Merge pull request MannLabs#106 from MannLabs/develop

Develop

.github/workflows/test4release.yml → .github/workflows/publish_and_release.yml

@@ -4,34 +4,40 @@ on:
       release_name:
         description: 'Define release name'
         required: true
+      body:
+        description: 'Define body'
+        required: true
       prerelease:
         description: 'Pre-Release?'
         required: true
-        default: true
+        default: false
       draft:
         description: 'Draft?'
         required: true
         default: true
 
-name: Create all Release
+name: Create all GUI releases and publish on PyPi
 
 jobs:
-  Create_Draft_Release:
+  Create_Draft_On_GitHub:
     runs-on: ubuntu-latest
+    outputs:
+      upload_url: ${{ steps.draft_release.outputs.upload_url }}
     steps:
-      - name: Create Release
-        id: create_release
+      - name: Draft Release
+        id: draft_release
         uses: actions/create-release@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
         with:
           tag_name: ${{ github.event.inputs.release_name }}
           release_name: Release ${{ github.event.inputs.release_name }}
+          body: Release ${{ github.event.inputs.body }}
           draft: ${{ github.event.inputs.draft }}
           prerelease: ${{ github.event.inputs.prerelease }}
   Create_Linux_Release:
     runs-on: ubuntu-latest
-    needs: Create_Draft_Release
+    needs: Create_Draft_On_GitHub
     steps:
       - name: Checkout code
         uses: actions/checkout@v2
@@ -53,13 +59,13 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
-          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
+          upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
           asset_path: misc/one_click_linux/dist/alphatims_gui_installer_linux.deb
           asset_name: alphatims_gui_installer_linux.deb
           asset_content_type: application/octet-stream
   Create_MacOS_Release:
     runs-on: macos-latest
-    needs: Create_Draft_Release
+    needs: Create_Draft_On_GitHub
     steps:
       - name: Checkout code
         uses: actions/checkout@v2
@@ -81,13 +87,13 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
-          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
+          upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
           asset_path: misc/one_click_macos/dist/alphatims_gui_installer_macos.pkg
           asset_name: alphatims_gui_installer_macos.pkg
           asset_content_type: application/octet-stream
   Create_Windows_Release:
     runs-on: windows-latest
-    needs: Create_Draft_Release
+    needs: Create_Draft_On_GitHub
     steps:
       - name: Checkout code
         uses: actions/checkout@v2
@@ -102,19 +108,20 @@ jobs:
         shell: bash -l {0}
         run: |
           cd misc/one_click_windows
-          . ./create_installer_windows.bat
+          # . ./create_installer_windows.bat
+          . ./create_installer_windows.sh
       - name: Upload Windows Installer
         id: upload-release-asset
         uses: actions/upload-release-asset@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
-          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
+          upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
           asset_path: misc/one_click_windows/dist/alphatims_gui_installer_windows.exe
           asset_name: alphatims_gui_installer_windows.exe
           asset_content_type: application/octet-stream
   Create_PyPi_Release:
-    runs-on: macos-latest
+    runs-on: ubuntu-latest
     needs: [Create_Linux_Release, Create_MacOs_Release, Create_Windows_Release]
     steps:
       - name: Checkout code
@@ -126,7 +133,27 @@ jobs:
       - name: Conda info
         shell: bash -l {0}
         run: conda info
-      - name: Push release to PyPi
+      - name: Prepare distribution
         shell: bash -l {0}
         run: |
-          cd misc/one_click_windows
+          conda env create --force --name alphatims --file misc/conda_development_environment.yaml
+          conda activate alphatims
+          rm -rf dist
+          rm -rf build
+          python setup.py sdist bdist_wheel
+          twine check dist/*
+          conda deactivate
+      # - name: Publish to PyPI
+      #   uses: pypa/gh-action-pypi-publish@release/v1
+      #   with:
+      #     user: __token__
+      #     password: ${{ secrets.PYPI_API_TOKEN }}
+      - name: Publish distribution to Test PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -136,3 +136,4 @@ misc/releases/*
 misc/one_click_macos/alphatims.pkg
 misc/one_click_macos/resources/LICENSE.txt
 misc/one_click_macos/resources/alpha_logo.png
+misc/one_click_windows/inno

README.md

@@ -159,7 +159,7 @@ A ddaPASEF dataset is available for [download from the release page](https://git
 
