{cm^{-2}}$]') plt.colorbar().set_label('Density', labelpad=-28, y=1.14, rotation=0) diff --git a/py_diaid/main.py b/py_diaid/main.py index c262b1e..2ad432c 100644 --- a/py_diaid/main.py +++ b/py_diaid/main.py @@ -3,17 +3,6 @@ from py_diaid import method_evaluation from py_diaid import graphs -# import logging -# -# logger = logging.getLogger('root') -# formatter = logging.Formatter( -# '%(asctime)s> %(message)s', "%Y-%m-%d %H:%M:%S" -# ) -# logger.setLevel(logging.INFO) -# logger.setFormatter(formatter) - -import time - # for data manipulation: import pandas as pd @@ -80,12 +69,6 @@ def library_information( '/input_library/Histogram_precursor_distribution_in_library.pdf' ) - #graphs.plot_precursor_distribution_as_histogrami_IM( - # library, method_conf["graphs"], - # save_at + - # '/input_library/Histogram_precursor_distribution_in_library_IM.pdf' - # ) - graphs.plot_density( xi, yi, @@ -131,7 +114,6 @@ def precursor_within_scan_area( method_parameters["mz"], method_parameters["ion_mobility"] ) - print(time.asctime()) print(dict_precursors_within_scan_area) pd.DataFrame({ From 8ca0b9eb2effd3b0423d7240c3057b6bca2f1e17 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 15:38:19 +0100 Subject: [PATCH 09/58] FIX: rename diaid_pasef to py_diaid --- py_diaid/cli.py | 2 +- release/one_click_macos_gui/Resources/conclusion.html | 2 +- release/one_click_macos_gui/Resources/welcome.html | 6 +++--- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/py_diaid/cli.py b/py_diaid/cli.py index ab90855..492eea5 100644 --- a/py_diaid/cli.py +++ b/py_diaid/cli.py @@ -36,7 +36,7 @@ @click.pass_context @click.version_option(py_diaid.__version__, "-v", "--version") def run(ctx, **kwargs): - name = f"diAID-PASEF {py_diaid.__version__}" + name = f"py_diAID {py_diaid.__version__}" click.echo("*" * (len(name) + 4)) click.echo(f"* {name} *") click.echo("*" * (len(name) + 4)) diff --git a/release/one_click_macos_gui/Resources/conclusion.html b/release/one_click_macos_gui/Resources/conclusion.html index 8fcfe60..1444839 100644 --- a/release/one_click_macos_gui/Resources/conclusion.html +++ b/release/one_click_macos_gui/Resources/conclusion.html @@ -7,7 +7,7 @@

py_diAID

-

Thank you for installing diAID-PASEF.

+

Thank you for installing py_diAID.

diff --git a/release/one_click_macos_gui/Resources/welcome.html b/release/one_click_macos_gui/Resources/welcome.html index f53d7f8..22c2a01 100644 --- a/release/one_click_macos_gui/Resources/welcome.html +++ b/release/one_click_macos_gui/Resources/welcome.html @@ -5,9 +5,9 @@
-

diAID-PASEF

-

diAID-PASEF is an open-source Python package of the AlphaPept ecosystem.

-

diAID-PASEF was developed by the Mann Labs at the Max Planck Institute of Biochemistry and is freely available with an Apache License. Since diAID-PASEF uses external Python packages, additional third-party licenses are applicable.

+

py_diAID

+

py_diAID is an open-source Python package of the AlphaPept ecosystem.

+

py_diAID was developed by the Mann Labs at the Max Planck Institute of Biochemistry and is freely available with an Apache License. Since diAID-PASEF uses external Python packages, additional third-party licenses are applicable.

