Merge pull request #38 from MannLabs/development

Development

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.0
+current_version = 1.3.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

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",

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",

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 <opensource@alphapept.com>
 Description: alphaviz

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

release/one_click_macos_gui/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphaviz.1.2.0</string>
+	<string>alphaviz.1.3.0</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.2.0</string>
+	<string>1.3.0</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

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

release/one_click_macos_gui/distribution.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>alphaviz 1.2.0</title>
+    <title>alphaviz 1.3.0</title>
     <background mime-type="image/png" file="alpha_logo.png" scaling="proportional"/>
     <welcome file="welcome.html" mime-type="text/html" />
     <conclusion file="conclusion.html" mime-type="text/html" />

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"

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
 

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],

requirements/requirements.txt

@@ -3,8 +3,6 @@ peptdeep
 alphabase
 alpharaw
 
-holoviews
 xarray
-dask
 multipledispatch
-plotly
+plotly

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

requirements/requirements_gui.txt

@@ -10,7 +10,3 @@ requests==2.27.1
 #selenium
 #chromedriver-binary
 jinja2==3.0.2
-
-alphatims
-peptdeep
-alphabase

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__,
     )