MAINT: update lock files (#317)

* DX: run `tox -e uv` with lock runner
* FIX: set correct ignore patterns for `sphinx-autobuild`
* MAINT: update developer environment

Author: grayson-helmholz

.github/workflows/ci.yml

@@ -36,7 +36,7 @@ jobs:
     uses: ComPWA/actions/.github/workflows/[email protected]
     with:
       coverage-target: qrules
-      macos-python-version: "3.9"
+      macos-python-version: "3.10"
       specific-pip-packages: ${{ inputs.specific-pip-packages }}
       test-output-path: tests/output/
     secrets:

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
       - id: check-useless-excludes
 
   - repo: https://github.com/ComPWA/policy
-    rev: 0.5.16
+    rev: 0.6.1
     hooks:
       - id: check-dev-files
         args:
@@ -30,6 +30,7 @@ repos:
           - --add-install-cell
           - --additional-packages=IPython
           - --extras-require=doc,viz
+      - id: set-nb-display-name
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.8.1
@@ -60,7 +61,7 @@ repos:
             metadata.vscode
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.2
+    rev: v0.9.3
     hooks:
       - id: ruff
         args: [--fix]
@@ -127,7 +128,7 @@ repos:
       - id: cspell
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: 3.0.3
+    rev: 3.2.0
     hooks:
       - id: editorconfig-checker
         name: editorconfig
@@ -153,6 +154,6 @@ repos:
       - id: pyright
 
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.5.20
+    rev: 0.5.25
     hooks:
       - id: uv-lock

.readthedocs.yml

@@ -14,7 +14,7 @@ build:
       uv run \
         --group doc \
         --no-dev \
-        --with tox \
+        --with tox-uv \
         tox -e doc
       mkdir -p $READTHEDOCS_OUTPUT
       mv docs/_build/html $READTHEDOCS_OUTPUT

.vscode/settings.json

@@ -57,6 +57,7 @@
   "notebook.gotoSymbols.showAllSymbols": true,
   "python.analysis.autoImportCompletions": false,
   "python.analysis.inlayHints.pytestParameters": true,
+  "python.defaultInterpreterPath": ".venv/bin/python",
   "python.terminal.activateEnvironment": false,
   "python.testing.pytestArgs": [
     "--color=no",

pyproject.toml

@@ -18,6 +18,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python",
     "Topic :: Scientific/Engineering :: Physics",
@@ -139,6 +140,11 @@ where = ["src"]
 [tool.setuptools_scm]
 write_to = "src/qrules/version.py"
 
+[tool.coverage.report]
+exclude_also = [
+    "if TYPE_CHECKING:",
+]
+
 [tool.coverage.run]
 branch = true
 source = ["src"]
@@ -193,16 +199,6 @@ ignore_missing_imports = true
 module = ["tqdm.*"]
 
 [tool.pyright]
-exclude = [
-    "**/.git",
-    "**/.ipynb_checkpoints",
-    "**/.mypy_cache",
-    "**/.pytest_cache",
-    "**/.tox",
-    "**/.venv/",
-    "**/__pycache__",
-    "**/_build",
-]
 reportArgumentType = false
 reportAssignmentType = false
 reportAttributeAccessIssue = false
@@ -397,6 +393,11 @@ trailing_comma_inline_array = true
 
 [tool.tox]
 env_list = [
+    "3.9",
+    "3.10",
+    "3.11",
+    "3.12",
+    "3.13",
     "cov",
     "docnb-force",
     "linkcheck",
@@ -409,15 +410,16 @@ skip_install = true
 skip_missing_interpreters = true
 
 [tool.tox.env_run_base]
-allowlist_externals = ["pytest"]
-commands = [
-    ["pytest", {replace = "posargs", default = ["src tests/unit"], extend = true}],
-]
-description = "Run all fast unit tests and doctests"
+commands = [["pytest", {replace = "posargs", extend = true}]]
+dependency_groups = ["test"]
+description = "Run test suite on Python {env_name}"
+no_package = false
 pass_env = ["*"]
+runner = "uv-venv-lock-runner"
+skip_install = false
+skip_missing_interpreters = false
 
 [tool.tox.env.cov]
-allowlist_externals = ["pytest"]
 commands = [
     [
         "pytest",
@@ -432,6 +434,7 @@ description = "Compute the test coverage of all unit tests"
 
 [tool.tox.env.doc]
 allowlist_externals = ["sphinx-build"]
+base = []
 commands = [
     [
         "sphinx-build",
@@ -440,90 +443,97 @@ commands = [
         "--keep-going",
         "--show-traceback",
         "docs/",
-        "docs/_build/html",
+        "docs/_build/html/",
     ],
 ]
 description = "Build documentation and API through Sphinx"
 set_env.PYTHONWARNINGS = ""
 