From b9429f86c86472cdb19b24ef6ef7f749d500ef15 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 16:09:53 +0100 Subject: [PATCH 10/58] FIX: rename py_diaid to pydiaid --- .github/ISSUE_TEMPLATE/bug-report.md | 4 +- .github/workflows/publish_and_release.yml | 18 +- .gitignore | 10 +- MANIFEST.in | 4 +- README.md | 50 +- misc/bumpversion.cfg | 4 +- misc/check_version.sh | 4 +- misc/loose_pip_install.sh | 6 +- misc/stable_pip_install.sh | 6 +- nbs/tutorial.ipynb | 4 +- py_diaid/lib/default_parameters.json | 73 - py_diaid/static/AlphaPept_results.csv | 20093 ---------------- py_diaid/static/DIAParameterspy3TC.txt | 68 - {py_diaid => pydiaid}/__init__.py | 6 +- {py_diaid => pydiaid}/cli.py | 16 +- {py_diaid => pydiaid}/docs/manual.pdf | Bin {py_diaid => pydiaid}/graphs.py | 2 +- {py_diaid => pydiaid}/graphs_for_gui.py | 0 {py_diaid => pydiaid}/gui.py | 60 +- {py_diaid => pydiaid}/img/github.png | Bin .../img/max-planck-gesellschaft.jpg | Bin {py_diaid => pydiaid}/img/mpi_logo.png | Bin {py_diaid => pydiaid}/loader.py | 0 {py_diaid => pydiaid}/main.py | 8 +- {py_diaid => pydiaid}/method_creator.py | 0 {py_diaid => pydiaid}/method_evaluation.py | 0 {py_diaid => pydiaid}/method_optimizer.py | 6 +- .../style/dashboard_style.css | 0 release/one_click_linux_gui/control | 4 +- .../create_installer_linux.sh | 20 +- release/one_click_macos_gui/Info.plist | 4 +- .../create_installer_macos.sh | 24 +- release/one_click_macos_gui/py_diaid_terminal | 2 +- .../create_installer_windows.sh | 10 +- .../py_diaid_innoinstaller.iss | 12 +- release/pyinstaller/py_diaid.spec | 10 +- release/pyinstaller/py_diaid_pyinstaller.py | 4 +- release/pypi/install_pypi_wheel.sh | 8 +- release/pypi/install_test_pypi_wheel.sh | 8 +- release/pypi/prepare_pypi_wheel.sh | 4 +- setup.py | 2 +- tests/run_tests.sh | 2 +- tests/test_cli.py | 4 +- tests/test_gui.py | 4 +- 44 files changed, 165 insertions(+), 20399 deletions(-) delete mode 100644 py_diaid/lib/default_parameters.json delete mode 100644 py_diaid/static/AlphaPept_results.csv delete mode 100644 py_diaid/static/DIAParameterspy3TC.txt rename {py_diaid => pydiaid}/__init__.py (92%) rename {py_diaid => pydiaid}/cli.py (97%) rename {py_diaid => pydiaid}/docs/manual.pdf (100%) rename {py_diaid => pydiaid}/graphs.py (99%) rename {py_diaid => pydiaid}/graphs_for_gui.py (100%) rename {py_diaid => pydiaid}/gui.py (96%) rename {py_diaid => pydiaid}/img/github.png (100%) rename {py_diaid => pydiaid}/img/max-planck-gesellschaft.jpg (100%) rename {py_diaid => pydiaid}/img/mpi_logo.png (100%) rename {py_diaid => pydiaid}/loader.py (100%) rename {py_diaid => pydiaid}/main.py (98%) rename {py_diaid => pydiaid}/method_creator.py (100%) rename {py_diaid => pydiaid}/method_evaluation.py (100%) rename {py_diaid => pydiaid}/method_optimizer.py (98%) rename {py_diaid => pydiaid}/style/dashboard_style.css (100%) diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-report.md index c38895c..138741f 100644 --- a/.github/ISSUE_TEMPLATE/bug-report.md +++ b/.github/ISSUE_TEMPLATE/bug-report.md @@ -8,7 +8,7 @@ assignees: '' --- **Describe the bug** -Make sure your bug is not addressed in the [troubleshooting section](https://github.com/MannLabs/py_diaid#troubleshooting) or in [previous issues](https://github.com/MannLabs/py_diaid/issues?q=is%3Aissue). If not, provide a clear and concise description of what the bug is. +Make sure your bug is not addressed in the [troubleshooting section](https://github.com/MannLabs/pydiaid#troubleshooting) or in [previous issues](https://github.com/MannLabs/pydiaid/issues?q=is%3Aissue). If not, provide a clear and concise description of what the bug is. **To Reproduce** Steps to reproduce the behavior: @@ -37,7 +37,7 @@ If applicable, add screenshots to help explain your problem. - processor [e.g. i386] - cpu count [e.g. 8] - Python information: - - py_diaid version [e.g. 0.1.2] + - pydiaid version [e.g. 0.1.2] - [other packages] **Additional context** diff --git a/.github/workflows/publish_and_release.yml b/.github/workflows/publish_and_release.yml index 6ffef55..628f5d1 100644 --- a/.github/workflows/publish_and_release.yml +++ b/.github/workflows/publish_and_release.yml @@ -62,7 +62,7 @@ jobs: - name: Test installer for Linux shell: bash -l {0} run: | - sudo dpkg -i release/one_click_linux_gui/dist/py_diaid_gui_installer_linux.deb + sudo dpkg -i release/one_click_linux_gui/dist/pydiaid_gui_installer_linux.deb - name: Upload Linux Installer id: upload-release-asset uses: actions/upload-release-asset@v1 @@ -70,8 +70,8 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} with: upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }} - asset_path: release/one_click_linux_gui/dist/py_diaid_gui_installer_linux.deb - asset_name: py_diaid_gui_installer_linux.deb + asset_path: release/one_click_linux_gui/dist/pydiaid_gui_installer_linux.deb + asset_name: pydiaid_gui_installer_linux.deb asset_content_type: application/octet-stream Create_MacOS_Release: runs-on: macos-latest @@ -94,7 +94,7 @@ jobs: - name: Test installer for MacOS shell: bash -l {0} run: | - sudo installer -pkg release/one_click_macos_gui/dist/py_diaid_gui_installer_macos.pkg -target / + sudo installer -pkg release/one_click_macos_gui/dist/pydiaid_gui_installer_macos.pkg -target / - name: Upload MacOS Installer id: upload-release-asset uses: actions/upload-release-asset@v1 @@ -102,8 +102,8 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} with: upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }} - asset_path: release/one_click_macos_gui/dist/py_diaid_gui_installer_macos.pkg - asset_name: py_diaid_gui_installer_macos.pkg + asset_path: release/one_click_macos_gui/dist/pydiaid_gui_installer_macos.pkg + asset_name: pydiaid_gui_installer_macos.pkg asset_content_type: application/octet-stream Create_Windows_Release: runs-on: windows-latest @@ -128,7 +128,7 @@ jobs: run: | cd release/one_click_windows_gui/dist/ echo "TODO, this test seems to freeze the runner..." - # ./py_diaid_gui_installer_windows.exe //verysilent //log=log.txt //noicons //tasks= //portable=1 + # ./pydiaid_gui_installer_windows.exe //verysilent //log=log.txt //noicons //tasks= //portable=1 # cat log.txt - name: Upload Windows Installer id: upload-release-asset @@ -137,8 +137,8 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} with: upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }} - asset_path: release/one_click_windows_gui/dist/py_diaid_gui_installer_windows.exe - asset_name: py_diaid_gui_installer_windows.exe + asset_path: release/one_click_windows_gui/dist/pydiaid_gui_installer_windows.exe + asset_name: pydiaid_gui_installer_windows.exe asset_content_type: application/octet-stream Create_PyPi_Release: runs-on: ubuntu-latest diff --git a/.gitignore b/.gitignore index 8e36902..4e0cdd2 100644 --- a/.gitignore +++ b/.gitignore @@ -129,10 +129,10 @@ dmypy.json .pyre/ # User defined: -py_diaid/logs +pydiaid/logs *.DS_Store *sandbox* -py_diaid/input -py_diaid/static -py_diaid/lib -output_py_diaid +pydiaid/input +pydiaid/static +pydiaid/lib +output_pydiaid diff --git a/MANIFEST.in b/MANIFEST.in index 049325b..600fcb0 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,4 +1,4 @@ -recursive-include py_diaid * +recursive-include pydiaid * include LICENSE.txt include README.md -recursive-exclude py_diaid/logs * +recursive-exclude pydiaid/logs * diff --git a/README.md b/README.md index e52e33c..647a947 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ -![Pip installation](https://github.com/MannLabs/py_diaid/workflows/Default%20installation%20and%20tests/badge.svg) -![GUI and PyPi releases](https://github.com/MannLabs/py_diaid/workflows/Publish%20on%20PyPi%20and%20release%20on%20GitHub/badge.svg) +![Pip installation](https://github.com/MannLabs/pydiaid/workflows/Default%20installation%20and%20tests/badge.svg) +![GUI and PyPi releases](https://github.com/MannLabs/pydiaid/workflows/Publish%20on%20PyPi%20and%20release%20on%20GitHub/badge.svg) # py_diAID -An open-source Python package of the AlphaPept ecosystem from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann). To enable all hyperlinks in this document, please view it at [GitHub](https://github.com/MannLabs/py_diaid). +An open-source Python package of the AlphaPept ecosystem from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann). To enable all hyperlinks in this document, please view it at [GitHub](https://github.com/MannLabs/pydiaid). * [**About**](#about) * [**License**](#license) @@ -43,32 +43,32 @@ There are three different types of installation possible: The GUI of py_diAID is a completely stand-alone tool that requires no knowledge of Python or CLI tools. Click on one of the links below to download the latest release for: -* [**Windows**](https://github.com/MannLabs/py_diaid/releases/latest/download/py_diaid_gui_installer_windows.exe) -* [**macOS**](https://github.com/MannLabs/py_diaid/releases/latest/download/py_diaid_gui_installer_macos.pkg) -* [**Linux**](https://github.com/MannLabs/py_diaid/releases/latest/download/py_diaid_gui_installer_linux.deb) +* [**Windows**](https://github.com/MannLabs/pydiaid/releases/latest/download/pydiaid_gui_installer_windows.exe) +* [**macOS**](https://github.com/MannLabs/pydiaid/releases/latest/download/pydiaid_gui_installer_macos.pkg) +* [**Linux**](https://github.com/MannLabs/pydiaid/releases/latest/download/pydiaid_gui_installer_linux.deb) -Older releases remain available on the [release page](https://github.com/MannLabs/py_diaid/releases), but no backwards compatibility is guaranteed. +Older releases remain available on the [release page](https://github.com/MannLabs/pydiaid/releases), but no backwards compatibility is guaranteed. ### Pip py_diAID can be installed in an existing Python 3.8 environment with a single `bash` command. *This `bash` command can also be run directly from within a Jupyter notebook by prepending it with a `!`*: ```bash -pip install py_diaid +pip install pydiaid ``` Installing py_diAID like this avoids conflicts when integrating it in other tools, as this does not enforce strict versioning of dependancies. However, if new versions of dependancies are released, they are not guaranteed to be fully compatible with py_diAID. While this should only occur in rare cases where dependencies are not backwards compatible, you can always force py_diAID to use dependancy versions which are known to be compatible with: ```bash -pip install "py_diaid[stable]" +pip install "pydiaid[stable]" ``` NOTE: You might need to run `pip install pip==21.0` before installing py_diAID like this. Also note the double quotes `"`. -For those who are really adventurous, it is also possible to directly install any branch (e.g. `@development`) with any extras (e.g. `#egg=py_diaid[stable,development-stable]`) from GitHub with e.g. +For those who are really adventurous, it is also possible to directly install any branch (e.g. `@development`) with any extras (e.g. `#egg=pydiaid[stable,development-stable]`) from GitHub with e.g. ```bash -pip install "git+https://github.com/MannLabs/py_diaid.git@development#egg=py_diaid[stable,development-stable]" +pip install "git+https://github.com/MannLabs/pydiaid.git@development#egg=pydiaid[stable,development-stable]" ``` ### Developer @@ -85,25 +85,25 @@ cd ~/folder/where/to/install/software Next, download the py_diAID repository from GitHub either directly or with a `git` command. This creates a new py_diAID subfolder in your current directory. ```bash -git clone https://github.com/MannLabs/py_diaid.git +git clone https://github.com/MannLabs/pydiaid.git ``` For any Python package, it is highly recommended to use a separate [conda virtual environment](https://docs.conda.io/en/latest/), as otherwise *dependancy conflicts can occur with already existing packages*. ```bash -conda create --name py_diaid python=3.8 -y -conda activate py_diaid +conda create --name pydiaid python=3.8 -y +conda activate pydiaid ``` Finally, py_diAID and all its [dependancies](requirements) need to be installed. To take advantage of all features and allow development (with the `-e` flag), this is best done by also installing the [development dependencies](requirements/requirements_development.txt) instead of only the [core dependencies](requirements/requirements.txt): ```bash -pip install -e "./py_diaid[development]" +pip install -e "./pydiaid[development]" ``` -By default this installs loose dependancies (no explicit versioning), although it is also possible to use stable dependencies (e.g. `pip install -e "./py_diaid[stable,development-stable]"`). +By default this installs loose dependancies (no explicit versioning), although it is also possible to use stable dependencies (e.g. `pip install -e "./pydiaid[stable,development-stable]"`). -***By using the editable flag `-e`, all modifications to the [py_diAID source code folder](py_diaid) are directly reflected when running py_diAID. Note that the py_diAID folder cannot be moved and/or renamed if an editable version is installed.*** +***By using the editable flag `-e`, all modifications to the [py_diAID source code folder](pydiaid) are directly reflected when running py_diAID. Note that the py_diAID folder cannot be moved and/or renamed if an editable version is installed.*** --- ## Usage @@ -121,24 +121,24 @@ NOTE: The first time you use a fresh installation of py_diAID, it is often quite If the GUI was not installed through a one-click GUI installer, it can be activate with the following `bash` command: ```bash -py_diaid gui +pydiaid gui ``` -Note that this needs to be prepended with a `!` when you want to run this from within a Jupyter notebook. When the command is run directly from the command-line, make sure you use the right environment (activate it with e.g. `conda activate py_diaid` or set an alias to the binary executable (can be obtained with `where py_diaid` or `which py_diaid`)). +Note that this needs to be prepended with a `!` when you want to run this from within a Jupyter notebook. When the command is run directly from the command-line, make sure you use the right environment (activate it with e.g. `conda activate pydiaid` or set an alias to the binary executable (can be obtained with `where pydiaid` or `which pydiaid`)). ### CLI -The CLI can be run with the following command (after activating the `conda` environment with `conda activate py_diaid` or if an alias was set to the py_diaid executable): +The CLI can be run with the following command (after activating the `conda` environment with `conda activate pydiaid` or if an alias was set to the pydiaid executable): ```bash -py_diaid -h +pydiaid -h ``` It is possible to get help about each function and their (required) parameters by using the `-h` flag. ### Python and Jupyter notebooks -diAID-PASEF can be imported as a Python package into any Python script or notebook with the command `import py_diaid`. +diAID-PASEF can be imported as a Python package into any Python script or notebook with the command `import pydiaid`. A brief [Jupyter notebook tutorial](nbs/tutorial.ipynb) on how to use the API is also present in the [nbs folder](nbs). @@ -147,8 +147,8 @@ A brief [Jupyter notebook tutorial](nbs/tutorial.ipynb) on how to use the API is In case of issues, check out the following: -* [Issues](https://github.com/MannLabs/py_diaid/issues): Try a few different search terms to find out if a similar problem has been encountered before -* [Discussions](https://github.com/MannLabs/py_diaid/discussions): Check if your problem or feature requests has been discussed before. +* [Issues](https://github.com/MannLabs/pydiaid/issues): Try a few different search terms to find out if a similar problem has been encountered before +* [Discussions](https://github.com/MannLabs/pydiaid/discussions): Check if your problem or feature requests has been discussed before. --- ## Citations @@ -158,7 +158,7 @@ There are currently no plans to draft a manuscript. --- ## How to contribute -If you like this software, you can give us a [star](https://github.com/MannLabs/py_diaid/stargazers) to boost our visibility! All direct contributions are also welcome. Feel free to post a new [issue](https://github.com/MannLabs/py_diaid/issues) or clone the repository and create a [pull request](https://github.com/MannLabs/py_diaid/pulls) with a new branch. For an even more interactive participation, check out the [discussions](https://github.com/MannLabs/py_diaid/discussions) and the [the Contributors License Agreement](misc/CLA.md). +If you like this software, you can give us a [star](https://github.com/MannLabs/pydiaid/stargazers) to boost our visibility! All direct contributions are also welcome. Feel free to post a new [issue](https://github.com/MannLabs/pydiaid/issues) or clone the repository and create a [pull request](https://github.com/MannLabs/pydiaid/pulls) with a new branch. For an even more interactive participation, check out the [discussions](https://github.com/MannLabs/pydiaid/discussions) and the [the Contributors License Agreement](misc/CLA.md). --- ## Changelog diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index 5cc2bbe..a9d5897 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -11,7 +11,7 @@ serialize = [bumpversion:part:build] -[bumpversion:file:../py_diaid/__init__.py] +[bumpversion:file:../pydiaid/__init__.py] [bumpversion:file:../release/one_click_linux_gui/control] @@ -25,6 +25,6 @@ serialize = [bumpversion:file:../release/one_click_windows_gui/create_installer_windows.sh] -[bumpversion:file:../release/one_click_windows_gui/py_diaid_innoinstaller.iss] +[bumpversion:file:../release/one_click_windows_gui/pydiaid_innoinstaller.iss] search = {current_version} replace = {new_version} diff --git a/misc/check_version.sh b/misc/check_version.sh index 605b764..fd89c01 100644 --- a/misc/check_version.sh +++ b/misc/check_version.sh @@ -1,9 +1,9 @@ -current_version=$(grep "__version__" ../py_diaid/__init__.py | cut -f3 -d ' ' | sed 's/"//g') +current_version=$(grep "__version__" ../pydiaid/__init__.py | cut -f3 -d ' ' | sed 's/"//g') current_version_as_regex=$(echo $current_version | sed 's/\./\\./g') conda create -n version_check python=3.8 pip=20.1 -y conda activate version_check set +e -already_on_pypi=$(pip install py_diaid== 2>&1 | grep -c "$current_version_as_regex") +already_on_pypi=$(pip install pydiaid== 2>&1 | grep -c "$current_version_as_regex") set -e conda deactivate if [ $already_on_pypi -ne 0 ]; then diff --git a/misc/loose_pip_install.sh b/misc/loose_pip_install.sh index 82de603..fab10ae 100644 --- a/misc/loose_pip_install.sh +++ b/misc/loose_pip_install.sh @@ -1,5 +1,5 @@ -conda create -n py_diaid python=3.8 -y -conda activate py_diaid +conda create -n pydiaid python=3.8 -y +conda activate pydiaid pip install -e '../.[development]' -py_diaid +pydiaid conda deactivate diff --git a/misc/stable_pip_install.sh b/misc/stable_pip_install.sh index 7059bbb..5a93d29 100644 --- a/misc/stable_pip_install.sh +++ b/misc/stable_pip_install.sh @@ -1,5 +1,5 @@ -conda create -n py_diaid python=3.8 -y -conda activate py_diaid +conda create -n pydiaid python=3.8 -y +conda activate pydiaid pip install -e '../.[stable,development-stable]' -py_diaid +pydiaid conda deactivate diff --git a/nbs/tutorial.ipynb b/nbs/tutorial.ipynb index 5cdc260..f735b44 100644 --- a/nbs/tutorial.ipynb +++ b/nbs/tutorial.ipynb @@ -8,9 +8,9 @@ ], "metadata": { "kernelspec": { - "display_name": "Python [conda env:py_diaid]", + "display_name": "Python [conda env:pydiaid]", "language": "python", - "name": "conda-env-py_diaid-py" + "name": "conda-env-pydiaid-py" }, "language_info": { "codemirror_mode": { diff --git a/py_diaid/lib/default_parameters.json b/py_diaid/lib/default_parameters.json deleted file mode 100644 index 3e96f75..0000000 --- a/py_diaid/lib/default_parameters.json +++ /dev/null @@ -1,73 +0,0 @@ -{ - "input": { - "save_at": "D:\\output_test2", - "PTM": "None", - "library_name": "D:\\Input_for_py_diaid\\library21min24fractions.tsv", - "analysis_software": "MS_Fragger", - "diaPASEF_method_only_used_for_evaluate": "D:/py_diaid/py_diaid/static/DIAParameterspy3TC.txt" - }, - "method_parameters": { - "mz": [ - 300, - 1200 - ], - "ion_mobility": [ - 0.6, - 1.6 - ], - "num_dia_pasef_scans": 12, - "im_steps": 2, - "overlap": 0, - "shift_of_final_method": 0.022, - "scan_area_A1_A2_B1_B2_only_used_for_create": [ - 0.68, - 1.04, - 0.9, - 1.3 - ], - "scan_area_A1_A2_B1_B2_only_used_for_specific_diaPASEF": [ - 0.5752575470522289, - 0.7128990257352522, - 1.4241557523881094, - 1.6972373193612142 - ] - }, - "graphs": { - "plot_mz": [ - 250, - 1250 - ], - "plot_IM": [ - 0.6, - 1.6 - ], - "numbins": 50, - "window_frame_color": "black", - "window_color": "white", - "window_transparency": 0.5 - }, - "optimizer": { - "optimizer": "Gauss", - "n_random_starts": null, - "n_calls": 5, - "n_start": 2, - "initial_points": 2, - "YA1": [ - 0.5, - 0.9 - ], - "YA2": [ - 0.6, - 1.0 - ], - "YB1": [ - 0.9, - 1.5 - ], - "YB2": [ - 1.0, - 1.8 - ], - "evaluation_parameter": "No. of covered precursors" - } -} diff --git a/py_diaid/static/AlphaPept_results.csv b/py_diaid/static/AlphaPept_results.csv deleted file mode 100644 index 015dcdd..0000000 --- a/py_diaid/static/AlphaPept_results.csv +++ /dev/null @@ -1,20093 +0,0 @@ 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a/py_diaid/static/DIAParameterspy3TC.txt +++ /dev/null @@ -1,68 +0,0 @@ -#---------------------------------------------------------------------------------------------------- -# MS Type | Cycle Id | 1/K0 Begin [Vs/cm2] | 1/K0 End [Vs/cm2] | Start Mass [m/z] | End Mass [m/z] | CE [eV] -#---------------------------------------------------------------------------------------------------- - MS1, 0, - , - , - , - , - - PASEF, 1, 1.22, 1.40, 1000.0, 1025.0, - - PASEF, 1, 1.04, 1.22, 800.0, 825.0, - - PASEF, 1, 0.87, 1.04, 600.0, 625.0, - - PASEF, 1, 0.69, 0.87, 400.0, 425.0, - - PASEF, 2, 1.24, 1.41, 1025.0, 1050.0, - - PASEF, 2, 1.06, 1.24, 825.0, 850.0, - - PASEF, 2, 0.89, 1.06, 625.0, 650.0, - - PASEF, 2, 0.71, 0.89, 425.0, 450.0, - - PASEF, 3, 1.25, 1.42, 1050.0, 1075.0, - - PASEF, 3, 1.07, 1.25, 850.0, 875.0, - - PASEF, 3, 0.90, 1.07, 650.0, 675.0, - - PASEF, 3, 0.73, 0.90, 450.0, 475.0, - - PASEF, 4, 1.26, 1.43, 1075.0, 1100.0, - - PASEF, 4, 1.09, 1.26, 875.0, 900.0, - - PASEF, 4, 0.92, 1.09, 675.0, 700.0, - - PASEF, 4, 0.75, 0.92, 475.0, 500.0, - - PASEF, 5, 1.27, 1.44, 1100.0, 1125.0, - - PASEF, 5, 1.10, 1.27, 900.0, 925.0, - - PASEF, 5, 0.94, 1.10, 700.0, 725.0, - - PASEF, 5, 0.77, 0.94, 500.0, 525.0, - - PASEF, 6, 1.29, 1.45, 1125.0, 1150.0, - - PASEF, 6, 1.12, 1.29, 925.0, 950.0, - - PASEF, 6, 0.96, 1.12, 725.0, 750.0, - - PASEF, 6, 0.79, 0.96, 525.0, 550.0, - - PASEF, 7, 1.30, 1.46, 1150.0, 1175.0, - - PASEF, 7, 1.14, 1.30, 950.0, 975.0, - - PASEF, 7, 0.97, 1.14, 750.0, 775.0, - - PASEF, 7, 0.81, 0.97, 550.0, 575.0, - - PASEF, 8, 1.31, 1.47, 1175.0, 1200.0, - - PASEF, 8, 1.15, 1.31, 975.0, 1000.0, - - PASEF, 8, 0.99, 1.15, 775.0, 800.0, - - PASEF, 8, 0.83, 0.99, 575.0, 600.0, - - PASEF, 9, 1.10, 1.28, 1000.0, 1025.0, - - PASEF, 9, 0.92, 1.10, 800.0, 825.0, - - PASEF, 9, 0.75, 0.92, 600.0, 625.0, - - PASEF, 9, 0.57, 0.75, 400.0, 425.0, - - PASEF, 10, 1.12, 1.29, 1025.0, 1050.0, - - PASEF, 10, 0.94, 1.12, 825.0, 850.0, - - PASEF, 10, 0.77, 0.94, 625.0, 650.0, - - PASEF, 10, 0.59, 0.77, 425.0, 450.0, - - PASEF, 11, 1.13, 1.30, 1050.0, 1075.0, - - PASEF, 11, 0.95, 1.13, 850.0, 875.0, - - PASEF, 11, 0.78, 0.95, 650.0, 675.0, - - PASEF, 11, 0.61, 0.78, 450.0, 475.0, - - PASEF, 12, 1.14, 1.31, 1075.0, 1100.0, - - PASEF, 12, 0.97, 1.14, 875.0, 900.0, - - PASEF, 12, 0.80, 0.97, 675.0, 700.0, - - PASEF, 12, 0.63, 0.80, 475.0, 500.0, - - PASEF, 13, 1.15, 1.32, 1100.0, 1125.0, - - PASEF, 13, 0.98, 1.15, 900.0, 925.0, - - PASEF, 13, 0.82, 0.98, 700.0, 725.0, - - PASEF, 13, 0.65, 0.82, 500.0, 525.0, - - PASEF, 14, 1.17, 1.33, 1125.0, 1150.0, - - PASEF, 14, 1.00, 1.17, 925.0, 950.0, - - PASEF, 14, 0.84, 1.00, 725.0, 750.0, - - PASEF, 14, 0.67, 0.84, 525.0, 550.0, - - PASEF, 15, 1.18, 1.34, 1150.0, 1175.0, - - PASEF, 15, 1.02, 1.18, 950.0, 975.0, - - PASEF, 15, 0.85, 1.02, 750.0, 775.0, - - PASEF, 15, 0.69, 0.85, 550.0, 575.0, - - PASEF, 16, 1.19, 1.35, 1175.0, 1200.0, - - PASEF, 16, 1.03, 1.19, 975.0, 1000.0, - - PASEF, 16, 0.87, 1.03, 775.0, 800.0, - - PASEF, 16, 0.71, 0.87, 575.0, 600.0, - diff --git a/py_diaid/__init__.py b/pydiaid/__init__.py similarity index 92% rename from py_diaid/__init__.py rename to pydiaid/__init__.py index 536eb34..eea0d1e 100644 --- a/py_diaid/__init__.py +++ b/pydiaid/__init__.py @@ -1,13 +1,13 @@ #!python -__project__ = "py_diaid" +__project__ = "pydiaid" __version__ = "0.0.3" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" __author_email__ = "opensource@alphapept.com" -__github__ = "https://github.com/MannLabs/py_diaid" +__github__ = "https://github.com/MannLabs/pydiaid" __keywords__ = [ "bioinformatics", "software", @@ -36,7 +36,7 @@ "Topic :: Scientific/Engineering :: Bio-Informatics", ] __console_scripts__ = [ - "py_diaid=py_diaid.cli:run", + "pydiaid=pydiaid.cli:run", ] __urls__ = { "Mann Labs at MPIB": "https://www.biochem.mpg.de/mann", diff --git a/py_diaid/cli.py b/pydiaid/cli.py similarity index 97% rename from py_diaid/cli.py rename to pydiaid/cli.py index 492eea5..6e34296 100644 --- a/py_diaid/cli.py +++ b/pydiaid/cli.py @@ -5,10 +5,10 @@ import click # local -import py_diaid -from py_diaid import loader -from py_diaid import main -from py_diaid import method_optimizer +import pydiaid +from pydiaid import loader +from pydiaid import main +from pydiaid import method_optimizer # for data manipulation: import pandas as pd @@ -34,9 +34,9 @@ invoke_without_command=True ) @click.pass_context -@click.version_option(py_diaid.__version__, "-v", "--version") +@click.version_option(pydiaid.__version__, "-v", "--version") def run(ctx, **kwargs): - name = f"py_diAID {py_diaid.__version__}" + name = f"py_diAID {pydiaid.__version__}" click.echo("*" * (len(name) + 4)) click.echo(f"* {name} *") click.echo("*" * (len(name) + 4)) @@ -46,8 +46,8 @@ def run(ctx, **kwargs): @run.command("gui", help="Start graphical user interface.") def gui(): - import py_diaid.gui - py_diaid.gui.run() + import pydiaid.gui + pydiaid.gui.run() @run.command("optimize", help="Optimize a dia-PASEF method.") diff --git a/py_diaid/docs/manual.pdf b/pydiaid/docs/manual.pdf similarity index 100% rename from py_diaid/docs/manual.pdf rename to pydiaid/docs/manual.pdf diff --git a/py_diaid/graphs.py b/pydiaid/graphs.py similarity index 99% rename from py_diaid/graphs.py rename to pydiaid/graphs.py index 2c931d6..46ecdd1 100644 --- a/py_diaid/graphs.py +++ b/pydiaid/graphs.py @@ -14,7 +14,7 @@ # for suppressing warnings import warnings -from py_diaid.method_evaluation import boxes +from pydiaid.method_evaluation import boxes # importing components for visualization mpl.rcParams['font.family'] = 'Arial' diff --git a/py_diaid/graphs_for_gui.py b/pydiaid/graphs_for_gui.py similarity index 100% rename from py_diaid/graphs_for_gui.py rename to pydiaid/graphs_for_gui.py diff --git a/py_diaid/gui.py b/pydiaid/gui.py similarity index 96% rename from py_diaid/gui.py rename to pydiaid/gui.py index 7bbd4c7..49c98fc 100644 --- a/py_diaid/gui.py +++ b/pydiaid/gui.py @@ -14,12 +14,12 @@ import bokeh.server.views.ws # modules -import py_diaid -import py_diaid.loader -import py_diaid.main -import py_diaid.graphs -import py_diaid.method_optimizer -import py_diaid.method_evaluation +import pydiaid +import pydiaid.loader +import pydiaid.main +import pydiaid.graphs +import pydiaid.method_optimizer +import pydiaid.method_evaluation import warnings warnings.filterwarnings("ignore") @@ -39,13 +39,13 @@ method_conf = json.load(infile) if platform.system() == 'Windows': - method_path_placeholder = 'D:\py_diaid\static\DIAParameterspy3TC.txt' - library_path_placeholder = 'D:\py_diaid\static\AlphaPept_results.csv' - save_folder_placeholder = 'D:\py_diaid\static' + method_path_placeholder = 'D:\pydiaid\static\DIAParameterspy3TC.txt' + library_path_placeholder = 'D:\pydiaid\static\AlphaPept_results.csv' + save_folder_placeholder = 'D:\pydiaid\static' else: - method_path_placeholder = '/Users/py_diaid/static/DIAParameterspy3TC.txt' - library_path_placeholder = '/Users/py_diaid/static/AlphaPept_results.csv' - save_folder_placeholder = '/Users/py_diaid/static' + method_path_placeholder = '/Users/pydiaid/static/DIAParameterspy3TC.txt' + library_path_placeholder = '/Users/pydiaid/static/AlphaPept_results.csv' + save_folder_placeholder = '/Users/pydiaid/static' class BaseWidget(object): @@ -429,7 +429,7 @@ def update_parameters_plotting(self, event): def upload_data(self, *args): self.upload_progress.active = True - self.library = py_diaid.loader.load_library( + self.library = pydiaid.loader.load_library( self.path_library.value, method_conf["input"]["analysis_software"], method_conf["input"]["PTM"] @@ -446,13 +446,13 @@ def upload_data(self, *args): 'final_method' ), ] - py_diaid.main.create_folder(folder_paths) - self.xi, self.yi, self.zi = py_diaid.graphs.kernel_density_calculation( + pydiaid.main.create_folder(folder_paths) + self.xi, self.yi, self.zi = pydiaid.graphs.kernel_density_calculation( self.library, method_conf["graphs"]["numbins"] ) self.layout[4][0] = pn.pane.Matplotlib( - py_diaid.graphs.plot_precursor_distribution_as_histogram( + pydiaid.graphs.plot_precursor_distribution_as_histogram( self.library, method_conf["graphs"], os.path.join( @@ -465,7 +465,7 @@ def upload_data(self, *args): tight=True ) self.layout[4][1] = pn.pane.Matplotlib( - py_diaid.graphs.plot_density( + pydiaid.graphs.plot_density( self.xi, self.yi, self.zi, @@ -479,7 +479,7 @@ def upload_data(self, *args): ), tight=True ) - dict_charge_of_precursor = py_diaid.method_evaluation.calculate_percentage_multiple_charged_precursors(self.library) + dict_charge_of_precursor = pydiaid.method_evaluation.calculate_percentage_multiple_charged_precursors(self.library) mult_charged_precursor_info = pd.DataFrame( { "charge state of precursors": list(dict_charge_of_precursor.keys()), @@ -680,7 +680,7 @@ def update_parameters(self, event): method_conf['method_parameters'][convertion_dict[event.obj.name]] = event.new def run_calculation(self, *args): - dict_precursors_within_scan_area = py_diaid.method_evaluation.calculate_precursor_within_scan_area( + dict_precursors_within_scan_area = pydiaid.method_evaluation.calculate_precursor_within_scan_area( self.data.library, method_conf['method_parameters']["mz"], method_conf['method_parameters']["ion_mobility"] @@ -927,9 +927,9 @@ def run_optimization(self, *args): 'optimization_plots' ) ] - py_diaid.main.create_folder(self.folder_path) + pydiaid.main.create_folder(self.folder_path) - self.opt_result = py_diaid.method_optimizer.optimization( + self.opt_result = pydiaid.method_optimizer.optimization( self.data.library, method_conf["method_parameters"], self.data.xi, @@ -941,7 +941,7 @@ def run_optimization(self, *args): self.scan_area_A1_A2_B1_B2_only_used_for_specific_diaPASEF.value = self.opt_result - self.filenames_plots = py_diaid.loader.get_file_names_from_directory( + self.filenames_plots = pydiaid.loader.get_file_names_from_directory( self.folder_path[0], 'png' ) @@ -955,7 +955,7 @@ def run_optimization(self, *args): margin=(0, 0, 50, 0) ) - opt_plot_df = py_diaid.loader.create_opt_plot_df( + opt_plot_df = pydiaid.loader.create_opt_plot_df( self.filenames_plots[self.player.value] ) @@ -989,7 +989,7 @@ def run_optimization(self, *args): self.optimize_spinner.value = False def update_kde_plot_df(self, event): - self.kde_plot_table.value = py_diaid.loader.create_opt_plot_df( + self.kde_plot_table.value = pydiaid.loader.create_opt_plot_df( self.filenames_plots[event.new] ) self.kde_plot.object = os.path.join( @@ -1095,7 +1095,7 @@ def update_parameters(self, event): method_conf['method_parameters'][convertion_dict[event.obj.name]] = event.new def create_method(self, event): - df_parameters_final = py_diaid.main.create_final_method( + df_parameters_final = pydiaid.main.create_final_method( self.data.library, method_conf["method_parameters"], self.opt_widget.scan_area_A1_A2_B1_B2_only_used_for_specific_diaPASEF.value, @@ -1244,7 +1244,7 @@ def evaluate_method(self, event): names=["MS Type", "Cycle Id", "Start IM", "End IM", "Start Mass", "End Mass", "CE"] ) - py_diaid.main.final_method_information( + pydiaid.main.final_method_information( df_parameters_final, self.data.xi, self.data.yi, @@ -1257,12 +1257,12 @@ def evaluate_method(self, event): ) # save parameters for method evaluation as .csv - dict_precursors_within_mz = py_diaid.method_evaluation.calculate_precursor_within_scan_area( + dict_precursors_within_mz = pydiaid.method_evaluation.calculate_precursor_within_scan_area( self.data.library, method_conf["method_parameters"]["mz"], method_conf["method_parameters"]["ion_mobility"] ) - dict_precursors_coverage = py_diaid.method_evaluation.coverage( + dict_precursors_coverage = pydiaid.method_evaluation.coverage( df_parameters_final, self.data.library, ) @@ -1400,9 +1400,9 @@ class DiAIDPasefGUI(GUI): def __init__(self, start_server=False): super().