diff --git a/.cspell.json b/.cspell.json index 1803f925..f6372538 100644 --- a/.cspell.json +++ b/.cspell.json @@ -33,8 +33,7 @@ "CITATION.cff", "codecov.yml", "docs/conf.py", - "pyproject.toml", - "typings" + "pyproject.toml" ], "ignoreWords": [ "FURB", @@ -145,7 +144,6 @@ "pypi", "pyplot", "pyproject", - "pyright", "pytestconfig", "qrules", "rightarrow", @@ -219,7 +217,6 @@ "mathbb", "matplotlib", "mkdir", - "mypy", "nishijima", "numpy", "optimizable", diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index fc96db3c..73a4b036 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -12,11 +12,6 @@ on: - main - epic/* workflow_dispatch: - inputs: - specific-pip-packages: - description: Run benchmarks with specific pip packages - required: false - type: string jobs: benchmark: @@ -30,26 +25,8 @@ jobs: with: python-version: "3.13" - uses: astral-sh/setup-uv@v6 - - id: with - if: inputs.specific-pip-packages - name: Determine additional packages to install - run: | - additional_packages='' - for package in ${{ inputs.specific-pip-packages }}; do - additional_packages="$additional_packages --with $package" - done - echo "packages=$additional_packages" | tee -a $GITHUB_OUTPUT - name: Run pytest-benchmark - run: | - uv run \ - --group test \ - --no-dev \ - ${{ steps.with.outputs.packages }} \ - pytest \ - -k benchmark \ - --benchmark-json output.json \ - --durations=0 - working-directory: benchmarks + run: uvx --from poethepoet poe benchmark - name: Warn on performance decrease if: github.event_name == 'pull_request' uses: benchmark-action/github-action-benchmark@v1 diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 4e32c200..d1243746 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -9,9 +9,9 @@ on: jobs: milestone: if: startsWith(github.ref, 'refs/tags') - uses: ComPWA/actions/.github/workflows/close-milestone.yml@v3 + uses: ComPWA/actions/.github/workflows/close-milestone.yml@v4 package-name: - uses: ComPWA/actions/.github/workflows/get-pypi-name.yml@v3 + uses: ComPWA/actions/.github/workflows/get-pypi-name.yml@v4 pypi: environment: name: PyPI @@ -24,9 +24,9 @@ jobs: id-token: write runs-on: ubuntu-24.04 steps: - - uses: ComPWA/actions/build-pypi-distribution@v3 + - uses: ComPWA/actions/build-pypi-distribution@v4 - uses: pypa/gh-action-pypi-publish@release/v1 push: if: startsWith(github.ref, 'refs/tags') && !github.event.release.prerelease secrets: inherit - uses: ComPWA/actions/.github/workflows/push-to-version-branches.yml@v3 + uses: ComPWA/actions/.github/workflows/push-to-version-branches.yml@v4 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d03294c5..97fb9552 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,33 +17,25 @@ on: - epic/* - "[0-9]+.[0-9]+.x" workflow_dispatch: - inputs: - specific-pip-packages: - description: Run CI with specific pip packages - required: false - type: string jobs: doc: - uses: ComPWA/actions/.github/workflows/ci-docs.yml@v3.0 + uses: ComPWA/actions/.github/workflows/ci-docs.yml@v4.0 permissions: pages: write id-token: write with: apt-packages: graphviz - specific-pip-packages: ${{ inputs.specific-pip-packages }} - pytest: - uses: ComPWA/actions/.github/workflows/pytest.yml@v3.0 + style: + secrets: + token: ${{ secrets.PAT }} + uses: ComPWA/actions/.github/workflows/pre-commit.yml@v4.0 + test: + uses: ComPWA/actions/.github/workflows/test.yml@v4.0 + secrets: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} with: - coverage-target: tensorwaves + coverage-python-version: "3.13" macos-python-version: "3.10" multithreaded: false - specific-pip-packages: ${{ inputs.specific-pip-packages }} test-output-path: tests/output/ - secrets: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} - style: - if: inputs.specific-pip-packages == '' - secrets: - token: ${{ secrets.PAT }} - uses: ComPWA/actions/.github/workflows/pre-commit.yml@v3.0 diff --git a/.github/workflows/clean-caches.yml b/.github/workflows/clean-caches.yml index 2de0c959..b241bf56 100644 --- a/.github/workflows/clean-caches.yml +++ b/.github/workflows/clean-caches.yml @@ -16,7 +16,7 @@ jobs: name: Remove caches runs-on: ubuntu-24.04 steps: - - uses: ComPWA/actions/clean-caches@v3 + - uses: ComPWA/actions/clean-caches@v4 with: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} ref: ${{ inputs.ref }} diff --git a/.github/workflows/lock.yml b/.github/workflows/lock.yml index 41aa0268..05fafad2 100644 --- a/.github/workflows/lock.yml +++ b/.github/workflows/lock.yml @@ -17,6 +17,6 @@ on: jobs: lock: - uses: ComPWA/actions/.github/workflows/lock.yml@v3 + uses: ComPWA/actions/.github/workflows/lock.yml@v4 secrets: token: ${{ secrets.PAT }} diff --git a/.github/workflows/pr-linting.yml b/.github/workflows/pr-linting.yml index 638dfc1e..e15b56f9 100644 --- a/.github/workflows/pr-linting.yml +++ b/.github/workflows/pr-linting.yml @@ -11,4 +11,4 @@ on: jobs: lint-pr: - uses: ComPWA/actions/.github/workflows/pr-linting.yml@v3 + uses: ComPWA/actions/.github/workflows/pr-linting.yml@v4 diff --git a/.gitignore b/.gitignore index 349ba591..75ea126f 100644 --- a/.gitignore +++ b/.gitignore @@ -25,7 +25,6 @@ version.py .coverage.