 ### DIA
 
-The same sample was also acquired with diaPASEF and is also available for [download from the release page](https://github.com/MannLabs/alphatims/releases/download/0.1.210317/20201207_tims03_Evo03_PS_SA_HeLa_200ng_EvoSep_prot_high_speed_21min_8cm_S1-C8_1_22474.d.zip). The "high-speed" method (mass range: m/z 400 to 1000, 1/K0: 0.6 – 1.6 Vs cm- 2, diaPASEF windows: 8 x 25 Th) was used, as described in [Meier et al](https://www.nature.com/articles/s41592-020-00998-0).
+The same sample was acquired with diaPASEF and is also available for [download from the release page](https://github.com/MannLabs/alphatims/releases/download/0.1.210317/20201207_tims03_Evo03_PS_SA_HeLa_200ng_EvoSep_prot_high_speed_21min_8cm_S1-C8_1_22474.d.zip). The "high-speed" method (mass range: m/z 400 to 1000, 1/K0: 0.6 – 1.6 Vs cm- 2, diaPASEF windows: 8 x 25 Th) was used, as described in [Meier et al](https://www.nature.com/articles/s41592-020-00998-0).
 
 ---
 ## Usage
@@ -170,7 +170,7 @@ There are three ways to use AlphaTims:
 * [**CLI:**](#cli) This allows to incorporate AlphaTims in automated workflows.
 * [**Python:**](#python-and-jupyter-notebooks) This allows to access data and explore it interactively.
 
-The first time you use a fresh installation of AlphaTims is often quite slow because some functions might still need compilation on you local operating system and architecture. Subsequent use should be a lot faster.
+NOTE: The first time you use a fresh installation of AlphaTims, it is often quite slow because some functions might still need compilation on you local operating system and architecture. Subsequent use should be a lot faster.
 
 ### GUI
 

alphatims/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "alphatims"
-__version__ = "0.2.0"
+__version__ = "0.2.2"
 __license__ = "Apache"
 __description__ = "A Python package to index Bruker TimsTOF raw data for fast and easy accession and visualization"
 __author__ = "Sander Willems, Eugenia Voytik"

alphatims/cli.py

@@ -313,9 +313,9 @@ def export_mgf(**kwargs):
 @cli_option("quad_mz_bounds")
 @cli_option("tof_mz_bounds")
 @cli_option("intensity_bounds")
+@cli_option("format")
 @cli_option("x_axis")
 @cli_option("y_axis")
-@cli_option("format")
 @cli_option("output_folder")
 @cli_option("log_file")
 @cli_option("threads")

misc/bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.0
+current_version = 0.2.2
 commit = False
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
@@ -15,12 +15,16 @@ serialize =
 
 [bumpversion:file:one_click_linux/control]
 
+[bumpversion:file:one_click_linux/create_installer_linux.sh]
+
 [bumpversion:file:one_click_macos/distribution.xml]
 
 [bumpversion:file:one_click_macos/Info.plist]
 
 [bumpversion:file:one_click_macos/create_installer_macos.sh]
 
+[bumpversion:file:one_click_windows/create_installer_windows.bat]
+
 [bumpversion:file:one_click_windows/alphatims_innoinstaller.iss]
 search = {current_version}
 replace = {new_version}

misc/one_click_linux/control

@@ -1,5 +1,5 @@
 Package: AlphaTims
-Version: 0.2.0
+Version: 0.2.2
 Architecture: all
 Maintainer: Mann Labs <[email protected]>
 Description: AlphaTims GUI

misc/one_click_linux/create_installer_linux.sh

@@ -1,7 +1,6 @@
 #!bash
 rm -rf dist
 rm -rf build
-conda env remove -n alphatimsinstaller
 conda create -n alphatimsinstaller python=3.8 -y
 # conda create -n alphatimsinstaller python=3.8
 conda activate alphatimsinstaller
@@ -13,7 +12,7 @@ rm -rf dist
 rm -rf build
 python setup.py sdist bdist_wheel
 cd misc/one_click_linux
-pip install "../../dist/alphatims-0.2.0-py3-none-any.whl[plotting]"
+pip install "../../dist/alphatims-0.2.2-py3-none-any.whl[plotting]"
 pip install pyinstaller==4.2
 pyinstaller ../pyinstaller/alphatims.spec -y
 conda deactivate

misc/one_click_macos/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphatims.0.2.0</string>
+	<string>alphatims.0.2.2</string>
 	<key>CFBundleShortVersionString</key>
-	<string>0.2.0</string>
+	<string>0.2.2</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

