diff --git a/.cspell.json b/.cspell.json index 13b60c26..03ceb463 100644 --- a/.cspell.json +++ b/.cspell.json @@ -29,6 +29,7 @@ ".pre-commit-config.yaml", ".prettierignore", ".readthedocs.yml", + ".taplo.toml", ".vscode/*", "CITATION.cff", "codecov.yml", @@ -61,7 +62,6 @@ "celltoolbar", "clim", "cmap", - "codacy", "codecov", "codemirror", "colab", diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 636b28bc..76b74175 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -38,6 +38,8 @@ jobs: coverage-target: ampform 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 index cc2ee8e0..fb6662c3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,7 +14,7 @@ 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: @@ -60,7 +60,7 @@ 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] @@ -114,7 +114,7 @@ repos: - --in-place - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.30.0 + rev: 0.31.0 hooks: - id: check-jsonschema name: Check CITATION.cff @@ -158,6 +158,6 @@ 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 index 5bf72252..52dd314b 100644 --- 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 index 0db1df7c..71fcb1be 100644 --- 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/CONTRIBUTING.md b/CONTRIBUTING.md index e240627b..e17757b6 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -12,7 +12,7 @@ git clone https://github.com/ComPWA/ampform cd ampform ``` -Now it's simply a matter of creating and activating the [virtual environment](https://docs.astral.sh/uv/pip/environments) with [`uv sync`](https://docs.astral.sh/uv/reference/cli/#uv-sync). The dependencies for the project are 'pinned' in each commit through the [`uv.lock` file](https://docs.astral.sh/uv/concepts/projects/#project-lockfile). +Now it's simply a matter of creating and activating the [virtual environment](https://docs.astral.sh/uv/pip/environments) with [`uv sync`](https://docs.astral.sh/uv/reference/cli/#uv-sync). The dependencies for the project are 'pinned' in each commit through the [`uv.lock` file](https://docs.astral.sh/uv/concepts/projects/layout/#the-lockfile). ```shell uv sync --all-extras diff --git a/README.md b/README.md index 69ca8b46..b5fbcb74 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,6 @@ [![pytest](https://github.com/ComPWA/ampform/workflows/pytest/badge.svg)](https://github.com/ComPWA/ampform/actions?query=branch%3Amain+workflow%3Apytest) [![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy.readthedocs.io) [![Test coverage](https://codecov.io/gh/ComPWA/ampform/branch/main/graph/badge.svg)](https://codecov.io/gh/ComPWA/ampform) -[![Codacy Badge](https://api.codacy.com/project/badge/Grade/70fc5fb0f3954a9d82d142efeff4df31)](https://www.codacy.com/gh/ComPWA/ampform) [![Spelling checked](https://img.shields.io/badge/cspell-checked-brightgreen.svg)](https://github.com/streetsidesoftware/cspell/tree/master/packages/cspell) [![code style: prettier](https://img.shields.io/badge/code_style-prettier-ff69b4.svg?style=flat-square)](https://github.com/prettier/prettier) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) diff --git a/codecov.yml b/codecov.yml index 64157f16..dd23fbcf 100644 --- a/codecov.yml +++ b/codecov.yml @@ -9,32 +9,22 @@ coverage: status: project: default: - # basic - target: 75% # can't go below this percentage - threshold: 1% # allow drops by this percentage + target: 75% + 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% 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 index 42fb2c5c..bf094871 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -429,146 +429,157 @@ 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:bench] -allowlist_externals = - pytest -commands = - pytest {posargs:benchmarks} \ - --durations=0 \ - --benchmark-autosave \ - -k benchmark -description = Run benchmark tests and visualize in histogram - -[testenv:cov] -allowlist_externals = - pytest -commands = - pytest {posargs:src tests} \ - --cov-fail-under=75 \ - --cov-report=html \ - --cov-report=xml \ - --cov=ampform -description = Compute test coverage - -[testenv:doc] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - --builder=html \ - --fail-on-warning \ - --keep-going \ - --show-traceback \ - docs/ docs/_build/html -description = Build documentation and API through Sphinx -setenv = - PYTHONWARNINGS = - -[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 \ - --builder=html \ - --ignore=docs/_build/ \ - --ignore=docs/_images/ \ - --ignore=docs/api/ \ - --open-browser \ - --port=0 \ - --re-ignore='.*/__pycache__/.*' \ - --re-ignore='.*/.ipynb_checkpoints/.*' \ - --re-ignore='.*/.virtual_documents/.*' \ - --re-ignore='.*\\.csv' \ - --re-ignore='.*\\.gif' \ - --re-ignore='.*\\.gitignore' \ - --re-ignore='.*\\.gv' \ - --re-ignore='.*\\.inv' \ - --re-ignore='.*\\.json' \ - --re-ignore='.*\\.pickle' \ - --re-ignore='.*\\.png' \ - --re-ignore='.*\\.svg' \ - --re-ignore='.*\\.tmp' \ - --re-ignore='.