* .ipynb_checkpoints/ .jupyter_ystore.db -.mypy*/ .pytest_cache/ .virtual_documents/ __pycache__/ @@ -50,4 +49,3 @@ pyvenv*/ !.vscode/*.json !.zenodo.json !codecov.yml -!pyrightconfig.json diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 07d99c7a..604bc86a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,8 +4,7 @@ ci: autoupdate_schedule: quarterly skip: - check-jsonschema - - mypy - - pyright + - ty - uv-lock repos: @@ -15,7 +14,7 @@ repos: - id: check-useless-excludes - repo: https://github.com/ComPWA/policy - rev: 0.7.3 + rev: 0.8.2rc5 hooks: - id: check-dev-files args: @@ -24,19 +23,17 @@ repos: - --pytest-single-threaded - --repo-name=tensorwaves - --repo-title=TensorWaves + - --type-checker=ty - --update-lock-files=outsource - id: colab-toc-visible - id: fix-nbformat-version - id: remove-empty-tags - id: set-nb-cells - args: - - --add-install-cell - - --additional-packages=IPython - - --extras-require=doc,jax,pwa,viz + args: [autolink-concat] - id: set-nb-display-name - repo: https://github.com/kynan/nbstripout - rev: 0.8.1 + rev: 0.8.2 hooks: - id: nbstripout args: @@ -64,7 +61,7 @@ repos: metadata.vscode - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.14.0 + rev: v0.14.11 hooks: - id: ruff-check args: [--fix] @@ -117,7 +114,7 @@ repos: - --in-place - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.34.1 + rev: 0.36.0 hooks: - id: check-jsonschema name: Check CITATION.cff @@ -130,12 +127,12 @@ repos: pass_filenames: false - repo: https://github.com/streetsidesoftware/cspell-cli - rev: v9.2.0 + rev: v9.4.0 hooks: - id: cspell - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: 3.4.0 + rev: 3.6.0 hooks: - id: editorconfig-checker name: editorconfig @@ -147,20 +144,15 @@ repos: - repo: local hooks: - - id: mypy - name: mypy - entry: mypy - language: system + - id: ty + name: ty + entry: ty check + args: [--no-progress, --output-format=concise] require_serial: true - types: - - python - - - repo: https://github.com/ComPWA/pyright-pre-commit - rev: v1.1.406 - hooks: - - id: pyright + language: system + types_or: [python, pyi, jupyter] - repo: https://github.com/astral-sh/uv-pre-commit - rev: 0.9.3 + rev: 0.9.24 hooks: - id: uv-lock diff --git a/.readthedocs.yml b/.readthedocs.yml index ebee9afb..cc704ce0 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -11,11 +11,7 @@ build: pixi global install graphviz uv - |- export UV_LINK_MODE=copy - uv run \ - --group doc \ - --no-dev \ - --with poethepoet \ - poe doc + uvx --from poethepoet poe doc mkdir -p $READTHEDOCS_OUTPUT mv docs/_build/html $READTHEDOCS_OUTPUT diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 354e350e..feb6fed9 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -1,5 +1,6 @@ { "recommendations": [ + "astral-sh.ty", "charliermarsh.ruff", "christian-kohler.path-intellisense", "eamodio.gitlens", @@ -9,9 +10,7 @@ "github.vscode-github-actions", "github.vscode-pull-request-github", "mhutchie.git-graph", - "ms-python.mypy-type-checker", "ms-python.python", - "ms-python.vscode-pylance", "ms-toolsai.jupyter", "ms-toolsai.vscode-jupyter-cell-tags", "ms-vscode.live-server", @@ -30,7 +29,9 @@ "ms-python.black-formatter", "ms-python.flake8", "ms-python.isort", + "ms-python.mypy-type-checker", "ms-python.pylint", + "ms-python.vscode-pylance", "ms-toolsai.vscode-jupyter-slideshow", "ryanluker.vscode-coverage-gutters", "travisillig.vscode-json-stable-stringify", diff --git a/.vscode/settings.json b/.vscode/settings.json index d6e6f57d..72d84418 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -45,15 +45,13 @@ ], "livePreview.defaultPreviewPath": "docs/_build/html", "multiDiffEditor.experimental.enabled": true, - "mypy-type-checker.args": ["--config-file=${workspaceFolder}/pyproject.toml"], "notebook.codeActionsOnSave": { "notebook.source.organizeImports": "explicit" }, "notebook.formatOnSave.enabled": true, "notebook.gotoSymbols.showAllSymbols": true, - "python.analysis.autoImportCompletions": false, - "python.analysis.inlayHints.pytestParameters": true, "python.defaultInterpreterPath": ".venv/bin/python", + "python.languageServer": "None", "python.terminal.activateEnvironment": false, "python.testing.pytestEnabled": true, "python.testing.unittestEnabled": false, @@ -70,6 +68,9 @@ "telemetry.telemetryLevel": "off", "testing.coverageToolbarEnabled": true, "testing.showCoverageInExplorer": true, + "ty.completions.autoImport": false, + "ty.diagnosticMode": "workspace", + "ty.importStrategy": "fromEnvironment", "yaml.schemas": { "https://citation-file-format.github.io/1.2.0/schema.json": "CITATION.cff", "https://json.schemastore.org/github-workflow.json": "./.github/workflows/requirements.yml" diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 