everything except tox

Author: flying-sheep

.github/workflows/build.yml

@@ -14,16 +14,13 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v5
+      - name: Set up Python 3.12
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.10"
-          cache: "pip"
-          cache-dependency-path: "**/pyproject.toml"
-      - name: Install build dependencies
-        run: python -m pip install --upgrade pip wheel twine build
+          python-version: "3.12"
+          enable-cache: true
       - name: Build package
-        run: python -m build
+        run: uvx hatch build
       - name: Check package
-        run: twine check --strict dist/*.whl
+        run: uvx twine check --strict dist/*.whl

.github/workflows/deployment.yml

@@ -17,21 +17,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - name: Set up Python 3.12
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.10"
-
-      - name: Install hatch
-        run: pip install hatch
+          python-version: "3.12"
 
       # this will fail if the last commit is not tagged
       - name: Build project for distribution
-        run: hatch build
+        run: uvx hatch build
 
       - name: Publish on PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
@@ -46,14 +43,14 @@ jobs:
     needs: deploy
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
       - name: Extract branch name
         id: vars
         run: |
           echo ::set-output name=branch::${GITHUB_REF#refs/*/}
 
       - name: Merge release into main
-        uses: everlytic/branch-merge@1.1.2
+        uses: everlytic/branch-merge@1.1.5
         with:
           github_token: ${{ secrets.RELEASE_DISPATCH_TOKEN }}
           target_branch: main

.github/workflows/release.yml

@@ -9,22 +9,16 @@ jobs:
     runs-on: ubuntu-latest
     if: startsWith(github.ref, 'refs/tags/v')
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
       - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+        uses: astral-sh/setup-uv@v6
         with:
           python-version: "3.12"
-          cache: pip
-      - name: Install build dependencies
-        run: python -m pip install --upgrade pip wheel twine build
+          enable-cache: true
       - name: Build package
-        run: python -m build
+        run: uvx hatch build
       - name: Check package
-        run: twine check --strict dist/*.whl
-      - name: Install hatch
-        run: pip install hatch
-      - name: Build project for distribution
-        run: hatch build
+        run: uvx twine check --strict dist/*.whl
       - name: Publish a Python distribution to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:

.github/workflows/test.yml

@@ -33,37 +33,25 @@ jobs:
       PYTHON: ${{ matrix.python }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5
+        uses: astral-sh/setup-uv@v6
         with:
           python-version: ${{ matrix.python }}
-
-      - name: Get pip cache dir
-        id: pip-cache-dir
-        run: |
-          echo "::set-output name=dir::$(pip cache dir)"
-
-      - name: Restore pip cache
-        uses: actions/cache@v3
-        with:
-          path: ${{ steps.pip-cache-dir.outputs.dir }}
-          key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            pip-${{ runner.os }}-${{ env.pythonLocation }}-
+          enable-cache: true
+          activate-environment: true
 
       - name: Install dependencies
         run: |
           ./.scripts/ci/install_dependencies.sh
 
       - name: Install pip dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install tox tox-gh-actions
+          uv pip install tox tox-gh-actions
 
       - name: Restore data cache
         id: data-cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             ~/.cache/squidpy/*.h5ad
@@ -77,10 +65,10 @@ jobs:
       # caching .tox is not encouraged, but since we're private and this shaves off ~1min from the step
       # if any problems occur and/or once the package is public, this can be removed
       - name: Restore tox cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .tox
-          key: tox-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/requirements.txt', '**/tox.ini') }}
+          key: tox-${{ runner.os }}-${{ matrix.python }}-${{ hashFiles('**/requirements.txt', '**/tox.ini') }}
 
       - name: Test
         timeout-minutes: 60
@@ -103,7 +91,7 @@ jobs:
           path: /home/runner/work/squidpy/squidpy/tests/figures/*
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           name: coverage
           verbose: true