__init__( - name=f"py_diAID {py_diaid.__version__}", + name=f"py_diAID {pydiaid.__version__}", img_folder_path=IMG_PATH, - github_url='https://github.com/MannLabs/py_diaid', + github_url='https://github.com/MannLabs/pydiaid', ) self.project_description = """#### py_diAID uses an Automated Isolation Design to generate optimal dia-PASEF methods with respect to the peptide precursor density. It designs isolation windows with dynamic widths, which enable short acquisition cycles, while essentially covering the complete m/z-ion mobility-range.""" self.load_library_description = "#### Please load the library for the indicated analysis software’s to check the distribution of the precursors in the m/z-ion mobility plain." diff --git a/py_diaid/img/github.png b/pydiaid/img/github.png similarity index 100% rename from py_diaid/img/github.png rename to pydiaid/img/github.png diff --git a/py_diaid/img/max-planck-gesellschaft.jpg b/pydiaid/img/max-planck-gesellschaft.jpg similarity index 100% rename from py_diaid/img/max-planck-gesellschaft.jpg rename to pydiaid/img/max-planck-gesellschaft.jpg diff --git a/py_diaid/img/mpi_logo.png b/pydiaid/img/mpi_logo.png similarity index 100% rename from py_diaid/img/mpi_logo.png rename to pydiaid/img/mpi_logo.png diff --git a/py_diaid/loader.py b/pydiaid/loader.py similarity index 100% rename from py_diaid/loader.py rename to pydiaid/loader.py diff --git a/py_diaid/main.py b/pydiaid/main.py similarity index 98% rename from py_diaid/main.py rename to pydiaid/main.py index 2ad432c..1fbd6ef 100644 --- a/py_diaid/main.py +++ b/pydiaid/main.py @@ -1,7 +1,7 @@ -from py_diaid import loader -from py_diaid import method_creator -from py_diaid import method_evaluation -from py_diaid import graphs +from pydiaid import loader +from pydiaid import method_creator +from pydiaid import method_evaluation +from pydiaid import graphs # for data manipulation: import pandas as pd diff --git a/py_diaid/method_creator.py b/pydiaid/method_creator.py similarity index 100% rename from py_diaid/method_creator.py rename to pydiaid/method_creator.py diff --git a/py_diaid/method_evaluation.py b/pydiaid/method_evaluation.py similarity index 100% rename from py_diaid/method_evaluation.py rename to pydiaid/method_evaluation.py diff --git a/py_diaid/method_optimizer.py b/pydiaid/method_optimizer.py similarity index 98% rename from py_diaid/method_optimizer.py rename to pydiaid/method_optimizer.py index 992d450..ef655c7 100644 --- a/py_diaid/method_optimizer.py +++ b/pydiaid/method_optimizer.py @@ -1,6 +1,6 @@ -from py_diaid import method_creator -from py_diaid import method_evaluation -from py_diaid import graphs +from pydiaid import method_creator +from pydiaid import method_evaluation +from pydiaid import graphs # for data manipulation: import pandas as pd diff --git a/py_diaid/style/dashboard_style.css b/pydiaid/style/dashboard_style.css similarity index 100% rename from py_diaid/style/dashboard_style.css rename to pydiaid/style/dashboard_style.css diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index 6976373..3aad531 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,7 +1,7 @@ -Package: py_diaid +Package: pydiaid Version: 0.0.3 Architecture: all Maintainer: Mann Labs Description: py_diAID py_diAIDF is an open-source Python package in the AlphaPept ecosystem. - py_diAID was developed by the Mann Labs at the Max Planck Institute of Biochemistry and is freely available with an Apache License. Additional third-party licenses are applicable for external Python packages (see https://github.com/MannLabs/py_diaid for more details.). + py_diAID was developed by the Mann Labs at the Max Planck Institute of Biochemistry and is freely available with an Apache License. Additional third-party licenses are applicable for external Python packages (see https://github.com/MannLabs/pydiaid for more details.). diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index c4be644..0f805e0 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -8,8 +8,8 @@ rm -rf dist rm -rf build # Creating a conda environment -conda create -n py_diaid_installer python=3.8 -y -conda activate py_diaid_installer +conda create -n pydiaid_installer python=3.8 -y +conda activate pydiaid_installer # Creating the wheel python setup.py sdist bdist_wheel @@ -17,20 +17,20 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/py_diaid-0.0.3-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.3-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 -pyinstaller ../pyinstaller/py_diaid.spec -y +pyinstaller ../pyinstaller/pydiaid.spec -y conda deactivate # If needed, include additional source such as e.g.: -# cp ../../py_diaid/data/*.fasta dist/py_diaid/data +# cp ../../pydiaid/data/*.fasta dist/pydiaid/data # WARNING: this probably does not work!!!! # Wrapping the pyinstaller folder in a .deb package -mkdir -p dist/py_diaid_gui_installer_linux/usr/local/bin -mv dist/py_diaid dist/py_diaid_gui_installer_linux/usr/local/bin/py_diaid -mkdir dist/py_diaid_gui_installer_linux/DEBIAN -cp control dist/py_diaid_gui_installer_linux/DEBIAN -dpkg-deb --build --root-owner-group dist/py_diaid_gui_installer_linux/ +mkdir -p dist/pydiaid_gui_installer_linux/usr/local/bin +mv dist/pydiaid dist/pydiaid_gui_installer_linux/usr/local/bin/pydiaid +mkdir dist/pydiaid_gui_installer_linux/DEBIAN +cp control dist/pydiaid_gui_installer_linux/DEBIAN +dpkg-deb --build --root-owner-group dist/pydiaid_gui_installer_linux/ diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index fd733dc..d8fff83 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -5,11 +5,11 @@ CFBundleDisplayName py_diAID CFBundleExecutable - MacOS/py_diaid_terminal + MacOS/pydiaid_terminal CFBundleIconFile alpha_logo.icns CFBundleIdentifier - py_diaid.0.0.3 + pydiaid.0.0.3 CFBundleShortVersionString 0.0.3 CFBundleInfoDictionaryVersion diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 16ac4c2..7d9c7b0 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -12,33 +12,33 @@ rm -rf dist rm -rf build # Creating a conda environment -conda create -n py_diaidinstaller python=3.8 -y -conda activate py_diaidinstaller +conda create -n pydiaidinstaller python=3.8 -y +conda activate pydiaidinstaller # Creating the wheel python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/py_diaid-0.0.3-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.3-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 -pyinstaller ../pyinstaller/py_diaid.spec -y +pyinstaller ../pyinstaller/pydiaid.spec -y conda deactivate # If needed, include additional source such as e.g.: -# cp ../../py_diaid/data/*.fasta dist/py_diaid/data +# cp ../../pydiaid/data/*.fasta dist/pydiaid/data # Wrapping the pyinstaller folder in a .pkg package -mkdir -p dist/py_diaid/Contents/Resources -cp ../logos/alpha_logo.icns dist/py_diaid/Contents/Resources -mv dist/py_diaid_gui dist/py_diaid/Contents/MacOS -cp Info.plist dist/py_diaid/Contents -cp py_diaid_terminal dist/py_diaid/Contents/MacOS +mkdir -p dist/pydiaid/Contents/Resources +cp ../logos/alpha_logo.icns dist/pydiaid/Contents/Resources +mv dist/pydiaid_gui dist/pydiaid/Contents/MacOS +cp Info.plist dist/pydiaid/Contents +cp pydiaid_terminal dist/pydiaid/Contents/MacOS cp ../../LICENSE.txt Resources/LICENSE.txt cp ../logos/alpha_logo.png Resources/alpha_logo.png chmod 777 scripts/* -pkgbuild --root dist/py_diaid --identifier de.mpg.biochem.py_diaid.app --version 0.3.0 --install-location /Applications/py_diAID.app --scripts scripts py_diAID.pkg -productbuild --distribution distribution.xml --resources Resources --package-path py_diAID.pkg dist/py_diaid_gui_installer_macos.pkg +pkgbuild --root dist/pydiaid --identifier de.mpg.biochem.pydiaid.app --version 0.3.0 --install-location /Applications/py_diAID.app --scripts scripts py_diAID.pkg +productbuild --distribution distribution.xml --resources Resources --package-path py_diAID.pkg dist/pydiaid_gui_installer_macos.pkg diff --git a/release/one_click_macos_gui/py_diaid_terminal b/release/one_click_macos_gui/py_diaid_terminal index bcef270..e5ae6b9 100644 --- a/release/one_click_macos_gui/py_diaid_terminal +++ b/release/one_click_macos_gui/py_diaid_terminal @@ -1,3 +1,3 @@ #!/bin/sh -open -a Terminal "${BASH_SOURCE%/*}/py_diaid_gui" +open -a Terminal "${BASH_SOURCE%/*}/pydiaid_gui" diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 958f013..274abaf 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -9,7 +9,7 @@ rm -rf build # Creating a conda environment conda create -n py_installer python=3.8 -y -conda activate py_diaid_installer +conda activate pydiaid_installer # Creating the wheel python setup.py sdist bdist_wheel @@ -17,16 +17,16 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/py_diaid-0.0.3-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.3-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 -pyinstaller ../pyinstaller/py_diaid.spec -y +pyinstaller ../pyinstaller/pydiaid.spec -y conda deactivate # If needed, include additional source such as e.g.: -# cp ../../py_diaid/data/*.fasta dist/py_diaid/data +# cp ../../pydiaid/data/*.fasta dist/pydiaid/data # Wrapping the pyinstaller folder in a .exe package -"C:\Program Files (x86)\Inno Setup 6\ISCC.exe" py_diaid_innoinstaller.iss +"C:\Program Files (x86)\Inno Setup 6\ISCC.exe" pydiaid_innoinstaller.iss # WARNING: this assumes a static location for innosetup diff --git a/release/one_click_windows_gui/py_diaid_innoinstaller.iss b/release/one_click_windows_gui/py_diaid_innoinstaller.iss index 50495b9..1ff4c4c 100644 --- a/release/one_click_windows_gui/py_diaid_innoinstaller.iss +++ b/release/one_click_windows_gui/py_diaid_innoinstaller.iss @@ -4,13 +4,13 @@ #define MyAppName "py_diAID" #define MyAppVersion "0.0.3" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" -#define MyAppURL "https://github.com/MannLabs/py_diaid" -#define MyAppExeName "py_diaid_gui.exe" +#define MyAppURL "https://github.com/MannLabs/pydiaid" +#define MyAppExeName "pydiaid_gui.exe" [Setup] ; NOTE: The value of AppId uniquely identifies this application. Do not use the same AppId value in installers for other applications. ; (To generate a new GUID, click Tools | Generate GUID inside the IDE.) -AppId={{py_diaid_Mann_Labs_MPI} +AppId={{pydiaid_Mann_Labs_MPI} AppName={#MyAppName} AppVersion={#MyAppVersion} ;AppVerName={#MyAppName} {#MyAppVersion} @@ -25,7 +25,7 @@ LicenseFile=..\..\LICENSE.txt PrivilegesRequired=lowest PrivilegesRequiredOverridesAllowed=dialog OutputDir=dist -OutputBaseFilename=py_diaid_gui_installer_windows +OutputBaseFilename=pydiaid_gui_installer_windows SetupIconFile=..\logos\alpha_logo.ico Compression=lzma SolidCompression=yes @@ -38,8 +38,8 @@ Name: "english"; MessagesFile: "compiler:Default.isl" Name: "desktopicon"; Description: "{cm:CreateDesktopIcon}"; GroupDescription: "{cm:AdditionalIcons}"; Flags: unchecked [Files] -Source: "dist\py_diaid_gui\{#MyAppExeName}"; DestDir: "{app}"; Flags: ignoreversion -Source: "dist\py_diaid_gui\*"; DestDir: "{app}"; Flags: ignoreversion recursesubdirs createallsubdirs +Source: "dist\pydiaid_gui\{#MyAppExeName}"; DestDir: "{app}"; Flags: ignoreversion +Source: "dist\pydiaid_gui\*"; DestDir: "{app}"; Flags: ignoreversion recursesubdirs createallsubdirs ; NOTE: Don't use "Flags: ignoreversion" on any shared system files [Icons] diff --git a/release/pyinstaller/py_diaid.spec b/release/pyinstaller/py_diaid.spec index 1f2bd9f..cda8d34 100644 --- a/release/pyinstaller/py_diaid.spec +++ b/release/pyinstaller/py_diaid.spec @@ -7,21 +7,21 @@ from PyInstaller.building.build_main import Analysis, PYZ, EXE, COLLECT, BUNDLE, import PyInstaller.utils.hooks import pkg_resources import importlib.metadata -import py_diaid +import pydiaid ##################### User definitions -exe_name = 'py_diaid_gui' -script_name = 'py_diaid_pyinstaller.py' +exe_name = 'pydiaid_gui' +script_name = 'pydiaid_pyinstaller.py' if sys.platform[:6] == "darwin": icon = '../logos/alpha_logo.icns' else: icon = '../logos/alpha_logo.ico' block_cipher = None location = os.getcwd() -project = "py_diaid" +project = "pydiaid" remove_tests = True -bundle_name = "py_diaid" +bundle_name = "pydiaid" ##################### diff --git a/release/pyinstaller/py_diaid_pyinstaller.py b/release/pyinstaller/py_diaid_pyinstaller.py index 6f0fc36..9e08524 100644 --- a/release/pyinstaller/py_diaid_pyinstaller.py +++ b/release/pyinstaller/py_diaid_pyinstaller.py @@ -1,5 +1,5 @@ if __name__ == "__main__": - import py_diaid.gui + import pydiaid.gui import multiprocessing multiprocessing.freeze_support() - py_diaid.gui.run() + pydiaid.gui.run() diff --git a/release/pypi/install_pypi_wheel.sh b/release/pypi/install_pypi_wheel.sh index 876cb53..6d46a3e 100644 --- a/release/pypi/install_pypi_wheel.sh +++ b/release/pypi/install_pypi_wheel.sh @@ -1,5 +1,5 @@ -conda create -n py_diaid_pip_test python=3.8 -y -conda activate py_diaid_pip_test -pip install "py_diaid[stable]" -py_diaid +conda create -n pydiaid_pip_test python=3.8 -y +conda activate pydiaid_pip_test +pip install "pydiaid[stable]" +pydiaid conda deactivate diff --git a/release/pypi/install_test_pypi_wheel.sh b/release/pypi/install_test_pypi_wheel.sh index 37571bf..7a68a76 100644 --- a/release/pypi/install_test_pypi_wheel.sh +++ b/release/pypi/install_test_pypi_wheel.sh @@ -1,5 +1,5 @@ -conda create -n py_diaid_pip_test python=3.8 -y -conda activate py_diaid_pip_test -pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "py_diaid[stable]" -py_diaid +conda create -n pydiaid_pip_test python=3.8 -y +conda activate pydiaid_pip_test +pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "pydiaid[stable]" +pydiaid conda deactivate diff --git a/release/pypi/prepare_pypi_wheel.sh b/release/pypi/prepare_pypi_wheel.sh index 1bd28a2..8ee0d73 100644 --- a/release/pypi/prepare_pypi_wheel.sh +++ b/release/pypi/prepare_pypi_wheel.sh @@ -1,6 +1,6 @@ cd ../.. -conda create -n py_diaid_pypi_wheel python=3.8 -conda activate py_diaid_pypi_wheel +conda create -n pydiaid_pypi_wheel python=3.8 +conda activate pydiaid_pypi_wheel pip install twine rm -rf dist rm -rf build diff --git a/setup.py b/setup.py index 88f3c24..2ffa09c 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ import re import os # local -import py_diaid as package2install +import pydiaid as package2install def get_long_description(): diff --git a/tests/run_tests.sh b/tests/run_tests.sh index f869207..2d9a018 100644 --- a/tests/run_tests.sh +++ b/tests/run_tests.sh @@ -1,4 +1,4 @@ -conda activate py_diaid +conda activate pydiaid python -m unittest test_cli python -m unittest test_gui conda deactivate diff --git a/tests/test_cli.py b/tests/test_cli.py index bc60254..cee94be 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,11 +1,11 @@ #!python -m unittest tests.test_utils -"""This module provides unit tests for py_diaid.cli.""" +"""This module provides unit tests for pydiaid.cli.""" # builtin import unittest # local -import py_diaid.cli +import pydiaid.cli if __name__ == "__main__": unittest.main() diff --git a/tests/test_gui.py b/tests/test_gui.py index c9f4323..5a120b4 100644 --- a/tests/test_gui.py +++ b/tests/test_gui.py @@ -1,11 +1,11 @@ #!python -m unittest tests.test_utils -"""This module provides unit tests for py_diaid.gui.""" +"""This module provides unit tests for pydiaid.gui.""" # builtin import unittest # local -import py_diaid.gui +import pydiaid.gui if __name__ == "__main__": unittest.main() From c4eec306f00e8073865bd0f743d52bf91cc13c47 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 16:13:47 +0100 Subject: [PATCH 11/58] FIX: rename to pydiaid --- .../one_click_macos_gui/{py_diaid_terminal => pydiaid_terminal} | 0 .../{py_diaid_innoinstaller.iss => pydiaid_innoinstaller.iss} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename release/one_click_macos_gui/{py_diaid_terminal => pydiaid_terminal} (100%) rename release/one_click_windows_gui/{py_diaid_innoinstaller.iss => pydiaid_innoinstaller.iss} (100%) diff --git a/release/one_click_macos_gui/py_diaid_terminal b/release/one_click_macos_gui/pydiaid_terminal similarity index 100% rename from release/one_click_macos_gui/py_diaid_terminal rename to release/one_click_macos_gui/pydiaid_terminal diff --git a/release/one_click_windows_gui/py_diaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss similarity index 100% rename from release/one_click_windows_gui/py_diaid_innoinstaller.iss rename to release/one_click_windows_gui/pydiaid_innoinstaller.iss From 4724b9af669668e3186e22e977a7c01850750cdc Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 16:13:58 +0100 Subject: [PATCH 12/58] =?UTF-8?q?Bump=20version:=200.0.3=20=E2=86=92=200.0?= =?UTF-8?q?.4?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- misc/bumpversion.cfg | 4 ++-- pydiaid/__init__.py | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 2 +- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/pydiaid_innoinstaller.iss | 2 +- 9 files changed, 11 insertions(+), 11 deletions(-) diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index a9d5897..d2d6015 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,9 +1,9 @@ [bumpversion] -current_version = 0.0.3 +current_version = 0.0.4 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? -serialize = +serialize = {major}.{minor}.{patch} {major}.{minor}.{patch} diff --git a/pydiaid/__init__.py b/pydiaid/__init__.py index eea0d1e..9a4e19a 100644 --- a/pydiaid/__init__.py +++ b/pydiaid/__init__.py @@ -2,7 +2,7 @@ __project__ = "pydiaid" -__version__ = "0.0.3" +__version__ = "0.0.4" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index 3aad531..ebf0215 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: pydiaid -Version: 0.0.3 +Version: 0.0.4 Architecture: all Maintainer: Mann Labs Description: py_diAID diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index 0f805e0..be0ab8c 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.3-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.4-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index d8fff83..2d80d0b 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - pydiaid.0.0.3 + pydiaid.0.0.4 CFBundleShortVersionString - 0.0.3 + 0.0.4 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 7d9c7b0..3af9447 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/pydiaid-0.0.3-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.4-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index adcb914..be93f7e 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - py_diAID 0.0.3 + py_diAID 0.0.4 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 274abaf..6f7b1b4 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.3-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.4-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_windows_gui/pydiaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss index 1ff4c4c..7b893b6 100644 --- a/release/one_click_windows_gui/pydiaid_innoinstaller.iss +++ b/release/one_click_windows_gui/pydiaid_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "py_diAID" -#define MyAppVersion "0.0.3" +#define MyAppVersion "0.0.4" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" #define MyAppURL "https://github.com/MannLabs/pydiaid" #define MyAppExeName "pydiaid_gui.exe" From f06e854a8c3f7912c1d0360224a932f3b937e99c Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 16:16:44 +0100 Subject: [PATCH 13/58] FIX: reinclude gitignored files --- .gitignore | 3 +- pydiaid/lib/default_parameters.json | 73 +++++++++++++++++++++++++++ pydiaid/static/DIAParameterspy3TC.txt | 68 +++++++++++++++++++++++++ 3 files changed, 142 insertions(+), 2 deletions(-) create mode 100644 pydiaid/lib/default_parameters.json create mode 100644 pydiaid/static/DIAParameterspy3TC.txt diff --git a/.gitignore b/.gitignore index 4e0cdd2..9bdd43d 100644 --- a/.gitignore +++ b/.gitignore @@ -133,6 +133,5 @@ pydiaid/logs *.DS_Store *sandbox* pydiaid/input -pydiaid/static -pydiaid/lib +pydiaid/static/AlphaPept_results.csv output_pydiaid diff --git a/pydiaid/lib/default_parameters.json b/pydiaid/lib/default_parameters.json new file mode 100644 index 0000000..5b11e05 --- /dev/null +++ b/pydiaid/lib/default_parameters.json @@ -0,0 +1,73 @@ +{ + "input": { + "save_at": "D:\\output_test2", + "PTM": "None", + "library_name": "D:\\Input_for_pydiaid\\library21min24fractions.tsv", + "analysis_software": "MS_Fragger", + "diaPASEF_method_only_used_for_evaluate": "D:/pydiaid/pydiaid/static/DIAParameterspy3TC.txt" + }, + "method_parameters": { + "mz": [ + 300, + 1200 + ], + "ion_mobility": [ + 0.6, + 1.6 + ], + "num_dia_pasef_scans": 12, + "im_steps": 2, + "overlap": 0, + "shift_of_final_method": 0.022, + "scan_area_A1_A2_B1_B2_only_used_for_create": [ + 0.68, + 1.04, + 0.9, + 1.3 + ], + "scan_area_A1_A2_B1_B2_only_used_for_specific_diaPASEF": [ + 0.5752575470522289, + 0.7128990257352522, + 1.4241557523881094, + 1.6972373193612142 + ] + }, + "graphs": { + "plot_mz": [ + 250, + 1250 + ], + "plot_IM": [ + 0.6, + 1.6 + ], + "numbins": 50, + "window_frame_color": "black", + "window_color": "white", + "window_transparency": 0.5 + }, + "optimizer": { + "optimizer": "Gauss", + "n_random_starts": null, + "n_calls": 5, + "n_start": 2, + "initial_points": 2, + "YA1": [ + 0.5, + 0.9 + ], + "YA2": [ + 0.6, + 1.0 + ], + "YB1": [ + 0.9, + 1.5 + ], + "YB2": [ + 1.0, + 1.8 + ], + "evaluation_parameter": "No. of covered precursors" + } +} diff --git a/pydiaid/static/DIAParameterspy3TC.txt b/pydiaid/static/DIAParameterspy3TC.txt new file mode 100644 index 0000000..593c56b --- /dev/null +++ b/pydiaid/static/DIAParameterspy3TC.txt @@ -0,0 +1,68 @@ +#---------------------------------------------------------------------------------------------------- +# MS Type | Cycle Id | 1/K0 Begin [Vs/cm2] | 1/K0 End [Vs/cm2] | Start Mass [m/z] | End Mass [m/z] | CE [eV] +#---------------------------------------------------------------------------------------------------- + MS1, 0, - , - , - , - , - + PASEF, 1, 1.22, 1.40, 1000.0, 1025.0, - + PASEF, 1, 1.04, 1.22, 800.0, 825.0, - + PASEF, 1, 0.87, 1.04, 600.0, 625.0, - + PASEF, 1, 0.69, 0.87, 400.0, 425.0, - + PASEF, 2, 1.24, 1.41, 1025.0, 1050.0, - + PASEF, 2, 1.06, 1.24, 825.0, 850.0, - + PASEF, 2, 0.89, 1.06, 625.0, 650.0, - + PASEF, 2, 0.71, 0.89, 425.0, 450.0, - + PASEF, 3, 1.25, 1.42, 1050.0, 1075.0, - + PASEF, 3, 1.07, 1.25, 850.0, 875.0, - + PASEF, 3, 0.90, 1.07, 650.0, 675.0, - + PASEF, 3, 0.73, 0.90, 450.0, 475.0, - + PASEF, 4, 1.26, 1.43, 1075.0, 1100.0, - + PASEF, 4, 1.09, 1.26, 875.0, 900.0, - + PASEF, 4, 0.92, 1.09, 675.0, 700.0, - + PASEF, 4, 0.75, 0.92, 475.0, 500.0, - + PASEF, 5, 1.27, 1.44, 1100.0, 1125.0, - + PASEF, 5, 1.10, 1.27, 900.0, 925.0, - + PASEF, 5, 0.94, 1.10, 700.0, 725.0, - + PASEF, 5, 0.77, 0.94, 500.0, 525.0, - + PASEF, 6, 1.29, 1.45, 1125.0, 1150.0, - + PASEF, 6, 1.12, 1.29, 925.0, 950.0, - + PASEF, 6, 0.96, 1.12, 725.0, 750.0, - + PASEF, 6, 0.79, 0.96, 525.0, 550.0, - + PASEF, 7, 1.30, 1.46, 1150.0, 1175.0, - + PASEF, 7, 1.14, 1.30, 950.0, 975.0, - + PASEF, 7, 0.97, 1.14, 750.0, 775.0, - + PASEF, 7, 0.81, 0.97, 550.0, 575.0, - + PASEF, 8, 1.31, 1.47, 1175.0, 1200.0, - + PASEF, 8, 1.15, 1.31, 975.0, 1000.0, - + PASEF, 8, 0.99, 1.15, 775.0, 800.0, - + PASEF, 8, 0.83, 0.99, 575.0, 600.0, - + PASEF, 9, 1.10, 1.28, 1000.0, 1025.0, - + PASEF, 9, 0.92, 1.10, 800.0, 825.0, - + PASEF, 9, 0.75, 0.92, 600.0, 625.0, - + PASEF, 9, 0.57, 0.75, 400.0, 425.0, - + PASEF, 10, 1.12, 1.29, 1025.0, 1050.0, - + PASEF, 10, 0.94, 1.12, 825.0, 850.0, - + PASEF, 10, 0.77, 0.94, 625.0, 650.0, - + PASEF, 10, 0.59, 0.77, 425.0, 450.0, - + PASEF, 11, 1.13, 1.30, 1050.0, 1075.0, - + PASEF, 11, 0.95, 1.13, 850.0, 875.0, - + PASEF, 11, 0.78, 0.95, 650.0, 675.0, - + PASEF, 11, 0.61, 0.78, 450.0, 475.0, - + PASEF, 12, 1.14, 1.31, 1075.0, 1100.0, - + PASEF, 12, 0.97, 1.14, 875.0, 900.0, - + PASEF, 12, 0.80, 0.97, 675.0, 700.0, - + PASEF, 12, 0.63, 0.80, 475.0, 500.0, - + PASEF, 13, 1.15, 1.32, 1100.0, 1125.0, - + PASEF, 13, 0.98, 1.15, 900.0, 925.0, - + PASEF, 13, 0.82, 0.98, 700.0, 725.0, - + PASEF, 13, 0.65, 0.82, 500.0, 525.0, - + PASEF, 14, 1.17, 1.33, 1125.0, 1150.0, - + PASEF, 14, 1.00, 1.17, 925.0, 950.0, - + PASEF, 14, 0.84, 1.00, 725.0, 750.0, - + PASEF, 14, 0.67, 0.84, 525.0, 550.0, - + PASEF, 15, 1.18, 1.34, 1150.0, 1175.0, - + PASEF, 15, 1.02, 1.18, 950.0, 975.0, - + PASEF, 15, 0.85, 1.02, 750.0, 775.0, - + PASEF, 15, 0.69, 0.85, 550.0, 575.0, - + PASEF, 16, 1.19, 1.35, 1175.0, 1200.0, - + PASEF, 16, 1.03, 1.19, 975.0, 1000.0, - + PASEF, 16, 0.87, 1.03, 775.0, 800.0, - + PASEF, 16, 0.71, 0.87, 575.0, 600.0, - From c4fb0116307663f55df20c1dd5b3ba6736ef6c6d Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 16:22:12 +0100 Subject: [PATCH 14/58] FIX: release workflows typos --- release/pyinstaller/{py_diaid.spec => pydiaid.spec} | 0 .../{py_diaid_pyinstaller.py => pydiaid_pyinstaller.py} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename release/pyinstaller/{py_diaid.spec => pydiaid.spec} (100%) rename release/pyinstaller/{py_diaid_pyinstaller.py => pydiaid_pyinstaller.py} (100%) diff --git a/release/pyinstaller/py_diaid.spec b/release/pyinstaller/pydiaid.spec similarity index 100% rename from release/pyinstaller/py_diaid.spec rename to release/pyinstaller/pydiaid.spec diff --git a/release/pyinstaller/py_diaid_pyinstaller.py b/release/pyinstaller/pydiaid_pyinstaller.py similarity index 100% rename from release/pyinstaller/py_diaid_pyinstaller.py rename to release/pyinstaller/pydiaid_pyinstaller.py From 55048f787816c887d9494296fb022665fd41ee92 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 16:22:21 +0100 Subject: [PATCH 15/58] =?UTF-8?q?Bump=20version:=200.0.4=20=E2=86=92=200.0?= =?UTF-8?q?.5?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- misc/bumpversion.cfg | 2 +- pydiaid/__init__.py | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 2 +- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/pydiaid_innoinstaller.iss | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index d2d6015..a5b3ec6 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.4 +current_version = 0.0.5 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/pydiaid/__init__.py b/pydiaid/__init__.py index 9a4e19a..b88fde2 100644 --- a/pydiaid/__init__.py +++ b/pydiaid/__init__.py @@ -2,7 +2,7 @@ __project__ = "pydiaid" -__version__ = "0.0.4" +__version__ = "0.0.5" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index ebf0215..f86a405 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: pydiaid -Version: 0.0.4 +Version: 0.0.5 Architecture: all Maintainer: Mann Labs Description: py_diAID diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index be0ab8c..5165678 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.4-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.5-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index 2d80d0b..4620c59 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - pydiaid.0.0.4 + pydiaid.0.0.5 CFBundleShortVersionString - 0.0.4 + 0.0.5 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 3af9447..1e36af5 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/pydiaid-0.0.4-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.5-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index be93f7e..1e3a5e8 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - py_diAID 0.0.4 + py_diAID 0.0.5 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 6f7b1b4..7488e17 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.4-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.5-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_windows_gui/pydiaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss index 7b893b6..2a3292d 100644 --- a/release/one_click_windows_gui/pydiaid_innoinstaller.iss +++ b/release/one_click_windows_gui/pydiaid_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "py_diAID" -#define MyAppVersion "0.0.4" +#define MyAppVersion "0.0.5" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" #define MyAppURL "https://github.com/MannLabs/pydiaid" #define MyAppExeName "pydiaid_gui.exe" From 339379cfd1058ac5a7fb31093fef65a86ea6f0e3 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 16:28:18 +0100 Subject: [PATCH 16/58] FIX windows release typo --- release/one_click_windows_gui/create_installer_windows.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 7488e17..dea0ec5 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -8,7 +8,7 @@ rm -rf dist rm -rf build # Creating a conda environment -conda create -n py_installer python=3.8 -y +conda create -n pydiaid_installer python=3.8 -y conda activate pydiaid_installer # Creating the wheel From 542124de6f741cf6f41c919a9206ba88270f7167 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 16:28:27 +0100 Subject: [PATCH 17/58] =?UTF-8?q?Bump=20version:=200.0.5=20=E2=86=92=200.0?= =?UTF-8?q?.6?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- misc/bumpversion.cfg | 2 +- pydiaid/__init__.py | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 2 +- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/pydiaid_innoinstaller.iss | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index a5b3ec6..1477dd6 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.5 +current_version = 0.0.6 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/pydiaid/__init__.py b/pydiaid/__init__.py index b88fde2..9faba0a 100644 --- a/pydiaid/__init__.py +++ b/pydiaid/__init__.py @@ -2,7 +2,7 @@ __project__ = "pydiaid" -__version__ = "0.0.5" +__version__ = "0.0.6" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index f86a405..976f495 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: pydiaid -Version: 0.0.5 +Version: 0.0.6 Architecture: all Maintainer: Mann Labs Description: py_diAID diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index 5165678..d3859ba 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.5-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.6-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index 4620c59..082c5ab 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - pydiaid.0.0.5 + pydiaid.0.0.6 CFBundleShortVersionString - 0.0.5 + 0.0.6 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 1e36af5..fbcf431 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/pydiaid-0.0.5-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.6-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index 1e3a5e8..f165395 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - py_diAID 0.0.5 + py_diAID 0.0.6 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index dea0ec5..1fceca7 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.5-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.6-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_windows_gui/pydiaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss index 2a3292d..d510433 100644 --- a/release/one_click_windows_gui/pydiaid_innoinstaller.iss +++ b/release/one_click_windows_gui/pydiaid_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "py_diAID" -#define MyAppVersion "0.0.5" +#define MyAppVersion "0.0.6" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" #define MyAppURL "https://github.com/MannLabs/pydiaid" #define MyAppExeName "pydiaid_gui.exe" From ee5e748576ab83d671241ee7a5f6a7c2492b3d79 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 16:58:44 +0100 Subject: [PATCH 18/58] FIX: windows installer --- release/pyinstaller/pydiaid.spec | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/release/pyinstaller/pydiaid.spec b/release/pyinstaller/pydiaid.spec index cda8d34..10e29f3 100644 --- a/release/pyinstaller/pydiaid.spec +++ b/release/pyinstaller/pydiaid.spec @@ -152,6 +152,7 @@ else: ) import shutil import sklearn.neighbors._partition_nodes + import sklearn.utils._typedefs if sys.platform[:6] == "darwin": import cmath shutil.copyfile( @@ -169,3 +170,14 @@ else: sklearn.neighbors._partition_nodes.