MAINT: update lock files (#149)

* DX: convert Tox config to native TOML * DX: increase minimal test coverage to 58% * FIX: correctly set `EXECUTE_NB` * FIX: downgrade `pygments` and `sphinx-codeautolink` * FIX: set `sphinx.configuration` * MAINT: clean up Codecov configuration Co-authored-by: GitHub <[email protected]>
ComPWA · Jan 13, 2025 · 7c2db34 · 7c2db34
1 parent 182d69b
commit 7c2db34
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Showing 8 changed files with 838 additions and 717 deletions.
diff --git a/.cspell.json b/.cspell.json
@@ -29,8 +29,8 @@
     ".pre-commit-config.yaml",
     ".prettierignore",
     ".readthedocs.yml",
+    ".taplo.toml",
     ".vscode/*",
-    ".vscode/.gitignore",
     "codecov.yml",
     "docs/conf.py",
     "pyproject.toml"

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -39,6 +39,8 @@ jobs:
       coverage-target: ampform_dpd
       macos-python-version: "3.9"
       specific-pip-packages: ${{ inputs.specific-pip-packages }}
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   style:
     if: inputs.specific-pip-packages == ''
     secrets:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -13,7 +13,7 @@ repos:
       - id: check-useless-excludes
 
   - repo: https://github.com/ComPWA/policy
-    rev: 0.5.8
+    rev: 0.5.15
     hooks:
       - id: check-dev-files
         args:
@@ -53,7 +53,7 @@ repos:
             metadata.vscode
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.4
+    rev: v0.9.1
     hooks:
       - id: ruff
         args: [--fix]
@@ -125,6 +125,6 @@ repos:
       - id: pyright
 
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.5.11
+    rev: 0.5.18
     hooks:
       - id: uv-lock
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -13,9 +13,11 @@ build:
       export UV_LINK_MODE=copy
       uv run \
         --group doc \
-        --locked \
         --no-dev \
         --with tox \
         tox -e doc
       mkdir -p $READTHEDOCS_OUTPUT
       mv docs/_build/html $READTHEDOCS_OUTPUT
+
+sphinx:
+  configuration: docs/conf.py
diff --git a/.taplo.toml b/.taplo.toml
@@ -10,3 +10,10 @@ compact_inline_tables = true
 indent_string = "    "
 reorder_arrays = true
 reorder_keys = true
+
+[[rule]]
+include = ["**/pyproject.toml"]
+keys = ["tool.tox"]
+
+[rule.formatting]
+reorder_arrays = false
diff --git a/codecov.yml b/codecov.yml
@@ -9,32 +9,22 @@ coverage:
   status:
     project:
       default:
-        # basic
-        target: 50% # can't go below this percentage
-        threshold: 1% # allow drops by this percentage
+        target: 58%
+        threshold: 1%
         base: auto
-        # advanced
-        branches: []
         if_no_uploads: error
         if_not_found: success
         if_ci_failed: error
         only_pulls: false
-        flags: []
-        paths: []
     patch:
       default:
-        # basic
         target: 0
-        threshold: 5%
+        threshold: 0%
         base: auto
-        # advanced
-        branches: null
         if_no_uploads: error
         if_not_found: success
         if_ci_failed: error
         only_pulls: false
-        flags: null
-        paths: null
     changes: false
 
 parsers:

diff --git a/pyproject.toml b/pyproject.toml
@@ -351,123 +351,133 @@ sort_first = [
     "project",
     "tool.setuptools",
     "tool.setuptools_scm",
+    "tool.tox.env_run_base",
 ]
 spaces_indent_inline_array = 4
 trailing_comma_inline_array = true
 
