From 645a28a278323bedfeabd3fa7ddfd9ea23fa377a Mon Sep 17 00:00:00 2001
From: RalfG <ralfg@hotmail.be>
Date: Fri, 16 Feb 2024 14:47:22 +0100
Subject: [PATCH] Update CI to use pyproject.toml; add tests for more py
 versions; upgrade action versions

---
 .github/workflows/publish.yml | 39 ++++++++++++++++++-----------------
 .github/workflows/test.yml    | 13 ++++++------
 2 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index f388cc1..24f7a38 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -8,45 +8,46 @@ on:
 jobs:
   python-package:
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.8'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel flake8 twine
+        pip install build flake8
     - name: Check for syntax errors
       run: |
         flake8 ./deeplc --count --select=E9,F63,F7,F82 --show-source --statistics
-    - name: Build and publish to PyPI
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+    - name: Build package
       run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        python -m build . --sdist --wheel
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
     - name: Upload compiled wheels
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: dist
         path: dist/*.whl
+
   windows-installer:
     runs-on: windows-latest
     needs: python-package
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.8'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install . gooey pyinstaller
+        pip install .[gui] pyinstaller
     - name: Install Inno Setup
-      uses: crazy-max/ghaction-chocolatey@v1
+      uses: crazy-max/ghaction-chocolatey@v3
       with:
         args: install innosetup -y --allow-unofficial --force
     - name: Run pyinstaller
@@ -56,7 +57,7 @@ jobs:
     - name: Run Inno Setup
       run: ISCC.exe ./deeplc_innosetup.iss /DMyAppVersion=$(python setup.py --version)
     - name: Upload installer
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: dist
         path: dist/*.exe
@@ -66,7 +67,7 @@ jobs:
     needs: [python-package, windows-installer]
     steps:
     - name: Download installer
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: dist
         path: dist
@@ -85,20 +86,20 @@ jobs:
     runs-on: ubuntu-latest
     needs: python-package
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - id: latest_release
       uses: pozetroninc/github-action-get-latest-release@master
       with:
         owner: compomics
         repo: DeepLC
     - name: Login to GitHub Container Registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v3
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
         password: ${{ secrets.GITHUB_TOKEN }}
     - name: Build and push to ghcr.io
-      uses: docker/build-push-action@v2
+      uses: docker/build-push-action@v5
       with:
         context: streamlit
         push: true
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ffc2927..88dee15 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -8,17 +8,16 @@ on:
 
 jobs:
   test:
-    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        system: [["3.8", "windows-latest"], ["3.8", "macos-latest"], ["3.8", "ubuntu-latest"], ["3.9", "ubuntu-latest"], ["3.10", "ubuntu-latest"], ["3.11", "ubuntu-latest"]]
+    runs-on: ${{ matrix.system[1] }}
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.system[0] }}
+        uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.system[0] }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip