YosefLab · adamgayoso · Mar 3, 2023 · Mar 3, 2023 · Mar 3, 2023 · Mar 3, 2023
diff --git a/.flake8 b/.flake8
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -1,39 +1,39 @@
 name: Release
 
 on:
-  push:
-    tags:
-      - '*.*.*'
+    push:
+        tags:
+            - "*.*.*"
 
 jobs:
-  release:
-    name: Release
-    runs-on: ubuntu-latest
-    steps:
-      # will use ref/SHA that triggered it
-      - name: Checkout code
-        uses: actions/checkout@v3
+    release:
+        name: Release
+        runs-on: ubuntu-latest
+        steps:
+            # will use ref/SHA that triggered it
+            - name: Checkout code
+              uses: actions/checkout@v3
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.9"
+            - name: Set up Python 3.9
+              uses: actions/setup-python@v2
+              with:
+                  python-version: "3.9"
 
-      - name: Install poetry
-        uses: abatilo/actions-poetry@v2.0.0
-        with:
-          poetry-version: 1.1.11
+            - name: Install poetry
+              uses: abatilo/actions-poetry@v2.0.0
+              with:
+                  poetry-version: 1.1.11
 
-      - name: Build project for distribution
-        run: poetry build
+            - name: Build project for distribution
+              run: poetry build
 
-      - name: Check Version
-        id: check-version
-        run: |
-          [[ "$(poetry version --short)" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]] \
-            || echo ::set-output name=prerelease::true
+            - name: Check Version
+              id: check-version
+              run: |
+                  [[ "$(poetry version --short)" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]] \
+                    || echo ::set-output name=prerelease::true
 
-      - name: Publish to PyPI
-        env:
-          POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
-        run: poetry publish
+            - name: Publish to PyPI
+              env:
+                  POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
+              run: poetry publish
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -4,40 +4,39 @@
 name: velovi
 
 on:
-  push:
-    branches: [main]
-  pull_request:
-    branches: [main]
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
 
 jobs:
-  build:
+    build:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version: ["3.8", "3.9", "3.10"]
 
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache pip
-      uses: actions/cache@v2
-      with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-    - name: Install dependencies
-      run: |
-        pip install pytest-cov
-        pip install .[dev]
-    - name: Test with pytest
-      run: |
-        pytest --cov-report=xml --cov=velovi
-    - name: After success
-      run: |
-        bash <(curl -s https://codecov.io/bash)
-        pip list
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v2
+              with:
+                  python-version: ${{ matrix.python-version }}
+            - name: Cache pip
+              uses: actions/cache@v2
+              with:
+                  path: ~/.cache/pip
+                  key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+                  restore-keys: |
+                      ${{ runner.os }}-pip-
+            - name: Install dependencies
+              run: |
+                  pip install pytest-cov
+                  pip install .[dev]
+            - name: Test with pytest
+              run: |
+                  pytest --cov-report=xml --cov=velovi
+            - name: After success
+              run: |
+                  bash <(curl -s https://codecov.io/bash)
+                  pip list
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,15 +1,50 @@
+fail_fast: false
+default_language_version:
+    python: python3
+default_stages:
+    - commit
+    - push
+minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 22.6.0
+      rev: "23.1.0"
       hooks:
           - id: black
-    - repo: https://github.com/PyCQA/flake8
-      rev: 4.0.1
+    - repo: https://github.com/asottile/blacken-docs
+      rev: 1.13.0
       hooks:
-          - id: flake8
-    - repo: https://github.com/pycqa/isort
-      rev: 5.10.1
+          - id: blacken-docs
+    - repo: https://github.com/pre-commit/mirrors-prettier
+      rev: v3.0.0-alpha.4
       hooks:
-          - id: isort
-            name: isort (python)
-            additional_dependencies: [toml]
+          - id: prettier
+            # Newer versions of node don't work on systems that have an older version of GLIBC
+            # (in particular Ubuntu 18.04 and Centos 7)
+            # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+            # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+            # https://github.com/jupyterlab/jupyterlab/issues/12675
+            language_version: "17.9.1"
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.253
+      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: detect-private-key
+          - id: check-ast
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: trailing-whitespace
+          - id: check-case-conflict
+    - repo: local
+      hooks:
+          - id: forbid-to-commit
+            name: Don't commit rej files
+            entry: |
+                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+                Fix the merge conflicts manually and remove the .rej files.
+            language: fail
+            files: '.*\.rej$'
diff --git a/codecov.yml b/codecov.yml
@@ -1,9 +1,9 @@
 # Run to check if valid
 # curl --data-binary @codecov.yml https://codecov.io/validate
 coverage:
-  status:
-    project:
-      default:
-        target: 80%
-        threshold: 1%
-    patch: off
+    status:
+        project:
+            default:
+                target: 80%
+                threshold: 1%
+        patch: off
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
@@ -1,14 +1,14 @@
 /* influenced by and borrowed from: https://github.com/cvxgrp/pymde/blob/main/docs_src/source/_static/css/custom.css */
 
