Prettier (#115)

theislab · Jul 14, 2023 · 4d7befb · 4d7befb
1 parent 83be262
commit 4d7befb
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Showing 7 changed files with 129 additions and 105 deletions.
diff --git a/.editorconfig b/.editorconfig
@@ -0,0 +1,13 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+max_line_length = 120
+indent_size = 4
+indent_style = space
+
+[*.{yml,yaml}]
+indent_size = 2
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -3,51 +3,51 @@ name: Publish Python 🐍 distributions 📦 to PyPI
 on:
   push:
     branches:
-    - 'main'
-    - 'test_deploy'
+      - main
+      - test_deploy
     tags:
-    - '*'
+      - "*"
 
 jobs:
   build-n-publish:
     name: Build and publish Python 🐍 distributions 📦 to PyPI
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-      with:
-        fetch-depth: 0  # allow deriving correct version from git tags
-
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.11
-        cache: pip
-
-    - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-
-    - name: Build a binary wheel and a source tarball
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-        .
-
-    - name: Publish distribution 📦 to Test PyPI
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        skip_existing: true
-        password: ${{ secrets.TEST_PYPI_PASSWORD }}
-        repository_url: https://test.pypi.org/legacy/
-
-    - name: Publish distribution 📦 to PyPI
-      if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        password: ${{ secrets.PYPI_PASSWORD }}
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # allow deriving correct version from git tags
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+          cache: pip
+
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+
+      - name: Publish distribution 📦 to Test PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          skip_existing: true
+          password: ${{ secrets.TEST_PYPI_PASSWORD }}
+          repository_url: https://test.pypi.org/legacy/
+
+      - name: Publish distribution 📦 to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.PYPI_PASSWORD }}
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -3,10 +3,10 @@ name: Unit Tests
 on:
   push:
     branches:
-    - 'main'
+      - main
   pull_request:
     branches:
-    - '*'
+      - "*"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -27,57 +27,57 @@ jobs:
       fail-fast: false
       matrix:
         config:
-        - { name: '3.11', os: ubuntu-latest, python: '3.11', r: 'release' }
-        - { name: '3.10', os: ubuntu-latest, python: '3.10', r: 'release' }
-        - { name: '3.9', os: ubuntu-latest, python: '3.9', r: 'release' }
-        - { name: '3.8', os: ubuntu-latest, python: '3.8', r: 'oldrel' }
+          - { name: "3.11", os: ubuntu-latest, python: "3.11", r: release }
+          - { name: "3.10", os: ubuntu-latest, python: "3.10", r: release }
+          - { name: "3.9", os: ubuntu-latest, python: "3.9", r: release }
+          - { name: "3.8", os: ubuntu-latest, python: "3.8", r: oldrel }
 
     steps:
-    - uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
 
-    - name: Install system dependencies
-      if: runner.os == 'Linux'
-      uses: awalsh128/cache-apt-pkgs-action@latest
-      with:
-        packages: pandoc gfortran libblas-dev liblapack-dev libedit-dev llvm-dev libcurl4-openssl-dev ffmpeg libhdf5-dev
-        version: 1.0
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: pandoc gfortran libblas-dev liblapack-dev libedit-dev llvm-dev libcurl4-openssl-dev ffmpeg libhdf5-dev
+          version: 1.0
 
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.config.python }}
-        cache: pip
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.config.python }}
+          cache: pip
 
-    - name: Set up R
-      id: setup-r
-      uses: r-lib/actions/setup-r@v2
-      with:
-        r-version: ${{ matrix.config.r }}
+      - name: Set up R
+        id: setup-r
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
 
-    - name: Install python tools
-      run: |
-        python -m pip install --upgrade pip wheel
-        pip install --upgrade build
+      - name: Install python tools
+        run: |
+          python -m pip install --upgrade pip wheel
+          pip install --upgrade build
 
-    - name: Set up rpy2
-      run: |
-        pip install rpy2
-        echo "LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}" >> $GITHUB_ENV
+      - name: Set up rpy2
+        run: |
+          pip install rpy2
+          echo "LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}" >> $GITHUB_ENV
 
-    - uses: r-lib/actions/setup-r-dependencies@v2
-      with:
-        cache-version: 1  # increment to bust cache
-        packages: |
-          bioc::SingleCellExperiment
-          bioc::scRNAseq
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 1 # increment to bust cache
+          packages: |
+            bioc::SingleCellExperiment
+            bioc::scRNAseq
 
-    - name: Install anndata2ri
-      run: |
-        python -m build --wheel
-        pip install $(ls -1 dist/anndata2ri*.whl)[test]
-        python -c "import anndata2ri"
+      - name: Install anndata2ri
+        run: |
+          python -m build --wheel
+          pip install $(ls -1 dist/anndata2ri*.whl)[test]
+          python -c "import anndata2ri"
 
-    - name: Run tests
-      run: pytest --verbose --color=yes
+      - name: Run tests
+        run: pytest --verbose --color=yes
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,15 +1,19 @@
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
-  hooks:
-  - id: trailing-whitespace
-- repo: https://github.com/psf/black
-  rev: 23.3.0
-  hooks:
-  - id: black
-    language_version: python3
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.0.278
-  hooks:
-    - id: ruff
-      args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: "23.3.0"
+    hooks:
+      - id: black
+        language_version: python3
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.278
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.0
+    hooks:
+      - id: prettier
diff --git a/.prettierrc.yaml b/.prettierrc.yaml
@@ -0,0 +1,7 @@
+overrides:
+  # JSON with comments and trailing commas
+  - files: .vscode/*.json
+    options:
+      parser: json5
+      quoteProps: preserve
+      singleQuote: false
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -5,9 +5,9 @@ build:
     python: "3.11"
 python:
   install:
-  - method: pip
-    path: .
-    extra_requirements:
-    - doc
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
 sphinx:
   configuration: docs/conf.py
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -11,4 +11,4 @@
     "python.testing.unittestEnabled": false,
     "python.testing.pytestEnabled": true,
     "python.terminal.activateEnvironment": false,
-}
+}