772cdd85..7572d4b6 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -22,7 +22,7 @@ source .venv/bin/activate Formatting and linting checks are automatically performed when committing changes. This is done with [pre-commit](https://pre-commit.com). To install the hooks in your local repository, run install `pre-commit` with `uv`: ```shell -uv tool install pre-commit --with pre-commit-uv --force-reinstall +uv tool install pre-commit --with pre-commit-uv --force-reinstall --python=3.13 ``` and [`pre-commit install`](https://pre-commit.com/#3-install-the-git-hook-scripts) **once**: @@ -31,7 +31,13 @@ and [`pre-commit install`](https://pre-commit.com/#3-install-the-git-hook-script pre-commit install --install-hooks ``` -[Poe the Poet](https://poethepoet.natn.io) is used as a task runner. You can see which local CI checks it defines by running +[Poe the Poet](https://poethepoet.natn.io) is used as a task runner. Install it globally (within your home folder) with `uv`: + +```shell +uv tool install poethepoet --force-reinstall --python=3.13 +``` + +You can see which local CI checks it defines by running ```shell poe diff --git a/README.md b/README.md index a4ed476b..20368088 100644 --- a/README.md +++ b/README.md @@ -14,12 +14,12 @@ [![Documentation build status](https://readthedocs.org/projects/tensorwaves/badge/?version=latest)](https://tensorwaves.readthedocs.io) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/ComPWA/tensorwaves/main.svg)](https://results.pre-commit.ci/latest/github/ComPWA/tensorwaves/main) [![CI](https://github.com/ComPWA/tensorwaves/actions/workflows/ci.yml/badge.svg)](https://github.com/ComPWA/tensorwaves/actions/workflows/ci.yml) -[![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy.readthedocs.io) [![Test coverage](https://codecov.io/gh/ComPWA/tensorwaves/branch/main/graph/badge.svg)](https://codecov.io/gh/ComPWA/tensorwaves) [![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) [![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv) +[![ty](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ty/main/assets/badge/v0.json)](https://github.com/astral-sh/ty) TensorWaves is a fitter package that optimizes mathematical models to data samples. The models can be any _symbolic_ mathematical expression that is then converted to any diff --git a/benchmarks/expression.py b/benchmarks/expression.py index f65e62ae..cb28f8a9 100644 --- a/benchmarks/expression.py +++ b/benchmarks/expression.py @@ -8,7 +8,8 @@ from tensorwaves.estimator import UnbinnedNLL from tensorwaves.function.sympy import create_parametrized_function -from tensorwaves.optimizer import Minuit2, ScipyMinimizer +from tensorwaves.optimizer.minuit import Minuit2 +from tensorwaves.optimizer.scipy import ScipyMinimizer if TYPE_CHECKING: from tensorwaves.interface import DataSample, Function @@ -65,7 +66,7 @@ def _generate_data( rng: np.random.Generator, bunch_size: int = 10_000, ) -> DataSample: - collected_sample = {var: np.array([]) for var in domain_boundaries} # type: ignore[var-annotated] + collected_sample = {var: np.array([]) for var in domain_boundaries} some_variable = next(iter(domain_boundaries)) while len(collected_sample[some_variable]) < size: phsp = _generate_domain(bunch_size, rng) @@ -125,7 +126,7 @@ def test_fit( ) original_parameters = function.parameters - estimator = UnbinnedNLL(function, data, domain, backend=backend) # type: ignore[arg-type] + estimator = UnbinnedNLL(function, data, domain, backend=backend) original_nll = estimator(function.parameters) optimizer = optimizer_type() result = benchmark(optimizer.optimize, estimator, function.parameters) diff --git a/docs/amplitude-analysis.ipynb b/docs/amplitude-analysis.ipynb index f2f39658..0f7a3710 100644 --- a/docs/amplitude-analysis.ipynb +++ b/docs/amplitude-analysis.ipynb @@ -1,62 +1,14 @@ { "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell", - "skip-execution" - ] - }, - "outputs": [], - "source": [ - "# WARNING: advised to install a specific version, e.g. tensorwaves==0.1.2\n", - "%pip install -q tensorwaves[doc,jax,pwa,viz] IPython" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ + "# Amplitude analysis\n", "```{autolink-concat}\n", "```" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Amplitude analysis" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -76,22 +28,6 @@ ":::" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "from __future__ import annotations" - ] - }, { "cell_type": "markdown", "metadata": { @@ -1956,7 +1892,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.13" + "version": "3.13.11" } }, "nbformat": 4, diff --git a/docs/amplitude-analysis/analytic-continuation.ipynb b/docs/amplitude-analysis/analytic-continuation.ipynb index 97b64cc0..363a5e7d 100644 --- a/docs/amplitude-analysis/analytic-continuation.ipynb +++ b/docs/amplitude-analysis/analytic-continuation.ipynb @@ -1,62 +1,14 @@ { "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell", - "skip-execution" - ] - }, - "outputs": [], - "source": [ - "# WARNING: advised to install a specific version, e.g. tensorwaves==0.1.2\n", - "%pip install -q tensorwaves[doc,jax,pwa,viz] IPython" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ + "# Analytic continuation\n", "```{autolink-concat}\n", "```" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Analytic continuation" - ] - }, { "cell_type": "code", "execution_count": null, @@ -205,10 +157,10 @@ "metadata": {}, "outputs": [], "source": [ - "for par in model.parameter_defaults:\n", - " if not par.name.startswith(\"C\") or \"a_{0}(980)^{0}\" not in par.name:\n", + "for symbol in model.parameter_defaults:\n", + " if not str(symbol).startswith(\"C\") or \"a_{0}(980)^{0}\" not in str(symbol):\n", " continue\n", - " model.parameter_defaults[par] = 0.1\n", + " model.parameter_defaults[symbol] = 0.1\n", "\n", "intensity = create_parametrized_function(\n", " expression=model.expression.doit(),\n", @@ -283,7 +235,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.17" + "version": "3.13.11" } }, "nbformat": 4, diff --git a/docs/conf.py b/docs/conf.py index d152e241..69200fbd 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -40,7 +40,9 @@ def get_tensorflow_url() -> str: create_tensorflow_inventory() set_intersphinx_version_remapping({ + "ampform": {"0.15.12.dev25+gfc1d4e292": "0.15.11"}, "matplotlib": {"3.5.1": "3.5.0"}, + "qrules": {"0.10.7.dev21+g33be556be": "0.10.6"}, "scipy": {"1.7.3": "1.7.1"}, }) @@ -59,6 +61,7 @@ def get_tensorflow_url() -> str: "np.ndarray": "numpy.ndarray", "ParameterValue": "tensorwaves.interface.ParameterValue", "Path": "pathlib.Path", + "sp.Basic": "sympy.core.basic.Basic", "sp.Expr": "sympy.core.expr.Expr", "sp.Symbol": "sympy.core.symbol.Symbol", "TypeAliasForwardRef": "typing.TypeAlias", @@ -203,7 +206,6 @@ def get_tensorflow_url() -> str: "matplotlib": (f"https://matplotlib.org/{pin('matplotlib')}", None), "numpy": (f"https://numpy.org/doc/{pin_minor('numpy')}", None), "pandas": (f"https://pandas.pydata.org/pandas-docs/version/{pin('pandas')}", None), - "pwa": ("https://pwa.readthedocs.io", None), "python": ("https://docs.python.org/3", None), "qrules": (f"https://qrules.readthedocs.io/{pin('qrules')}", None), "scipy": (get_scipy_url(), None), @@ -251,6 +253,7 @@ def get_tensorflow_url() -> str: project = REPO_TITLE pygments_style = "sphinx" release = get_package_version("tensorwaves") +suppress_warnings = ["myst.directive_unknown"] thebe_config = { "repository_url": html_theme_options["repository_url"], "repository_branch": html_theme_options["repository_branch"], diff --git a/docs/usage.ipynb b/docs/usage.ipynb index e8d2dbb2..78e3717c 100644 --- a/docs/usage.ipynb +++ b/docs/usage.ipynb @@ -1,62 +1,14 @@ { "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell", - "skip-execution" - ] - }, - "outputs": [], - "source": [ - "# WARNING: advised to install a specific version, e.g. tensorwaves==0.1.2\n", - "%pip install -q tensorwaves[doc,jax,pwa,viz] IPython" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ + "# General examples\n", "```{autolink-concat}\n", "```" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# General examples" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -683,8 +635,8 @@ "fig.canvas.toolbar_visible = False\n", "fig.canvas.header_visible = False\n", "fig.canvas.footer_visible = False\n", - "ax1.hist2d(*cartesian_data.values(), bins=100, cmap=plt.cm.coolwarm)\n", - "ax2.hist2d(polar_data[\"phi\"], polar_data[\"r\"], bins=100, cmap=plt.cm.coolwarm)\n", + "ax1.hist2d(*cartesian_data.values(), bins=100, cmap=\"coolwarm\")\n", + "ax2.hist2d(polar_data[\"phi\"], polar_data[\"r\"], bins=100, cmap=\"coolwarm\")\n", "fig.suptitle(\"Hit-and-miss intensity distribution\")\n", "ax1.set_title(\"cartesian\")\n", "ax2.set_title(\"polar\")\n", @@ -783,7 +735,7 @@ " Z = polar_function(polar_domain)\n", " if color_mesh is not None:\n", " color_mesh.remove()\n", - " color_mesh = ax_interactive.pcolormesh(X, Y, Z, cmap=plt.cm.coolwarm)" + " color_mesh = ax_interactive.pcolormesh(X, Y, Z, cmap=\"coolwarm\")" ] }, { @@ -837,7 +789,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.17" + "version": "3.13.11" } }, "nbformat": 4, diff --git a/docs/usage/basics.ipynb b/docs/usage/basics.ipynb index da3ed442..ff9a856e 100644 --- a/docs/usage/basics.ipynb +++ b/docs/usage/basics.ipynb @@ -1,62 +1,14 @@ { "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell", - "skip-execution" - ] - }, - "outputs": [], - "source": [ - "# WARNING: advised to install a specific version, e.g. tensorwaves==0.1.2\n", - "%pip install -q tensorwaves[doc,jax,pwa,viz] IPython" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ + "# Core ideas illustrated\n", "```{autolink-concat}\n", "```" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Core ideas illustrated" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -97,13 +49,14 @@ "\n", "from tensorwaves.estimator import UnbinnedNLL\n", "from tensorwaves.function.sympy import create_parametrized_function\n", - "from tensorwaves.optimizer import Minuit2, ScipyMinimizer\n", "from tensorwaves.optimizer.callbacks import (\n", " CallbackList,\n", " CSVSummary,\n", " TFSummary,\n", " YAMLSummary,\n", ")\n", + "from tensorwaves.optimizer.minuit import Minuit2\n", + "from tensorwaves.optimizer.scipy import ScipyMinimizer\n", "\n", "os.environ[\"TF_CPP_MIN_LOG_LEVEL\"] = \"3\"\n", "warnings.filterwarnings(\"ignore\", category=MatplotlibDeprecationWarning)" @@ -1296,7 +1249,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" } }, "nbformat": 4, diff --git a/docs/usage/binned-fit.ipynb b/docs/usage/binned-fit.ipynb index 999bb463..80e16546 100644 --- a/docs/usage/binned-fit.ipynb +++ b/docs/usage/binned-fit.ipynb @@ -1,62 +1,14 @@ { "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell", - "skip-execution" - ] - }, - "outputs": [], - "source": [ - "# WARNING: advised to install a specific version, e.g. tensorwaves==0.1.2\n", - "%pip install -q tensorwaves[doc,jax,pwa,viz] IPython" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ + "# Binned fit\n", "```{autolink-concat}\n", "```" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Binned fit" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -317,7 +269,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.17" + "version": "3.13.11" } }, "nbformat": 4, diff --git a/docs/usage/caching.ipynb b/docs/usage/caching.ipynb index e292dc11..37b9ef6a 100644 --- a/docs/usage/caching.ipynb +++ b/docs/usage/caching.ipynb @@ -1,62 +1,14 @@ { "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell", - "skip-execution" - ] - }, - "outputs": [], - "source": [ - "# WARNING: advised to install a specific version, e.g. tensorwaves==0.1.2\n", - "%pip install -q tensorwaves[doc,jax,pwa,viz] IPython" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ + "# Constant sub-expressions\n", "```{autolink-concat}\n", "```" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Constant sub-expressions" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -531,7 +483,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.17" + "version": "3.13.11" } }, "nbformat": 4, diff --git a/docs/usage/chi-squared.ipynb b/docs/usage/chi-squared.ipynb index f56e1dcc..a42b287f 100644 --- a/docs/usage/chi-squared.ipynb +++ b/docs/usage/chi-squared.ipynb @@ -1,62 +1,14 @@ { "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell", - "skip-execution" - ] - }, - "outputs": [], - "source": [ - "# WARNING: advised to install a specific version, e.g. tensorwaves==0.1.2\n", - "%pip install -q tensorwaves[doc,jax,pwa,viz] IPython" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ + "# Chi-squared estimator\n", "```{autolink-concat}\n", "```" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Chi-squared estimator" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -179,7 +131,7 @@ " ax.scatter(x_values, observed_y, s=2, label=\"generated data\")\n", " ax.set_xlabel(\"$x$\")\n", " ax.set_ylabel(\"$y$\")\n", - " ax.set_ylim([-30, 50])\n", + " ax.set_ylim((-30, 50))\n", " ax.legend(loc=\"upper left\")\n", " plt.show()\n", "\n", @@ -277,7 +229,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.17" + "version": "3.13.11" } }, "nbformat": 4, diff --git a/docs/usage/faster-lambdify.ipynb b/docs/usage/faster-lambdify.ipynb index 8279472f..38b0c8a0 100644 --- a/docs/usage/faster-lambdify.ipynb +++ b/docs/usage/faster-lambdify.ipynb @@ -1,62 +1,14 @@ { "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell", - "skip-execution" - ] - }, - "outputs": [], - "source": [ - "# WARNING: advised to install a specific version, e.g. tensorwaves==0.1.2\n", - "%pip install -q tensorwaves[doc,jax,pwa,viz] IPython" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ + "# Speed up lambdifying\n", "```{autolink-concat}\n", "```" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Speed up lambdifying" - ] - }, { "cell_type": "code", "execution_count": null, @@ -230,18 +182,18 @@ "for symbol, definition in sub_expressions.items():\n", " dot = sp.dotprint(definition, bgcolor=\"none\")\n", " graph = graphviz.Source(dot)\n", - " graph.render(filename=f\"sub_expr_{symbol.name}\", format=\"svg\")\n", + " graph.render(filename=f\"sub_expr_{symbol}\", format=\"svg\")\n", "\n", "html = \"\\n\"\n", "html += \" \\n\"\n", "html += \"\".join(\n", - " f' \\n'\n", + " f' \\n'\n", " for symbol in sub_expressions\n", ")\n", "html += \" \\n\"\n", "html += \" \\n\"\n", "for symbol in sub_expressions:\n", - " svg = SVG(f\"sub_expr_{symbol.name}.svg\").data\n", + " svg = SVG(f\"sub_expr_{symbol}.svg\").data\n", " html += f' \\n'\n", "html += \" \\n\"\n", "html += \"
