diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 1c6ca83..bbf471f 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.0 +current_version = 1.3.0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/alphaviz/__init__.py b/alphaviz/__init__.py index df596f2..7f95815 100644 --- a/alphaviz/__init__.py +++ b/alphaviz/__init__.py @@ -1,7 +1,7 @@ #!python __project__ = "alphaviz" -__version__ = "1.2.0" +__version__ = "1.3.0" __license__ = "Apache" __description__ = "A interactive Dashboard to explore mass spectrometry data." __author__ = "Eugenia Voytik" @@ -16,7 +16,7 @@ "bioinformatics", "visualization" ] -__python_version__ = ">=3.8,<3.9" +__python_version__ = ">=3.8,<3.12" __classifiers__ = [ # "Development Status :: 1 - Planning", # "Development Status :: 2 - Pre-Alpha", diff --git a/alphaviz/gui.py b/alphaviz/gui.py index 8074af6..3b9a8e8 100644 --- a/alphaviz/gui.py +++ b/alphaviz/gui.py @@ -4,7 +4,6 @@ import json import warnings import pandas as pd -from pandas.core.common import SettingWithCopyWarning from io import StringIO import alphatims.bruker @@ -23,8 +22,6 @@ import alphaviz.preprocessing import alphaviz.plotting -warnings.simplefilter(action="ignore", category=SettingWithCopyWarning) - def get_css_style( file_name="dashboard_style.css", diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index 53e0c5e..dad7aa4 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: alphaviz -Version: 1.2.0 +Version: 1.3.0 Architecture: all Maintainer: Mann Labs Description: alphaviz diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index 8eb7204..fbc36cc 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/alphaviz-1.2.0-py3-none-any.whl[stable,gui-stable]" +pip install "../../dist/alphaviz-1.3.0-py3-none-any.whl[stable,gui-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 9fe2dd1..b6c8d8f 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 - alphaviz.1.2.0 + alphaviz.1.3.0 CFBundleShortVersionString - 1.2.0 + 1.3.0 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 988fe4d..cb11662 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/alphaviz-1.2.0-py3-none-any.whl[stable,gui-stable]" +pip install "../../dist/alphaviz-1.3.0-py3-none-any.whl[stable,gui-stable]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.10 @@ -40,5 +40,5 @@ cp ../../LICENSE.txt Resources/LICENSE.txt cp ../logos/alpha_logo.png Resources/alpha_logo.png chmod 777 scripts/* -pkgbuild --root dist/alphaviz --identifier de.mpg.biochem.alphaviz.app --version 1.2.0 --install-location /Applications/alphaviz.app --scripts scripts alphaviz.pkg +pkgbuild --root dist/alphaviz --identifier de.mpg.biochem.alphaviz.app --version 1.3.0 --install-location /Applications/alphaviz.app --scripts scripts alphaviz.pkg productbuild --distribution distribution.xml --resources Resources --package-path alphaviz.pkg dist/alphaviz_gui_installer_macos.pkg diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index 3c38a85..85493eb 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - alphaviz 1.2.0 + alphaviz 1.3.0 diff --git a/release/one_click_windows_gui/alphaviz_innoinstaller.iss b/release/one_click_windows_gui/alphaviz_innoinstaller.iss index fb27ec0..f519055 100644 --- a/release/one_click_windows_gui/alphaviz_innoinstaller.iss +++ b/release/one_click_windows_gui/alphaviz_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "alphaviz" -#define MyAppVersion "1.2.0" +#define MyAppVersion "1.3.0" #define MyAppPublisher "Max Planck Institute of Biochemistry and the University of Copenhagen, Mann Labs" #define MyAppURL "https://github.com/MannLabs/alphaviz" #define MyAppExeName "alphaviz_gui.exe" diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 1a6e630..6660a40 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 alphaviz_installer python=3.8 -y +conda create -n alphaviz_installer python=3.9 -y conda activate alphaviz_installer # Creating the wheel @@ -17,10 +17,10 @@ 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/alphaviz-1.2.0-py3-none-any.whl[stable,gui-stable]" +pip