Merge pull request #208 from MannLabs/development

Development
MannLabs · Sep 12, 2024 · 5cb3d2c · 5cb3d2c
2 parents cda66bd + 6af58e5
commit 5cb3d2c
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Showing 119 changed files with 38,060 additions and 4,449 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.1
+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+))?
@@ -15,18 +15,30 @@ serialize =
 
 [bumpversion:file:./docs/conf.py]
 
-[bumpversion:file:./release/one_click_linux_gui/control]
+[bumpversion:file:./README.md]
 
-[bumpversion:file:./release/one_click_linux_gui/create_installer_linux.sh]
+[bumpversion:file:./release/linux/control]
 
-[bumpversion:file:./release/one_click_macos_gui/distribution.xml]
+[bumpversion:file:./release/linux/build_installer_linux.sh]
 
-[bumpversion:file:./release/one_click_macos_gui/Info.plist]
+[bumpversion:file:./release/linux/build_package_linux.sh]
 
-[bumpversion:file:./release/one_click_macos_gui/create_installer_macos.sh]
+[bumpversion:file:./release/linux/create_installer_linux.sh]
 
-[bumpversion:file:./release/one_click_windows_gui/create_installer_windows.sh]
+[bumpversion:file:./release/macos/distribution.xml]
 
-[bumpversion:file:./release/one_click_windows_gui/peptdeep_innoinstaller.iss]
+[bumpversion:file:./release/macos/Info.plist]
+
+[bumpversion:file:./release/macos/create_installer_macos.sh]
+
+[bumpversion:file:./release/macos/build_installer_macos.sh]
+
+[bumpversion:file:./release/macos/build_package_macos.sh]
+
+[bumpversion:file:./release/windows/create_installer_windows.sh]
+
+[bumpversion:file:./release/windows/build_installer_windows.ps1]
+
+[bumpversion:file:./release/windows/peptdeep_innoinstaller.iss]
 search = {current_version}
 replace = {new_version}
diff --git a/.github/workflows/pip_installation.yml b/.github/workflows/pip_installation.yml
@@ -21,7 +21,7 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-13, windows-latest]
         # macOS-latest and macos-latest-xlarge use Arm64, resulting in MPS OOM error in peptdeep
-        # os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
+        # os: [ubuntu-latest, macos-13, macos-latest, windows-latest, macos-latest-xlarge]
     uses: ./.github/workflows/_run_tests.yml
     with:
       os: ${{ matrix.os }}
@@ -34,7 +34,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-13, windows-latest]
-        # os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
+        # os: [ubuntu-latest, macos-13, macos-latest, windows-latest, macos-latest-xlarge]
     uses: ./.github/workflows/_run_tests.yml
     with:
       os: ${{ matrix.os }}

diff --git a/.github/workflows/publish_and_release.yml b/.github/workflows/publish_and_release.yml
@@ -1,3 +1,4 @@
+# TODO remove with old release workflow
 on:
   # push:
   #   branches: [ main ]
@@ -57,20 +58,20 @@ jobs:
       - name: Creating installer for Linux
         shell: bash -l {0}
         run: |
-          cd release/one_click_linux_gui
+          cd release/linux
           . ./create_installer_linux.sh CPU
       - name: Test installer for Linux
         shell: bash -l {0}
         run: |
-          sudo dpkg -i release/one_click_linux_gui/dist/peptdeep_gui_installer_linux.deb
+          sudo dpkg -i release/linux/dist/peptdeep_gui_installer_linux.deb
       - name: Upload Linux Installer
         id: upload-release-asset
         uses: actions/upload-release-asset@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_linux_gui/dist/peptdeep_gui_installer_linux.deb
+          asset_path: release/linux/dist/peptdeep_gui_installer_linux.deb
           asset_name: peptdeep_gui_installer_linux.deb
           asset_content_type: application/octet-stream
   Create_MacOS_Release:
@@ -89,25 +90,27 @@ jobs:
       - name: Creating installer for MacOS
         shell: bash -l {0}
         run: |
-          cd release/one_click_macos_gui
+          cd release/macos
           . ./create_installer_macos.sh
       - name: Test installer for MacOS
         shell: bash -l {0}
         run: |
-          sudo installer -pkg release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg -target /
+          sudo installer -pkg release/macos/dist/peptdeep_gui_installer_macos.pkg -target /
       - name: Upload MacOS Installer
         id: upload-release-asset
         uses: actions/upload-release-asset@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg
+          asset_path: release/macos/dist/peptdeep_gui_installer_macos.pkg
           asset_name: peptdeep_gui_installer_macos.pkg
           asset_content_type: application/octet-stream
   Create_Windows_Release:
     runs-on: windows-latest
     needs: Create_Draft_On_GitHub
+    env:
+      BUILD_NAME: peptdeep-1.2.1-win-x64
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
@@ -121,14 +124,14 @@ jobs:
       - name: Creating installer for Windows
         shell: bash -l {0}
         run: |
-          cd release/one_click_windows_gui
+          cd release/windows
           . ./create_installer_windows.sh
       - name: Test installer for Windows
         shell: bash -l {0}
         run: |
-          cd release/one_click_windows_gui/dist/
+          cd release/windows/dist/
           echo "TODO, this test seems to freeze the runner..."
-          # ./peptdeep_gui_installer_windows.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
+          # ./peptdeep-${{ needs.Version_Bumped.outputs.version }}-win-x64.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
           # cat log.txt
       - name: Upload Windows Installer
         id: upload-release-asset
@@ -137,9 +140,10 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_windows_gui/dist/peptdeep_gui_installer_windows.exe
-          asset_name: peptdeep_gui_installer_windows.exe
+          asset_path: release/windows/dist/peptdeep-${{ needs.Version_Bumped.outputs.version }}-win-x64.exe
+          asset_name: peptdeep-${{ needs.Version_Bumped.outputs.version }}-win-x64.exe
           asset_content_type: application/octet-stream
+
   Create_PyPi_Release:
     runs-on: ubuntu-latest
     needs: Version_Bumped

diff --git a/.github/workflows/release_installers.yml b/.github/workflows/release_installers.yml
@@ -1,3 +1,4 @@
+# TODO remove with old release workflow
 on:
   workflow_dispatch:
 