{symbol.name}{symbol}
{svg}
\"\n", @@ -417,7 +369,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" } }, "nbformat": 4, diff --git a/docs/usage/unbinned-fit.ipynb b/docs/usage/unbinned-fit.ipynb index f33956c1..4a6c4709 100644 --- a/docs/usage/unbinned-fit.ipynb +++ b/docs/usage/unbinned-fit.ipynb @@ -1,62 +1,14 @@ { "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell", - "skip-execution" - ] - }, - "outputs": [], - "source": [ - "# WARNING: advised to install a specific version, e.g. tensorwaves==0.1.2\n", - "%pip install -q tensorwaves[doc,jax,pwa,viz] IPython" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "hideCode": true, - "hideOutput": true, - "hidePrompt": true, - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "import os\n", - "\n", - "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ + "# Unbinned fit\n", "```{autolink-concat}\n", "```" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Unbinned fit" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -131,7 +83,7 @@ "\n", "bins_x, bins_y = 80, 50\n", "bin_values, bin_edges_x, bin_edges_y, _ = ax2d.hist2d(\n", - " data[\"x\"], data[\"y\"], bins=(bins_x, bins_y), cmap=plt.cm.coolwarm\n", + " data[\"x\"], data[\"y\"], bins=(bins_x, bins_y), cmap=\"coolwarm\"\n", ")\n", "xlim = 0, 4\n", "ylim = -3, +3\n", @@ -234,8 +186,8 @@ "fig, (ax1, ax2) = plt.subplots(figsize=(8, 7), nrows=2, sharex=True, tight_layout=True)\n", "ax1.set_title(\"Data distribution\")\n", "ax2.set_title(\"Initial fit model\")\n", - "ax1.hist2d(data[\"x\"], data[\"y\"], cmap=plt.cm.coolwarm, bins=(bins_x, bins_y))\n", - "ax2.pcolormesh(X, Y, Z, cmap=plt.cm.coolwarm)\n", + "ax1.hist2d(data[\"x\"], data[\"y\"], cmap=\"coolwarm\", bins=(bins_x, bins_y))\n", + "ax2.pcolormesh(X, Y, Z, cmap=\"coolwarm\")\n", "for ax in [ax1, ax2]:\n", " ax.set_xlim(*xlim)\n", " ax.set_ylim(*ylim)\n", @@ -310,8 +262,8 @@ "fig, (ax1, ax2) = plt.subplots(figsize=(8, 7), nrows=2, sharex=True, tight_layout=True)\n", "ax1.set_title(\"Data distribution\")\n", "ax2.set_title(\"Model with optimized parameters\")\n", - "ax1.hist2d(data[\"x\"], data[\"y\"], cmap=plt.cm.coolwarm, bins=(bins_x, bins_y))\n", - "ax2.pcolormesh(X, Y, Z, cmap=plt.cm.coolwarm)\n", + "ax1.hist2d(data[\"x\"], data[\"y\"], cmap=\"coolwarm\", bins=(bins_x, bins_y))\n", + "ax2.pcolormesh(X, Y, Z, cmap=\"coolwarm\")\n", "for ax in [ax1, ax2]:\n", " ax.set_xlim(*xlim)\n", " ax.set_ylim(*ylim)\n", @@ -338,7 +290,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.17" + "version": "3.13.11" } }, "nbformat": 4, diff --git a/pyproject.toml b/pyproject.toml index c309a88c..18975db9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -77,10 +77,7 @@ Tracker = "https://github.com/ComPWA/tensorwaves/issues" [dependency-groups] dev = [ - "nbmake", - "poethepoet", "ruff", - "sphinx-autobuild", {include-group = "doc"}, {include-group = "jupyter"}, {include-group = "style"}, @@ -109,7 +106,7 @@ jupyter = [ "jupyterlab-quickopen", "python-lsp-ruff", "python-lsp-server[rope]", - {include-group = "doc"}, + {include-group = "notebooks"}, ] notebooks = [ "black", @@ -119,15 +116,14 @@ notebooks = [ "tensorwaves[jax,pwa]", ] style = [ - "mypy", + "ty", + {include-group = "notebooks"}, {include-group = "types"}, ] test = [ - "ampform >=0.13", "pyarrow", "pytest-benchmark", "pytest-cov", - "tensorwaves[jax,numba,pwa]", {include-group = "test-types"}, ] test-types = [ @@ -136,6 +132,7 @@ test-types = [ "pytest-mock", ] types = [ + "numba", "sphinx-api-relink", "tensorwaves[jax,pwa]", "types-PyYAML", @@ -175,49 +172,10 @@ omit = [ ] source = ["src"] -[tool.mypy] -disallow_incomplete_defs = true -disallow_untyped_defs = true -exclude = "_build" -show_error_codes = true -warn_unused_configs = true - -[[tool.mypy.overrides]] -check_untyped_defs = true -disallow_incomplete_defs = false -disallow_untyped_defs = false -module = ["benchmarks.*", "tests.*"] - -[[tool.mypy.overrides]] -ignore_errors = true -module = ["typings.*"] - -[[tool.mypy.overrides]] -ignore_missing_imports = true -module = ["iminuit.*"] - -[[tool.mypy.overrides]] -ignore_missing_imports = true -module = ["numba.*"] - -[[tool.mypy.overrides]] -ignore_missing_imports = true -module = ["phasespace"] - -[[tool.mypy.overrides]] -ignore_missing_imports = true -module = ["scipy.optimize"] - -[[tool.mypy.overrides]] -ignore_missing_imports = true -module = ["sympy.