install "../../dist/alphaviz-1.3.0-py3-none-any.whl[stable,gui-stable]" # Creating the stand-alone pyinstaller folder -pip install pyinstaller==4.10 +pip install pyinstaller pyinstaller ../pyinstaller/alphaviz.spec -y conda deactivate diff --git a/release/pyinstaller/alphaviz.spec b/release/pyinstaller/alphaviz.spec index fa1894f..c88ed1b 100644 --- a/release/pyinstaller/alphaviz.spec +++ b/release/pyinstaller/alphaviz.spec @@ -9,6 +9,9 @@ import pkg_resources import importlib.metadata import alphaviz +from PyInstaller.utils.hooks import copy_metadata +from transformers.dependency_versions_check import pkgs_to_check_at_runtime + ##################### User definitions exe_name = 'alphaviz_gui' @@ -75,18 +78,26 @@ else: hidden_imports = [h for h in hidden_imports if "__pycache__" not in h] datas = [d for d in datas if ("__pycache__" not in d[0]) and (d[1] not in [".", "Resources", "scripts"])] -if sys.platform[:5] == "win32": - base_path = os.path.dirname(sys.executable) - library_path = os.path.join(base_path, "Library", "bin") - dll_path = os.path.join(base_path, "DLLs") - libcrypto_dll_path = os.path.join(dll_path, "libcrypto-1_1-x64.dll") - libssl_dll_path = os.path.join(dll_path, "libssl-1_1-x64.dll") - libcrypto_lib_path = os.path.join(library_path, "libcrypto-1_1-x64.dll") - libssl_lib_path = os.path.join(library_path, "libssl-1_1-x64.dll") - if not os.path.exists(libcrypto_dll_path): - datas.append((libcrypto_lib_path, ".")) - if not os.path.exists(libssl_dll_path): - datas.append((libssl_lib_path, ".")) +#if sys.platform[:5] == "win32": +# base_path = os.path.dirname(sys.executable) +# library_path = os.path.join(base_path, "Library", "bin") +# dll_path = os.path.join(base_path, "DLLs") +# libcrypto_dll_path = os.path.join(dll_path, "libcrypto-1_1-x64.dll") +# libssl_dll_path = os.path.join(dll_path, "libssl-1_1-x64.dll") +# libcrypto_lib_path = os.path.join(library_path, "libcrypto-1_1-x64.dll") +# libssl_lib_path = os.path.join(library_path, "libssl-1_1-x64.dll") +# if not os.path.exists(libcrypto_dll_path): +# datas.append((libcrypto_lib_path, ".")) +# if not os.path.exists(libssl_dll_path): +# datas.append((libssl_lib_path, ".")) + +for _pkg in ["python","accelerate"]: + if _pkg in pkgs_to_check_at_runtime: + pkgs_to_check_at_runtime.remove(_pkg) +for _pkg in pkgs_to_check_at_runtime: + datas += copy_metadata(_pkg) + +datas += copy_metadata('datashader') a = Analysis( [script_name], diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 486f724..bcfe222 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -3,8 +3,6 @@ peptdeep alphabase alpharaw -holoviews xarray -dask multipledispatch -plotly +plotly \ No newline at end of file diff --git a/requirements/requirements_development.txt b/requirements/requirements_development.txt index 431050f..80d6662 100644 --- a/requirements/requirements_development.txt +++ b/requirements/requirements_development.txt @@ -1,18 +1,14 @@ jupyter==1.0.0 jupyter_contrib_nbextensions==0.5.1 -pyinstaller==4.10 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 pytest==6.2.5 +tqdm +psutil +bumpversion +pyinstaller pywin32; sys_platform=='win32' - -alphatims -peptdeep -alphabase diff --git a/requirements/requirements_gui.txt b/requirements/requirements_gui.txt index fe091de..e197428 100644 --- a/requirements/requirements_gui.txt +++ b/requirements/requirements_gui.txt @@ -10,7 +10,3 @@ requests==2.27.1 #selenium #chromedriver-binary jinja2==3.0.2 - -alphatims -peptdeep -alphabase diff --git a/setup.py b/setup.py index b247616..f43c4b4 100644 --- a/setup.py +++ b/setup.py @@ -62,10 +62,7 @@ def create_pip_wheel(): entry_points={ "console_scripts": package2install.__console_scripts__, }, - install_requires=requirements + [ - # TODO Remove hardcoded requirement? - "pywin32==225; sys_platform=='win32'" - ], + install_requires=requirements, extras_require=extra_requirements, python_requires=package2install.__python_version__, )