__file__, new_location ) + new_location = os.path.join( + "dist", + exe_name, + "sklearn", + "utils", + os.path.basename(sklearn.utils._typedefs.__file__), + ) + shutil.copyfile( + sklearn.utils._typedefs.__file_, + new_location + ) From 7de0c60f2197b956a8bb6f2085f01b1bcb620e31 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Tue, 22 Feb 2022 16:59:00 +0100 Subject: [PATCH 19/58] =?UTF-8?q?Bump=20version:=200.0.6=20=E2=86=92=200.0?= =?UTF-8?q?.7?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- misc/bumpversion.cfg | 2 +- pydiaid/__init__.py | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 2 +- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/pydiaid_innoinstaller.iss | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index 1477dd6..b943741 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.6 +current_version = 0.0.7 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/pydiaid/__init__.py b/pydiaid/__init__.py index 9faba0a..4a1d86d 100644 --- a/pydiaid/__init__.py +++ b/pydiaid/__init__.py @@ -2,7 +2,7 @@ __project__ = "pydiaid" -__version__ = "0.0.6" +__version__ = "0.0.7" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index 976f495..1c6c92d 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: pydiaid -Version: 0.0.6 +Version: 0.0.7 Architecture: all Maintainer: Mann Labs Description: py_diAID diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index d3859ba..3102276 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.6-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.7-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index 082c5ab..b1bc69b 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - pydiaid.0.0.6 + pydiaid.0.0.7 CFBundleShortVersionString - 0.0.6 + 0.0.7 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index fbcf431..1b228d9 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/pydiaid-0.0.6-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.7-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index f165395..6b406e1 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - py_diAID 0.0.6 + py_diAID 0.0.7 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 1fceca7..9e7b690 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.6-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.7-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_windows_gui/pydiaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss index d510433..9eaab72 100644 --- a/release/one_click_windows_gui/pydiaid_innoinstaller.iss +++ b/release/one_click_windows_gui/pydiaid_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "py_diAID" -#define MyAppVersion "0.0.6" +#define MyAppVersion "0.0.7" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" #define MyAppURL "https://github.com/MannLabs/pydiaid" #define MyAppExeName "pydiaid_gui.exe" From d7a9074d09bd157f81adbfb27b2be35fc1b2fbc1 Mon Sep 17 00:00:00 2001 From: Sander Willems Date: Tue, 15 Mar 2022 16:55:33 +0100 Subject: [PATCH 20/58] FIX: typo in installer --- release/pyinstaller/pydiaid.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/release/pyinstaller/pydiaid.spec b/release/pyinstaller/pydiaid.spec index 10e29f3..d65ffec 100644 --- a/release/pyinstaller/pydiaid.spec +++ b/release/pyinstaller/pydiaid.spec @@ -178,6 +178,6 @@ else: os.path.basename(sklearn.utils._typedefs.__file__), ) shutil.copyfile( - sklearn.utils._typedefs.__file_, + sklearn.utils._typedefs.__file__, new_location ) From f82fa0893b62ced97d43e4700492f71dfbb60ce3 Mon Sep 17 00:00:00 2001 From: Sander Willems Date: Tue, 15 Mar 2022 16:56:17 +0100 Subject: [PATCH 21/58] =?UTF-8?q?Bump=20version:=200.0.7=20=E2=86=92=200.0?= =?UTF-8?q?.8?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- misc/bumpversion.cfg | 2 +- pydiaid/__init__.py | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 2 +- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/pydiaid_innoinstaller.iss | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index b943741..74d1b67 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.7 +current_version = 0.0.8 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/pydiaid/__init__.py b/pydiaid/__init__.py index 4a1d86d..280ef4b 100644 --- a/pydiaid/__init__.py +++ b/pydiaid/__init__.py @@ -2,7 +2,7 @@ __project__ = "pydiaid" -__version__ = "0.0.7" +__version__ = "0.0.8" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index 1c6c92d..ab28cd2 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: pydiaid -Version: 0.0.7 +Version: 0.0.8 Architecture: all Maintainer: Mann Labs Description: py_diAID diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index 3102276..d16b00f 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.7-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.8-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index b1bc69b..f9f48ac 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - pydiaid.0.0.7 + pydiaid.0.0.8 CFBundleShortVersionString - 0.0.7 + 0.0.8 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 1b228d9..9eb5441 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/pydiaid-0.0.7-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.8-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index 6b406e1..8c170b7 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - py_diAID 0.0.7 + py_diAID 0.0.8 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 9e7b690..722db03 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.7-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.8-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_windows_gui/pydiaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss index 9eaab72..a7e507a 100644 --- a/release/one_click_windows_gui/pydiaid_innoinstaller.iss +++ b/release/one_click_windows_gui/pydiaid_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "py_diAID" -#define MyAppVersion "0.0.7" +#define MyAppVersion "0.0.8" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" #define MyAppURL "https://github.com/MannLabs/pydiaid" #define MyAppExeName "pydiaid_gui.exe" From 8fd2d29fc251fc79e2d1662f9d0ec707b3062500 Mon Sep 17 00:00:00 2001 From: Sander Willems Date: Tue, 15 Mar 2022 17:21:50 +0100 Subject: [PATCH 22/58] FIX: downgrade scipy for mac --- requirements/requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 8a7b3d1..0fef9d1 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -6,3 +6,4 @@ pandas==1.3.4 matplotlib==3.4.3 seaborn==0.11.2 scikit-optimize==0.9.0 +scipy==1.7.3 From f7eb489f1028f03ec1c49a960d718870ec842229 Mon Sep 17 00:00:00 2001 From: Sander Willems Date: Tue, 15 Mar 2022 17:22:21 +0100 Subject: [PATCH 23/58] =?UTF-8?q?Bump=20version:=200.0.8=20=E2=86=92=200.0?= =?UTF-8?q?.9?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- misc/bumpversion.cfg | 2 +- pydiaid/__init__.py | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 2 +- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/pydiaid_innoinstaller.iss | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index 74d1b67..ac49b9f 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.8 +current_version = 0.0.9 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/pydiaid/__init__.py b/pydiaid/__init__.py index 280ef4b..df21d1c 100644 --- a/pydiaid/__init__.py +++ b/pydiaid/__init__.py @@ -2,7 +2,7 @@ __project__ = "pydiaid" -__version__ = "0.0.8" +__version__ = "0.0.9" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index ab28cd2..d087595 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: pydiaid -Version: 0.0.8 +Version: 0.0.9 Architecture: all Maintainer: Mann Labs Description: py_diAID diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index d16b00f..fed57fc 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.8-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.9-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index f9f48ac..64849fd 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - pydiaid.0.0.8 + pydiaid.0.0.9 CFBundleShortVersionString - 0.0.8 + 0.0.9 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 9eb5441..23f8ade 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/pydiaid-0.0.8-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.9-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index 8c170b7..d5d6a61 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - py_diAID 0.0.8 + py_diAID 0.0.9 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 722db03..d838a2c 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.8-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.9-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_windows_gui/pydiaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss index a7e507a..32162c8 100644 --- a/release/one_click_windows_gui/pydiaid_innoinstaller.iss +++ b/release/one_click_windows_gui/pydiaid_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "py_diAID" -#define MyAppVersion "0.0.8" +#define MyAppVersion "0.0.9" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" #define MyAppURL "https://github.com/MannLabs/pydiaid" #define MyAppExeName "pydiaid_gui.exe" From ed85e824607884ac17a81a16e979e6ae6f35dfed Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 18 Mar 2022 12:45:25 +0100 Subject: [PATCH 24/58] FIX: delete unnecessary import of seaborn package --- pydiaid/graphs.py | 1 - 1 file changed, 1 deletion(-) diff --git a/pydiaid/graphs.py b/pydiaid/graphs.py index 46ecdd1..5f19755 100644 --- a/pydiaid/graphs.py +++ b/pydiaid/graphs.py @@ -9,7 +9,6 @@ import matplotlib.pyplot as plt import matplotlib as mpl from matplotlib.collections import PatchCollection -import seaborn as sns # for suppressing warnings import warnings From f60a5dd98fb2237edfb639d312936ddc81b1c9ab Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 18 Mar 2022 12:45:52 +0100 Subject: [PATCH 25/58] FIX: changed value of widges in gui --- pydiaid/gui.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pydiaid/gui.py b/pydiaid/gui.py index 49c98fc..830eee2 100644 --- a/pydiaid/gui.py +++ b/pydiaid/gui.py @@ -564,7 +564,7 @@ def __init__(self, data, description): ) self.shift_of_final_method = pn.widgets.FloatInput( name='Shift of the final acquisition scheme (in IM dimension)', - start=0.0, + start=-0.5, end=1.0, value=method_conf['method_parameters']['shift_of_final_method'], step=0.01, From 47b5a9caf8d58a58e36146524a3d490b85419c68 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 18 Mar 2022 12:46:56 +0100 Subject: [PATCH 26/58] FIX: filter out singly charged ions for method creation --- pydiaid/main.py | 4 +++- pydiaid/method_optimizer.py | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/pydiaid/main.py b/pydiaid/main.py index 1fbd6ef..f83d931 100644 --- a/pydiaid/main.py +++ b/pydiaid/main.py @@ -161,8 +161,10 @@ def create_final_method( file_name_method = method_conf["input"]["save_at"] + '/final_method/diaPASEF_method.txt' # create the diaPASEF method scheme; dim[0],dim[1],dim[2],dim[3] == A1, A2, # B1, B2. + library_reduced = library[library['Charge'] != 1] + df_parameters_final = method_creator.method_creation( - library["mz"], + library_reduced["mz"], method_parameters, dim[0] + method_parameters["shift_of_final_method"], dim[1] + method_parameters["shift_of_final_method"], diff --git a/pydiaid/method_optimizer.py b/pydiaid/method_optimizer.py index ef655c7..8efb53e 100644 --- a/pydiaid/method_optimizer.py +++ b/pydiaid/method_optimizer.py @@ -136,8 +136,10 @@ def single_optimization_run( """ # create the diaPASEF method scheme; dim[0],dim[1],dim[2],dim[3] == A1, A2, # B1, B2. Calculate the optimization parameter. + library_reduced = library[library['Charge'] != 1] + df_parameters_final = method_creator.method_creation( - library["mz"], + library_reduced["mz"], method_parameters, dim[0], dim[0]+dim[1], From 4d58a7ab953655da46f3d434d25b77926a6e75a9 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Wed, 6 Apr 2022 13:46:15 +0200 Subject: [PATCH 27/58] FIX: updated readme. --- README.md | 69 +++++++++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 59 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 647a947..74e8e87 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ ![GUI and PyPi releases](https://github.com/MannLabs/pydiaid/workflows/Publish%20on%20PyPi%20and%20release%20on%20GitHub/badge.svg) # py_diAID -An open-source Python package of the AlphaPept ecosystem from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann). To enable all hyperlinks in this document, please view it at [GitHub](https://github.com/MannLabs/pydiaid). +The [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann) developed py_diAID, that generates dia-PASEF methods with an optimal window design. py_diAID stands for an open-source Python package for Data-Independent Acquisition with an Automated Isolation Design. To enable all hyperlinks in this document, please view it at [GitHub](https://github.com/MannLabs/pydiaid). * [**About**](#about) * [**License**](#license) @@ -22,12 +22,15 @@ An open-source Python package of the AlphaPept ecosystem from the [Mann Labs at --- ## About -An open-source Python package of the AlphaPept ecosystem from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann). +Data-independent acquisition coupled with parallel accumulation – serial fragmentation (dia-PASEF) has gained increasing attention from proteomics researchers over the last years. dia-PASEF offers comprehensive proteome coverage, a high degree of reproducibility, and quantitative accuracy while using a much higher ion beam proportion than conventional DIA methods. Previous tools generated dia-PASEF methods with equidistant isolation widths and required a fitting of the window design to the precursor density cloud by hand. We present py_diAID, a Python-based package for Data-Independent Acquisition offering an Automated Isolation Design. py_diAID generates optimal dia-PASEF methods with variable isolation widths adjusted to the precursor density in m/z and automatically, optimally placed in the m/z – ion mobility (IM) plane. Variable isolation widths enable short acquisition cycles while covering the complete m/z-IM-range essentially. We found dia-PASEF methods, generated with py_diAID, beneficial for optimizing proteomics workflows based on cell lines (HeLa) or clinical samples such as CSF and Plasma and for studying post-translational modifications such as phosphorylation. +We offer py_diAID as a Python module, command-line tool, and graphical user interface on all major operating systems under an Apache 2.0 license. py_diAID generates dia-PASEF methods with an optimal window design. It also allows for quality control of the precursors’ distribution of a dataset in the m/z-ion mobility plane and evaluating the suitability of already existing dia-PASEF methods for the individual experiment. + +py_diAID is an open-source Python package from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann). --- ## License -py_diAID was developed by the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann) and is freely available with an [Apache License](LICENSE.txt). External Python packages (available in the [requirements](requirements) folder) have their own licenses, which can be consulted on their respective websites. +py_diAID was developed by the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann) and is freely available with an [Apache License 2.0](LICENSE.txt). External Python packages (available in the [requirements](requirements) folder) have their own licenses, which can be consulted on their respective websites. --- ## Installation @@ -49,6 +52,8 @@ The GUI of py_diAID is a completely stand-alone tool that requires no knowledge Older releases remain available on the [release page](https://github.com/MannLabs/pydiaid/releases), but no backwards compatibility is guaranteed. +**IMPORTANT: Please refer to the [GUI manual](https://github.com/MannLabs/pydiaid/blob/development/pydiaid/docs/manual.pdf) for detailed instructions on the installation, troubleshooting and usage of the stand-alone py_diAID GUI.** + ### Pip py_diAID can be installed in an existing Python 3.8 environment with a single `bash` command. *This `bash` command can also be run directly from within a Jupyter notebook by prepending it with a `!`*: @@ -57,7 +62,7 @@ py_diAID can be installed in an existing Python 3.8 environment with a single `b pip install pydiaid ``` -Installing py_diAID like this avoids conflicts when integrating it in other tools, as this does not enforce strict versioning of dependancies. However, if new versions of dependancies are released, they are not guaranteed to be fully compatible with py_diAID. While this should only occur in rare cases where dependencies are not backwards compatible, you can always force py_diAID to use dependancy versions which are known to be compatible with: +Installing py_diAID like this avoids conflicts when integrating it in other tools, as this does not enforce strict versioning of dependencies. However, if new versions of dependencies are released, they are not guaranteed to be fully compatible with py_diAID. While this should only occur in rare cases where dependencies are not backwards compatible, you can always force py_diAID to use dependency versions which are known to be compatible with: ```bash pip install "pydiaid[stable]" @@ -88,14 +93,14 @@ Next, download the py_diAID repository from GitHub either directly or with a `gi git clone https://github.com/MannLabs/pydiaid.git ``` -For any Python package, it is highly recommended to use a separate [conda virtual environment](https://docs.conda.io/en/latest/), as otherwise *dependancy conflicts can occur with already existing packages*. +For any Python package, it is highly recommended to use a separate [conda virtual environment](https://docs.conda.io/en/latest/), as otherwise *dependency conflicts can occur with already existing packages*. ```bash conda create --name pydiaid python=3.8 -y conda activate pydiaid ``` -Finally, py_diAID and all its [dependancies](requirements) need to be installed. To take advantage of all features and allow development (with the `-e` flag), this is best done by also installing the [development dependencies](requirements/requirements_development.txt) instead of only the [core dependencies](requirements/requirements.txt): +Finally, py_diAID and all its [dependencies](requirements) need to be installed. To take advantage of all features and allow development (with the `-e` flag), this is best done by also installing the [development dependencies](requirements/requirements_development.txt) instead of only the [core dependencies](requirements/requirements.txt): ```bash pip install -e "./pydiaid[development]" @@ -126,6 +131,8 @@ pydiaid gui Note that this needs to be prepended with a `!` when you want to run this from within a Jupyter notebook. When the command is run directly from the command-line, make sure you use the right environment (activate it with e.g. `conda activate pydiaid` or set an alias to the binary executable (can be obtained with `where pydiaid` or `which pydiaid`)). +**IMPORTANT: Please refer to the [GUI manual](https://github.com/MannLabs/pydiaid/blob/development/pydiaid/docs/manual.pdf) for detailed instructions on the installation, troubleshooting and usage of the stand-alone py_diAID GUI.** + ### CLI The CLI can be run with the following command (after activating the `conda` environment with `conda activate pydiaid` or if an alias was set to the pydiaid executable): @@ -134,13 +141,55 @@ The CLI can be run with the following command (after activating the `conda` envi pydiaid -h ``` -It is possible to get help about each function and their (required) parameters by using the `-h` flag. +It is possible to get help about each function and their (required) parameters by using the `-h` flag. For instance, the command ```pydiaid create -h``` will produce the following output: + +``` +****************** +* py_diAID 0.0.9 * +****************** +Usage: pydiaid create [OPTIONS] + + Create a specific dia-PASEF method. + +Options: + -p TEXT Parameter file (check out + d:\pydiaid\pydiaid\lib\default_parameters.json for an example) + [required] + -h, --help Show this message and exit. +``` + +py_diAID provides several options: +- charge Evaluate a dia-PASEF method for multiple charged precursors. +- create Create a specific dia-PASEF method. +- evaluate Evaluate a dia-PASEF method. +- gui Start graphical user interface. +- optimize Optimize a dia-PASEF method. + +All options can be executed with ```pydiaid [option] -p [Text]```. All parameters are saved in a .json file and have to adjusted in this file. For instance, the command ```pydiaid optimize -p "d:\pydiaid\pydiaid\lib\default_parameters.json"``` will give following result: + +``` +****************** +* py_diAID 0.0.9 * +****************** +Using parameter file d:\pydiaid\pydiaid\lib\default_parameters.json +{'precursors within m/z-range [%]': 97.59} +RUN WITH: [0.7435820751492209, 0.9789579174732773, 1.73455196349983, 1.5945652845606708] | RESULT: 10823.0 +RUN WITH: [0.7468616079634967, 0.8864876711590428, 1.6545030790686948, 1.6033036772717069] | RESULT: 11168.0 +RUN WITH: [0.7346248237666703, 0.8734794138726382, 1.5853169071713897, 1.6400014924345845] | RESULT: 11138.0 +RUN WITH: [0.8118354704659128, 0.9634373141944189, 1.7636724593721786, 1.5662199385632] | RESULT: 10794.0 +RUN WITH: [0.8150009805616482, 1.0092137143383832, 1.274205264719582, 1.5310500464391847] | RESULT: 11918.0 +######## +BEST RESULT +INPUT: [0.8150009805616482, 1.0092137143383832, 1.274205264719582, 1.5310500464391847] +OUTPUT: 11918.0 +######## +``` ### Python and Jupyter notebooks -diAID-PASEF can be imported as a Python package into any Python script or notebook with the command `import pydiaid`. +py_diAID can be imported as a Python package into any Python script or notebook with the command `import pydiaid`. -A brief [Jupyter notebook tutorial](nbs/tutorial.ipynb) on how to use the API is also present in the [nbs folder](nbs). +An ‘nbs’ folder in the GitHub repository contains several Jupyter Notebooks as tutorials on how to use py_diAID as a Python package. --- ## Troubleshooting @@ -153,7 +202,7 @@ In case of issues, check out the following: --- ## Citations -There are currently no plans to draft a manuscript. +A manuscript is currently in preparation. --- ## How to contribute From 06bac93837e2eb91d1fd9c9d3dd5e677c57eac86 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Wed, 6 Apr 2022 13:56:48 +0200 Subject: [PATCH 28/58] FIX: typos in README.md --- README.md | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 74e8e87..513372d 100644 --- a/README.md +++ b/README.md @@ -23,6 +23,7 @@ The [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem. ## About Data-independent acquisition coupled with parallel accumulation – serial fragmentation (dia-PASEF) has gained increasing attention from proteomics researchers over the last years. dia-PASEF offers comprehensive proteome coverage, a high degree of reproducibility, and quantitative accuracy while using a much higher ion beam proportion than conventional DIA methods. Previous tools generated dia-PASEF methods with equidistant isolation widths and required a fitting of the window design to the precursor density cloud by hand. We present py_diAID, a Python-based package for Data-Independent Acquisition offering an Automated Isolation Design. py_diAID generates optimal dia-PASEF methods with variable isolation widths adjusted to the precursor density in m/z and automatically, optimally placed in the m/z – ion mobility (IM) plane. Variable isolation widths enable short acquisition cycles while covering the complete m/z-IM-range essentially. We found dia-PASEF methods, generated with py_diAID, beneficial for optimizing proteomics workflows based on cell lines (HeLa) or clinical samples such as CSF and Plasma and for studying post-translational modifications such as phosphorylation. + We offer py_diAID as a Python module, command-line tool, and graphical user interface on all major operating systems under an Apache 2.0 license. py_diAID generates dia-PASEF methods with an optimal window design. It also allows for quality control of the precursors’ distribution of a dataset in the m/z-ion mobility plane and evaluating the suitability of already existing dia-PASEF methods for the individual experiment. py_diAID is an open-source Python package from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann). @@ -141,15 +142,15 @@ The CLI can be run with the following command (after activating the `conda` envi pydiaid -h ``` -It is possible to get help about each function and their (required) parameters by using the `-h` flag. For instance, the command ```pydiaid create -h``` will produce the following output: +It is possible to get help about each function and their (required) parameters by using the `-h` flag. For instance, the command ```pydiaid optimize -h``` will produce the following output: ``` ****************** * py_diAID 0.0.9 * ****************** -Usage: pydiaid create [OPTIONS] +Usage: pydiaid optimize [OPTIONS] - Create a specific dia-PASEF method. + Optimize a dia-PASEF method. Options: -p TEXT Parameter file (check out @@ -159,13 +160,13 @@ Options: ``` py_diAID provides several options: -- charge Evaluate a dia-PASEF method for multiple charged precursors. -- create Create a specific dia-PASEF method. -- evaluate Evaluate a dia-PASEF method. -- gui Start graphical user interface. -- optimize Optimize a dia-PASEF method. +- charge: Evaluate a dia-PASEF method for multiple charged precursors. +- create: Create a specific dia-PASEF method. +- evaluate: Evaluate a dia-PASEF method. +- gui: Start graphical user interface. +- optimize: Optimize a dia-PASEF method. -All options can be executed with ```pydiaid [option] -p [Text]```. All parameters are saved in a .json file and have to adjusted in this file. For instance, the command ```pydiaid optimize -p "d:\pydiaid\pydiaid\lib\default_parameters.json"``` will give following result: +All options can be executed with ```pydiaid [option] -p [Text]```. All parameters are saved in a .json file and have to be adjusted in this file. For instance, the command ```pydiaid optimize -p "d:\pydiaid\pydiaid\lib\default_parameters.json"``` will execute one complete optimization process. py_diAID will create a folder at the location specified in the .json parameter file with all generated information and give following result in the terminal window: ``` ****************** From 3408e5beeaf00d186915bbf8ce35694f924e3898 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Wed, 6 Apr 2022 15:09:57 +0200 Subject: [PATCH 29/58] FIX: typos in README.md --- README.md | 42 +++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index 513372d..94a0b3c 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ ![GUI and PyPi releases](https://github.com/MannLabs/pydiaid/workflows/Publish%20on%20PyPi%20and%20release%20on%20GitHub/badge.svg) # py_diAID -The [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann) developed py_diAID, that generates dia-PASEF methods with an optimal window design. py_diAID stands for an open-source Python package for Data-Independent Acquisition with an Automated Isolation Design. To enable all hyperlinks in this document, please view it at [GitHub](https://github.com/MannLabs/pydiaid). +The [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann) developed py_diAID generating dia-PASEF methods with an optimal window design. py_diAID stands for an open-source Python package for Data-Independent Acquisition with an Automated Isolation Design. To enable all hyperlinks in this document, please view it on [GitHub](https://github.com/MannLabs/pydiaid). * [**About**](#about) * [**License**](#license) @@ -36,24 +36,24 @@ py_diAID was developed by the [Mann Labs at the Max Planck Institute of Biochemi --- ## Installation -py_diAID can be installed and used on all major operating systems (Windows, macOS and Linux). +py_diAID can be installed and used on all major operating systems (Windows, macOS, and Linux). There are three different types of installation possible: -* [**One-click GUI installer:**](#one-click-gui) Choose this installation if you only want the GUI and/or keep things as simple as possible. -* [**Pip installer:**](#pip) Choose this installation if you want to use py_diAID as a Python package in an existing Python 3.8 environment (e.g. a Jupyter notebook). If needed, the GUI and CLI can be installed with pip as well. -* [**Developer installer:**](#developer) Choose this installation if you are familiar with CLI tools, [conda](https://docs.conda.io/en/latest/) and Python. This installation allows access to all available features of py_diAID and even allows to modify its source code directly. Generally, the developer version of py_diAID outperforms the precompiled versions which makes this the installation of choice for high-throughput experiments. +* [**One-click GUI installer:**](#one-click-gui) Choose this installation if you only want the GUI and/or keep things simple. +* [**Pip installer:**](#pip) Choose this installation if you want to use py_diAID as a Python package in an existing Python 3.8 environment (e.g. a Jupyter notebook). If needed, the GUI and CLI can be installed with pip. +* [**Developer installer:**](#developer) Choose this installation if you are familiar with CLI tools, [conda](https://docs.conda.io/en/latest/), and Python. This installation allows access to all available features of py_diAID and even allows to modify its source code directly. Generally, the developer version of py_diAID outperforms the precompiled versions making this the installation of choice for high-throughput experiments. ### One-click GUI -The GUI of py_diAID is a completely stand-alone tool that requires no knowledge of Python or CLI tools. Click on one of the links below to download the latest release for: +The GUI of py_diAID is a stand-alone tool that requires no knowledge of Python or CLI tools. Click on one of the links below to download the latest release for: * [**Windows**](https://github.com/MannLabs/pydiaid/releases/latest/download/pydiaid_gui_installer_windows.exe) * [**macOS**](https://github.com/MannLabs/pydiaid/releases/latest/download/pydiaid_gui_installer_macos.pkg) * [**Linux**](https://github.com/MannLabs/pydiaid/releases/latest/download/pydiaid_gui_installer_linux.deb) -Older releases remain available on the [release page](https://github.com/MannLabs/pydiaid/releases), but no backwards compatibility is guaranteed. +Older releases remain available on the [release page](https://github.com/MannLabs/pydiaid/releases), but no backward compatibility is guaranteed. -**IMPORTANT: Please refer to the [GUI manual](https://github.com/MannLabs/pydiaid/blob/development/pydiaid/docs/manual.pdf) for detailed instructions on the installation, troubleshooting and usage of the stand-alone py_diAID GUI.** +**IMPORTANT: Please refer to the [GUI manual](https://github.com/MannLabs/pydiaid/blob/development/pydiaid/docs/manual.pdf) for detailed instructions on installing, troubleshooting, and using the stand-alone py_diAID GUI.