*"] - -[[tool.mypy.overrides]] -ignore_missing_imports = true -module = ["tensorflow.python.ops.numpy_ops"] - -[tool.poe] -executor.type = "uv" +[tool.poe.executor] +isolated = true +no-group = "dev" +type = "uv" [tool.poe.tasks.all] help = "Run all continuous integration (CI) tasks locally" @@ -235,9 +193,11 @@ sequence = [ cmd = """ pytest benchmarks \ --benchmark-autosave \ + --benchmark-json benchmarks/output.json \ --durations=0 \ -k benchmark """ +executor = {extra = ["jax", "numba", "pwa"], group = "test"} help = "Run benchmark tests and visualize performance" [tool.poe.tasks.cov] @@ -249,10 +209,11 @@ pytest \ --cov-report=xml \ ${paths} """ +executor = {extra = ["jax", "numba", "pwa"], group = "test"} help = "Compute how much of the source code is covered by tests" [[tool.poe.tasks.cov.args]] -default = "src tests" +default = "" multiple = true name = "paths" positional = true @@ -268,6 +229,7 @@ sphinx-build \ docs/_build/html/ """ env = {PYTHONWARNINGS = ""} +executor = {group = "doc"} help = "Build documentation and API" [tool.poe.tasks.doclive] @@ -305,6 +267,7 @@ sphinx-autobuild \ docs/ \ docs/_build/html/ """ +executor = {group = "doc", with = "sphinx-autobuild"} help = "Set up a server to directly preview changes to the HTML pages" [tool.poe.tasks.docnb] @@ -324,13 +287,13 @@ sequence = ["doclive"] [tool.poe.tasks.jax] cmd = """ -uv run --extra jax --group test --isolated --no-dev \ - pytest \ - -k 'benchmark or not benchmark' \ - -k 'not (ampform or four_momenta or numba or tensorflow or tf)' \ - --benchmark-disable \ - ${paths} +pytest \ + -k 'benchmark or not benchmark' \ + -k 'not (ampform or four_momenta or numba or tensorflow or tf)' \ + --benchmark-disable \ + ${paths} """ +executor = {extra = "jax", group = "test"} help = "Run tests with JAX only" [[tool.poe.tasks.jax.args]] @@ -342,7 +305,8 @@ positional = true [tool.poe.tasks.lab] args = [{name = "paths", default = "", positional = true}] cmd = "jupyter lab ${paths}" -help = "Run Jupyter Lab" +executor = {group = "jupyter"} +help = "Launch Jupyter Lab" [tool.poe.tasks.linkcheck] cmd = """ @@ -353,18 +317,23 @@ sphinx-build \ docs/_build/linkcheck/ """ env = {PYTHONWARNINGS = ""} +executor = {group = "doc"} help = "Check external links in the documentation (requires internet connection)" [tool.poe.tasks.nb] -cmd = "pytest --nbmake --nbmake-timeout=0 docs" +args = [{name = "paths", default = "docs", multiple = true, positional = true}] +cmd = "pytest --nbmake --nbmake-timeout=0 ${paths}" +executor = {group = "notebooks", with = "nbmake"} help = "Run all notebooks" [tool.poe.tasks.style] -cmd = "uv run --group style --isolated --no-dev pre-commit run --all-files" +cmd = "pre-commit run --all-files" +executor = {group = "style"} help = "Perform all linting, formatting, and spelling checks" [tool.poe.tasks.test] -cmd = "pytest ${paths}" +cmd = "pytest --benchmark-disable -m 'slow or not slow' ${paths}" +executor = {extra = ["jax", "numba", "pwa"], group = "test"} help = "Run all unit tests" [[tool.poe.tasks.test.args]] @@ -376,56 +345,33 @@ positional = true [tool.poe.tasks.test-all] help = "Run all tests on each supported Python version" sequence = [ - {ref = "test-py 3.10"}, - {ref = "test-py 3.11"}, - {ref = "test-py 3.12"}, - {ref = "test-py 3.13"}, + {ref = "test-py310 ${paths}"}, + {ref = "test-py311 ${paths}"}, + {ref = "test-py312 ${paths}"}, + {ref = "test-py313 ${paths}"}, ] -[tool.poe.tasks.test-py] -cmd = """ -uv run \ - --group=test \ - --isolated \ - --no-dev \ - --python=${version} \ - pytest \ - --benchmark-disable \ - -m 'slow or not slow' -""" -help = "Run all tests on a specific Python version" - -[[tool.poe.tasks.test-py.args]] -default = "3.13" -help = "Selected Python version" -name = "version" +[[tool.poe.tasks.test-all.args]] +default = "" +multiple = true +name = "paths" positional = true -[tool.pyright] -reportArgumentType = false -reportAttributeAccessIssue = false -reportGeneralTypeIssues = false -reportMissingParameterType = false -reportMissingTypeArgument = false -reportMissingTypeStubs = false -reportOperatorIssue = false -reportPrivateImportUsage = false -reportReturnType = false -reportUnboundVariable = false -reportUnknownArgumentType = false -reportUnknownLambdaType = false -reportUnknownMemberType = false -reportUnknownParameterType = false -reportUnknownVariableType = false -reportUnnecessaryComparison = true -reportUnnecessaryIsInstance = false -reportUnusedClass = true -reportUnusedFunction = true -reportUnusedImport = true -reportUnusedVariable = true -typeCheckingMode = "strict" -venv = ".venv" -venvPath = "." +[tool.poe.tasks.test-py310] +env = {UV_PYTHON = "3.10"} +ref = "test" + +[tool.poe.tasks.test-py311] +env = {UV_PYTHON = "3.11"} +ref = "test" + +[tool.poe.tasks.test-py312] +env = {UV_PYTHON = "3.12"} +ref = "test" + +[tool.poe.tasks.test-py313] +env = {UV_PYTHON = "3.13"} +ref = "test" [tool.pytest.ini_options] addopts = ["--color=yes"] @@ -438,12 +384,13 @@ filterwarnings = [ "ignore:.*Using or importing the ABCs.*:DeprecationWarning", "ignore:.*jax.xla_computation is deprecated*:DeprecationWarning", "ignore:.*the imp module is deprecated in favour of importlib.