 [tool.tox.env.doclive]
 allowlist_externals = ["sphinx-autobuild"]
+base = []
 commands = [
     [
         "sphinx-autobuild",
-        "--builder=html",
-        "--ignore=docs/_build/",
-        "--ignore=docs/_images/",
-        "--ignore=docs/_static/logo.*",
-        "--ignore=docs/api/",
-        "--open-browser",
         "--port=0",
-        "--re-ignore='.*/__pycache__/.*'",
-        "--re-ignore='.*/.ipynb_checkpoints/.*'",
-        "--re-ignore='.*/.virtual_documents/.*'",
-        "--re-ignore='.*\\.csv'",
-        "--re-ignore='.*\\.gv'",
-        "--re-ignore='.*\\.inv'",
-        "--re-ignore='.*\\.json'",
-        "--re-ignore='.*\\.pickle'",
-        "--re-ignore='.*\\.tmp'",
-        "--re-ignore='.*\\.ya?ml'",
-        "--watch=docs",
+        "--re-ignore=/__pycache__(/.*)?$",
+        "--re-ignore=/_build(/.*)?$",
+        "--re-ignore=/_images(/.*)?$",
+        "--re-ignore=/\\.cache(/.*)?$",
+        "--re-ignore=/\\.egg-info(/.*)?$",
+        "--re-ignore=/\\.ipynb_checkpoints(/.*)?$",
+        "--re-ignore=/\\.virtual_documents(/.*)?$",
+        "--re-ignore=/api(/.*)?$",
+        "--re-ignore=/docs$",
+        "--re-ignore=/version\\.py$",
+        "--re-ignore=\\.csv$",
+        "--re-ignore=\\.egg-info(/.*)?$",
+        "--re-ignore=\\.gif$",
+        "--re-ignore=\\.gitignore$",
+        "--re-ignore=\\.gv$",
+        "--re-ignore=\\.inv$",
+        "--re-ignore=\\.json$",
+        "--re-ignore=\\.pickle$",
+        "--re-ignore=\\.pkl$",
+        "--re-ignore=\\.png$",
+        "--re-ignore=\\.root$",
+        "--re-ignore=\\.svg$",
+        "--re-ignore=\\.tmp$",
+        "--re-ignore=\\.ya?ml$",
         "--watch=src",
         "docs/",
-        "docs/_build/html",
+        "docs/_build/html/",
     ],
 ]
 description = "Set up a server to directly preview changes to the HTML pages"
 
 [tool.tox.env.docnb]
-base = ["tool.tox.env.doc", "tool.tox.env_run_base"]
+base = ["tool.tox.env.doc"]
 set_env = [
     {replace = "ref", of = ["tool.tox.env.doc.set_env"]},
     {EXECUTE_NB = "yes"},
 ]
 
 [tool.tox.env.docnb-force]
-base = ["tool.tox.env.doc", "tool.tox.env_run_base"]
+base = ["tool.tox.env.doc"]
 description = "Execute Jupyter notebooks without cache and build documentation with Sphinx"
 set_env = [
     {replace = "ref", of = ["tool.tox.env.doc.set_env"]},
     {FORCE_EXECUTE_NB = "yes"},
 ]
 
 [tool.tox.env.docnblive]
-base = ["tool.tox.env.doclive", "tool.tox.env_run_base"]
+base = ["tool.tox.env.doclive"]
 set_env = [
     {replace = "ref", of = ["tool.tox.env.doclive.set_env"]},
     {EXECUTE_NB = "yes"},
 ]
 
 [tool.tox.env.linkcheck]
-allowlist_externals = ["sphinx-build"]
-base = ["tool.tox.env.doc", "tool.tox.env_run_base"]
+base = ["tool.tox.env.doc"]
 commands = [
     [
         "sphinx-build",
         "--builder=linkcheck",
         "--show-traceback",
         "docs/",
-        "docs/_build/linkcheck",
+        "docs/_build/linkcheck/",
     ],
 ]
 description = "Check external links in the documentation (requires internet connection)"
 
 [tool.tox.env.nb]
-allowlist_externals = ["pytest"]
 commands = [["pytest", "--nbmake", "{posargs:docs}"]]
 description = "Run all notebooks with pytest"
+with_dev = true
 
 [tool.tox.env.sty]
 allowlist_externals = ["pre-commit"]
+base = []
 commands = [["pre-commit", "run", "--all-files", {replace = "posargs", extend = true}]]
 description = "Perform all linting, formatting, and spelling checks"
 
 [tool.tox.env.test]
-allowlist_externals = ["pytest"]
 commands = [
     [
         "pytest",
@@ -535,3 +545,16 @@ commands = [
     ],
 ]
 description = "Run ALL tests, including the slow channel tests, and compute coverage"
+
+[tool.tox.labels]
+doc = [
+    "docnb-force",
+    "linkcheck",
+]
+test = [
+    "3.9",
+    "3.10",
+    "3.11",
+    "3.12",
+    "3.13",
+]