** ### Pip @@ -63,15 +63,15 @@ py_diAID can be installed in an existing Python 3.8 environment with a single `b pip install pydiaid ``` -Installing py_diAID like this avoids conflicts when integrating it in other tools, as this does not enforce strict versioning of dependencies. However, if new versions of dependencies are released, they are not guaranteed to be fully compatible with py_diAID. While this should only occur in rare cases where dependencies are not backwards compatible, you can always force py_diAID to use dependency versions which are known to be compatible with: +Installing py_diAID like this avoids conflicts when integrating it in other tools, as this does not enforce strict versioning of dependencies. However, if new versions of dependencies are released, they are not guaranteed to be fully compatible with py_diAID. While this should only occur in rare cases where dependencies are not backward compatible, you can always force py_diAID to use dependency versions that are known to be compatible with: ```bash pip install "pydiaid[stable]" ``` -NOTE: You might need to run `pip install pip==21.0` before installing py_diAID like this. Also note the double quotes `"`. +NOTE: You might need to run `pip install pip==21.0` before installing py_diAID like this. Also, note the double quotes `"`. -For those who are really adventurous, it is also possible to directly install any branch (e.g. `@development`) with any extras (e.g. `#egg=pydiaid[stable,development-stable]`) from GitHub with e.g. +For those who are adventurous, it is also possible to directly install any branch (e.g. `@development`) with any extras (e.g. `#egg=pydiaid[stable,development-stable]`) from GitHub with e.g. ```bash pip install "git+https://github.com/MannLabs/pydiaid.git@development#egg=pydiaid[stable,development-stable]" @@ -120,11 +120,11 @@ There are three ways to use py_diAID: * [**CLI**](#cli) * [**Python**](#python-and-jupyter-notebooks) -NOTE: The first time you use a fresh installation of py_diAID, it is often quite slow because some functions might still need compilation on your local operating system and architecture. Subsequent use should be a lot faster. +NOTE: The first time you use a fresh installation of py_diAID, it is often relatively slow because some functions might still need compilation on your local operating system and architecture. Subsequent use should be a lot faster. ### GUI -If the GUI was not installed through a one-click GUI installer, it can be activate with the following `bash` command: +If the GUI was not installed through a one-click GUI installer, it could be activated with the following `bash` command: ```bash pydiaid gui @@ -132,7 +132,7 @@ pydiaid gui Note that this needs to be prepended with a `!` when you want to run this from within a Jupyter notebook. When the command is run directly from the command-line, make sure you use the right environment (activate it with e.g. `conda activate pydiaid` or set an alias to the binary executable (can be obtained with `where pydiaid` or `which pydiaid`)). -**IMPORTANT: Please refer to the [GUI manual](https://github.com/MannLabs/pydiaid/blob/development/pydiaid/docs/manual.pdf) for detailed instructions on the installation, troubleshooting and usage of the stand-alone py_diAID GUI.** +**IMPORTANT: Please refer to the [GUI manual](https://github.com/MannLabs/pydiaid/blob/development/pydiaid/docs/manual.pdf) for detailed instructions on installing, troubleshooting, and using the stand-alone py_diAID GUI.** ### CLI @@ -142,7 +142,7 @@ The CLI can be run with the following command (after activating the `conda` envi pydiaid -h ``` -It is possible to get help about each function and their (required) parameters by using the `-h` flag. For instance, the command ```pydiaid optimize -h``` will produce the following output: +It is possible to get help with each function and its (required) parameters by using the `-h` flag. For instance, the command ```pydiaid optimize -h``` will produce the following output: ``` ****************** @@ -160,13 +160,13 @@ Options: ``` py_diAID provides several options: -- charge: Evaluate a dia-PASEF method for multiple charged precursors. +- charge: Evaluate a dia-PASEF method for multiply charged precursors. - create: Create a specific dia-PASEF method. - evaluate: Evaluate a dia-PASEF method. - gui: Start graphical user interface. - optimize: Optimize a dia-PASEF method. -All options can be executed with ```pydiaid [option] -p [Text]```. All parameters are saved in a .json file and have to be adjusted in this file. For instance, the command ```pydiaid optimize -p "d:\pydiaid\pydiaid\lib\default_parameters.json"``` will execute one complete optimization process. py_diAID will create a folder at the location specified in the .json parameter file with all generated information and give following result in the terminal window: +All options can be executed with ```pydiaid [option] -p [Text]```. The parameters are saved in a .json parameter file and have to be adjusted in this file. For instance, the command ```pydiaid optimize -p "d:\pydiaid\pydiaid\lib\default_parameters.json"``` will execute one complete optimization process. py_diAID will create a folder at the location specified in the .json parameter file with all generated information and give the following result in the terminal window: ``` ****************** @@ -190,7 +190,7 @@ OUTPUT: 11918.0 py_diAID can be imported as a Python package into any Python script or notebook with the command `import pydiaid`. -An ‘nbs’ folder in the GitHub repository contains several Jupyter Notebooks as tutorials on how to use py_diAID as a Python package. +An ‘nbs’ folder in the GitHub repository contains several Jupyter Notebooks as tutorials on using py_diAID as a Python package. --- ## Troubleshooting @@ -198,7 +198,7 @@ An ‘nbs’ folder in the GitHub repository contains several Jupyter Notebooks In case of issues, check out the following: * [Issues](https://github.com/MannLabs/pydiaid/issues): Try a few different search terms to find out if a similar problem has been encountered before -* [Discussions](https://github.com/MannLabs/pydiaid/discussions): Check if your problem or feature requests has been discussed before. +* [Discussions](https://github.com/MannLabs/pydiaid/discussions): Check if your problem or feature request has been discussed earlier. --- ## Citations @@ -208,9 +208,9 @@ A manuscript is currently in preparation. --- ## How to contribute -If you like this software, you can give us a [star](https://github.com/MannLabs/pydiaid/stargazers) to boost our visibility! All direct contributions are also welcome. Feel free to post a new [issue](https://github.com/MannLabs/pydiaid/issues) or clone the repository and create a [pull request](https://github.com/MannLabs/pydiaid/pulls) with a new branch. For an even more interactive participation, check out the [discussions](https://github.com/MannLabs/pydiaid/discussions) and the [the Contributors License Agreement](misc/CLA.md). +If you like this software, you can give us a [star](https://github.com/MannLabs/pydiaid/stargazers) to boost our visibility! All direct contributions are also welcome. Feel free to post a new [issue](https://github.com/MannLabs/pydiaid/issues) or clone the repository and create a [pull request](https://github.com/MannLabs/pydiaid/pulls) with a new branch. For even more interactive participation, check out the [discussions](https://github.com/MannLabs/pydiaid/discussions) and [the Contributors License Agreement](misc/CLA.md). --- ## Changelog -See the [HISTORY.md](HISTORY.md) for a full overview of the changes made in each version. +See the [HISTORY.md](HISTORY.md) for a complete overview of the changes made in each version. From 912150220084c37711c6d642b7b683f4aa0d4676 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Wed, 6 Apr 2022 15:10:30 +0200 Subject: [PATCH 30/58] FIX: typo in description --- pydiaid/cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pydiaid/cli.py b/pydiaid/cli.py index 6e34296..2aab4a0 100644 --- a/pydiaid/cli.py +++ b/pydiaid/cli.py @@ -95,7 +95,7 @@ def evaluate_diaPASEF_method(parameter_file_name,): library_plus_evaluate_method(method_conf) -@run.command("charge", help="Evaluate a dia-PASEF method for multiple charged precursors.") +@run.command("charge", help="Evaluate a dia-PASEF method for multiply charged precursors.") @click.option( "parameter_file_name", "-p", From 9cdc7f35ccc739cf839ebc8633691daf36a9b1a4 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Wed, 6 Apr 2022 15:11:21 +0200 Subject: [PATCH 31/58] FIX: Name of fields and widgets. --- pydiaid/gui.py | 61 ++++++++++++++++++++++++-------------------------- 1 file changed, 29 insertions(+), 32 deletions(-) diff --git a/pydiaid/gui.py b/pydiaid/gui.py index 830eee2..4935ae7 100644 --- a/pydiaid/gui.py +++ b/pydiaid/gui.py @@ -1,13 +1,9 @@ #!python -import sys import os -import re -import time import json import logging import platform import pandas as pd -import numpy as np # visualization import panel as pn @@ -232,13 +228,13 @@ def __init__(self, description): self.analysis_software = pn.widgets.Select( name='Analysis software', value=method_conf["input"]["analysis_software"], - options=['AlphaPept', 'MaxQuant', 'MS_Fragger', 'Spectronaut_single-shot', 'Spectronaut_library'], + options=['AlphaPept', 'MaxQuant', 'FragPipe', 'Spectronaut single-run', 'Spectronaut library'], width=200, margin=(15, 15, 15, 15) ) # PLOTS self.plot_mz = pn.widgets.EditableRangeSlider( - name='Plot m/z-range', + name='Plot m/z-range [Da]', start=100, end=1700, value=tuple(method_conf['graphs']['plot_mz']), @@ -247,7 +243,7 @@ def __init__(self, description): width=430, ) self.plot_im = pn.widgets.EditableRangeSlider( - name='Plot ion mobility-range', + name='Plot ion mobility-range [1/K0]', start=0.6, end=1.6, value=tuple(method_conf['graphs']['plot_IM']), @@ -554,7 +550,7 @@ def __init__(self, data, description): width=430, ) self.overlap = pn.widgets.IntInput( - name='Isolation window overlap', + name='Isolation window overlap [Da]', start=0, end=10, value=method_conf['method_parameters']['overlap'], @@ -563,7 +559,7 @@ def __init__(self, data, description): width=430, ) self.shift_of_final_method = pn.widgets.FloatInput( - name='Shift of the final acquisition scheme (in IM dimension)', + name='Shift of the final acquisition scheme (in IM dimension) [1/K0]', start=-0.5, end=1.0, value=method_conf['method_parameters']['shift_of_final_method'], @@ -709,7 +705,7 @@ def __init__(self, data, description): self.data = data self.opt_result_x = [0, 0, 0, 0] self.n_calls = pn.widgets.IntInput( - name='Number of calls', + name='Number of iterative optimization steps', start=1, end=200, value=method_conf['optimizer']['n_calls'], @@ -717,17 +713,17 @@ def __init__(self, data, description): margin=(15, 15, 0, 15), width=430, ) - self.n_start = pn.widgets.IntInput( - name='n_start', - start=1, - end=20, - value=method_conf['optimizer']['n_start'], - step=1, - margin=(15, 15, 0, 15), - width=430, - ) + #self.n_start = pn.widgets.IntInput( + # name='Number of starting points', + # start=1, + # end=20, + # value=method_conf['optimizer']['n_start'], + # step=1, + # margin=(15, 15, 0, 15), + # width=430, + #) self.initial_points = pn.widgets.IntInput( - name='initial_points', + name='Number of starting points', start=1, end=20, value=method_conf['optimizer']['initial_points'], @@ -736,7 +732,7 @@ def __init__(self, data, description): width=430, ) self.YA1 = pn.widgets.EditableRangeSlider( - name='YA1 range', + name='A1 range', start=0.2, end=2.0, value=tuple(method_conf['optimizer']['YA1']), @@ -745,7 +741,7 @@ def __init__(self, data, description): width=430, ) self.YA2 = pn.widgets.EditableRangeSlider( - name='YA2 range', + name='A2 range', start=0.2, end=2.0, value=tuple(method_conf['optimizer']['YA2']), @@ -754,7 +750,7 @@ def __init__(self, data, description): width=430, ) self.YB1 = pn.widgets.EditableRangeSlider( - name='YB1 range', + name='B1 range', start=0.2, end=2.0, value=tuple(method_conf['optimizer']['YB1']), @@ -763,7 +759,7 @@ def __init__(self, data, description): width=430, ) self.YB2 = pn.widgets.EditableRangeSlider( - name='YB2 range', + name='B2 range', start=0.2, end=2.0, value=tuple(method_conf['optimizer']['YB2']), @@ -802,7 +798,7 @@ def __init__(self, data, description): height=35 ) self.scan_area_A1_A2_B1_B2_only_used_for_specific_diaPASEF = pn.widgets.LiteralInput( - name='Scan area A1/A2/B1/B2 (only used for creating a specific dia-PASEF method)', + name='Scan area A1/A2/B1/B2', # value=method_conf['method_parameters']['scan_area_A1_A2_B1_B2_only_used_for_specific_diaPASEF'], value=[0,0,0,0], type=list, @@ -825,11 +821,12 @@ def create(self): pn.WidgetBox( pn.Row( self.n_calls, - self.n_start, + #self.n_start, + self.initial_points, sizing_mode='stretch_width', ), pn.Row( - self.initial_points, + #self.initial_points, self.evaluation_parameter, sizing_mode='stretch_width' ), @@ -884,7 +881,7 @@ def create(self): dependances = { self.n_calls: [self.update_parameters, 'value'], - self.n_start: [self.update_parameters, 'value'], + #self.n_start: [self.update_parameters, 'value'], self.initial_points: [self.update_parameters, 'value'], self.evaluation_parameter: [self.update_parameters, 'value'], self.YA1: [self.update_parameters, 'value'], @@ -905,7 +902,7 @@ def update_parameters(self, event): global method_conf convertion_dict = { self.n_calls.name: "n_calls", - self.n_start.name: "n_start", + #self.n_start.name: "n_start", self.initial_points: "initial_points", self.evaluation_parameter.name: "evaluation_parameter", self.YA1.name: "YA1", @@ -1404,9 +1401,9 @@ def __init__(self, start_server=False): img_folder_path=IMG_PATH, github_url='https://github.com/MannLabs/pydiaid', ) - self.project_description = """#### py_diAID uses an Automated Isolation Design to generate optimal dia-PASEF methods with respect to the peptide precursor density. It designs isolation windows with dynamic widths, which enable short acquisition cycles, while essentially covering the complete m/z-ion mobility-range.""" - self.load_library_description = "#### Please load the library for the indicated analysis software’s to check the distribution of the precursors in the m/z-ion mobility plain." - self.specify_parameter_description = "#### We found a strong correlation between a high theoretical and empirical precursor coverage. This result suggests using a scan area with a wide m/z-range and a narrow ion mobility range. Specify the number of dia-PASEF scans, which depend on the chromatographic peak width, and the number of ion mobility windows per dia-PASEF scan. We recommend two ion mobility windows." + self.project_description = """#### py_diAID uses an Automated Isolation Design to generate optimal dia-PASEF methods with respect to the precursor density. It designs isolation windows with variable widths, which enable short acquisition cycles, while essentially covering the complete m/z-ion mobility-range.""" + self.load_library_description = "#### Please load the library for the indicated analysis software’s to check the distribution of the precursors in the m/z-ion mobility plane." + self.specify_parameter_description = "#### We found a strong correlation between a high theoretical and empirical precursor coverage. This result suggests using a scan area with a wide m/z-range and a narrow ion mobility range. Specify the number of dia-PASEF scans, which depend on the chromatographic peak width, and the number of ion mobility windows per dia-PASEF scan. We recommend two ion mobility windows per dia-PASEF scan." self.optimization_description = "#### py_diAID uses a Bayesian optimization following a Gaussian process to find the optimal scan area." self.create_method_description = "#### Create a dia-PASEF method with an optimal or an individually specified scan area." self.evaluate_method_description = "#### Evaluate the optimal dia-PASEF method or confirm if an already existing dia-PASEF method is suitable for your experiment." From faae4a48abeedc59d4413e3577914c6b6e906a59 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Wed, 6 Apr 2022 15:11:46 +0200 Subject: [PATCH 32/58] FIX: Update to the latest layout and update default values for gui --- pydiaid/lib/default_parameters.json | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/pydiaid/lib/default_parameters.json b/pydiaid/lib/default_parameters.json index 5b11e05..6288a9c 100644 --- a/pydiaid/lib/default_parameters.json +++ b/pydiaid/lib/default_parameters.json @@ -1,9 +1,9 @@ { "input": { - "save_at": "D:\\output_test2", + "save_at": "D:/output_test2", "PTM": "None", - "library_name": "D:\\Input_for_pydiaid\\library21min24fractions.tsv", - "analysis_software": "MS_Fragger", + "library_name": "D:/pydiaid/pydiaid/static/AlphaPept_results.csv", + "analysis_software": "AlphaPept", "diaPASEF_method_only_used_for_evaluate": "D:/pydiaid/pydiaid/static/DIAParameterspy3TC.txt" }, "method_parameters": { @@ -25,12 +25,6 @@ 0.9, 1.3 ], - "scan_area_A1_A2_B1_B2_only_used_for_specific_diaPASEF": [ - 0.5752575470522289, - 0.7128990257352522, - 1.4241557523881094, - 1.6972373193612142 - ] }, "graphs": { "plot_mz": [ @@ -48,9 +42,7 @@ }, "optimizer": { "optimizer": "Gauss", - "n_random_starts": null, "n_calls": 5, - "n_start": 2, "initial_points": 2, "YA1": [ 0.5, From 3fc8038acdee6ca2682574e7b539eccf602010ae Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Wed, 6 Apr 2022 15:12:01 +0200 Subject: [PATCH 33/58] FIX: rename analysis softwares --- pydiaid/loader.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/pydiaid/loader.py b/pydiaid/loader.py index 1b21ec0..8098958 100644 --- a/pydiaid/loader.py +++ b/pydiaid/loader.py @@ -3,6 +3,7 @@ import os import re + def load_library( library_name: str, analysis_software: str, @@ -31,11 +32,11 @@ def load_library( return __parse_alpha_pept(dataframe, ptm) if analysis_software == 'MaxQuant': return __parse_max_quant(dataframe, ptm) - if analysis_software == 'MS_Fragger': + if analysis_software == 'FragPipe': return __parse_ms_fragger(dataframe, ptm) - if analysis_software == 'Spectronaut_single-shot': + if analysis_software == 'Spectronaut single-run': return __parse_spectronaut_single_shot(dataframe, ptm) - if analysis_software == 'Spectronaut_library': + if analysis_software == 'Spectronaut library': return __parse_spectronaut_library(dataframe, ptm) raise Exception('Analysis software not supported.') except Exception as e: From e695654482f14dcc85eeb5faaa0adef1b5388356 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Wed, 6 Apr 2022 15:12:46 +0200 Subject: [PATCH 34/58] FIX: delete not needed information for optimization function --- pydiaid/method_optimizer.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pydiaid/method_optimizer.py b/pydiaid/method_optimizer.py index 8efb53e..bb834b1 100644 --- a/pydiaid/method_optimizer.py +++ b/pydiaid/method_optimizer.py @@ -66,10 +66,10 @@ def optimization( optimizer_parameters["YB2"][1]-optimizer_parameters["YA1"][0] ) ], - optimizer_parameters["n_random_starts"], - optimizer_parameters["n_calls"], # n to test - optimizer_parameters["n_start"], # random starts - optimizer_parameters["initial_points"], # initial points + #n_random_starts = optimizer_parameters["n_random_starts"], + n_calls = optimizer_parameters["n_calls"], # n to test + #optimizer_parameters["n_start"], # random starts + n_initial_points = optimizer_parameters["initial_points"], # initial points ) From f8eadfd8cb769daf7ff618e5f6e2b25f1d6850b2 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Wed, 6 Apr 2022 18:20:16 +0200 Subject: [PATCH 35/58] Fix: typo of fields --- pydiaid/gui.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pydiaid/gui.py b/pydiaid/gui.py index 4935ae7..8f46e1a 100644 --- a/pydiaid/gui.py +++ b/pydiaid/gui.py @@ -243,7 +243,7 @@ def __init__(self, description): width=430, ) self.plot_im = pn.widgets.EditableRangeSlider( - name='Plot ion mobility-range [1/K0]', + name='Plot ion mobility range [1/K0]', start=0.6, end=1.6, value=tuple(method_conf['graphs']['plot_IM']), @@ -523,7 +523,7 @@ def __init__(self, data, description): width=430, ) self.ion_mobility = pn.widgets.EditableRangeSlider( - name='ion mobility-range [1/K0]', + name='Ion mobility range [1/K0]', start=0.6, end=1.6, value=tuple(method_conf['method_parameters']['ion_mobility']), From 5a8ea27f0705501f797353e8ca2531a3a0fde9c5 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Wed, 6 Apr 2022 18:20:32 +0200 Subject: [PATCH 36/58] FIX: Typo in parameter file. --- pydiaid/lib/default_parameters.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pydiaid/lib/default_parameters.json b/pydiaid/lib/default_parameters.json index 6288a9c..d54255b 100644 --- a/pydiaid/lib/default_parameters.json +++ b/pydiaid/lib/default_parameters.json @@ -24,7 +24,7 @@ 1.04, 0.9, 1.3 - ], + ] }, "graphs": { "plot_mz": [ From 640d97375cd06041f849e3599c1f5b161e881930 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Wed, 6 Apr 2022 18:20:53 +0200 Subject: [PATCH 37/58] FIX: Improved description in README.md --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 94a0b3c..6ebe731 100644 --- a/README.md +++ b/README.md @@ -120,7 +120,7 @@ There are three ways to use py_diAID: * [**CLI**](#cli) * [**Python**](#python-and-jupyter-notebooks) -NOTE: The first time you use a fresh installation of py_diAID, it is often relatively slow because some functions might still need compilation on your local operating system and architecture. Subsequent use should be a lot faster. +NOTE: The first time you use a fresh installation of py_diAID, it is often relatively slow because some functions might still need compilation on your local operating system and architecture. Subsequent executions should be a lot faster. ### GUI @@ -166,7 +166,7 @@ py_diAID provides several options: - gui: Start graphical user interface. - optimize: Optimize a dia-PASEF method. -All options can be executed with ```pydiaid [option] -p [Text]```. The parameters are saved in a .json parameter file and have to be adjusted in this file. For instance, the command ```pydiaid optimize -p "d:\pydiaid\pydiaid\lib\default_parameters.json"``` will execute one complete optimization process. py_diAID will create a folder at the location specified in the .json parameter file with all generated information and give the following result in the terminal window: +All options can be executed with ```pydiaid [option] -p [Text]```. The parameters are saved in a .json parameter file and have to be adjusted in this file. For instance, the command ```pydiaid optimize -p "d:\pydiaid\pydiaid\lib\default_parameters.json"``` will execute one complete optimization process. py_diAID will create a folder at the location specified in the .json parameter file with all generated information and print the following result in the terminal window: ``` ****************** @@ -195,9 +195,9 @@ An ‘nbs’ folder in the GitHub repository contains several Jupyter Notebooks --- ## Troubleshooting -In case of issues, check out the following: +In case of issues, check out the following links: -* [Issues](https://github.com/MannLabs/pydiaid/issues): Try a few different search terms to find out if a similar problem has been encountered before +* [Issues](https://github.com/MannLabs/pydiaid/issues): Try a few different search terms to find out if a similar problem has been encountered before. * [Discussions](https://github.com/MannLabs/pydiaid/discussions): Check if your problem or feature request has been discussed earlier. --- 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zWbc-bxYq;I`T(}E`r(H;8p9vH$Co9-FEgR!c0mF^Nb0w{@&?|U#Es*?Z`WRnz?ln{l$9!SW_!KCDVkE1&xfQ0^W0KN~3y($B{tpb6_ zs)@?nx(yM9!c<_QDzcJNqG~Ftw`A2MRHbBZ!BNZmAmRVj%vu-`q;V#({=`TO6~vc# zj^{k8g$iQ$5duN=Q$d$?WlsXy^u+I|nkmStK_ItPPUImnw^U#!!Y8W#EvocC&#>V8 zo|(sGD+Bv;hMTR`55ZLGrJ(nGw6u|?r?WPLZgionq8+)CZQ|(kMU+?yS#Q!TCI2#= z!goO`)F$X&F-tV-O%;Pm8bSprsJaRre9yA&K{-uwH1W~N{d^T Date: Thu, 7 Apr 2022 09:41:54 +0200 Subject: [PATCH 39/58] FIX: correct mistakes in Readme --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 6ebe731..17c4b06 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,10 @@ The [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem. --- ## About -Data-independent acquisition coupled with parallel accumulation – serial fragmentation (dia-PASEF) has gained increasing attention from proteomics researchers over the last years. dia-PASEF offers comprehensive proteome coverage, a high degree of reproducibility, and quantitative accuracy while using a much higher ion beam proportion than conventional DIA methods. Previous tools generated dia-PASEF methods with equidistant isolation widths and required a fitting of the window design to the precursor density cloud by hand. We present py_diAID, a Python-based package for Data-Independent Acquisition offering an Automated Isolation Design. py_diAID generates optimal dia-PASEF methods with variable isolation widths adjusted to the precursor density in m/z and automatically, optimally placed in the m/z – ion mobility (IM) plane. Variable isolation widths enable short acquisition cycles while covering the complete m/z-IM-range essentially. We found dia-PASEF methods, generated with py_diAID, beneficial for optimizing proteomics workflows based on cell lines (HeLa) or clinical samples such as CSF and Plasma and for studying post-translational modifications such as phosphorylation. +Data-independent acquisition coupled with parallel accumulation – serial fragmentation (dia-PASEF) has been gaining increasing traction, amongst proteomics researchers over the last years. dia-PASEF offers comprehensive proteome coverage, a high degree of reproducibility, and quantitative accuracy while using a much higher ion beam proportion than conventional DIA methods. Previous tools generated dia-PASEF methods with equidistant isolation widths and necessitated manual adjustment of the window design to the precursor density cloud. We present py_diAID, a Python-based package for Data-Independent Acquisition offering an Automated Isolation Design. py_diAID generates optimal dia-PASEF methods with variable isolation widths adjusted to the precursor density in m/z and automatically, optimally placed in the m/z – ion mobility (IM) plane. Variable isolation widths enable short acquisition cycles while covering essentially the complete m/z-IM-range. We found that the dia-PASEF methods, generated with py_diAID, are beneficial for optimizing proteomics workflows based on cell lines (HeLa) or clinical samples such as CSF and Plasma, as well as for studying post-translational modifications such as phosphorylation. + +We offer py_diAID as a Python module, command-line interface (CLI) tool, and Graphical User Interface (GUI) on all major operating systems under an Apache 2.0 license. py_diAID generates dia-PASEF methods with an optimal window design. It also allows for quality control of the precursors’ distribution of a dataset in the m/z-IM plane and evaluating the suitability of already existing dia-PASEF methods for the individual experiment. + We offer py_diAID as a Python module, command-line tool, and graphical user interface on all major operating systems under an Apache 2.0 license. py_diAID generates dia-PASEF methods with an optimal window design. It also allows for quality control of the precursors’ distribution of a dataset in the m/z-ion mobility plane and evaluating the suitability of already existing dia-PASEF methods for the individual experiment. From 128e6fdc23189a6d300ce6afafba715cdc1195fc Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Thu, 7 Apr 2022 09:49:24 +0200 Subject: [PATCH 40/58] FIX: description changed. --- README.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/README.md b/README.md index 17c4b06..09659ce 100644 --- a/README.md +++ b/README.md @@ -26,9 +26,6 @@ Data-independent acquisition coupled with parallel accumulation – serial fragm We offer py_diAID as a Python module, command-line interface (CLI) tool, and Graphical User Interface (GUI) on all major operating systems under an Apache 2.0 license. py_diAID generates dia-PASEF methods with an optimal window design. It also allows for quality control of the precursors’ distribution of a dataset in the m/z-IM plane and evaluating the suitability of already existing dia-PASEF methods for the individual experiment. - -We offer py_diAID as a Python module, command-line tool, and graphical user interface on all major operating systems under an Apache 2.0 license. py_diAID generates dia-PASEF methods with an optimal window design. It also allows for quality control of the precursors’ distribution of a dataset in the m/z-ion mobility plane and evaluating the suitability of already existing dia-PASEF methods for the individual experiment. - py_diAID is an open-source Python package from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann). --- From a864c5bedd3545f17dd8824e95ce6e0b4bbf367b Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Thu, 7 Apr 2022 16:35:37 +0200 Subject: [PATCH 41/58] FIX: Updated py_diAID tutorial. --- nbs/py_diAID_tutorial.ipynb | 937 ++++++++++++++++++++++++++++++++++++ nbs/tutorial.ipynb | 43 -- 2 files changed, 937 insertions(+), 43 deletions(-) create mode 100644 nbs/py_diAID_tutorial.ipynb delete mode 100644 nbs/tutorial.ipynb diff --git a/nbs/py_diAID_tutorial.ipynb b/nbs/py_diAID_tutorial.ipynb new file mode 100644 index 0000000..655bfdb --- /dev/null +++ b/nbs/py_diAID_tutorial.ipynb @@ -0,0 +1,937 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "5d235fe8", + "metadata": {}, + "source": [ + "## Optimize a dia-PASEF method in Jupyter notebook" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "c15f36f7", + "metadata": {}, + "outputs": [], + "source": [ + "import pydiaid.cli as cli" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "13911e3d", + "metadata": {}, + "outputs": [], + "source": [ + "method_conf = {\n", + " \"input\": {\n", + " \"save_at\": r\"D:\\test_optimization\",\n", + " \"PTM\": \"None\",\n", + " \"library_name\": r\"D:\\pydiaid\\pydiaid\\static\\AlphaPept_results.csv\",\n", + " \"analysis_software\": \"AlphaPept\",\n", + " },\n", + " \"method_parameters\": {\n", + " \"mz\": [300,1200],\n", + " \"ion_mobility\": [0.6,1.6],\n", + " \"num_dia_pasef_scans\": 20,\n", + " \"im_steps\": 2,\n", + " \"overlap\": 0,\n", + " \"shift_of_final_method\": 0,\n", + " },\n", + " \"graphs\": {\n", + " \"plot_mz\": [250, 1250],\n", + " \"plot_IM\": [0.6, 1.6],\n", + " \"numbins\": 50,\n", + " \"window_frame_color\": \"black\",\n", + " \"window_color\": \"white\",\n", + " \"window_transparency\": 0.5\n", + " },\n", + " \"optimizer\": {\n", + " \"optimizer\": \"Gauss\",\n", + " \"n_calls\": 5,\n", + " \"initial_points\": 2,\n", + " \"YA1\": [0.5, 0.9],\n", + " \"YA2\": [0.6, 1.0],\n", + " \"YB1\": [0.9, 1.5],\n", + " \"YB2\": [1.0, 1.8],\n", + " \"evaluation_parameter\": \"No. of covered precursors\"\n", + " }\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "6fccfdaa", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{'precursors within m/z-range [%]': 97.59}\n", + "RUN WITH: [0.783674287692417, 1.003750504251468, 1.5292554186172336, 1.464959421182495] | RESULT: 12152.0\n", + "RUN WITH: [0.8473093365152502, 1.0782547068873716, 1.8036297345076258, 1.413348018329967] | RESULT: 11125.0\n", + "RUN WITH: [0.5705251022476764, 0.9201738058748123, 1.3470463635085652, 1.5081446848805982] | RESULT: 16710.0\n", + "RUN WITH: [0.8359503735867329, 1.3020376043879844, 1.4211265934012072, 1.3690181964125474] | RESULT: 11408.0\n", + "RUN WITH: [0.5432663623821127, 0.839261707157508, 0.9527912009157502, 1.2823205638359028] | RESULT: 14901.0\n", + "########\n", + "BEST RESULT\n", + "INPUT: [0.5705251022476764, 0.9201738058748123, 1.3470463635085652, 1.5081446848805982]\n", + "OUTPUT: 16710.0\n", + "########\n" + ] + }, + { + "data": { + "text/plain": [ + "