misc/one_click_macos/create_installer_macos.sh

@@ -1,5 +1,9 @@
 rm -rf dist
 rm -rf build
+FILE=alphatims.pkg
+if test -f "$FILE"; then
+  rm alphatims.pkg
+fi
 conda env remove -n alphatimsinstaller
 conda create -n alphatimsinstaller python=3.8 -y
 # conda create -n alphatimsinstaller python=3.8
@@ -12,8 +16,9 @@ rm -rf dist
 rm -rf build
 python setup.py sdist bdist_wheel
 cd misc/one_click_macos
-pip install "../../dist/alphatims-0.2.0-py3-none-any.whl[plotting]"
 pip install pyinstaller==4.2
+pip install "../../dist/alphatims-0.2.2-py3-none-any.whl[plotting]"
+conda list
 pyinstaller ../pyinstaller/alphatims.spec -y
 conda deactivate
 mkdir -p dist/alphatims/Contents/Resources
@@ -23,6 +28,23 @@ cp Info.plist dist/alphatims/Contents
 cp alphatims_terminal dist/alphatims/Contents/MacOS
 cp ../../LICENSE.txt Resources/LICENSE.txt
 cp ../alpha_logo.png Resources/alpha_logo.png
-pkgbuild --root dist/alphatims --identifier org.alphatims.0.2.0 --version 0.2.0 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg
-productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg
-# productsign --sign "Developer ID Installer: John Doe" dist/alphatims_gui_installer_macos.pkg dist/alphatims_gui_installer_macos_signed.pkg
+
+if false; then
+  # https://scriptingosx.com/2019/09/notarize-a-command-line-tool/
+  for f in $(find dist/alphatims -name '*.so' -or -name '*.dylib'); do codesign --sign "Developer ID Application: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)" $f; done
+  codesign --sign "Developer ID Application: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)" dist/alphatims/Contents/MacOS/alphatims_gui --force --options=runtime --entitlements entitlements.xml
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 0.2.2 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
+  productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
+  requestUUID=$(xcrun altool --notarize-app --primary-bundle-id "de.mpg.biochem.alphatims.app" --username "[email protected]" --password "@keychain:Alphatims-develop" --asc-provider 7QSY5527AQ --file dist/alphatims_gui_installer_macos.pkg 2>&1 | awk '/RequestUUID/ { print $NF; }')
+  request_status="in progress"
+  while [[ "$request_status" == "in progress" ]]; do
+      echo "$request_status"
+      sleep 10
+      request_status=$(xcrun altool --notarization-info "$requestUUID" --username "[email protected]" --password "@keychain:Alphatims-develop" | awk -F ': ' '/Status:/ { print $2; }' )
+  done
+  xcrun altool --notarization-info "$requestUUID" --username "[email protected]" --password "@keychain:Alphatims-develop"
+  xcrun stapler staple dist/alphatims_gui_installer_macos.pkg
+else
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 0.2.2 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg
+  productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg
+fi

misc/one_click_macos/distribution.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>AlphaTims 0.2.0</title>
+    <title>AlphaTims 0.2.2</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" />

misc/one_click_macos/entitlements.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+    <key>com.apple.security.cs.allow-jit</key>
+    <true/>
+    <key>com.apple.security.cs.allow-unsigned-executable-memory</key>
+    <true/>
+    <key>com.apple.security.network.client</key>
+    <true/>
+    <key>com.apple.security.network.server</key>
+    <true/>
+</dict>
+</plist>

misc/one_click_windows/alphatims_innoinstaller.iss

@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "AlphaTims"
-#define MyAppVersion "0.2.0"
+#define MyAppVersion "0.2.2"
 #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann department"
 #define MyAppURL "https://github.com/MannLabs/alphatims"
 #define MyAppExeName "alphatims_gui.exe"

misc/one_click_windows/create_installer_windows.bat

@@ -15,9 +15,19 @@ call rmdir dist /s /q
 call rmdir build /s /q
 call python setup.py sdist bdist_wheel
 call cd misc/one_click_windows
-call pip install "../../dist/alphatims-0.2.0-py3-none-any.whl[plotting]"
+call pip install "../../dist/alphatims-0.2.2-py3-none-any.whl[plotting]"
 call pip install pyinstaller==4.2
 call pyinstaller ../pyinstaller/alphatims.spec -y
 call conda deactivate
-call "C:\Program Files (x86)\Inno Setup 6\ISCC.exe" alphatims_innoinstaller.iss
-REM call iscc alphatims_innoinstaller.iss
+
+
+if false; then
+  REM call mkdir inno
+  REM call pip install wget
+  REM call python -m wget https://jrsoftware.org/download.php/is.exe
+  call is.exe /SILENT /DIR=.
+  call inno\ISCC.exe alphatims_innoinstaller.iss
+else
+  call "C:\Program Files (x86)\Inno Setup 6\ISCC.exe" alphatims_innoinstaller.iss
+  REM call iscc alphatims_innoinstaller.iss
+fi