Fixup linter setup

Author: vladistan

.editorconfig

@@ -1,4 +1,4 @@
-# Check http://editorconfig.org for more information
+# Check https://editorconfig.org for more information
 # This is the main config file for this project:
 root = true
 

.github/workflows/main.yaml

@@ -8,16 +8,15 @@ name: Build and test linkml-runtime
 on:
   push:
     branches:
-    - main
+      - main
   pull_request:
   workflow_dispatch:
 
 jobs:
-
   quality-checks:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4.2.2
+      - uses: actions/checkout@4.2.2
       - name: Install Poetry
         run: |
           pipx install poetry
@@ -29,10 +28,10 @@ jobs:
         run: poetry check
       - name: Install tox
         run: python -m pip install tox
-      - name: Run codespell
-        run: tox -e codespell
-      - name: Run code format checks
-        run: tox -e format_check
+      - name: Run pre-commit checks
+        uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --all-files
 
   test:
     needs:
@@ -42,61 +41,49 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        # Test on Windows with only the oldest and newest Python versions
         exclude:
-        - os: windows-latest
-          python-version: "3.10"
-        - os: windows-latest
-          python-version: "3.11"
-        - os: windows-latest
-          python-version: "3.12"
+          - os: windows-latest
+            python-version: "3.10"
+          - os: windows-latest
+            python-version: "3.11"
+          - os: windows-latest
+            python-version: "3.12"
+    # See https://github.com/snok/install-poetry#running-on-windows
+    defaults:
+      run:
+        shell: bash
 
     runs-on: ${{ matrix.os }}
 
     steps:
+      - name: Check out repository
+        uses: actions/checkout@4.2.2
+        with:
+          fetch-depth: 0
+
 
-      #----------------------------------------------
-      #          install poetry
-      #----------------------------------------------
       - name: Install Poetry
         run: |
           pipx install poetry
           pipx inject poetry poetry-dynamic-versioning
 
-      #----------------------------------------------
-      #       check-out repo and set-up python
-      #----------------------------------------------
-      - name: Check out repository
-        uses: actions/checkout@v4.2.2
-        with:
-          fetch-depth: 0
-
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5.6.0
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'poetry'
 
-      #----------------------------------------------
-      #    install your root project, if required
-      #----------------------------------------------
       - name: Install library
         run: |
           poetry install --no-interaction
-
-      #----------------------------------------------
-      #              coverage report
-      #----------------------------------------------
       - name: Generate coverage results
         # Set bash shell to fail correctly on Windows https://github.com/actions/runner-images/issues/6668
         shell: bash
         run: |
           poetry run coverage run -m pytest
           poetry run coverage xml
           poetry run coverage report -m
-
-      #----------------------------------------------
-      #           upload coverage results
-      #----------------------------------------------
       - name: Upload coverage report
         uses: codecov/codecov-action@v5
         with:

.pre-commit-config.yaml

@@ -9,12 +9,8 @@ repos:
   - id: end-of-file-fixer
     exclude: __snapshots__
   - id: check-yaml
-    exclude: (__snapshots__|test_utils/input)
   - id: check-toml
   - id: trailing-whitespace
-    # TODO: This is temporary while bioliank is being fixed upstream.
-    # TODO: Should look at snapshot exclusion to find upstream problems
-    exclude: (__snapshots__|biolink-model.yaml)
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ensure this version stays in sync with tox.ini
   rev: v0.11.13

pyproject.toml

@@ -75,9 +75,21 @@ style = "pep440"
 coverage = "^6.2"
 requests-cache = "^1.2.0"
 
+
+[tool.codespell]
+skip = [
+  ".git", "*.pdf", "*.svg", "*.dill",
+  "poetry.lock",
+]
+# Ignore table where words could be split across rows
+ignore-regex = '(\|.*\|.*\|.*\||\[[A-Z][a-z]\][a-z][a-z])'
+ignore-words-list = [
+]
+quiet-level = 3
 # https://docs.astral.sh/ruff/settings/
 [tool.ruff]
-extend-exclude = []
+extend-exclude = [
+]
 force-exclude = true
 line-length = 120
 # Assume Python 3.9
@@ -86,12 +98,11 @@ target-version = "py39"
 [tool.ruff.lint]
 
 select = [
-    # core
-    "F", # Pyflakes
-    "E", # pycodestyle errors
+    "E",  # pycodestyle errors
+    "F",  # Pyflakes
+    "I", # isort
     "W", # pycodestyle warnings
     "C90", # mccabe +
-    "I", # isort
     "N", # pep8-naming
     # "D", # pydocstyle
     "UP", # pyupgrade
@@ -177,6 +188,14 @@ max-complexity = 15
 requires = ["tox>=4"]
 env_list = ["lint", "py{39,310,311,312,313}"]
 
+[tool.tox.env_run_base]
+allowlist_externals = ["poetry"]
+deps = ["pytest"]
+commands = [
+  ["poetry", "install", "--no-root", "--sync", "--all-extras"],
+  ["poetry", "run", "pytest", "{posargs}"],
+]
+
 [tool.tox.env.codespell]
 description = "Run spell checkers."
 skip_install = true
@@ -189,25 +208,23 @@ commands = [
 ]
 
 [tool.tox.env.format]
-description = "Run ruff code formatter."
+description = "Run code formatter and code-fixing linter."
 skip_install = true
-deps = ["ruff==0.11.13"]
+deps = ["pre-commit"]
 commands = [
-  ["ruff", "format", "{posargs:.}"],
+  ["pre-commit", "run", "--all-files", "--show-diff-on-failure", { replace = "posargs", extend = true }]
 ]
 
 [tool.tox.env.format_check]
 description = "Check that code is correctly formatted by ruff."
 skip_install = true
 deps = ["ruff==0.11.13"]
-commands = [
-  ["ruff", "format", "--check", "{posargs:.}"],
-]
 
 [tool.tox.env.lint]
-description = "Run code linter (no fixes)."
+description = "Run code linter and formatter (no fixes)."
 skip_install = true
 deps = ["ruff==0.11.13"]
 commands = [
   ["ruff", "check", "{posargs:.}"],
+  ["ruff", "format", "{posargs:.}"],
 ]