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" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "cli.run_all(\n", + " method_conf\n", + ")\n", + "\n", + "# The output can be found in the folder specified at \"save_at\"." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "62f918c6", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "id": "4adf1f65", + "metadata": {}, + "source": [ + "## Here, we present the method evaluation steps:" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "63eef647", + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import pydiaid.loader as loader\n", + "import pydiaid.graphs as graphs" + ] + }, + { + "cell_type": "markdown", + "id": "10224636", + "metadata": {}, + "source": [ + "#### Loading of the dia-PASEF method and the AlphaPept library." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "4f3d4c35", + "metadata": {}, + "outputs": [], + "source": [ + "lib_name = method_conf[\"input\"][\"library_name\"]\n", + "dia_PASEF = r\".\\Input\\dia-PASEF-methods\\used_for_measurements\\DIAParameters.optimal_dia-PASEF_300-1200_2steps_12scans_vs2.txt\"" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "a6a7b00d", + "metadata": {}, + "outputs": [], + "source": [ + "df_parameters_final = pd.read_csv(\n", + " dia_PASEF,\n", + " skiprows=4,\n", + " names=[\"MS Type\", \"Cycle Id\", \"Start IM\", \"End IM\", \"Start Mass\", \"End Mass\", \"CE\"]\n", + " )" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "b4806119", + "metadata": {}, + "outputs": [], + "source": [ + "dataframe = pd.read_csv(lib_name) # .xls, .tsv, .txt\n", + "lib = loader.__parse_alpha_pept(dataframe, 'None')" + ] + }, + { + "cell_type": "markdown", + "id": "093b0c21", + "metadata": {}, + "source": [ + "#### Generating the plots that belong only to the library." + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "66a6a6c8", + "metadata": {}, + "outputs": [], + "source": [ + "x, y, z = graphs.kernel_density_calculation(\n", + " lib,\n", + " 50,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "25eb8fef", + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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A84A9gFlZ2sHAV4GzSd05NwKHRcSCJi9/FPAZ4COkkXXzgGkR8f2+Cg40IF1P/lDBehYBswd4XTOzrjEYG/RFxLmk5rO8czNYe/m1BcCx2dHI+x9TkP4caZj3KQ1XNjOggBQRe/SjzBxSVDazFurPHKCi+Tx1DavTTxQFc4fq9NNovYI5RWMK+nyAmJA39QZWr58zp6gPPc+XsPlRjUCs6vUYsz6/A5I2lDRd0lWSPlBz7seDVzUzs6GjrKWDOlkjIfn7pKF63wOOl/TtqnPbDkqtzMyGkkhNdo0c3ayRJrspEXEIgKSZwG8l/WdEfGlwq2ZmNjQMRh9SJ2okIPVIGh0Rz0fEYklvB34vaR7p+2hmbapf/UQjRqyT69R9v6J15ADG1S5AkKx66fjcdICVY/M/6oYtL14VZ70nn82v26IluekD5YDUWED6IXCzpOMi4oaIeFTSgcA1wJjBrZ6ZWfcLxGoPaug7IEXE1yTdDDxdlXanpNcDJw5i3czMhoxuH7DQiIaGfUfETQCSNoiIJVna34GPDmLdzMyGhAg32UHz85CeBppvYDazwVW0JlydteI0ovk5RUVzgPpLG4zNTe99yYTCMks3z19/btXo4nsdubB237lkxKN1VrJZnN9XFM8tLS4zAOGA1HRA8nfMzKx03T+kuxHNBiSPqjMzGwR+QvIGfWZmLRcBq3sdkNxkZ9Yp6vUHFcwD6hnV/Fpt1OlbUlEd6u15NKF4ftCyV26Ym774FcVd1VEw5WmDh1YWlhk9t2BfuIXFa0P3Ls3vK4oVKwrLDIRH2TUfkN47KLUwMxvCAjfZQZMBKSK8mKqZWek8qAFK7EOSNAI4DngjMCEnS0TEvmVdz6wr9aNZDuo0zdXbWnxkQbNYwXbfqVD+h2bvJhMLiyx6Vf7QboDFr8i/355VxVXY6K78prkxc54sLBMLFuanP/98cZnV+UPFo3dwxnYV7cQxlJQ5qOE7wPtIW9Y+3UdeMzOr4ia7cgPSO4DPRsTpJb6nmVnXS6PsvJZdmQEpgD+U+H5mZkOGm+zKDUgzgPdJujYiitd0N7PCviLVGT5dd6mfgnMaVWcbh6JtJoYX9zste2V+X9Ezrykepr3kFcWftCMKVu6Z9OfiIdxj7n48N713fnFPQazIf7+ifqJ0ct1+jLnJrtyA9FngNuBvkm4Fnqs5HxHxvjIuJGlH4E/AlhHxcJ18mwCnAfsAGwH3AGdGxM/LqIeZWRkCOSBRbkA6E9gGWAT8S875Uh5IJU0FLqOPuksaCVxJGvH3WeBR4FDgIklHRcTPyqiPmVkZ3GJXbkA6mhSUPhVRfmuopOHAB4EvAcXP8y/YD9gBeENE/ClLu1rSy4FPAg5IZtYeAsJLB5UakFYDMwcjGGV2IQW8s4BHgO/1kX8xcC5wS036Pdl7mbVMUV9Rve3De8bmb7sAQNGW33W2Ao/18vuKFm47obDM09vm932t3Kx4OZ1RDxTf0yY35/9tOfqe/H4igN4n85cBqrekT+HcoTbq7naTXbkB6aekeUjXlfie1eYAkyPiSUnH9JU5Iq4Frq1Ok7QecABw16DU0MysnzzKrtyA9ATwHklzSQMOane3ioj4YH/fPCKeGEjlMv8NbA0clHdS0jRgGsAoxpRwOTOzvnktu6TMgPR+4BlgGLBzzvmWxX9JIjX3nQicFRG/yssXEdOB6QDjNNF/r5jZuhGAA1J5ASkitqxNk6RB7FNqSDbabgZwBCkYndzK+tjQUW/tuaK+op46WzVQpw8pRue/3+r1i/tvntgp//0W//PywjIj18/vpxlzywaFZTb5U533uy+/4aP+nKL8OtSdU9QB3GQHpa5VIelDkqpHr71J0n2Sji7zOk3UZxxwNXAYcKKDkZm1JxG9jR3drLSAJOl40gKr1Tte/QOYDfxA0rvKulaD9RkG/IrUfHh4RHxjXV7fzKwp0eDRxcrsQ/oI8PmIOK2SEBEPkJYTegg4GfhJidd7EUmTgK2AuyNiMfAhYHfS0O+HJVX3a0VE3DxYdTEza0p4UAOUG5C2AH5XcO4G0mTUwXQAcB6wBzALOCRL/2B2VFtNufduQ1hRX5FGFm8f3rPhhNz02LC4L6Z3THF/0IoN8+cbPbxH8fp3r3j9P/JPPFu8fxHX5m85/tI/5W/3DTD8weIBsr1PL8hNj1XFc98Haz+iluvS22pGmX1IfycFgzxvIk1mLUVEzIgIVa9jV5U2K3u9Z/Y673AwMrM2owaP7lXmB/N04L+zyae/BJ4EJgEHAp8APlPitczMukv7LBrRMmUO+/6apE2Bk0gBqGIV8K2IOKusa5mZdRXPQwJK7keJiE9IOp00sm0j0srfN0dE/uJTZh2i7pyigr6inon5/S0AvRvlzzfqHVPc5/PcZqMLzz16YH6fy7t3nF1Y5lcPbpebPvyy4npPujV/A6Oeh58sLNO7qHbRlhcU9RXV7Sdqo/XnyuR5SIPQsR8Ri4Cryn5fM7Ou5oDkkWZmZm3BTXYOSGZm7UB+QnJAMnsR5c+EqLtPUcGcoqJ+IoDVG+S/36Ipxf1Ew48o7qc5d+tLc9NPuP2IwjLjfpU/32jiHc8UltGj83PTe5fU6Seqs8Zc184palYIunxZoEY4IJmZtQPH5tIXVx0r6WXZ/68n6aOSvirpX8u8jplZ1yl5LTtJR0q6S9Lzkub0tch19vn9HUmPS3pW0uWStq6T/7hs/7u8cydImptd+zZJ+zVS5zIXV90JeAj4jyzpm8BXgGOAWZIOLOtaZmZdp8SAJOkw0i7eV5E2JJ0FnC/p0DrFLgTeSVrm7WhgM+A6SWu1PUs6GPhawbU/QfrsnwEcDNwPXFqznmiuMpvsTgfuAaZLGkO6of+JiOMlnQt8Gvh1idcz65+CfiKAnn7sU1S0/tyq8cVr2T21Q35f0e7H/LGwzGdfekPhuZ1/96Hc9I1/WdwnNf7P+XsO6cnivYiK+oo6fS+ilit/YuwZwEURcVL2+ipJE4HTgItrM0vaBdgf2C8irszSbgAeIC1UfWaWtiHwBeB4YGHO+6wPnAqcHRGnZ2lXAjcBnwPqPimV2WS3E3BatsL3PsAo4MfZuQuAbUu8lplZV1E0dvT5PtJk0s4Hl9ScuhiYKmmtzVRJn9lLSPvHARAR84HrSYGq4gTgHcDhQN5Imp2A8dXXzjZp/QWwl6Ti0UGUG5B6gWXZ/+9Lip6VP/fGAcXLAZuZDXXlNdlNzb7eW5Ne6e/ZpqDM3IiofdSdW5P/f4EpEfHzflx7ODC5qNJQbpPdLcAHJD1P2qH1sogISS8BTgH+VOK1zMy6SonzkCrty4tr0ivtreMKytTmr5RZkz8i/tbgtWvbdutde40yA9LJwJXAEcB8Up8SwF9Ja6bvU+K1zPqtZ73iH/uecQV7AY0v3qdo+Sb55x57Y3HrxLnHnpOb/qb8bY0AmHLdvxee2+SX+f1V4/9a3B/E/Pz5Rr3PPldYpHDeUJ1+uXrUk78u3ZDsk2q8D2ljSbdUvZ4eEdOrXvf1Rnnf9Hplmlk8sD/XXqPM1b5vk7QV8BrgrxFR+ameBvwua480M7NazQ3pfioiXlfnfGUF3Nq/lMbVnK8tk9ecNq4gf1/XHsuLn5LqXXuNAfUhSbpY0lskCSAilkTEzVXBiIj4PwcjM7M+lNeHVOm/mVKTPqXmfG2ZyZXP8poyefn7c+3lpI1cCw30CWln0oiLRyXNAM6LiPsH+J5mpdDw/K0cNGZMcaGN8rdeePZVxVsyPPzm/L/r5r0zv1munskz31t4brNLi39dx91d0DRX0CwH0Lu0+XFG9bbhKFRnu4jelV6eoEIl7aoREXMlPQAcStosteIQ4L6IeCin2EzScO29yEbaSZoE7EoaQt6om4Dnsmvfnr2PSPORZkfEinqFBxqQtiDdwNHAicCnJM0Gvg9cEhHL6pQ1M7OKcmPzF4HzJC0ALgPeThpsdgSsCTZbAXdHxOKImC1pFnCBpJOBZ4DPk0ZLN/yXVUQslXQ28BlJq4A/AO8FXgvs3lf5ATXZRXJ1RLwb2AQ4lrRD7PnAY5L+R9JrB3INM7Nu1+gcpEZH4kXEDNKE1n2B/wN2A46OiAuzLAcAvwf+parYwaS5RWeTVll4GHhzRCxo8na+SJoEeyxp/tFk4G0R8bu+CpY5qOE54EfAjyRtBrwb+DfgQ5L+AvwgIr5Z1vXMzLpKyfshRcS5wLkF52aQgk512gJSEDm2wfc/piC9lzTK+vS88/UMymrfEfEI8GXgy5J2I31TvkZa386sNPX6NHpG54+h1iaTCsss+OeNctOfPuj5wjLz3vSjwnNFtrz8/bnpm19RfD/j7nqq8FzML+hDWpG/RTgAa/VfZ8kjij8WCodj19l/O+r1E3XpduT94u60wQlIkiaQFuk7EngTaV7SWYNxLTOzbuAN+koMSJJGkTrOjiK1W4rUmXYQcGXOkhRmZgYQ5Y2y62QDCkiSekjB5yhSMBpLWpnhFOAnEVHcxmBmZi/wE9KAn5AeBzYizb79MWke0i31i5g1qd52EaOLt1fQZpvkpj+188aFZTY+Jn/e3k2vuqKwTJHJl36g8Nxmv82/p3F3Fs8hj6eL5xRRtKTP8DrLJI3In6cVz9eZrVHQVxQrVxUXGYrLAPWHA9KAA9IdwHnALyJi+cCrY2Y2NLkPaeDbT8wArmomGEnaSNJRA7yumZl1mYEGpB+TZvs2YwovbNxnZmZQ6hbmnWqgTXYiLRfUzOKpxZNAbGgr6Csqmk8Exf1EAE/smv+jtteHbyos8+WX/rnwXJHJv5qWm/6yWcUTHcff/mRuejxTPCledfqDKJqPVWeeVix5Nj99VXF/EAX9QXX7iTzXqG8eZQcMPCA9BOzYz3L9JmlH0oZ/W0bEw3XyjSXtBX8IaQTgbOCEiLhvINc3Mytdlz/9NGJAASkiXllSPRomaSppflMjdb8QeD3wCdLeHJ8DrpP0TxHRzB4fZmaDRnhQAwy8D2mdkTRc0nHAH4Hisb4v5N8F2J+0oOD5EfEL0srkE0iLDpqZtQ/3IQ3O0kGDZBdS89tZwCPA9/rIvw/pqejqSkJEzJd0PSlQnTlI9bR+6hmVvw13zxabFpZ5fM+XFJ77yAmX5KYfMy6//6aeenOKivqKJtxa5zoL8h/Q6+7VVDBvqJ54urhPKpblD46t1x8Uq+qsjWf918RK3t2sY56QgDnA5Ij4AmmLi75MBebmLFk0F9im7MqZmQ1Ib4NHF+uYJ6SIeKLJIuOBxTnpS3hhf3czs7bgJ6QOCkj9UG9zkdy/MyRNA6YBjKJO04mZWdkckAY/IGX7qb+XtADrZqRg8DBppNx3BnEV8EWknQprjcvOrSUipgPTAcZpon88BkHPyOI5RT2b5s8penyP4n6i//r4DwrPvWX0isYrltnysvy+oqK15wDG31EwDW/xkuILjd8gNzlGjigsojp7G8WT+esYR70yBf1BXnuuBYbAgIVGrIsnpK8Bm5IGETySpW1KClLbAcW9xQNzL7CXJEW8aEXIKdk5M7O24Sa7dROQ9ouI2kEEd0m6Brh7EK87EziVNNT7agBJk4BdgTMG8bpmZs1zQFono+xWSMpri9kUaL5NpYCkSZJ2ljQOICJmA7OACyS9T9I7gGuAhcA5ZV3XzKwM6m3s6Gbr4gnpM8Ctkm7kxU12uwDHlXidA0hbYexBCkQABwNfBc4mBd8bgcMionhyhpVCw/PnzPS8tHgvovm75vchffkTxVPO9h7dyAyAF9vy8vcXnnvZdQX7FP21zl5ES5/PT584obBIjMj/1dOzBe9FcT8RQKzI/9uut84+RV5jro24DwlYBwEpIv5P0u+BvUmDGnqA20hryjU7lLvynjNIW1/0lbYAODY7zMzakqg/LHioWCfDvrPA85N1cS0zs47kJ6SB9SFJ2q3BfOtJ+sZArmVm1s0UjR3dbKBPSL+W9JaIKNxgRtI2wAXA9sAJA7yetRHV2Wtn2EYb5qYvesPmhWVO+s8Lc9P7008EMHnm+3LTX3p98Y/9hLsW5qZrefH4m5iYv/BH9BT/vdezIG8REeid/3Txder0BxXOHXI/Uefo8mDTiIGOspsHXCFpp7yTkt4P3AK8hjQE28zMaoVH2cHAA9KepKB0paTXVhIljZd0EWnVgweBN0TElwd4LTOz7uXtJwYWkLJRbHuSVtCeKWlHSf8K/Jk05PorwGsjovl9oc3MhhD3IZUwyi4iFkp6M2k1hFnAGNJ8oz2zyanW6ZT/d0vPBvnrsQEs2/7luelv/syNhWWOGNv89LCtr39P4bmNr8+fC7Xh3cVrzGl5/vpuvRPWL67E6vxPiZ4ni+cu9T6zMD+9YD4R4P6gbtflwaYRpazUEBGLSUv0zMne80gHIzOzxvkJqcSlgyJiCWny6x+AX0iaWtZ7m5l1tcAb9DHAJjtJM3OShwGbALMl3VGVHhGx70CuZ63RMzp/y4jeKVsUlhl16qO56V+YdFfT19/xT0cUnptwTfG+VRvOeS43vahZDmD1+NG56T1Li5vS9Fj+kj69S4qbBguX9HGz3JAkuv/ppxED7UPKa6RfBlxf57yZmdVyQBpwQPolcHlEzC2jMmZmQ5XCEWmgfUj7AX+WNFfStyTtJym/zcPMzPI1Ogepy2PWgJ6QImI/SaNIc5HeAnwT2EzSDcAVwJURcc/Aq2mDre7W4ltsmpt+zwnFLbLzXnVF03XY/a6356YPvyx/GSKACfcVb9fQsyK/n6Z3/ZGFZYYtXJqbHo8XbFMOrH6uoEy9rcDdV2Q13IdUzjykZcDl2YGkrUnBaT/gDElP8EJwunSg1zMz60bdvixQI0rfMTYi7ouIb0XE/sBE4MPASuCssq9lZtY13GQ3uPshZU9PV2aHmZnlGQKTXhuxTjbos/ZQtK04QE/BdhEA9x/1ktz0eW8+p+k67Hfv/oXnllyS31c14cHiOUA9q4p/i2O9/O0xhs3P3/oBoPfxJ/Pfa/ny4uv0FtTB/UTWDAekAU+Mzf8EKRAR+bMlzcyGME+MTQb6hPQgaWWGRjWT18xsyFDRk/YQMtCA9AbgMmAkcArQv609zcyGskEYsCDpSODTwGTSw8OXIuJHdfKPBc4EDgHGArOBEyLivqo8w4HPAccAGwG3Ah+LiD9W5dkc+EfOJe6KiG3r1Xmg85DukLQXcDPwsog4fSDvZyUp2i5ibPEWCvP3fWXhuTkfaL6vaM+73pabvuBXmxWWGfdY0TbcxdfRiuK5PsOezN/OoveJ/LXnoI/tH4q4r8hKUOawb0mHAT8Fvg5cBRwEnC9paURcXFDsQuD1wCeAJaTAc52kf4qIRVmeb5CC0SeBvwMnAddI2jEi7s/y7JB93Sd7n4r8CXtVypiHdI+kTwFfkvTdiCj+bTczs3zlPiGdAVwUESdlr6+SNBE4DVgrIEnaBdgf2C8irszSbgAeAD4EnCnplcAHgeMj4rtZnpnA30hB7MPZ2+0APBERVzdb6bLmIX0XOJDUN2dmZk0qaz8kSZOBrYBLak5dDEyVtGVOscrTzJogEhHzSQtlV4bG7kkaB3BJVZ7lpG6b6uGzOwJ39l3TtZW1Qd/qiLg+uwEzM2tGABGNHX2r7EV3b016ZRHsbQrKzI2I2jbwuVX5pwILcj7n5wIvr1rHdAdgtKQbJS2T9ISkL0nqc/cHz0PqQj0jRuSmr9xxcmGZ/U68oenrbPuHowrPDZs9Pjd97FPFDeU9K/LPjXimznp1j9fZJvypp/PTi/YiAvcHWcs00Ye0saRbql5Pj4jpVa8rv3y1E+4q/Tnjct5zfE7+SplxDeQB2ECSgCmkVXpOBk4lPVmdAmwKvCen/BoOSGZmLdbkPKSnIuJ1fbxdPXmhr16Z3gbyVPKtIjX/PRgR87L06yWtAE6XdHr1qL1apa9lZ2ZmTWq0ua6xJrvKiLgNatLH1ZyvLVObv1JmUQN5ABZHxIqI+G1VMKr4TfZ1B+pwQDIzawNlDWrghb6jKTXpU2rO15aZnDW51Za5tyrPREm164xNAR6IiBWStpQ0TdLGNXkq/Ut1R2G7ya5DaVjxohc9L8+f6zPviOJ/7o+NLXyKZvIV789NHzunuI9y9DP5vzkjlhQ3lI9+5NncdD1eZ97Qwrw/9rJzRX1F7ieydlTSsO+ImCvpAeBQ0q7eFYcA90XEQznFZpL6e/YiG2knaRKwK2kIObwwAu9Q4HtZnpHAW3lhAe0NgXOBUaT98SoOJz1h3V6v7g5IZmZtoOS17L4InCdpAWlY9tuBw4AjYE2w2Qq4OyIWR8RsSbOACySdDDwDfB5YCJwDEBF/l3Q+8M1sVYf7SBNjJwD/neW5TdKlpL3whgF/JQ0J/w/gpKoJtrk6qslO0pGS7pL0vKQ5ko7uI/8kSedJelTSM5IuyzYQNDNrHwGsjsaORt4uYgZpQuu+wP8BuwFHR8SFWZYDgN8D/1JV7GDgUuBsYAbwMPDmiKhe8uSDpHmnp5BWdhgO7B0Rc6vyHAV8G/gI8GvSIIdpEfH1vurdMU9IzS6FkbWF/pLUvnky8DTwBdJSGNvVfJPNzFqq7NW+I+JcUvNZ3rkZpKBTnbYAODY7it5zOfDR7CjK8xwpYJ3SbJ07JiDR5FIYwNbAvwLvqSwoKGkOMA94G3D+4Fe5BAXr0g2bMKGwyJO7vTQ3fcJmxXN2/uPn7ys8t0H+FkGMfqr4N2j9x1bmpo/6R50n9vn59et99rnCIp5TZF2jsRF0Xa0jmuz6uRTGqOxr9eJ+lU+8jcqtoZnZwJQ4yq5jdURAoh9LYUTEncB1wGclTc068b4JPEtqUzUzaw/RxNHFOqXJrj9LYUBaffYqYE72ejlwUNUy6S8iaRowDWAUY/pdWTOzZghQgwMWulmnBKSml8KQ9GrgJtJT1ImkvTg+AFwi6S0Rsdbibdl6UNMBxmliW/x09IwamZu+apstCss8V7Dl0HrXTSwss0GdnUpGF6w/t/4jxWvMDX9sYW56PF3cjxXLl+emu5/IhgK5D6ljAlJ/lsKojALZpzKiTtLVwA3A14B6a0GZma07Q6A5rhGd0ofUn6UwXkGa9LVmeHdEBHAj8E+l19DMrN9KXcuuY3VEQMomXVWWwqhWbymMe4FtJU2oSd+ZtL+8mVnb8Ci7zmmygyaXwgC+CrwLmCnpy6Q+pKNJM5aPWPfVL1Z3XbpJ+SPUl2w2KjcdYPzc/J/aYcuLf5pHLizupxn5WN4WKKCnFhaW6V28JDc96vQHxeravcEqJ9xPZENAlz/9NKIjnpCg+aUwIuJB0sTYx4DzgAuALUjLXFyImVm7iDTKrpGjm3XSE1J/lsKYQ3qSMjNrb90daxrSUQGp4xUsA9QzpnjOU++kCbnpo+evKL7MqvwmrmFLisv01Gl+i4Lmt9XPLyssU9TMVtgsZzbEedi3A5KZWXtwQHJAMjNruSBnev/Q44BkZtZiItxkhwPSOtWzXv63WxuMLSyjZ/P7aUYsLN6SgeX5fUWxJH+LcIDeZfnL9gD0rijueyrkodpmzen174wDkplZq7nJDnBAMjNrC26yc0AyM2sPDkgOSOvU8IJvd0GfD0AsK5jrs7r4+T6ez98Wot4cIM8PMmul7l84tREOSGZmrRZAly8L1AgHJDOzNuA+JAckM7P24IDkgLROFfT79C7JXyuuHm/rbdZFAuh1QHJAMjNrOQ9qAAckM7P24IDkgGRm1nJB3akcQ4UD0jrUrzXh+qNg3yUzGyQDfrgJ9/3igGRm1h7cZOeAZGbWch5lBzggmZm1Bz8hOSCZmbUFByQHJDOzlosAL3DsgGRm1hb8hOSAZGbWFhyQHJDMzFovPMoOByQzs9YLCE+MdUAyM2sLXjrIAcnMrOUioNcByQHJzKwdeFCDA5KZWTsIPyHRUctCSzpS0l2Snpc0R9LRfeTvkXSqpPuzMn+RdMS6qq+ZWWOyDfoaORrUj8/LsZK+I+lxSc9KulzS1jV5hks6TdI/JC2VdIOkN+S81wmS5mbXvk3Sfo3UuWMCkqTDgJ8CVwEHAbOA8yUdWqfY14HPAN8G3gr8AfjfRr85ZmbrRGVx1UaOBvTz8/JC4J3AJ4Gjgc2A6ySNr8rzDeAk4EzgcGAVcI2kyVXX/gTwFWAGcDBwP3CppJ37rHd0SLulpLnALRFxRFXahcD2EfHqnPxbAX8DpkXED6rSrwfuiIgT6l1vnCbGTj17l1Z/M+te1/RedGtEvK6/5cf1bBQ7D9+3obxXr/xZn9fqx+flLsANwH4RcWWWNgl4ADgtIs6U9EpgLnB8RHw3yzOS9Dl7eUR8WNL6wCPAdyPilCyPgJuAhRFR92GgI56Qsui7FXBJzamLgamStswpdhCwFPhRdWJE7NZXMDIzW6ci26CvkaMP/fy83AdYAlz9QpViPnA9sH+WtCcwrPp9I2I5cFlVnp2A8TV5AvgFsJekEfXq3hEBCZiafb23Jn1u9nWbnDLbZ/n3lvRnSask3Sfp8MGqpJlZf0VvNHQ0oD+fl1OBuRFRu8Lr3Kr8U4EFWaCqzfNySaP7uPZwYDJ1dEpAqrRhLq5JX5J9HZdTZhLwcuCHpD6ktwC3AhdI2mMwKmlm1m8lPSHRv8/L8Tn5K2XGNZAHYIOqay8pyJN37TU6Zdi3+jif9680ghSUDoyIywAkXUuK4J8HrlvrItI0YFr28tlrei+qjfLtZGPgqVZXYhB043114z1Bd95Xf+/pFQO56BIWXHVNXLxxg9lHSbql6vX0iJhe9bo/n5f1yvQ2kKeSrz/XXqNTAtKi7OsGNenjas5XWwKsBmZWEiKiV9LVwPvzLpL9o07PO9duJN0ykE7UdtWN99WN9wTdeV+tuqeIeEuJb9efz8tF5DenjavKvyjnPavfd3FV3rG8+Cmp3rXX6JQmu8qTypSa9Ck156vdR7q/9WrSR5AGWZqZdaP+fF7eC0zORsTVlrm3Ks9ESRvm5HkgIlb0ce3lwN/rVbwjAlJEzCUNP6wdQ38IcF9EPJRT7ErS4+NhlQRJw0l9STcMUlXNzFqqn5+XM4EJwF6VhGzY967ANVlSZQTeoVV5RpLmeFby3AQ8V5NHpPlIs7OgVahTmuwAvgicJ2kBaZjh20nB5ghY883bCrg7IhZHxLWSLge+KWksaaz8vwNbAke14gZK1hFNi/3QjffVjfcE3Xlf3XJPzX5ezpY0izTo62TgGVJf+0LgHICI+Luk83nhM/U+0iTZCcB/Z3mWSjob+IykVaTFCN4LvBbYvc9aR0THHMAHs2/CMuBu4N1V544hNcXtXpU2GjiLNFHreVL03q3V9+HDhw8fg3304/NyQ+A8YAGpr+c3wDY17zkS+BrwBOlJaDawU02eHuDTwEPZ5+6tpAm3fda5Y1ZqMDOz7tYRfUhDkaRfZMt/VKftI+lP2aKGD0j6WE6510malS2O+KikMyTVDuxYpyTtKunGrN6PSvpW9shfOd9x9yXpQ9mClc9JulPSv9Wc75h7krSjpJWSNq9JL+UeJG0t6deSFkp6StI5kvJGa62r+3pndl9LlBYJPU/SS5qts6SXSvqppKclLZL0M0mbDPZ9dbVWP1b6yH3UfhfpcXpuVdr/A1YAPyYNzDidNKb/41V5ppAeta8gLeXxMdLj+rdbeC87k0bXXEzqMP0QqUnggk69L9JctQDOzu7pq9nrd3baPZHm5T2c1X/zsn/eSM1A/wD+CLwN+ED2739Zi+7r8Cztu6Tlct5DGvl1JzCy0TqT+t/vIK1A8E5Sv/RDWdrwVv2+dfrR8gr4qPkHgU1JHYr/4MUB6RrgDzV5z8x+USq/SN/PfilGVOX5MGlF3s1adD/XZ4eq0o4D5gFjOvG+SH2R19akzQau65R/q+wD9TjS3JGncz64S7kHUl/Cs8BGVXn2y663Uwvu6w7gNzVldsryHdRonXnhj8ZXV+V5DSloH76ufya75XCTXfv5PmkI5m8rCZJGkYZf5i2WOIH01yykv/h+HS8eWnkxaUHEfQapvoUkbQy8CTgnst9YgIj4TkRsRfrl7bj7Akax9tIoTwMbddC/1S6kAPMV0nYDa5R8D/sA10fE01V5ZpK+f/tTvnr3JVKgrR1Jd0/2davsayN13oc0Qm1OJUNE3A3MYXDua0hwQGojkt5PGh55fM2pyaQJvoWLJUoaA2xRmyfSQoiLyV9QcbBtR5oL9oykC7P+lkVZe/xoOve+vgHsl/VFjFPaY+atpOatTrmnOcDkiPgC6YmmWpn3MDUnz2rSPJnBuM/C+4rk4xHxq5oyB2Vf78q+NlLntfJkqhcjtSZ10jykribpFaS+iGMj4im9eMJ0I4slFuWp5Ku7qOEgmZR9nQH8EjgQ2IHUHzEaODc732n39TPSUvwXVaWdHxFnSXpj9rqt7ykinqhzusyft0YW7SxNH/e1FqV9084GbuOFZcYaXWj07oI8W+ekWwMckNpA1pTwQ9ImV7XNJLAOFjUcJJW9T26KiOOy/782u9+z6XsSYrve16WkZquTSB9kOwGflbQYuKCPsu16T9XK/HlrZNHOlpA0lRSEVgGHRUQzdW7b++pkDkjt4TjS/k3bKS1vBNkPfPa6kcUSFxfkqeSru6jhIKn8RX15TfpVpDb+12evO+a+JP0/YF/Sk+yMLPl6SQtJT3yV3Yk75p5ylPnzVm9Bzrrrmg0mSbuTNo17FtgjIuZVnW6kzvXytPrfr2O5D6k9HEpa9v4xYGV2HE3qZF1JGhiwmjqLJUbEs6QVKV6UJ5tfsQH57d2D7b7s68ia9MqT0wN03n1Vthn4XU367OzrjnTePdWaR3n3cG9OnmGkJbxacp9Km3ReRRoW/saIuKcmSyN1XitPpnoxUmuSA1J7+CDpaaH6uIz0C/N64OekD7yD9eLOpUNIf41V9kaZCRyoF28TfAjpw2XWINa/yBzSX5RH1KS/ldRM8ns6774qHza71KRX+o7uofPu6UUiYhnl3cNMYA9JE6vy7EPanuAa1jFJ+wI/Jf3s7RIRj+Rka6TOM4FtJa0ZwCDpNcCracF9dY1Wjzv3kX+QBgJUz0Pak9Q2fSFpTsRp2euTq/JMJa0ddQ3pQ/8k0kTF/2nhfRye1fMnpEmknyRNlP1qp94XaYDGYuCjpAUjP569vrwT74kX1jWrnq9Tyj2QBrbMB24H3kHai+yZyvdqXd4X6Un9YdJcqr1Jk7arj80arXP2XveQnvKPzI7KBFtPjO3vv1mrK+Cj4B+mJiBlae/IfuCXA/cDH8sp9ybSCrvLsl++M4D1WnwvB5E6/5eRJlKeCvR06n1lH0ZnZPeyLPtg+izZhNFOu6e8gFTmPQDbZkFrKWlRzu8CG6zr+yLNrYo6x6ebqTNp2PsvSH2lT5NGX76sFT+T3XJ4cVUzM2sL7kMyM7O24IBkZmZtwQHJzMzaggOSmZm1BQckMzNrCw5IZmbWFhyQzMysLTggmZlZW3BAMhsAScMlLZR0XN+5zaweBySzgflX0mZttVtsmFmTHJDMBmZ/4J6IeKDVFTHrdA5INmRJui47dpN0o6Slku6W9Kbs/GGS7pD0nKSbJOXtf7M/2dORpNdIioJjXk5ZM6vixVVtyJL0FGkl57HA90hbKZxK2kX0G8CxwHmkXUD/E7g6Ig6oKr8FacXvvSLit5I2JW3bUG0H0vYU342IDw/uHZl1Nm9hbkOSpJcBG5G2TfjniJifpY8Bvgi8E3hdpM3qyJ6O9qp5m/1JWw/cABARj5L2fapcYyrwVeAK4ITBvB+zbuAmOxuqtsu+froSjDKLsq8nVoJRZjGwouY99gd+GxG16UjakrSfzt3AIXl5zOzFHJBsqNqOtCnbr2vSX0Vqxru5Jv3VwN8qL7Jtu99Mzug6SZsBvwUeAQ6MiOfLq7ZZ93JAsqFqe+DvEfF0TfoOwO2xdufqdsBfql7vBqxPTUCSNIn0ZLQEeEtELCm11mZdzAHJhqrtSNtz19q+Nj0brDCxJn1/4M6IeKQq3wRgJiBg74hYUHKdzbqaA5INOZKGkZrgagPPK0kj6moDVaW/qfoJac1w76zsWNLghQ1Jo+6eLLfWZt3Po+xsKNoaGMXagWeH7GteQOoF7gKQtBWpr6m6ue7HwE7AF4DdJVWXvyMi/lpKzc26mAOSDUWVJ57awLM9aSTdPTn550XE0uz1/sBC4CYApeizF6mp7vM513sP4IBk1gdPjDVrkqQrgMURcXir62LWTfyEZNa8WcDsVlfCrNv4CcnMzNqCR9mZmVlbcEAyM7O24IBkZmZtwQHJzMzaggOSmZm1BQckMzNrCw5IZmbWFv4/ez9Y4x5kd4QAAAAASUVORK5CYII=\n", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "plt_proteomics = graphs.plot_density(\n", + " x,\n", + " y,\n", + " z,\n", + " method_conf[\"graphs\"],\n", + " r\".\\Output\\tutorial\\Plot_proteomics_precursors.pdf\",\n", + " gui = True\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "c8ad871e", + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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\n", 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" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "hist_mz = graphs.plot_precursor_distribution_as_histogram(\n", + " lib,\n", + " method_conf[\"graphs\"],\n", + " r\".\\Output\\tutorial\\histogram_proteomics_precursors_mz.pdf\",\n", + " gui = True \n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "5ee190cb", + "metadata": {}, + "source": [ + "#### Plotting the dia-PASEF method on to of the kernel density distribution." + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "0b860e9b", + "metadata": {}, + "outputs": [ + { + "data": { + "application/javascript": [ + "\n", + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " var force = true;\n", + "\n", + " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, js_modules, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + " if (js_modules == null) js_modules = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls.length === 0 && js_modules.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error() {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (var i = 0; i < css_urls.length; i++) {\n", + " var url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error;\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " 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url;\n", + " element.type = \"module\";\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " if (!js_urls.length && !js_modules.length) {\n", + " on_load()\n", + " }\n", + " };\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-2.4.2.min.js\", \"https://unpkg.com/@holoviz/panel@0.12.4/dist/panel.min.js\"];\n", + " var js_modules = [];\n", + " var css_urls = 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((root.Bokeh !== undefined) || (force === true)) {\n", + " for (var i = 0; i < inline_js.length; i++) {\n", + " inline_js[i].call(root, root.Bokeh);\n", + " }} else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(run_inline_js, 100);\n", + " } else if (!root._bokeh_failed_load) {\n", + " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", + " root._bokeh_failed_load = true;\n", + " }\n", + " }\n", + "\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", + " run_inline_js();\n", + " } else {\n", + " load_libs(css_urls, js_urls, js_modules, function() {\n", + " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + " run_inline_js();\n", + " });\n", + " }\n", + "}(window));" + ], + "application/vnd.holoviews_load.v0+json": "\n(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n\n if (typeof root._bokeh_onload_callbacks === 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append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n" + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "import panel as pn\n", + "pn.extension()" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "133d881b", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "save_figure_at = r\".\\Output\\tutorial\\Plot_method.png\"\n", + "\n", + "graphs.plot_density_and_method(\n", + " df_parameters_final,\n", + " x,\n", + " y,\n", + " z,\n", + " method_conf[\"graphs\"],\n", + " save_figure_at,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "7466bb09", + "metadata": {}, + "outputs": [ + { + "data": {}, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/vnd.holoviews_exec.v0+json": "", + "text/html": [ + "
\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
\n", + "
\n", + "" + ], + "text/plain": [ + "PNG(str, align='center', height=345, margin=(0, 20, 0, 0), sizing_mode='fixed', width=460)" + ] + }, + "execution_count": 13, + "metadata": { + "application/vnd.holoviews_exec.v0+json": { + "id": "1002" + } + }, + "output_type": "execute_result" + } + ], + "source": [ + "pn.pane.PNG(\n", + " save_figure_at,\n", + " height=345,\n", + " width=460,\n", + " align='center',\n", + " margin=(0, 20, 0, 0)\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "594021a0", + "metadata": {}, + "source": [ + "#### Evaluate the die-PASEF method." + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "eef44047", + "metadata": {}, + "outputs": [], + "source": [ + "import pydiaid.method_evaluation as evaluator" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "528b2f9e", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'unique proteins in the library': 3420,\n", + " 'unique precursors in the library': 19998,\n", + " 'smallest diaPASEF window': 17.03,\n", + " 'biggest diaPASEF window': 198.07,\n", + " 'average diaPASEF window size': 37.4,\n", + " 'No. of covered proteins': 3397,\n", + " 'No. of covered precursors': 19257,\n", + " 'No. of covered, doubly charged precursors': 15056,\n", + " 'No. of covered, triply charged precursors': 3792,\n", + " 'No. of covered, quadruply charged precursors': 232,\n", + " 'all proteins covered': '99.3%',\n", + " 'all precursors covered': '96.3%',\n", + " 'all doubly charged precursors covered': '96.9%',\n", + " 'all triply charged precursors covered': '93.9%',\n", + " 'all quadruply charged precursors covered': '97.5%'}" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dict_coverage = evaluator.coverage(\n", + " df_parameters_final,\n", + " lib,\n", + ")\n", + "dict_coverage" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c558b36d", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python [conda env:.conda-pydiaid2]", + "language": "python", + "name": "conda-env-.conda-pydiaid2-py" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.13" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/nbs/tutorial.ipynb b/nbs/tutorial.ipynb deleted file mode 100644 index f735b44..0000000 --- a/nbs/tutorial.ipynb +++ /dev/null @@ -1,43 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python [conda env:pydiaid]", - "language": "python", - "name": "conda-env-pydiaid-py" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.8.10" - }, - "toc": { - "base_numbering": 1, - "nav_menu": {}, - "number_sections": true, - "sideBar": true, - "skip_h1_title": false, - "title_cell": "Table of Contents", - "title_sidebar": "Contents", - "toc_cell": false, - "toc_position": {}, - "toc_section_display": true, - "toc_window_display": false - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} From 08ca284b30e0ae7a03e705a6cafdb77c2adba716 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Thu, 7 Apr 2022 16:38:55 +0200 Subject: [PATCH 42/58] FIX: Update py_diAID tutorial --- nbs/{py_diAID_tutorial.ipynb => py_diAID_tutorial_v1.ipynb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename nbs/{py_diAID_tutorial.ipynb => py_diAID_tutorial_v1.ipynb} (100%) diff --git a/nbs/py_diAID_tutorial.ipynb b/nbs/py_diAID_tutorial_v1.ipynb similarity index 100% rename from nbs/py_diAID_tutorial.ipynb rename to nbs/py_diAID_tutorial_v1.ipynb From 870a7bb779794e2063729e74beaaff61f19f697e Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Thu, 7 Apr 2022 16:40:32 +0200 Subject: [PATCH 43/58] FIX: typo in turotial --- nbs/py_diAID_tutorial_v1.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nbs/py_diAID_tutorial_v1.ipynb b/nbs/py_diAID_tutorial_v1.ipynb index 655bfdb..45bbb7e 100644 --- a/nbs/py_diAID_tutorial_v1.ipynb +++ b/nbs/py_diAID_tutorial_v1.ipynb @@ -330,7 +330,7 @@ "id": "5ee190cb", "metadata": {}, "source": [ - "#### Plotting the dia-PASEF method on to of the kernel density distribution." + "#### Plotting the dia-PASEF method on top of the kernel density distribution." ] }, { From 06bac49694d8ac4616124e434f4640aef98fe39f Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Thu, 7 Apr 2022 16:45:39 +0200 Subject: [PATCH 44/58] FIX: tutorial did not show one plot. --- nbs/{py_diAID_tutorial_v1.ipynb => py_diAID_tutorial_v2.ipynb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename nbs/{py_diAID_tutorial_v1.ipynb => py_diAID_tutorial_v2.ipynb} (100%) diff --git a/nbs/py_diAID_tutorial_v1.ipynb b/nbs/py_diAID_tutorial_v2.ipynb similarity index 100% rename from nbs/py_diAID_tutorial_v1.ipynb rename to nbs/py_diAID_tutorial_v2.ipynb From 877cbd5e4c3a96c560f2590dbc958c0178ff165f Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Thu, 7 Apr 2022 20:33:49 +0200 Subject: [PATCH 45/58] FIX: Raise exception if the modification filter is on but the modification is not present in the dataset. --- pydiaid/loader.