Split linting and testing job (#596)

Co-authored-by: giovp <giov.pll@gmail.com>
scverse · Sep 17, 2022 · d24dd13 · d24dd13
1 parent 2cf664f
commit d24dd13
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Showing 5 changed files with 66 additions and 32 deletions.
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -0,0 +1,38 @@
+name: Lint
+
+on:
+    schedule:
+        - cron: 00 00 * * 1 # every Monday at 00:00
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+jobs:
+    lint:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python 3.9
+              uses: actions/setup-python@v2
+              with:
+                  python-version: 3.9
+
+            - uses: actions/cache@v2
+              with:
+                  path: ~/.cache/pre-commit
+                  key: precommit-${{ env.pythonLocation }}-${{ hashFiles('**/.pre-commit-config.yaml') }}
+
+            - name: Install dependencies
+              run: |
+                  sudo apt install pandoc
+                  python -m pip install --upgrade pip
+                  pip install tox
+
+            - name: Lint code
+              run: |
+                  tox -e lint
+
+            - name: Lint documentation
+              run: |
+                  tox -e check-docs
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -15,29 +15,20 @@ on:
                 default: release
 
 jobs:
-    lint:
-        runs-on: ubuntu-latest
+    cancel_previous_runs:
+        if: |
+            !endsWith(github.event.head_commit.message, '# ci skip') &&
+            (
+              startsWith(github.ref, 'refs/heads') ||
+              startsWith(github.ref, 'refs/tags') ||
+              github.event.pull_request.draft == false
+            )
+        runs-on: ${{ matrix.os }}
         steps:
-            - uses: actions/checkout@v2
-            - name: Set up Python 3.9
-              uses: actions/setup-python@v2
-              with:
-                  python-version: 3.9
-
-            - uses: actions/cache@v2
+            - name: Cancel Previous Runs
+              uses: styfle/cancel-workflow-action@0.10.0
               with:
-                  path: ~/.cache/pre-commit
-                  key: precommit-${{ env.pythonLocation }}-${{ hashFiles('**/.pre-commit-config.yaml') }}
-
-            - name: Install dependencies
-              run: |
-                  sudo apt install pandoc
-                  python -m pip install --upgrade pip
-                  pip install tox
-
-            - name: Lint
-              run: |
-                  tox -e lint,check-docs
+                  access_token: ${{ github.token }}
 
     test:
         runs-on: ${{ matrix.os }}
@@ -121,7 +112,7 @@ jobs:
                   codecov --no-color --required --flags unittests
 
     regenerate-notebooks:
-        needs: [lint, test]
+        needs: test
         if: ${{ (github.event_name == 'push' && (github.ref == 'refs/heads/main')) || (github.event_name == 'workflow_dispatch' && github.event.inputs.reason == 'release') }}
         runs-on: ubuntu-latest
         steps:
@@ -135,7 +126,7 @@ jobs:
 
     release:
         if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.reason == 'release' }}
-        needs: [lint, test]
+        needs: test
         runs-on: ubuntu-latest
         steps:
             - name: Invoke deployment workflow

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -14,12 +14,12 @@ repos:
                 [numpy==1.21.0, scipy, pandas, types-requests]
             exclude: .scripts/ci/download_data.py|squidpy/datasets/_(dataset|image).py # See https://github.com/pre-commit/mirrors-mypy/issues/33
     - repo: https://github.com/psf/black
-      rev: 22.6.0
+      rev: 22.8.0
       hooks:
           - id: black
             additional_dependencies: [toml]
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v2.7.1
+      rev: v3.0.0-alpha.0
       hooks:
           - id: prettier
     - repo: https://github.com/timothycrosley/isort
@@ -68,7 +68,7 @@ repos:
           - id: check-toml
           - id: requirements-txt-fixer
     - repo: https://github.com/myint/autoflake
-      rev: v1.4
+      rev: v1.5.3
       hooks:
           - id: autoflake
             args:
@@ -106,7 +106,7 @@ repos:
           - id: blacken-docs
             additional_dependencies: [black==20.8b1]
     - repo: https://github.com/asottile/pyupgrade
-      rev: v2.37.3
+      rev: v2.38.0
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py38-plus, --keep-runtime-typing]

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,15 +1,20 @@
 -r ../requirements.txt
 gitpython
 ipython
-Jinja2<3.1.0  # https://github.com/spatialaudio/nbsphinx/issues/641
+ipywidgets>=8.0.0
+# Jinja2<3.1.0  # https://github.com/spatialaudio/nbsphinx/issues/641
+Jinja2>=3.1.1
+nbconvert>=6.4.5
 # very slow build
+# nbsphinx>=0.8.1,<0.8.7
 nbsphinx>=0.8.1,<0.8.7
 pyenchant>=3.1.1
 requests
-sphinx>=4,<4.0.3  # https://github.com/spatialaudio/nbsphinx/issues/584
+# sphinx>=4,<4.0.3  # https://github.com/spatialaudio/nbsphinx/issues/584
+sphinx>=5.1.1
 sphinx-autodoc-annotation
 sphinx-autodoc-typehints>=1.10.3
-sphinx_gallery>=0.8.2
+sphinx_gallery>=0.8.2,<0.11 # https://github.com/spatialaudio/nbsphinx/pull/666
 sphinx_rtd_theme
 sphinxcontrib-bibtex>=2.2.0
 sphinxcontrib-spelling
diff --git a/tox.ini b/tox.ini
@@ -26,7 +26,7 @@ per-file-ignores =
 # RST301 Unexpected indentation.
 # RST306 Unknown target name:
 # RST203 Definition list ends without a blank line; unexpected unindent.
-ignore = D100,D107,B008,W503,D105,E203,P101,RST201,RST301,RST306,RST203
+ignore = D100,D107,B008,W503,D105,E203,P101,RST201,RST301,RST306,RST203,B024
 exclude =
     .git
     .tox
@@ -163,7 +163,7 @@ commands =
 [testenv:lint]
 description = Perform linting.
 basepython = python3.9
-deps = pre-commit>=2.9.3
+deps = pre-commit>=2.20.0
 skip_install = true
 commands = pre-commit run --all-files --show-diff-on-failure {posargs:}