Prepare for new release workflow

.bumpversion.cfg

@@ -15,18 +15,31 @@ 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]  # TODO remove with old release workflow
 
-[bumpversion:file:./release/one_click_windows_gui/create_installer_windows.sh]
+[bumpversion:file:./release/macos/distribution.xml]
+
+[bumpversion:file:./release/macos/Info.plist]
+
+[bumpversion:file:./release/macos/create_installer_macos.sh]  # TODO remove with old release workflow
+
+[bumpversion:file:./release/macos/build_installer_macos.sh]
+
+[bumpversion:file:./release/macos/build_package_macos.sh]
+
+[bumpversion:file:./release/windows/create_installer_windows.sh]  # TODO remove with old release workflow
+
+[bumpversion:file:./release/windows/build_installer_windows.ps1]
+
+[bumpversion:file:./release/windows/peptdeep_innoinstaller.iss]
 
-[bumpversion:file:./release/one_click_windows_gui/peptdeep_innoinstaller.iss]
 search = {current_version}
 replace = {new_version}

.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

.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

.gitignore

@@ -34,6 +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

README.md

@@ -112,19 +112,23 @@ The GUI of peptdeep 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/alphapeptdeep/releases/latest/download/peptdeep_gui_installer_windows.exe)
-- [**macOS**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep_gui_installer_macos.pkg)
-- [**Linux**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep_gui_installer_linux.deb)
+- [**Windows**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.2.1-windows-amd64.exe)
+- [**macOS**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.2.1-macos-darwin-x64.pkg)
+- [**macOS ARM**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.2.1-macos-darwin-arm64.pkg )
+- [**Linux**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.2.1-linux-x64.deb)
 
 Older releases remain available on the [release
 page](https://github.com/MannLabs/alphapeptdeep/releases), but no
 backwards compatibility is guaranteed.
 
-Note that, as GitHub does not allow large release files, these installers do not have GPU support. To create GPU version installers, clone the source code and install GPU-version pytorch (#use-gpu), and then use `release/one_click_xxx_gui/create_installer_xxx.sh` to build installer locally. For example in Windows, run
-
+Note that, as GitHub does not allow large release files, these installers do not have GPU support.
+To create GPU version installers: clone the source code, install the GPU-version of pytorch [see here](#use-gpu),
+and then use the `build_installer_*.sh` and `build_package_*.sh`
+script in the respective `release/[macos, linux, windows]` folder to build the installer locally.
+For Linux you need to additionally pass the "GPU" flag, i.e. run
 ```bash
-cd release/one_click_windows_gui
-. ./create_installer_windows.sh
+release/linux/build_installer_linux.sh GPU
+release/linux/build_package_linux.sh
 ```
 
 ### Pip
@@ -945,6 +949,17 @@ branch. For an even more interactive participation, check out the
 the [Contributors License Agreement](misc/CLA.md).
 
 ### Notes for developers
+
+#### Tagging of changes
+In order to have release notes automatically generated, changes need to be tagged with labels.
+The following labels are used (should be safe-explanatory):
+`breaking-change`, `bug`, `enhancement`.
+
+#### Release a new version
+This package uses a shared release process defined in the
+[alphashared](https://github.com/MannLabs/alphashared) repository. Please see the instructions
+[there](https://github.com/MannLabs/alphashared/blob/reusable-release-workflow/.github/workflows/README.md#release-a-new-version).
+
 #### pre-commit hooks
 It is highly recommended to use the provided pre-commit hooks, as the CI pipeline enforces all checks therein to
 pass in order to merge a branch.

release/linux/build_installer_linux.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+set -e -u
+
+# Build the installer for Linux.
+# This script must be run from the root of the repository.
+
+CPU_OR_GPU=${1:-CPU}
+
+rm -rf dist build *.egg-info
+rm -rf dist_pyinstaller build_pyinstaller
+
+# Creating the wheel
+python setup.py sdist bdist_wheel
+
+# Setting up the local package
+# Make sure you include the required extra packages and always use the stable or very-stable options!
+pip install "dist/peptdeep-1.2.1-py3-none-any.whl[stable]"
+
+if [ "${CPU_OR_GPU}" != "GPU" ]; then
+    pip install torch -U --extra-index-url https://download.pytorch.org/whl/cpu
+fi
+
+# Creating the stand-alone pyinstaller folder
+pyinstaller release/pyinstaller/peptdeep.spec --distpath dist_pyinstaller --workpath build_pyinstaller -y

release/linux/build_package_linux.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+set -e -u
+
+# Build the install package for Linux.
+# This script must be run from the root of the repository after running build_installer_linux.sh
+
+PACKAGE_NAME=peptdeep
+
+# BUILD_NAME is taken from environment variables, e.g. 'peptdeep-1.2.1-linux-x64'
+rm -rf ${BUILD_NAME}.deb
+
+# If needed, include additional source such as e.g.:
+# cp ../../peptdeep/data/*.fasta dist/peptdeep/data
+# WARNING: this probably does not work!!!!
+
+# Wrapping the pyinstaller folder in a .deb package
+mkdir -p dist_pyinstaller/${BUILD_NAME}/usr/local/bin
+mv dist_pyinstaller/${PACKAGE_NAME} dist_pyinstaller/${BUILD_NAME}/usr/local/bin/${PACKAGE_NAME}
+mkdir dist_pyinstaller/${BUILD_NAME}/DEBIAN
+cp release/linux/control dist_pyinstaller/${BUILD_NAME}/DEBIAN
+dpkg-deb --build --root-owner-group dist_pyinstaller/${BUILD_NAME}
+
+# release workflow expects artifact at root of repository
+mv dist_pyinstaller/${BUILD_NAME}.deb .

release/one_click_linux_gui/create_installer_linux.sh → release/linux/create_installer_linux.sh

@@ -1,5 +1,5 @@
 #!bash
-
+# TODO remove with old release workflow
 # Initial cleanup
 rm -rf dist
 rm -rf build
@@ -15,7 +15,7 @@ conda activate peptdeep_installer
 python setup.py sdist bdist_wheel
 
 # Setting up the local package
-cd release/one_click_linux_gui
+cd release/linux
 # Make sure you include the required extra packages and always use the stable or very-stable options!
 pip install "../../dist/peptdeep-1.2.1-py3-none-any.whl[stable]"
 

release/macos/build_installer_macos.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+set -e -u
+
+# Build the installer for MacOS.
+# This script must be run from the root of the repository.
+
+rm -rf dist
+rm -rf build
+
+# Creating the wheel
+python setup.py sdist bdist_wheel
+pip install "dist/peptdeep-1.2.1-py3-none-any.whl[stable]"
+
+# Creating the stand-alone pyinstaller folder
+pyinstaller release/pyinstaller/peptdeep.spec --distpath dist_pyinstaller --workpath build_pyinstaller -y