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/pydiaid/loader.py b/pydiaid/loader.py index 8098958..1190f5a 100644 --- a/pydiaid/loader.py +++ b/pydiaid/loader.py @@ -41,7 +41,7 @@ def load_library( raise Exception('Analysis software not supported.') except Exception as e: print(e) - raise Exception("error while processing: Did you choose the correct analysis_software?") + raise Exception("error while processing: Did you choose the correct analysis_software and is the modification present in the dataset?") def __load_dataframe_from_file( @@ -301,7 +301,12 @@ def library_loader( library[ptm] = library[modified_peptide].apply( lambda x: find_PTM(x, ptm) ) - library_filtered = library[library[ptm] == True] + try: + library_filtered = library[library[ptm] == True] + raise Exception('Modification not in dataset.') + except Exception as e: + print(e) + raise Exception("Is this modification present in the dataset?") library_subset = library_filtered.drop_duplicates( [modified_peptide, charge] ) From 3988b6350d0eda1acd0695c6d2740c5c28260a17 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Thu, 7 Apr 2022 20:37:22 +0200 Subject: [PATCH 46/58] DOC: updated --- pydiaid/method_creator.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/pydiaid/method_creator.py b/pydiaid/method_creator.py index 73c6681..44cf0df 100644 --- a/pydiaid/method_creator.py +++ b/pydiaid/method_creator.py @@ -82,12 +82,6 @@ def method_creation( x_splits ) - # enable this for returning the actuall windows without elongaiton - #return pd.DataFrame( - # results_sorted, - # columns=["MS Type", "Cycle Id", "Start IM", "End IM", "Start Mass", "End Mass"] - #) - return enhance_diaPASEF_windows_to_edges_of_IM_ranges( results_sorted, method_parameters["ion_mobility"], From 2e9a558265125efa7486fe0abbcfb565dcde9a09 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Thu, 7 Apr 2022 20:39:19 +0200 Subject: [PATCH 47/58] DOC: update documentation. --- pydiaid/main.py | 4 ---- pydiaid/method_creator.py | 14 +++++++------- pydiaid/method_evaluation.py | 2 +- 3 files changed, 8 insertions(+), 12 deletions(-) diff --git a/pydiaid/main.py b/pydiaid/main.py index f83d931..aba4b40 100644 --- a/pydiaid/main.py +++ b/pydiaid/main.py @@ -12,10 +12,6 @@ # importing for scientific and numeric manipulations import numpy as np -# todo: accelerate slow steps: loading of proteomics library, kernel density -# estimation, Bayesian optimization -# todo: change file locations to general solution - def create_folder( paths: list, diff --git a/pydiaid/method_creator.py b/pydiaid/method_creator.py index 44cf0df..3d5f5b0 100644 --- a/pydiaid/method_creator.py +++ b/pydiaid/method_creator.py @@ -8,8 +8,8 @@ def method_creation( - library_mz_values: list, # todo or pd.Series? - method_parameters: dict, # todo Is this correct? + library_mz_values: list, + method_parameters: dict, A1: float, A2: float, B1: float, @@ -92,12 +92,12 @@ def method_creation( def calculate_diaPASEF_window_coordinates( num_steps: int, num_scans: int, - window_position: list, # todo correct? + window_position: list, m_bottom: float, c_bottom: float, m_top: float, c_top: float, - x_splits: list, # todo correct? + x_splits: list, ) -> pd.DataFrame: """This function calculates the diaPASEF window parameters. The x start and end coordinate of each window (= rectangle) is already defined in @@ -225,7 +225,7 @@ def divide_mz_range_in_equally_filled_parts( x_series: list, mz_range: tuple, num_splits: int, -) -> list: # todo correct? how to describe it better? +) -> list: """This function calculates the lower and upper m/z value of each ion mobility window equalizing the number of precursors per diaPASEF window across the m/z dimension. @@ -266,9 +266,9 @@ def divide_mz_range_in_equally_filled_parts( def line_equation( - l1: tuple, # todo (x,y) correct? + l1: tuple, l2: tuple, -) -> float: # todo m: float, c: float; how to write this with two output values? +) -> float: """This function calculates the line equation of two coordinates. Parameters: l1 (tuple): x and y coordinate of the 1st point. Line encoded as l=(x,y). diff --git a/pydiaid/method_evaluation.py b/pydiaid/method_evaluation.py index 57db0c1..0cb634d 100644 --- a/pydiaid/method_evaluation.py +++ b/pydiaid/method_evaluation.py @@ -117,7 +117,7 @@ def coverage( def boxes( df: pd.DataFrame, -) -> int: # todo: how to describe multiple values? +) -> int: """This function calculates diaPASEF window specific information regarding the window size and creates two lists. One is for plotting the dia-PASEF window scheme on top of a kernel density estimation plot. The second is From 53525e8ba6297136151b80fdd692bf8423ac325c Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Thu, 7 Apr 2022 20:43:46 +0200 Subject: [PATCH 48/58] FIX: also include singly charged precursors. --- pydiaid/main.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pydiaid/main.py b/pydiaid/main.py index aba4b40..2558de4 100644 --- a/pydiaid/main.py +++ b/pydiaid/main.py @@ -157,10 +157,9 @@ def create_final_method( file_name_method = method_conf["input"]["save_at"] + '/final_method/diaPASEF_method.txt' # create the diaPASEF method scheme; dim[0],dim[1],dim[2],dim[3] == A1, A2, # B1, B2. - library_reduced = library[library['Charge'] != 1] df_parameters_final = method_creator.method_creation( - library_reduced["mz"], + library["mz"], method_parameters, dim[0] + method_parameters["shift_of_final_method"], dim[1] + method_parameters["shift_of_final_method"], From 9f035bc3b383538497d475f17597fdcd2b99b6af Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 8 Apr 2022 13:24:31 +0200 Subject: [PATCH 49/58] DOC: typos in docstrings --- pydiaid/cli.py | 19 ++-- pydiaid/graphs.py | 28 +++-- pydiaid/graphs_for_gui.py | 208 ----------------------------------- pydiaid/loader.py | 30 ++--- pydiaid/main.py | 16 +-- pydiaid/method_creator.py | 66 +++++------ pydiaid/method_evaluation.py | 10 +- pydiaid/method_optimizer.py | 5 +- 8 files changed, 83 insertions(+), 299 deletions(-) delete mode 100644 pydiaid/graphs_for_gui.py diff --git a/pydiaid/cli.py b/pydiaid/cli.py index 2aab4a0..dfa4842 100644 --- a/pydiaid/cli.py +++ b/pydiaid/cli.py @@ -1,6 +1,5 @@ #!python - # external import click @@ -10,7 +9,7 @@ from pydiaid import main from pydiaid import method_optimizer -# for data manipulation: +# for data manipulation import pandas as pd # for saving input data as json: @@ -116,10 +115,10 @@ def run_all( """This function carries out all sub-functions step by step: creating a folder for the output information, loading of the proteomics library, calculation of the kernel density estimation for the density plots, - Bayesian optimization of diaPASEF method parameters by trying multiple scan + Bayesian optimization of dia-PASEF method parameters by trying multiple scan area coordinates using a Gaussian process, writing all input and output information in json or csv files, creating final dia-PASEF method, plotting - diaPASEF windows on top of a kernel density estimation of precursors and + dia-PASEF windows on top of a kernel density estimation of precursors and calculating method evaluation information. Parameters: @@ -142,7 +141,7 @@ def run_all( # save input parameters as json file for reusing out_file = open(save_at+"/input_parameters.json", "w") - json.dump(method_conf, out_file, indent = 4) + json.dump(method_conf, out_file, indent=4) out_file.close() xi, yi, zi, library = main.library_information( @@ -194,7 +193,7 @@ def library_plus_evaluate_method( kernel density estimation for the density plots, writing all input and output information in json or csv files, plotting of the diaPASEF windows on top of a kernel density estimation of precursors, and calculating method - evaluation information + evaluation information. Parameters: method_conf (dict): this dictionary contains all input parameters for all @@ -214,7 +213,7 @@ def library_plus_evaluate_method( # save input parameters as json file for reusing out_file = open(save_at+"/input_parameters.json", "w") - json.dump(method_conf, out_file, indent = 4) + json.dump(method_conf, out_file, indent=4) out_file.close() df_parameters_final = pd.read_csv( @@ -270,7 +269,7 @@ def library_plus_create_methods( # save input parameters as json file for reusing out_file = open(save_at+"/input_parameters.json", "w") - json.dump(method_conf, out_file, indent = 4) + json.dump(method_conf, out_file, indent=4) out_file.close() library = loader.load_library( @@ -299,7 +298,7 @@ def multiple_charged_prec( method_conf: dict ) -> None: """This function carries out all sub-functions required for method - evaluation of precursor with multiple charge state: creating a folder for + evaluation of precursor with multiple charge states: creating a folder for the output information, loading of the proteomics library, loading of the acquisition scheme, calculation of the kernel density estimation for the density plots depending on the charge state, writing all input information @@ -322,7 +321,7 @@ def multiple_charged_prec( # save input parameters as json file for reusing out_file = open(save_at+"/input_parameters.json", "w") - json.dump(method_conf, out_file, indent = 4) + json.dump(method_conf, out_file, indent=4) out_file.close() df_parameters_final = pd.read_csv( diff --git a/pydiaid/graphs.py b/pydiaid/graphs.py index 5f19755..cf6e3d7 100644 --- a/pydiaid/graphs.py +++ b/pydiaid/graphs.py @@ -1,4 +1,4 @@ -# for data manipulation: +# for data manipulation import pandas as pd # importing for scientific and numeric manipulations @@ -27,7 +27,7 @@ def kernel_density_calculation( library_subset: pd.DataFrame, nbins: int, -) -> np.ndarray: # todo: how to describe multiple values? +) -> np.ndarray: """Calculate the kernel density estimation of a data frame representing a filtered proteomics library or single-shot measurement. @@ -43,7 +43,7 @@ def kernel_density_calculation( x = library_subset['mz'] y = library_subset['IM'] - k = kde.gaussian_kde([x,y]) + k = kde.gaussian_kde([x, y]) xi, yi = np.mgrid[x.min():x.max():nbins*1j, y.min():y.max():nbins*1j] zi = k(np.vstack([xi.flatten(), yi.flatten()])) @@ -63,16 +63,16 @@ def plot_density( Parameters: xi, yi, zi (numpy.ndarray): coordinates of the kernel density estimation, - where zi indicates the density + where zi indicates the density. plot_parameters (dict): dictionary, which contains all input parameters for - creating plots (e.g., displayed m/z-range, ion mobility-range) + creating plots (e.g., displayed m/z-range, ion mobility-range). file_name: file path and file name where the plot should be saved gui (bool): whether to use in the GUI or not. Defaults is False. """ fig, ax = plt.subplots() plt.pcolormesh( xi, yi, zi.reshape(xi.shape), - vmax = 0.02, + vmax=0.02, cmap=plt.cm.viridis ) ax.set_xlim(plot_parameters["plot_mz"][0], plot_parameters["plot_mz"][1]) @@ -101,7 +101,7 @@ def plot_precursor_distribution_as_histogram( library_subset (pd.DataFrame): pre-filtered data frame with unified column names. plot_parameters (dict): dictionary, which contains all input parameters for - creating plots (e.g., displayed m/z-range, ion mobility-range) + creating plots (e.g., displayed m/z-range, ion mobility-range). file_name: file path and file name where the plot should be saved gui (bool): whether to use in the GUI or not. Defaults is False. """ @@ -117,7 +117,7 @@ def plot_precursor_distribution_as_histogram( histtype='step', fill=True, alpha=0.5, - color = ['#267FA5', '#4EA7BB', '#7AC7C9'], + color=['#267FA5', '#4EA7BB', '#7AC7C9'], label=[ 'triply charged precursors', 'doubly charged precursors', @@ -128,7 +128,7 @@ def plot_precursor_distribution_as_histogram( plt.xlim([plot_parameters["plot_mz"][0], plot_parameters["plot_mz"][1]]) plt.ylabel('No. of precursors') plt.legend(bbox_to_anchor=(0.8, 1.42)) - plt.xlabel('$m/z$') # can be used as $some_text$ to make some_text italic + plt.xlabel('$m/z$') fig.savefig(file_name, bbox_inches='tight', pad_inches=0, dpi=300) if gui: plt.legend( @@ -140,8 +140,6 @@ def plot_precursor_distribution_as_histogram( plt.clf() - - def plot_density_and_method( df: pd.DataFrame, xi: np.ndarray, @@ -155,12 +153,12 @@ def plot_density_and_method( Parameters: df (pd.DataFrame): data frame that contains the scan type (PASEF), scan - number and the corresponding diaPASEF window coordinates for each + number and the corresponding di-aPASEF window coordinates for each window per scan. xi, yi, zi (numpy.ndarray): coordinates of the kernel density estimation, where zi indicates the density. plot_parameters (dict): dictionary, which contains all input parameters for - creating plots (e.g., displayed m/z-range, ion mobility-range) + creating plots (e.g., displayed m/z-range, ion mobility-range). file_name: file path and file name where the plot should be saved. """ @@ -194,7 +192,7 @@ def kernel_density_calculation_multiple_charge( library_subset: pd.DataFrame, nbins: int, charge_setting: int, -) -> np.ndarray: # todo: how to describe multiple values? +) -> np.ndarray: """Calculate the kernel density estimation for specific multiple charged precursors. @@ -210,7 +208,7 @@ def kernel_density_calculation_multiple_charge( x = library_subset['mz'][library_subset['Charge'] == charge_setting] y = library_subset['IM'][library_subset['Charge'] == charge_setting] - k = kde.gaussian_kde([x,y]) + k = kde.gaussian_kde([x, y]) xi, yi = np.mgrid[x.min():x.max():nbins*1j, y.min():y.max():nbins*1j] zi = k(np.vstack([xi.flatten(), yi.flatten()])) diff --git a/pydiaid/graphs_for_gui.py b/pydiaid/graphs_for_gui.py deleted file mode 100644 index 105a25a..0000000 --- a/pydiaid/graphs_for_gui.py +++ /dev/null @@ -1,208 +0,0 @@ -# importing components for visualization -import holoviews as hv -import plotly.express as px - -# for data manipulation: -import pandas as pd - -# importing for scientific and numeric manipulations -from scipy.stats import kde -import numpy as np - -hv.extension("bokeh") - -# --------------------------------------------------------------------------- -# example code for you, Jane :) -xi, yi, zi = kernel_density_calculation_GUI( - library, - method_conf["graphs"]["numbins"] - ) - - -qmesh = density_plot_GUI(xi, yi, zi) - - -plot_window_scheme_on_top_of_density(df_parameters_final, qmesh, plot_parameters) - - -histogram_plots(library, "mz") - - -histogram_plots(library, "IM") - -# -------------------------------------------------------------------------- - - -def kernel_density_calculation_GUI( - library_subset: pd.DataFrame, - nbins: int, -) -> np.ndarray: # todo: how to describe multiple values? - """This function calculates the kernel density estimation of a data frame - representing a filtered proteomics library or single-shot measurement. - - Parameters: - library_subset (pd.DataFrame): pre-filtered data frame with unified column - names. - nbins (int): number of bins for the kernel density estimation. - - Returns: - xi, yi, zi (numpy.ndarray): coordinates of the kernel density estimation, - where zi indicates the density. - """ - - x = library_subset['mz'] - y = library_subset['IM'] - - # Creating density plot - nbins=150 - k = kde.gaussian_kde([x,y]) - xi, yi = np.mgrid[x.min():x.max():nbins*1j, y.min():y.max():nbins*1j] - positions = np.vstack([xi.ravel(), yi.ravel()]) - zi = np.reshape(k(positions).T, xi.shape) - - return xi, yi, zi - - -def boxes_GUI( - df: pd.DataFrame, -) -> list: - """This function calculates dia-PASEF window specific information. It - creates a list, containing information for plotting the dia-PASEF - window scheme on top of a kernel density estimation plot. - - Parameters: - df (pd.DataFrame): data frame that contains the scan type (PASEF), scan - number, and the corresponding diaPASEF window coordinates for each - window per scan. - - Returns: - rect (list): This list contains all information to print the diaPASEF - windows on top of a kernel density estimation plot. - """ - - rect = list() - - count = dict() - for item in df["Cycle Id"].values: - count[item] = count.get(item, 0) + 1 - - for i in count.keys(): - df_2 = df[df["Cycle Id"] == i] - df_2["xw"] = df_2.apply(lambda x: x["End Mass"]-x["Start Mass"], axis=1) - df_2["yw"] = df_2.apply(lambda x: x["End IM"]-x["Start IM"], axis=1) - df_2["rect"] = df_2.apply(lambda x: [ - x["Start Mass"], - x["Start IM"], - x["xw"], - x["yw"] - ], axis=1) - rect += list(df_2["rect"].values) - - return rect - - -def density_plot_GUI( - xi: np.ndarray, - yi: np.ndarray, - zi: np.ndarray -): - """Creates an interactive density plot from a data frame representing a - filtered proteomics library or single-shot measurement. - - Parameters: - xi, yi, zi (numpy.ndarray): coordinates of the kernel density estimation, - where zi indicates the density - """ - - qmesh = hv.QuadMesh((xi, yi, zi)).options( - cmap=plt.get_cmap('viridis'), - colorbar = True, - width = 500, - line_width = 0.00001, - bgcolor= '#440256', - xlabel = "m/z, Th", - ylabel= "Inversed IM, V·s·cm\u207B\u00B2", - colorbar_opts = {'title': 'Density'} - ) - - return qmesh - - -def plot_window_scheme_on_top_of_density( - df: pd.DataFrame, - qmesh: hv.element.raster.QuadMesh, - plot_parameters: dict, -): - """Plot the dia-PASEF acquisition scheme on top of a density plot - representing a filtered proteomics library or single-shot measurement. - - Parameters: - df (pd.DataFrame): data frame that contains the scan type (PASEF), scan - number and the corresponding diaPASEF window coordinates for each - window per scan. - qmesh (holoviews.element.raster.QuadMesh): interactive density plot, where - the dia-PASEF windows are plotted on top. - plot_parameters (dict): dictionary, which contains all input parameters for - creating plots (e.g., displayed m/z-range, ion mobility-range) - """ - - rect = boxes_GUI(df) - - polys = hv.Polygons( - [ - hv.Box( - rectangle[0], - rectangle[1], - (rectangle[2], rectangle[3]) - ) for rectangle in rect - ] - ) - polys.opts( - color=plot_parameters["window_color"], - line_width=1, - alpha=plot_parameters["window_transparency"] - ) - - qmesh.opts(colorbar_opts = {'title': 'Density'}) - - plot = qmesh * polys - - plot.opts(bgcolor='#440256', - xlabel = "m/z, Th", - ylabel= "Inversed IM, V·s·cm\u207B\u00B2" - ) - - return plot - - -def histogram_plots( - library_subset: pd.DataFrame, - x_axis: str, -) -> None: - """Plot histograms with the precursor distribution in the m/z or ion - mobility dimension sorted by charge state. - - Parameters: - library_subset (pd.DataFrame): pre-filtered data frame with unified column - names. - x_axis (str): the histogram can be build for the m/z- or ion Mobility - dimesion. This value selects the correct column in the data frame. - """ - - axis_dict = { - "mz": "m/z, Th", - "IM": "Inversed IM, V·s·cm\u207B\u00B2", - } - - x_axis_label = axis_dict[x_axis] - - - fig = px.histogram(library_subset, x = x_axis, color = 'Charge') - # Overlay both histograms - fig.update_layout(barmode = 'overlay', - xaxis_title_text = x_axis_label, # xaxis label - yaxis_title_text = 'No. of precursors', # yaxis label - ) - # Reduce opacity to see both histograms - fig.update_traces(opacity = 0.75) - fig.show() diff --git a/pydiaid/loader.py b/pydiaid/loader.py index 1190f5a..c21543c 100644 --- a/pydiaid/loader.py +++ b/pydiaid/loader.py @@ -1,4 +1,4 @@ -# for data manipulation: +# for data manipulation import pandas as pd import os import re @@ -153,24 +153,15 @@ def __parse_ms_fragger( Returns: pd.DataFrame: returns a pre-filtered data frame with unified column names. """ - #dataframe["ModifiedPeptideSequence"] = dataframe.apply( - # lambda x: combine_columns(x), - # axis=1 - #) library_subset = library_loader( dataframe, ptm, - #'Calibrated Observed M/Z', - #'Ion Mobility', - #'Charge', - #'Protein ID', - #"ModifiedPeptideSequence" - 'PrecursorMz', - 'PrecursorIonMobility', - 'PrecursorCharge', - 'ProteinId', - 'ModifiedPeptideSequence' + 'PrecursorMz', + 'PrecursorIonMobility', + 'PrecursorCharge', + 'ProteinId', + 'ModifiedPeptideSequence' ) return library_subset @@ -347,7 +338,8 @@ def get_file_names_from_directory( directory: str, extensions_list: list )-> list: - """Search for files with the specified extension in the repository and return a list of all file names with that extention. + """Search for files with the specified extension in the repository and + return a list of all file names with that extention. Parameters ---------- @@ -368,7 +360,8 @@ def get_file_names_from_directory( def create_opt_plot_df( filename: str )-> pd.DataFrame: - """Return the dataframe containing information about the optimized scan area coordinates and coverage based on the filename of the .png file. + """Return the dataframe containing information about the optimized scan + area coordinates and coverage based on the filename of the .png file. Parameters ---------- @@ -380,7 +373,8 @@ def create_opt_plot_df( pd.DataFrame The data frame contains several columns: - parameters: ['A1', 'A2', 'B1', 'B2', 'coverage']; - - values: showing the values for each parameter extracted from the filename. + - values: showing the values for each parameter extracted from the + filename. """ diff --git a/pydiaid/main.py b/pydiaid/main.py index 2558de4..ea62e33 100644 --- a/pydiaid/main.py +++ b/pydiaid/main.py @@ -3,10 +3,10 @@ from pydiaid import method_evaluation from pydiaid import graphs -# for data manipulation: +# for data manipulation import pandas as pd -# for creating new folders: +# for creating new folders import os # importing for scientific and numeric manipulations @@ -101,7 +101,7 @@ def precursor_within_scan_area( names. method_conf (dict): this dictionary contains all input parameters for all sub-functions. - save_at (str): location, where all information shouldbe stored. + save_at (str): location, where all information should be stored. """ # save parameters for method evaluation as .csv @@ -127,7 +127,7 @@ def create_final_method( method_conf: dict, ) -> pd.DataFrame: """This function calculates the final dia-PASEF window scheme with the - optimized scan area coordinates and writes the .txt diaPASEF parameter + optimized scan area coordinates and writes the .txt dia-PASEF parameter file as input file for timsControl. By default, the scan area coordinates are up-shifted by 0.022 1/K0 since the quadrupole has a dead time at the beginning of the dia-PASEF window where no signal is @@ -190,7 +190,7 @@ def final_method_information( Parameters: df_parameters_final (pd.DataFrame): data frame that contains the scan type - (PASEF), scan number, and the corresponding diaPASEF window coordinates + (PASEF), scan number, and the corresponding dia-PASEF window coordinates for each window per scan. xi, yi, zi (numpy.ndarray): coordinates of the kernel density estimation, where zi indicates the density. @@ -200,7 +200,7 @@ def final_method_information( library (pd.DataFrame): a pre-filtered data frame with unified column names containing all required precursor information. method_parameters (dict): dictionary, which includes all input parameters - for creating a diaPASEF method. + for creating a dia-PASEF method. dim (list): y-coordinates of the scan area = A1, A2, B1, B2. x-coordinate for A1 and B1 is the lower m/z-range value, x-coordinate for A2 and B2 is the upper m/z-range value. @@ -261,11 +261,11 @@ def evaluate_for_multiple_charged_prec( Parameters: method_conf (dict): this dictionary contains all input parameters for all sub-functions. - save_at (str): location, where all information shouldbe stored. + save_at (str): location, where all information should be stored. library (pd.DataFrame): a pre-filtered data frame with unified column names containing all required precursor information. df_parameters_final (pd.DataFrame): data frame that contains the scan type - (PASEF), scan number, and the corresponding diaPASEF window coordinates + (PASEF), scan number, and the corresponding dia-PASEF window coordinates for each window per scan. """ diff --git a/pydiaid/method_creator.py b/pydiaid/method_creator.py index 3d5f5b0..6337084 100644 --- a/pydiaid/method_creator.py +++ b/pydiaid/method_creator.py @@ -1,4 +1,4 @@ -# for data manipulation: +# for data manipulation import pandas as pd # importing for scientific and numeric manipulations @@ -15,7 +15,7 @@ def method_creation( B1: float, B2: float, ) -> pd.DataFrame: - """This function calculates the diaPASEF window coordinates based on the + """This function calculates the dia-PASEF window coordinates based on the input parameters with dynamic isolation widths, adjusted to the precursor density in the m/z dimension. All dia-PASEF windows together add up to the dia-PASEF window scheme. @@ -23,19 +23,19 @@ def method_creation( Parameters: library_mz_values (list): list of all mz precursor values. method_parameters (dict): dictionary, which contains all input parameters - for creating a diaPASEF method (e.g., m/z-range, ion mobility-range, - number of diaPASEF scans, number of ion mobility steps, the overlap of + for creating a dia-PASEF method (e.g., m/z-range, ion mobility-range, + number of dia-PASEF scans, number of ion mobility steps, the overlap of the diaPASEF windows, the shift of the final window scheme in the ion mobility axis to account for the blind spot of the changing quadrupole - at the top of each diaPASEF window) + at the top of each dia-PASEF window). A1 (float): bottom left y-coordinate of the rectangle, which