Update pre-commit hooks (#964)

* Updates pre-commit hooks to align with scverse packages.

* Updates and fixes docstrings to pass pre-commit hooks. If the fix is not permanent, a corresponding TODO comment is added.

* Updates spacing if needed.

* Update exception handling to not rely on bare excepts.

* Update arguments to non-mutable objects.

* Avoid redundant list comprehension.

* Update for loops to remove redundant operations and variables.

.editorconfig

@@ -8,8 +8,5 @@ end_of_line = lf
 charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
-max_line_length = 88
-
-[*.py]
-indent_size = 4
 indent_style = space
+indent_size = 4

.flake8

@@ -1,11 +1,63 @@
 [flake8]
-max-line-length = 88
-filename = *.py
-exclude =
-    .git,
-    __pycache__,
-    docs/*
-# F403: unable to detect undefined names
-# F405: undefined, or defined from star imports
-# W503: Linebreak before binary operator
-ignore = F403, F405, W503
+max-line-length = 119
+ignore =
+    # Unnecessary dict call - rewrite as a literal.
+    C408
+    # line break before a binary operator -> black does not adhere to PEP8
+    W503
+    # line break occured after a binary operator -> black does not adhere to PEP8
+    W504
+    # line too long -> we accept long comment lines; black gets rid of long code lines
+    E501
+    # whitespace before : -> black does not adhere to PEP8
+    E203
+    # missing whitespace after ,', ';', or ':' -> black does not adhere to PEP8
+    E231
+    # continuation line over-indented for hanging indent -> black does not adhere to PEP8
+    E126
+    # too many leading '#' for block comment -> this is fine for indicating sections
+    E262
+    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+    E731
+    # allow I, O, l as variable names -> I is the identity matrix
+    E741
+    # Missing docstring in public package
+    D104
+    # Missing docstring in public module
+    D100
+    # Missing docstring in __init__
+    D107
+    # Missing docstring in magic method
+    D105
+    # format string does contain unindexed parameters
+    P101
+    # first line should end with a period [Bug: doesn't work with single-line docstrings]
+    D400
+    # First line should be in imperative mood; try rephrasing
+    D401
+exclude = .git,__pycache__,build,docs/_build,dist,scvi/__init__.py
+per-file-ignores =
+    tests/*: D
+    */__init__.py: F401
+extend-immutable-calls =
+    # Add functions returning immutable values here to avoid B008
+    pathlib.Path
+    Path
+rst-roles =
+    class,
+    func,
+    ref,
+    meth,
+    doc,
+    py:class,
+    method,
+    attr,
+    cite:p,
+    cite:t,
+rst-directives =
+    envvar,
+    exception,
+rst-substitutions =
+    version,
+extend-ignore =
+    RST307,RST210,RST201,RST203,RST301

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,21 +1,21 @@
 ---
 name: Bug report
 about: scVelo doesn’t do what it should? Please help us fix it!
-title: ''
+title: ""
 labels: bug
-assignees: ''
+assignees: ""
 ---
 
 <!-- Description of the bug -->
-...
 
+...
 
 <!-- Reproducible example -->
+
 ```python
 # paste your code here, if applicable
 ```
 
-
 <!-- Error Output -->
 <details>
 
@@ -24,13 +24,14 @@ assignees: ''
 ```pytb
 # paste the error output here, if applicable
 ```
-</details>
 
+</details>
 
 <!-- Versions -->
 <details> <summary> Versions </summary>
 
 ```pytb
 # paste the ouput of scv.logging.print_versions() here
 ```
+
 </details>

.github/ISSUE_TEMPLATE/enhancement_request.md

@@ -1,10 +1,9 @@
 ---
 name: Enhancement request
 about: Anything you’d like to see in scVelo?
-title: ''
+title: ""
 labels: enhancement
-assignees: ''
+assignees: ""
 ---
 
 <!-- What kind of feature would you like to request? -->
-

.github/pull_request_template.md

@@ -1,19 +1,23 @@
 ## Changes
+
 <!-- Please remove section if this PR does change an existing feature -->
 
-* ...
+-   ...
 
 ## Bug fixes
+
 <!-- Please give section if this PR does not fix any bugs -->
 
-* ...
+-   ...
 