 [tool.tox]
-legacy_tox_ini = """
-[tox]
-envlist =
-    cov,
-    docnb-force,
-    linkcheck,
-    sty,
-skip_install = True
-skip_missing_interpreters = True
-skipsdist = True
-
-[testenv]
-allowlist_externals =
-    pytest
-commands =
-    pytest {posargs}
-description = Run all unit tests
-passenv = *
-
-[testenv:cov]
-allowlist_externals =
-    pytest
-commands =
-    pytest {posargs:src tests} \
-        --cov-fail-under=50 \
-        --cov-report=html \
-        --cov-report=xml \
-        --cov=ampform_dpd
-description = Compute test coverage
-
-[testenv:doc]
-allowlist_externals =
-    sphinx-build
-commands =
-    sphinx-build \
-        --builder=html \
-        --fail-on-warning \
-        --keep-going \
-        docs/ docs/_build/html
-description = Build documentation with Sphinx
-
-[testenv:docnb]
-base = doc
-description = {[testenv:doc]description} with cached notebook execution
-setenv =
-    {[testenv:doc]setenv}
-    EXECUTE_NB = yes
-
-[testenv:docnb-force]
-base = doc
-description = {[testenv:doc]description} with notebook execution (no cache)
-setenv =
-    {[testenv:doc]setenv}
-    FORCE_EXECUTE_NB = yes
-
-[testenv:doclive]
-allowlist_externals =
-    sphinx-autobuild
-commands =
-    sphinx-autobuild \
-        --ignore=docs/_build/ \
-        --ignore=docs/_images/ \
-        --ignore=docs/api/ \
-        --ignore=docs/export/ \
-        --open-browser \
-        --port=0 \
-        --re-ignore='.*/__pycache__/.*' \
-        --re-ignore='.*/.ipynb_checkpoints/.*' \
-        --re-ignore='.*/.virtual_documents/.*' \
-        --re-ignore='.*\\.pdf' \
-        --re-ignore='.*\\.pkl' \
-        --re-ignore='.*\\.png' \
-        --re-ignore='.*\\.svg' \
-        --re-ignore='.*\\.tmp' \
-        --watch=docs \
-        --watch=src \
-        docs/ docs/_build/html
-description = Set up a server to directly preview changes to the HTML pages
-
-[testenv:docnblive]
-base = doclive
-description = {[testenv:doclive]description} with cached notebook execution
-setenv =
-    {[testenv:doclive]setenv}
-    EXECUTE_NB = yes
-
-[testenv:linkcheck]
-allowlist_externals =
-    sphinx-build
-commands =
-    sphinx-build \
-        --builder=linkcheck \
-        --show-traceback \
-        docs/ docs/_build/linkcheck
-description = Check external links in the documentation (requires internet connection)
-setenv =
-    PYTHONWARNINGS =
-
-[testenv:nb]
-allowlist_externals =
-    pytest
-commands =
-    pytest --nbmake --nbmake-timeout=3600 {posargs:docs}
-description = Run all notebooks with pytest
-
-[testenv:sty]
-allowlist_externals =
-    pre-commit
-commands =
-    pre-commit run --all-files {posargs}
-description = Perform all linting, formatting, and spelling checks
-"""
+env_list = [
+    "cov",
+    "docnb-force",
+    "linkcheck",
+    "sty",
+]
+no_package = true
+requires = ["tox>=4.21.0"]
+skip_install = true
+skip_missing_interpreters = true
+
+[tool.tox.env_run_base]
+allowlist_externals = ["pytest"]
+commands = [["pytest", {replace = "posargs", extend = true}]]
+description = "Run all unit tests"
+pass_env = ["*"]
+
+[tool.tox.env.cov]
+allowlist_externals = ["pytest"]
+commands = [
+    [
+        "pytest",
+        {replace = "posargs", extend = true},
+        "--cov-fail-under=58",
+        "--cov-report=html",
+        "--cov-report=xml",
+        "--cov=ampform_dpd",
+    ],
+]
+description = "Compute test coverage"
+
+[tool.tox.env.doc]
+allowlist_externals = ["sphinx-build"]
+commands = [
+    [
+        "sphinx-build",
+        "--builder=html",
+        "--fail-on-warning",
+        "--keep-going",
+        "docs/",
+        "docs/_build/html",
+    ],
+]
+description = "Build documentation with Sphinx"
+
+[tool.tox.env.doclive]
+allowlist_externals = ["sphinx-autobuild"]
+commands = [
+    [
+        "sphinx-autobuild",
+        "--ignore=docs/_build/",
+        "--ignore=docs/_images/",
+        "--ignore=docs/api/",
+        "--ignore=docs/export/",
+        "--open-browser",
+        "--port=0",
+        "--re-ignore='.*/__pycache__/.*'",
+        "--re-ignore='.*/.ipynb_checkpoints/.*'",
+        "--re-ignore='.*/.virtual_documents/.*'",
+        "--re-ignore='.*\\.pdf'",
+        "--re-ignore='.*\\.pkl'",
+        "--re-ignore='.*\\.png'",
+        "--re-ignore='.*\\.svg'",
+        "--re-ignore='.*\\.tmp'",
+        "--watch=docs",
+        "--watch=src",
+        "docs/",
+        "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"]
+description = "{[tool.tox.env.doc]description} with cached notebook execution"
+set_env.EXECUTE_NB = "yes"
+
+[tool.tox.env.docnb-force]
+base = ["tool.tox.env.doc", "tool.tox.env_run_base"]
+description = "{[tool.tox.env.doc]description} with notebook execution (no cache)"
+set_env.FORCE_EXECUTE_NB = "yes"
+
+[tool.tox.env.docnblive]
+base = ["tool.tox.env.doclive", "tool.tox.env_run_base"]
+description = "{[tool.tox.env.doclive]description} with cached notebook execution"
+set_env.EXECUTE_NB = "yes"
+
+[tool.tox.env.linkcheck]
+allowlist_externals = ["sphinx-build"]
+commands = [
+    [
+        "sphinx-build",
+        "--builder=linkcheck",
+        "--show-traceback",
+        "docs/",
+        "docs/_build/linkcheck",
+    ],
+]
+description = "Check external links in the documentation (requires internet connection)"
+set_env.PYTHONWARNINGS = ""
+
+[tool.tox.env.nb]
+allowlist_externals = ["pytest"]
+commands = [
+    [
+        "pytest",
+        "--nbmake",
+        "--nbmake-timeout=0",
+        "{posargs:docs}",
+    ],
+]
+description = "Run all notebooks with pytest"
+
+[tool.tox.env.sty]
+allowlist_externals = ["pre-commit"]
+commands = [["pre-commit", "run", "--all-files", {replace = "posargs", extend = true}]]
+description = "Perform all linting, formatting, and spelling checks"
 
 [tool.uv]
-constraint-dependencies = ["numpy~=1.0"]
+constraint-dependencies = [
+    "numpy~=1.0",
+    "pygments!=2.19.*", # https://github.com/felix-hilden/sphinx-codeautolink/issues/152
+    "sphinx-codeautolink!=0.16.0",
+]