Update pre-commit versions and run separate CI job for linting checks (#41)

Author: eriknw

.github/workflows/lint.yml

@@ -0,0 +1,21 @@
+name: Lint via pre-commit
+
+on:
+  pull_request:
+  push:
+    branches-ignore:
+      - main
+
+permissions:
+  contents: read
+
+jobs:
+  pre-commit:
+    name: pre-commit-hooks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - uses: pre-commit/action@v3.0.0

.github/workflows/test.yml

@@ -12,7 +12,7 @@ jobs:
       run:
         shell: bash -l {0}
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         python-version: ["3.8", "3.9", "3.10"]
@@ -30,21 +30,16 @@ jobs:
           activate-environment: testing
       - name: Install dependencies
         run: |
-          conda install -c conda-forge python-graphblas scipy pandas \
-            pytest-cov pytest-randomly black flake8-comprehensions flake8-bugbear
+          conda install -c conda-forge python-graphblas scipy pandas pytest-cov pytest-randomly
             # matplotlib lxml pygraphviz pydot sympy  # Extra networkx deps we don't need yet
           pip install git+https://github.com/networkx/networkx.git@main --no-deps
           pip install -e . --no-deps
-      - name: Style checks
-        run: |
-          flake8
-          black . --check --diff
       - name: PyTest
         run: |
           python -c 'import sys, graphblas_algorithms; assert "networkx" not in sys.modules'
-          coverage run --branch -m pytest -v --check-structure
+          coverage run --branch -m pytest --color=yes -v --check-structure
           coverage report
-          NETWORKX_GRAPH_CONVERT=graphblas pytest --pyargs networkx --cov --cov-append
+          NETWORKX_GRAPH_CONVERT=graphblas pytest --color=yes --pyargs networkx --cov --cov-append
           coverage report
           coverage xml
       - name: Coverage

.pre-commit-config.yaml

@@ -5,9 +5,11 @@
 # To update: `pre-commit autoupdate`
 #  - &flake8_dependencies below needs updated manually
 fail_fast: true
+default_language_version:
+    python: python3
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -17,40 +19,45 @@ repos:
       - id: end-of-file-fixer
       - id: mixed-line-ending
       - id: trailing-whitespace
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.11
+    hooks:
+      - id: validate-pyproject
+        name: Validate pyproject.toml
   - repo: https://github.com/myint/autoflake
-    rev: v1.7.7
+    rev: v2.0.0
     hooks:
       - id: autoflake
         args: [--in-place]
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
-        language_version: python3
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.2
+    rev: v3.3.1
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
   - repo: https://github.com/MarcoGorelli/auto-walrus
-    rev: v0.2.1
+    rev: v0.2.2
     hooks:
-    - id: auto-walrus
+      - id: auto-walrus
+        args: [--line-length, "100"]
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 22.12.0
     hooks:
       - id: black
-        language_version: python3
         args: [--target-version=py38]
   - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+    rev: 6.0.0
     hooks:
       - id: flake8
         additional_dependencies: &flake8_dependencies
         # These versions need updated manually
-        - flake8==5.0.4
+        - flake8==6.0.0
         - flake8-comprehensions==3.10.1
-        - flake8-bugbear==22.10.27
+        - flake8-bugbear==23.1.20
+        - flake8-simplify==0.19.3
   - repo: https://github.com/asottile/yesqa
     rev: v1.4.0
     hooks:
@@ -62,9 +69,7 @@ repos:
       - id: codespell
         types_or: [python, rst, markdown]
         files: ^(graphblas_algorithms|docs)/
-        # args: ["--ignore-words-list=coo,ba"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: no-commit-to-branch  # no commit directly to main
-# Maybe: black-jupyter, blacken-docs, blackdoc mypy, velin

pyproject.toml

@@ -3,3 +3,4 @@ requires = ["setuptools", "wheel"]
 
 [tool.black]
 line-length = 100
+target-version = ["py38", "py39", "py310", "py311"]

scripts/bench.py

@@ -132,17 +132,21 @@ def getfunction(functionname, backend):
     return getattr(nx, functionname)
 
 
-def main(dataname, backend, functionname, time=3.0, n=None, extra=None, display=True):
+def getgraph(dataname, backend="graphblas", functionname=None):
     filename = find_data(dataname)
     is_symmetric = get_symmetry(filename) == "symmetric"
-    if not is_symmetric and functionname in undirected_only:
+    if not is_symmetric and functionname is not None and functionname in undirected_only:
         # Should we automatically symmetrize?
         raise ValueError(
             f"Data {dataname!r} is not symmetric, but {functionname} only works on undirected"
         )
     if is_symmetric and functionname in directed_only:
         is_symmetric = False  # Make into directed graph
-    G = readfile(filename, is_symmetric, backend)
+    return readfile(filename, is_symmetric, backend)
+
+
+def main(dataname, backend, functionname, time=3.0, n=None, extra=None, display=True):
+    G = getgraph(dataname, backend, functionname)
     func = getfunction(functionname, backend)
     benchstring = functioncall.get(functionname, "func(G)")
     if extra is not None:

setup.cfg

@@ -6,16 +6,20 @@ max-line-length = 100
 inline-quotes = "
 exclude =
     versioneer.py,
+    graphblas_algorithms/_version.py,
     graphblas_algorithms/*/tests/,
     graphblas_algorithms/*/*/tests/,
     build/
 extend-ignore =
     E203,
+    SIM105,
+    SIM401,
 # E203 whitespace before ':' (to be compatible with black)
 per-file-ignores =
     __init__.py:F401,F403,  # allow unused and star imports
     test_*.py:F401,F403,
     graphblas_algorithms/nxapi/exception.py:F401,
+    graphblas_algorithms/**/__init__.py:F401,F403
 
 [isort]
 sections = FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER
@@ -26,7 +30,8 @@ default_section = THIRDPARTY
 known_first_party = graphblas_algorithms
 line_length = 100
 skip =
-    graphblas_algorithms/nxapi/__init__.py
+    graphblas_algorithms/nxapi/__init__.py,
+    scripts/bench.py
 
 [coverage:run]
 source = graphblas_algorithms