-@import url('https://fonts.googleapis.com/css2?family=Roboto:ital,wght@0,300;0,400;0,600;1,300;1,400;1,600&display=swap');
+@import url("https://fonts.googleapis.com/css2?family=Roboto:ital,wght@0,300;0,400;0,600;1,300;1,400;1,600&display=swap");
 
 :root {
     --sidebarcolor: #003262;
     --sidebarfontcolor: #ffffff;
     --sidebarhover: #295e97;
 
     --bodyfontcolor: #333;
-    --webfont: 'Roboto';
+    --webfont: "Roboto";
 
     --contentwidth: 1000px;
 }
@@ -20,7 +20,7 @@ h3,
 h4,
 h5,
 h6 {
-    font-family: var(--webfont), 'Helvetica Neue', Helvetica, Arial, sans-serif;
+    font-family: var(--webfont), "Helvetica Neue", Helvetica, Arial, sans-serif;
     font-weight: 400;
 }
 
@@ -38,7 +38,7 @@ h1 {
 }
 
 body {
-    font-family: var(--webfont), 'Helvetica Neue', Helvetica, Arial, sans-serif;
+    font-family: var(--webfont), "Helvetica Neue", Helvetica, Arial, sans-serif;
     color: var(--bodyfontcolor);
 }
 
@@ -47,7 +47,6 @@ p {
     line-height: 150%;
 }
 
-
 /* Sidebar */
 .wy-side-nav-search {
     background-color: var(--sidebarcolor);
@@ -66,7 +65,7 @@ p {
     color: var(--sidebarfontcolor);
 }
 
-.wy-side-nav-search>div.version {
+.wy-side-nav-search > div.version {
     color: var(--sidebarfontcolor);
 }
 
@@ -79,8 +78,13 @@ p {
     max-width: var(--contentwidth);
 }
 
-
-html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple) dl:not(.field-list)>dt {
+html.writer-html5
+    .rst-content
+    dl[class]:not(.option-list):not(.field-list):not(.footnote):not(
+        .glossary
+    ):not(.simple)
+    dl:not(.field-list)
+    > dt {
     margin-bottom: 6px;
     border-left: none;
     background: none;
@@ -110,10 +114,10 @@ div.nbinput.container {
 
 div.nbinput.container div.input_area {
     /* Code cell border that works in both dark and light mode */
-    border-color: rgba(127, 127, 127, .25) !important;
+    border-color: rgba(127, 127, 127, 0.25) !important;
 }
 
-div.nbinput.container div.input_area div[class*="highlight"]>pre {
+div.nbinput.container div.input_area div[class*="highlight"] > pre {
     padding: 10px !important;
     margin: 0;
 }

diff --git a/docs/conf.py b/docs/conf.py
@@ -68,19 +68,19 @@
 master_doc = "index"
 
 
-intersphinx_mapping = dict(
-    anndata=("https://anndata.readthedocs.io/en/stable/", None),
-    ipython=("https://ipython.readthedocs.io/en/stable/", None),
-    matplotlib=("https://matplotlib.org/", None),
-    numpy=("https://docs.scipy.org/doc/numpy/", None),
-    pandas=("https://pandas.pydata.org/pandas-docs/stable/", None),
-    python=("https://docs.python.org/3", None),
-    scipy=("https://docs.scipy.org/doc/scipy/reference/", None),
-    sklearn=("https://scikit-learn.org/stable/", None),
-    torch=("https://pytorch.org/docs/master/", None),
-    scanpy=("https://scanpy.readthedocs.io/en/stable/", None),
-    pytorch_lightning=("https://pytorch-lightning.readthedocs.io/en/stable/", None),
-)
+intersphinx_mapping = {
+    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+    "ipython": ("https://ipython.readthedocs.io/en/stable/", None),
+    "matplotlib": ("https://matplotlib.org/", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "python": ("https://docs.python.org/3", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
+    "sklearn": ("https://scikit-learn.org/stable/", None),
+    "torch": ("https://pytorch.org/docs/master/", None),
+    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+    "pytorch_lightning": ("https://pytorch-lightning.readthedocs.io/en/stable/", None),
+}
 
 
 # General information about the project.

diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
@@ -7,6 +7,7 @@
 
 
 def process_return(lines):
+    """Process the return section of a docstring."""
     for line in lines:
         m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
         if m:
@@ -17,6 +18,7 @@ def process_return(lines):
 
 
 def scanpy_parse_returns_section(self, section):
+    """Parse the returns section of the docstring."""
     lines_raw = list(process_return(self._dedent(self._consume_to_next_section())))
     lines = self._format_block(":returns: ", lines_raw)
     if lines and lines[-1]:
@@ -25,4 +27,5 @@ def scanpy_parse_returns_section(self, section):
 
 
 def setup(app: Sphinx):
+    """Setup the extension."""
     NumpyDocstring._parse_returns_section = scanpy_parse_returns_section