*\\.ya?ml' \ - --watch=docs \ - --watch=src \ - docs/ docs/_build/html -description = Set up a server to directly preview changes to the HTML pages -setenv = - {[testenv:doc]setenv} - -[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 = - {[testenv:doclive]setenv} - -[testenv:nb] -allowlist_externals = - pytest -commands = - pytest --nbmake {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 = [ + "bench", + "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.bench] +allowlist_externals = ["pytest"] +commands = [ + [ + "pytest", + "{posargs:benchmarks}", + "--durations=0", + "--benchmark-autosave", + "-k", + "benchmark", + ], +] +description = "Run benchmark tests and visualize in histogram" + +[tool.tox.env.cov] +allowlist_externals = ["pytest"] +commands = [ + [ + "pytest", + {replace = "posargs", default = ["src", "tests"], extend = true}, + "--cov-fail-under=75", + "--cov-report=html", + "--cov-report=xml", + "--cov=ampform", + ], +] +description = "Compute test coverage" + +[tool.tox.env.doc] +allowlist_externals = ["sphinx-build"] +commands = [ + [ + "sphinx-build", + "--builder=html", + "--fail-on-warning", + "--keep-going", + "--show-traceback", + "docs/", + "docs/_build/html", + ], +] +description = "Build documentation and API through Sphinx" +set_env.PYTHONWARNINGS = "" + +[tool.tox.env.doclive] +allowlist_externals = ["sphinx-autobuild"] +commands = [ + [ + "sphinx-autobuild", + "--builder=html", + "--ignore=docs/_build/", + "--ignore=docs/_images/", + "--ignore=docs/api/", + "--open-browser", + "--port=0", + "--re-ignore='.*/__pycache__/.*'", + "--re-ignore='.*/.ipynb_checkpoints/.*'", + "--re-ignore='.*/.virtual_documents/.*'", + "--re-ignore='.*\\.csv'", + "--re-ignore='.*\\.gif'", + "--re-ignore='.*\\.gitignore'", + "--re-ignore='.*\\.gv'", + "--re-ignore='.*\\.inv'", + "--re-ignore='.*\\.json'", + "--re-ignore='.*\\.pickle'", + "--re-ignore='.*\\.png'", + "--re-ignore='.*\\.svg'", + "--re-ignore='.*\\.tmp'", + "--re-ignore='.*\\.ya?ml'", + "--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 = [ + {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"] +description = "{[tool.tox.env.doc]description} with notebook execution (no cache)" +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"] +description = "{[tool.tox.env.doclive]description} with cached notebook execution" +set_env = [ + {replace = "ref", of = ["tool.tox.env.doclive.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)" + +[tool.tox.env.nb] +allowlist_externals = ["pytest"] +commands = [["pytest", "--nbmake", "{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 = [ + "pygments!=2.19.*", # https://github.com/felix-hilden/sphinx-codeautolink/issues/152 "pytest-profiling!=1.8.0", + "sphinx-codeautolink!=0.16.0", ] diff --git a/uv.lock b/uv.lock index 82362bfb..07d6ae18 100644 --- a/uv.lock +++ b/uv.lock @@ -7,7 +7,11 @@ resolution-markers = [ ] [manifest] -constraints = [{ name = "pytest-profiling", specifier = "!=1.8.0" }] +constraints = [ + { name = "pygments", specifier = "!=2.19.*" }, + { name = "pytest-profiling", specifier = "!=1.8.0" }, + { name = "sphinx-codeautolink", specifier = "!=0.16.0" }, +] [[package]] name = "accessible-pygments" @@ -59,7 +63,7 @@ dependencies = [ [package.optional-dependencies] scipy = [ { name = "scipy", version = "1.13.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, - { name = "scipy", version = "1.14.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, + { name = "scipy", version = "1.15.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, ] viz = [ { name = "graphviz" }, @@ -84,7 +88,7 @@ dev = [ { name = "myst-nb" }, { name = "nbmake" }, { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, - { name = "numpy", version = "2.2.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, + { name = "numpy", version = "2.2.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, { name = "pytest" }, { name = "pytest-benchmark" }, { name = "pytest-cov" }, @@ -117,7 +121,7 @@ doc = [ { name = "mpl-interactions" }, { name = "myst-nb" }, { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, - { name = "numpy", version = "2.2.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, + { name = "numpy", version = "2.2.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, { name = "rich" }, { name = "sphinx", version = "7.4.7", source = { registry = 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"https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, + { name = "numpy", version = "2.2.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, { name = "pytest" }, { name = "pytest-benchmark" }, { name = "sphinx-api-relink" }, @@ -168,7 +172,7 @@ test = [ { name = "ipywidgets" }, { name = "nbmake" }, { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, - { name = "numpy", version = "2.2.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, + { name = "numpy", version = "2.2.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, { name = "pytest" }, { name = "pytest-benchmark" }, { name = "pytest-cov" }, @@ -180,7 +184,7 @@ types = [ { name = "ipython", version = "8.31.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= 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