 ## New
+
 <!-- Please give section if this PR does not implement a new feature -->
 
-* ...
+-   ...
 
 ## Related issues
+
 <!-- Please list related issues. If none exist, open one and reference it here. -->
 
 Closes #

.github/workflows/ci.yml

@@ -1,78 +1,78 @@
 name: CI
 
 on:
-  push:
-    branches: [master, develop, 'release/**']
-  pull_request:
-    branches: [master, develop, 'release/**']
+    push:
+        branches: [master, develop, "release/**"]
+    pull_request:
+        branches: [master, develop, "release/**"]
 
 jobs:
-  # Skip CI if commit message contains `[ci skip]` in the subject
-  init:
-    runs-on: ubuntu-latest
-    outputs:
-      skip: ${{ steps.ci-skip-step.outputs.ci-skip }}
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 0
-      - id: ci-skip-step
-        uses: mstachniuk/ci-skip@master
+    # Skip CI if commit message contains `[ci skip]` in the subject
+    init:
+        runs-on: ubuntu-latest
+        outputs:
+            skip: ${{ steps.ci-skip-step.outputs.ci-skip }}
+        steps:
+            - uses: actions/checkout@v2
+              with:
+                  fetch-depth: 0
+            - id: ci-skip-step
+              uses: mstachniuk/ci-skip@master
 
-  # Check if pre-commit hooks pass and if README.rst can be converted to HTML
-  linting:
-    needs: init
-    if: ${{ needs.init.outputs.skip == 'false' }}
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install pre-commit docutils
-      - name: Check pre-commit compatibility
-        run: pre-commit run --all-files --show-diff-on-failure
-      - name: Run rst2html.py
-        run: rst2html.py --halt=2 README.rst >/dev/null
+    # Check if pre-commit hooks pass and if README.rst can be converted to HTML
+    linting:
+        needs: init
+        if: ${{ needs.init.outputs.skip == 'false' }}
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v2
+            - name: Setup Python 3.8
+              uses: actions/setup-python@v2
+              with:
+                  python-version: 3.8
+            - name: Install dependencies
+              run: |
+                  python -m pip install --upgrade pip
+                  pip install pre-commit docutils
+            - name: Check pre-commit compatibility
+              run: pre-commit run --all-files --show-diff-on-failure
+            - name: Run rst2html.py
+              run: rst2html.py --halt=2 README.rst >/dev/null
 
-  # Run unit tests
-  test:
-    needs: linting
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest]
-        python-version: [3.8, 3.9]
-    steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: pip install -e '.[dev]'
-      - name: Unit tests
-        timeout-minutes: 60
-        run: python -m pytest --durations=25 --ignore=tests/datasets/test_datasets.py --hypothesis-profile=ci --cov=scvelo -vv
+    # Run unit tests
+    test:
+        needs: linting
+        runs-on: ${{ matrix.os }}
+        strategy:
+            fail-fast: false
+            matrix:
+                os: [ubuntu-latest]
+                python-version: [3.8, 3.9]
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v2
+              with:
+                  python-version: ${{ matrix.python-version }}
+            - name: Install dependencies
+              run: pip install -e '.[dev]'
+            - name: Unit tests
+              timeout-minutes: 60
+              run: python -m pytest --durations=25 --ignore=tests/datasets/test_datasets.py --hypothesis-profile=ci --cov=scvelo -vv
 
-  test-dataset-downloads:
-    needs: test
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - name: Install dependencies
-        run: |
-          pip install -e .
-          pip install hypothesis pytest pytest-cov
-      - name: Test dataset downloads
-        timeout-minutes: 60
-        run: python -m pytest tests/datasets/test_datasets.py -vv
+    test-dataset-downloads:
+        needs: test
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v2
+            - name: Setup Python 3.8
+              uses: actions/setup-python@v2
+              with:
+                  python-version: 3.8
+            - name: Install dependencies
+              run: |
+                  pip install -e .
+                  pip install hypothesis pytest pytest-cov
+            - name: Test dataset downloads
+              timeout-minutes: 60
+              run: python -m pytest tests/datasets/test_datasets.py -vv