@@ -54,20 +55,20 @@ jobs:
       - name: Creating installer for Linux
         shell: bash -l {0}
         run: |
-          cd release/one_click_linux_gui
+          cd release/linux
           . ./create_installer_linux.sh CPU
       - name: Test installer for Linux
         shell: bash -l {0}
         run: |
-          sudo dpkg -i release/one_click_linux_gui/dist/peptdeep_gui_installer_linux.deb
+          sudo dpkg -i release/linux/dist/peptdeep_gui_installer_linux.deb
       - name: Upload Linux Installer
         id: upload-release-asset
         uses: actions/upload-release-asset@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_linux_gui/dist/peptdeep_gui_installer_linux.deb
+          asset_path: release/linux/dist/peptdeep_gui_installer_linux.deb
           asset_name: peptdeep_gui_installer_linux.deb
           asset_content_type: application/octet-stream
   Create_MacOS_Release:
@@ -86,20 +87,20 @@ jobs:
       - name: Creating installer for MacOS
         shell: bash -l {0}
         run: |
-          cd release/one_click_macos_gui
+          cd release/macos
           . ./create_installer_macos.sh
       - name: Test installer for MacOS
         shell: bash -l {0}
         run: |
-          sudo installer -pkg release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg -target /
+          sudo installer -pkg release/macos/dist/peptdeep_gui_installer_macos.pkg -target /
       - name: Upload MacOS Installer
         id: upload-release-asset
         uses: actions/upload-release-asset@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg
+          asset_path: release/macos/dist/peptdeep_gui_installer_macos.pkg
           asset_name: peptdeep_gui_installer_macos.pkg
           asset_content_type: application/octet-stream
   Create_MacOS_Arm_Release:
@@ -118,25 +119,27 @@ jobs:
       - name: Creating installer for MacOS
         shell: bash -l {0}
         run: |
-          cd release/one_click_macos_gui
+          cd release/macos
           . ./create_installer_macos.sh
       - name: Test installer for MacOS
         shell: bash -l {0}
         run: |
-          sudo installer -pkg release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg -target /
+          sudo installer -pkg release/macos/dist/peptdeep_gui_installer_macos.pkg -target /
       - name: Upload MacOS Installer
         id: upload-release-asset
         uses: actions/upload-release-asset@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg
+          asset_path: release/macos/dist/peptdeep_gui_installer_macos.pkg
           asset_name: peptdeep_gui_installer_macos_arm.pkg
           asset_content_type: application/octet-stream
   Create_Windows_Release:
     runs-on: windows-latest
     needs: Create_Draft_On_GitHub
+    env:
+      BUILD_NAME: peptdeep-1.2.1-win-x64
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
@@ -150,14 +153,14 @@ jobs:
       - name: Creating installer for Windows
         shell: bash -l {0}
         run: |
-          cd release/one_click_windows_gui
+          cd release/windows
           . ./create_installer_windows.sh
       - name: Test installer for Windows
         shell: bash -l {0}
         run: |
-          cd release/one_click_windows_gui/dist/
+          cd release/windows/dist/
           echo "TODO, this test seems to freeze the runner..."
-          # ./peptdeep_gui_installer_windows.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
+          # ./peptdeep-1.2.1-win-x64.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
           # cat log.txt
       - name: Upload Windows Installer
         id: upload-release-asset
@@ -166,6 +169,6 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_windows_gui/dist/peptdeep_gui_installer_windows.exe
-          asset_name: peptdeep_gui_installer_windows.exe
+          asset_path: release/windows/dist/peptdeep-${{ needs.Version_Bumped.outputs.version }}-win-x64.exe
+          asset_name: peptdeep-${{ needs.Version_Bumped.outputs.version }}-win-x64.exe
           asset_content_type: application/octet-stream
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,11 @@
+# User defined:
+peptdeep/logs
+*.DS_Store
+*sandbox*
+*installed_models*
+*.last_checked*
+*mono_crash.*.blob
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -26,6 +34,8 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+dist_pyinstaller/
+build_pyinstaller/
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -128,19 +138,3 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
-
-# User defined:
-peptdeep/logs
-*.DS_Store
-*sandbox*
-*installed_models*
-*.last_checked*
-
-# nbdev2
-*.gitattributes
-_docs*
-# *_quarto.yml
-# *sidebar.yml
-*_proc*
-# .gitconfig is now autogenerated
-.gitconfig
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,10 +7,10 @@ repos:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
-# - repo: https://github.com/astral-sh/ruff-pre-commit
-#   rev: v0.4.0
-#   hooks:
-#     - id: ruff-format
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.0
+  hooks:
+    - id: ruff-format
 #     - id: ruff
 
 exclude: .bumpversion.cfg