defines the - scan area and the slope of the diaPASEF scan line. + scan area and the slope of the dia-PASEF scan line. A2 (float): bottom right y-coordinate of the rectangle, which defines the - scan area and the slope of the diaPASEF scan line. + scan area and the slope of the diaP-ASEF scan line. B1 (float): top left y-coordinate of the rectangle, which defines the scan - area and the slope of the diaPASEF scan line. + area and the slope of the dia-PASEF scan line. B2 (float): top right y-coordinate of the rectangle, which defines the scan - area and the slope of the diaPASEF scan line. + area and the slope of the dia-PASEF scan line. Returns: pd.DataFrame: data frame that contains the scan type (PASEF), scan number, @@ -99,35 +99,35 @@ def calculate_diaPASEF_window_coordinates( c_top: float, x_splits: list, ) -> pd.DataFrame: - """This function calculates the diaPASEF window parameters. The x start and + """This function calculates the dia-PASEF window parameters. The x start and end coordinate of each window (= rectangle) is already defined in x_splits, and the y coordinates are calculated through the intersection point of the x coordinates with the respective line equation. Parameters: - num_steps (int): number of ion mobility windows per diaPASEF scan. + num_steps (int): number of ion mobility windows per dia-PASEF scan. num_scans (int): number of diaPASEF scans. - window_position (list(int)): position of diaPASEF windows for each diaPASEF - scan. E.g., 3 diaPASEF scans * 2 ion mobility windows per diaPASEF scan - = 6 diaPASEF windows: [[0,3],[1,4],[2,5]], the first list describes the - window positions of the first diaPASEF scan. + window_position (list(int)): position of dia-PASEF windows for each dia-PASEF + scan. E.g., 3 dia-PASEF scans * 2 ion mobility windows per dia-PASEF scan + = 6 dia-PASEF windows: [[0,3],[1,4],[2,5]], the first list describes the + window positions of the first dia-PASEF scan. m_bottom (float): the slope of the line equation formed by A1 and A2; - corresponds to the slope of the bottom diaPASEF window border of the - last ion mobility windows per diaPASEF scan. + corresponds to the slope of the bottom dia-PASEF window border of the + last ion mobility windows per dia-PASEF scan. c_bottom (float): y-axis intersection of the line equation formed by A1 and A2. m_top (float): the slope of the line equation formed by B1 and B2; - corresponds to the slope of the top diaPASEF window border of the first - ion mobility windows per diaPASEF scan. + corresponds to the slope of the top dia-PASEF window border of the first + ion mobility windows per dia-PASEF scan. c_top (float): y-axis intersection of the line equation formed by B1 and B2. - x_splits (list(float)): start and end m/z value of each diaPASEF window - sorted after diaPASEF window position. + x_splits (list(float)): start and end m/z value of each dia-PASEF window + sorted after dia-PASEF window position. E.g., [[408.2423383, 484.3129605], [484.3129605, 506.2626105], [506.2626105, 522.7934549], ...] Returns: pd.DataFrame: data frame containing the scan type (PASEF), scan number, and - the corresponding diaPASEF window coordinates for each window per scan. + the corresponding dia-PASEF window coordinates for each window per scan. """ y_increments = dict() results = list() @@ -174,22 +174,22 @@ def enhance_diaPASEF_windows_to_edges_of_IM_ranges( overlap: float, ) -> pd.DataFrame: """This function recalculates the upper border of the first ion mobility - windows per diaPASEF scan and the lower border of the last ion mobility - windows per diaPASEF scan to enhance the diapASEF windows to the + windows per dia-PASEF scan and the lower border of the last ion mobility + windows per dia-PASEF scan to enhance the dia-PASEF windows to the borders of the ion mobility range. This enhances the overall precursor coverage without loss in sensitivity or acquisition speed. Parameters: df_without_column_names (pd.DataFrame): data frame containing the scan type - (PASEF), scan number, and the corresponding diaPASEF window coordinates + (PASEF), scan number, and the corresponding dia-PASEF window coordinates for each window per scan. ion_mobility (tuple): lower and upper value of the ion mobility range. - overlap (float): this value indicates how much the diaPASEF windows should + overlap (float): this value indicates how much the dia-PASEF windows should overlap in the m/z dimension (unit: Da). Returns: pd.DataFrame: data frame that contains the scan type (PASEF), scan number, - and the corresponding diaPASEF window coordinates for each window per + and the corresponding dia-PASEF window coordinates for each window per scan extended to the ion mobility borders. """ df = pd.DataFrame( @@ -233,12 +233,12 @@ def divide_mz_range_in_equally_filled_parts( Parameters: x_series (list(float)): list of all m/z precursor values. mz_range (tuple): lower and upper value of the m/z range. - num_splits (int): number of diaPASEF windows. Calculated by multiplying the - number of diaPASEF scans with the number of ion mobility windows per + num_splits (int): number of dia-PASEF windows. Calculated by multiplying the + number of dia-PASEF scans with the number of ion mobility windows per diaPASEF scan. Returns: - list(float): start and end m/z value of each diaPASEF window sorted after + list(float): start and end m/z value of each dia-PASEF window sorted after diaPASEF window position. E.g., [[408.2423383, 484.3129605], [484.3129605, 506.2626105], [506.2626105, 522.7934549], ...] """ @@ -287,14 +287,14 @@ def create_parameter_dataframe( df_parameters_final: pd.DataFrame, file_name: str, ) -> None: - """This function writes the diaPASEF parameter file as .txt. This file + """This function writes the dia-PASEF parameter file as .txt. This file serves as input for the generation of new dia-PASEF methods with timsControl (timsTof Pro 2 control software). Parameters: df_parameters_final (pd.DataFrame): data frame that contains the scan type - (PASEF), scan number, and the corresponding diaPASEF window coordinates + (PASEF), scan number, and the corresponding dia-PASEF window coordinates for each window per scan extended to the ion mobility borders. - file_name (str): file path and file name where the diaPASEF parameter file + file_name (str): file path and file name where the dia-PASEF parameter file should be saved. """ results_input = df_parameters_final.astype(str) diff --git a/pydiaid/method_evaluation.py b/pydiaid/method_evaluation.py index 0cb634d..8d2d1b3 100644 --- a/pydiaid/method_evaluation.py +++ b/pydiaid/method_evaluation.py @@ -1,4 +1,4 @@ -# for data manipulation: +# for data manipulation import pandas as pd # importing for scientific and numeric manipulations @@ -72,7 +72,7 @@ def coverage( Parameters: df (pd.DataFrame): data frame that contains the scan type (PASEF), scan - number, and the corresponding diaPASEF window coordinates for each + number, and the corresponding dia-PASEF window coordinates for each window per scan. library_subset (pd.DataFrame): a pre-filtered data frame with unified column names containing all required precursor information. @@ -118,7 +118,7 @@ def coverage( def boxes( df: pd.DataFrame, ) -> int: - """This function calculates diaPASEF window specific information regarding + """This function calculates dia-PASEF window specific information regarding the window size and creates two lists. One is for plotting the dia-PASEF window scheme on top of a kernel density estimation plot. The second is to calculate the number of proteins and precursors covered by the @@ -134,8 +134,8 @@ def boxes( windows on top of a kernel density estimation plot. border (list(tuples)): The list "borders" contains a list of tuples where each tuple represents the edge coordinates for each dia-PASEF window. - small_window (int): size of the smallest diaPASEF window [Da]. - big_window (int): size of the biggest diaPASEF window [Da]. + small_window (int): size of the smallest dia-PASEF window [Da]. + big_window (int): size of the biggest dia-PASEF window [Da]. mean_window (int): average dia-PASEF window size [Da]. """ rect = list() diff --git a/pydiaid/method_optimizer.py b/pydiaid/method_optimizer.py index bb834b1..3207cb8 100644 --- a/pydiaid/method_optimizer.py +++ b/pydiaid/method_optimizer.py @@ -2,10 +2,10 @@ from pydiaid import method_evaluation from pydiaid import graphs -# for data manipulation: +# for data manipulation import pandas as pd -# importing for scientific and numeric manipulations: +# importing for scientific and numeric manipulations import numpy as np import skopt @@ -98,6 +98,7 @@ def optimization( # return opt_result return optimized_results + def single_optimization_run( library: pd.DataFrame, method_parameters: dict, From 4238525fa004546c084e00402b840dbd46dbc312 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 8 Apr 2022 13:29:49 +0200 Subject: [PATCH 50/58] =?UTF-8?q?Bump=20version:=200.0.9=20=E2=86=92=200.0?= =?UTF-8?q?.10?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- misc/bumpversion.cfg | 2 +- pydiaid/__init__.py | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 2 +- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/pydiaid_innoinstaller.iss | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index ac49b9f..e37feb6 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.9 +current_version = 0.0.10 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/pydiaid/__init__.py b/pydiaid/__init__.py index df21d1c..ebf1c9d 100644 --- a/pydiaid/__init__.py +++ b/pydiaid/__init__.py @@ -2,7 +2,7 @@ __project__ = "pydiaid" -__version__ = "0.0.9" +__version__ = "0.0.10" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index d087595..fc8faca 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: pydiaid -Version: 0.0.9 +Version: 0.0.10 Architecture: all Maintainer: Mann Labs Description: py_diAID diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index fed57fc..c3bd593 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.9-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.10-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index 64849fd..3291366 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - pydiaid.0.0.9 + pydiaid.0.0.10 CFBundleShortVersionString - 0.0.9 + 0.0.10 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 23f8ade..256656c 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/pydiaid-0.0.9-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.10-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index d5d6a61..a44e1a6 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - py_diAID 0.0.9 + py_diAID 0.0.10 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index d838a2c..1c78c5f 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.9-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.10-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_windows_gui/pydiaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss index 32162c8..9c8e01c 100644 --- a/release/one_click_windows_gui/pydiaid_innoinstaller.iss +++ b/release/one_click_windows_gui/pydiaid_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "py_diAID" -#define MyAppVersion "0.0.9" +#define MyAppVersion "0.0.10" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" #define MyAppURL "https://github.com/MannLabs/pydiaid" #define MyAppExeName "pydiaid_gui.exe" From 1270d4bfe305a75abc3a99a818b4658f00a2e716 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 8 Apr 2022 13:59:29 +0200 Subject: [PATCH 51/58] CHORE: update pyinstaller version --- release/pyinstaller/pydiaid_pyinstaller.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/release/pyinstaller/pydiaid_pyinstaller.py b/release/pyinstaller/pydiaid_pyinstaller.py index 9e08524..9d1e31d 100644 --- a/release/pyinstaller/pydiaid_pyinstaller.py +++ b/release/pyinstaller/pydiaid_pyinstaller.py @@ -1,5 +1,13 @@ if __name__ == "__main__": - import pydiaid.gui - import multiprocessing - multiprocessing.freeze_support() - pydiaid.gui.run() + try: + import pydiaid.gui + import multiprocessing + multiprocessing.freeze_support() + pydiaid.gui.run() + except: + import traceback + import sys + exc_info = sys.exc_info() + # Display the *original* exception + traceback.print_exception(*exc_info) + input("Something went wrong, press any key to continue...") From 38a902b24ed025a689ce1db2fec339df2ba44d08 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 8 Apr 2022 14:00:47 +0200 Subject: [PATCH 52/58] =?UTF-8?q?Bump=20version:=200.0.10=20=E2=86=92=200.?= =?UTF-8?q?0.11?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- misc/bumpversion.cfg | 2 +- pydiaid/__init__.py | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 2 +- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/pydiaid_innoinstaller.iss | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index e37feb6..f26a246 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.10 +current_version = 0.0.11 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/pydiaid/__init__.py b/pydiaid/__init__.py index ebf1c9d..ac9ca40 100644 --- a/pydiaid/__init__.py +++ b/pydiaid/__init__.py @@ -2,7 +2,7 @@ __project__ = "pydiaid" -__version__ = "0.0.10" +__version__ = "0.0.11" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index fc8faca..1650120 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: pydiaid -Version: 0.0.10 +Version: 0.0.11 Architecture: all Maintainer: Mann Labs Description: py_diAID diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index c3bd593..16363d9 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.10-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.11-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index 3291366..587e28f 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - pydiaid.0.0.10 + pydiaid.0.0.11 CFBundleShortVersionString - 0.0.10 + 0.0.11 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 256656c..365db2a 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/pydiaid-0.0.10-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.11-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index a44e1a6..9ce79ab 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - py_diAID 0.0.10 + py_diAID 0.0.11 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 1c78c5f..8966311 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.10-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.11-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_windows_gui/pydiaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss index 9c8e01c..d5993a2 100644 --- a/release/one_click_windows_gui/pydiaid_innoinstaller.iss +++ b/release/one_click_windows_gui/pydiaid_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "py_diAID" -#define MyAppVersion "0.0.10" +#define MyAppVersion "0.0.11" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" #define MyAppURL "https://github.com/MannLabs/pydiaid" #define MyAppExeName "pydiaid_gui.exe" From 5ebb9299dd9777cc18412963c49e4e0bed0d9c67 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 8 Apr 2022 14:07:39 +0200 Subject: [PATCH 53/58] FIX: Update pyinstaller==4.2 to pyinstaller==4.10. --- requirements/requirements_development.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements/requirements_development.txt b/requirements/requirements_development.txt index 32ca26c..88d87b2 100644 --- a/requirements/requirements_development.txt +++ b/requirements/requirements_development.txt @@ -1,6 +1,6 @@ jupyter==1.0.0 jupyter_contrib_nbextensions==0.5.1 -pyinstaller==4.2 +pyinstaller==4.10 autodocsumm==0.2.6 sphinx-rtd-theme==0.5.2 twine==3.4.1 From 046a01dbb0850d9a34ba898c9709129cb34d10b0 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 8 Apr 2022 14:08:15 +0200 Subject: [PATCH 54/58] =?UTF-8?q?Bump=20version:=200.0.11=20=E2=86=92=200.?= =?UTF-8?q?0.12?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- misc/bumpversion.cfg | 2 +- pydiaid/__init__.py | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 2 +- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/pydiaid_innoinstaller.iss | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index f26a246..177ce61 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.11 +current_version = 0.0.12 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/pydiaid/__init__.py b/pydiaid/__init__.py index ac9ca40..314e738 100644 --- a/pydiaid/__init__.py +++ b/pydiaid/__init__.py @@ -2,7 +2,7 @@ __project__ = "pydiaid" -__version__ = "0.0.11" +__version__ = "0.0.12" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index 1650120..39b1943 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: pydiaid -Version: 0.0.11 +Version: 0.0.12 Architecture: all Maintainer: Mann Labs Description: py_diAID diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index 16363d9..e521f9e 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.11-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.12-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index 587e28f..01f38eb 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - pydiaid.0.0.11 + pydiaid.0.0.12 CFBundleShortVersionString - 0.0.11 + 0.0.12 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 365db2a..01a21c1 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/pydiaid-0.0.11-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.12-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index 9ce79ab..9cc984a 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - py_diAID 0.0.11 + py_diAID 0.0.12 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 8966311..fbb6b4f 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.11-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.12-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.2 diff --git a/release/one_click_windows_gui/pydiaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss index d5993a2..9d73e34 100644 --- a/release/one_click_windows_gui/pydiaid_innoinstaller.iss +++ b/release/one_click_windows_gui/pydiaid_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "py_diAID" -#define MyAppVersion "0.0.11" +#define MyAppVersion "0.0.12" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" #define MyAppURL "https://github.com/MannLabs/pydiaid" #define MyAppExeName "pydiaid_gui.exe" From f95cae93504e59591ea389f7d470a0121db2a14a Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 8 Apr 2022 14:21:50 +0200 Subject: [PATCH 55/58] FIX: change pyinstaller to 4.10 --- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index e521f9e..af0cb0a 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -20,7 +20,7 @@ cd release/one_click_linux_gui pip install "../../dist/pydiaid-0.0.12-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder -pip install pyinstaller==4.2 +pip install pyinstaller==4.10 pyinstaller ../pyinstaller/pydiaid.spec -y conda deactivate diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index fbb6b4f..4e6b681 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -20,7 +20,7 @@ cd release/one_click_windows_gui pip install "../../dist/pydiaid-0.0.12-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder -pip install pyinstaller==4.2 +pip install pyinstaller==4.10 pyinstaller ../pyinstaller/pydiaid.spec -y conda deactivate From 16a26d793622384455cafa417ce3f4dde7e89a19 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 8 Apr 2022 14:21:55 +0200 Subject: [PATCH 56/58] =?UTF-8?q?Bump=20version:=200.0.12=20=E2=86=92=200.?= =?UTF-8?q?0.13?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- misc/bumpversion.cfg | 2 +- pydiaid/__init__.py | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 2 +- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/pydiaid_innoinstaller.iss | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index 177ce61..791863f 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.12 +current_version = 0.0.13 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/pydiaid/__init__.py b/pydiaid/__init__.py index 314e738..a9b05d8 100644 --- a/pydiaid/__init__.py +++ b/pydiaid/__init__.py @@ -2,7 +2,7 @@ __project__ = "pydiaid" -__version__ = "0.0.12" +__version__ = "0.0.13" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index 39b1943..ef43d57 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: pydiaid -Version: 0.0.12 +Version: 0.0.13 Architecture: all Maintainer: Mann Labs Description: py_diAID diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index af0cb0a..24f3ded 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.12-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.13-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.10 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index 01f38eb..f1eaa52 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - pydiaid.0.0.12 + pydiaid.0.0.13 CFBundleShortVersionString - 0.0.12 + 0.0.13 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 01a21c1..40949d9 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/pydiaid-0.0.12-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.13-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index 9cc984a..ca4c869 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - py_diAID 0.0.12 + py_diAID 0.0.13 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 4e6b681..474daeb 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.12-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.13-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.10 diff --git a/release/one_click_windows_gui/pydiaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss index 9d73e34..db5643c 100644 --- a/release/one_click_windows_gui/pydiaid_innoinstaller.iss +++ b/release/one_click_windows_gui/pydiaid_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "py_diAID" -#define MyAppVersion "0.0.12" +#define MyAppVersion "0.0.13" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" #define MyAppURL "https://github.com/MannLabs/pydiaid" #define MyAppExeName "pydiaid_gui.exe" From dac66bdf41055becd0e0aa0cd5be9dfea561d732 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 8 Apr 2022 14:37:10 +0200 Subject: [PATCH 57/58] CHORE: move the jinja2 to the requirements_gui.txt --- requirements/requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 0fef9d1..808c0cc 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -7,3 +7,4 @@ matplotlib==3.4.3 seaborn==0.11.2 scikit-optimize==0.9.0 scipy==1.7.3 +jinja2==3.0.2 From fa154daab6210d4b9849d981ae35e7caa1e94c95 Mon Sep 17 00:00:00 2001 From: PatriciaSkowronek Date: Fri, 8 Apr 2022 15:24:35 +0200 Subject: [PATCH 58/58] =?UTF-8?q?Bump=20version:=200.0.13=20=E2=86=92=200.?= =?UTF-8?q?0.14?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- misc/bumpversion.cfg | 2 +- pydiaid/__init__.py | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 2 +- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/pydiaid_innoinstaller.iss | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index 791863f..4e28a90 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.13 +current_version = 0.0.14 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/pydiaid/__init__.py b/pydiaid/__init__.py index a9b05d8..c8c7e73 100644 --- a/pydiaid/__init__.py +++ b/pydiaid/__init__.py @@ -2,7 +2,7 @@ __project__ = "pydiaid" -__version__ = "0.0.13" +__version__ = "0.0.14" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Patricia Skowronek, Sander Willems, Eugenia Voytik" diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index ef43d57..c3ad600 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: pydiaid -Version: 0.0.13 +Version: 0.0.14 Architecture: all Maintainer: Mann Labs Description: py_diAID diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index 24f3ded..5051876 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.13-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.14-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.10 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index f1eaa52..2fb6257 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - pydiaid.0.0.13 + pydiaid.0.0.14 CFBundleShortVersionString - 0.0.13 + 0.0.14 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 40949d9..96be729 100644 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/pydiaid-0.0.13-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.14-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.7 diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index ca4c869..79b7122 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - py_diAID 0.0.13 + py_diAID 0.0.14 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 474daeb..a87f27c 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/pydiaid-0.0.13-py3-none-any.whl[stable]" +pip install "../../dist/pydiaid-0.0.14-py3-none-any.whl[stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.10 diff --git a/release/one_click_windows_gui/pydiaid_innoinstaller.iss b/release/one_click_windows_gui/pydiaid_innoinstaller.iss index db5643c..057ea71 100644 --- a/release/one_click_windows_gui/pydiaid_innoinstaller.iss +++ b/release/one_click_windows_gui/pydiaid_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "py_diAID" -#define MyAppVersion "0.0.13" +#define MyAppVersion "0.0.14" #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs" #define MyAppURL "https://github.com/MannLabs/pydiaid" #define MyAppExeName "pydiaid_gui.exe"