Update CI (#1025)

* dedupe readme

* everything except tox

* tox-uv

* no need to activate

* actually use pre-release flag

* add check for more flexibility for tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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/[email protected].2
+        uses: everlytic/[email protected].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

@@ -25,45 +25,32 @@ jobs:
         include:
           - python: "3.12"
             os: macos-latest
-            pip-flags: "--pre"
+            pre-release: "allow"
             name: "Python 3.12 (pre-release)"
 
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python }}
+      UV_PRERELEASE: ${{ matrix.pre-release || 'disallow' }}
 
     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
 
       - 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
+        run: uv tool install tox --with=tox-uv --with=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 +64,10 @@ 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
@@ -103,8 +90,17 @@ 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
           token: ${{ secrets.CODECOV_TOKEN }} # required
+
+  check:
+    if: always()
+    needs: [test]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: re-actors/alls-green@release/v1
+        with:
+          jobs: ${{ toJSON(needs) }}

README_pypi.rst

@@ -1,12 +1,11 @@
 [build-system]
 build-backend = "hatchling.build"
-requires = ["hatchling", "hatch-vcs"]
+requires = ["hatchling", "hatch-vcs", "hatch-fancy-pypi-readme"]
 
 [project]
 name = "squidpy"
-dynamic = ["version"]
+dynamic = ["readme", "version"]
 description = "Spatial Single Cell Analysis in Python"
-readme = "README.rst"
 requires-python = ">=3.10"
 license = "BSD-3-Clause"
 classifiers = [
@@ -121,6 +120,15 @@ source = "vcs"
 [tool.hatch.metadata]
 allow-direct-references = true
 
+[tool.hatch.metadata.hooks.fancy-pypi-readme]
+content-type = "text/x-rst"
+[[tool.hatch.metadata.hooks.fancy-pypi-readme.fragments]]
+text = "|PyPI| |Downloads| |CI| |Docs| |Coverage| |Discourse| |Zulip|"
+[[tool.hatch.metadata.hooks.fancy-pypi-readme.fragments]]
+path = "README.rst"
+start-after = "|NumFOCUS|"
+end-before = "Squidpy is part of the scverse® project"
+
 [tool.ruff]
 line-length = 120
 exclude = [