*:DeprecationWarning", + "ignore:In the future `np.object` will be defined as the corresponding NumPy scalar\\.:FutureWarning", + "ignore:Not saving anything, no benchmarks have been run!", "ignore:Passing a schema to Validator.iter_errors is deprecated.*:DeprecationWarning", "ignore:Please use `spmatrix` from the `scipy.sparse` namespace.*:DeprecationWarning", "ignore:Protobuf gencode version .*:UserWarning", "ignore:The distutils package is deprecated and slated for removal.*:DeprecationWarning", - "ignore:divide by zero encountered in divide:RuntimeWarning", - "ignore:divide by zero encountered in true_divide:RuntimeWarning", + "ignore:divide by zero encountered in (true_)?divide:RuntimeWarning", "ignore:invalid value encountered in .*:RuntimeWarning", "ignore:jax\\.xla_computation is deprecated\\. Please use the AOT APIs\\.:DeprecationWarning", "ignore:ml_dtypes\\.float8.*:DeprecationWarning", @@ -507,6 +454,7 @@ ignore = [ "PT001", "PTH", "RUF012", + "RUF067", "S307", "SIM108", ] @@ -625,3 +573,51 @@ sort_first = [ ] spaces_indent_inline_array = 4 trailing_comma_inline_array = true + +[[tool.ty.overrides]] +include = [ + "docs/amplitude-analysis.ipynb", + "docs/usage.ipynb", + "docs/usage/basics.ipynb", + "docs/usage/binned-fit.ipynb", +] + +[tool.ty.overrides.rules] +invalid-argument-type = "ignore" + +[[tool.ty.overrides]] +include = [ + "docs/amplitude-analysis.ipynb", + "docs/amplitude-analysis/analytic-continuation.ipynb", + "docs/usage.ipynb", + "docs/usage/caching.ipynb", +] + +[tool.ty.overrides.rules] +unresolved-attribute = "ignore" + +[[tool.ty.overrides]] +include = [ + "docs/amplitude-analysis.ipynb", + "docs/usage/basics.ipynb", + "docs/usage/binned-fit.ipynb", +] + +[tool.ty.overrides.rules] +possibly-missing-attribute = "ignore" + +[[tool.ty.overrides]] +include = ["docs/usage.ipynb"] + +[tool.ty.overrides.rules] +invalid-method-override = "ignore" + +[tool.ty.rules] +division-by-zero = "warn" +possibly-missing-import = "warn" +possibly-unresolved-reference = "warn" +unused-ignore-comment = "warn" + +[tool.uv.sources] +ampform = {git = "https://github.com/ComPWA/ampform", rev = "fc1d4e2920954738bb6620905f0de0a73a5a93cd"} +qrules = {git = "https://github.com/ComPWA/qrules", rev = "33be556be51fff52869034327bcf6157eb6cf726"} diff --git a/src/tensorwaves/data/__init__.py b/src/tensorwaves/data/__init__.py index 83c8527f..7c03e004 100644 --- a/src/tensorwaves/data/__init__.py +++ b/src/tensorwaves/data/__init__.py @@ -21,8 +21,6 @@ merge_events, select_events, ) - -# pyright: reportUnusedImport=false from .phasespace import ( TFPhaseSpaceGenerator, # noqa: F401 TFWeightedPhaseSpaceGenerator, # noqa: F401 @@ -135,8 +133,8 @@ def _generate_without_progress_bar( # https://github.com/ComPWA/tensorwaves/issues/395 show_progress = getattr(domain_generator, "show_progress", None) if show_progress is not None: - domain_generator.show_progress = False # type: ignore[attr-defined] + domain_generator.show_progress = False # ty:ignore[unresolved-attribute] domain = domain_generator.generate(bunch_size, rng) if show_progress is not None: - domain_generator.show_progress = show_progress # type: ignore[attr-defined] + domain_generator.show_progress = show_progress # ty:ignore[unresolved-attribute] return domain diff --git a/src/tensorwaves/data/phasespace.py b/src/tensorwaves/data/phasespace.py index 913e7d3b..9f7834d2 100644 --- a/src/tensorwaves/data/phasespace.py +++ b/src/tensorwaves/data/phasespace.py @@ -106,9 +106,8 @@ def __init__( import phasespace # noqa: PLC0415 except ImportError: # pragma: no cover raise_missing_module_error("phasespace", extras_require="phsp") - sorted_ids = sorted(final_state_masses) - self.__phsp_gen = phasespace.nbody_decay( + self.__phsp_gen = phasespace.nbody_decay( # ty:ignore[possibly-unresolved-reference] mass_top=initial_state_mass, masses=[final_state_masses[i] for i in sorted_ids], names=list(map(str, sorted_ids)), @@ -140,4 +139,4 @@ def generate(self, size: int, rng: RealNumberGenerator) -> DataSample: def _to_numpy(tensor: tf.Tensor) -> np.ndarray: - return tensor.numpy() # pyright: ignore[reportOptionalCall] + return tensor.numpy() diff --git a/src/tensorwaves/data/rng.py b/src/tensorwaves/data/rng.py index b82d8aa0..badcc8da 100644 --- a/src/tensorwaves/data/rng.py +++ b/src/tensorwaves/data/rng.py @@ -44,9 +44,8 @@ def __init__(self, seed: int | None = None) -> None: from tensorflow import float64 # noqa: PLC0415 except ImportError: # pragma: no cover raise_missing_module_error("tensorflow", extras_require="tf") - self.seed = seed - self.dtype = float64 + self.dtype = float64 # ty:ignore[possibly-unresolved-reference] def __call__( self, size: int, min_value: float = 0.0, max_value: float = 1.0 @@ -79,10 +78,10 @@ def _get_tensorflow_rng(seed: SeedLike | None = None) -> tf.random.Generator: raise_missing_module_error("tensorflow", extras_require="tf") if seed is None: - return tf.random.get_global_generator() + return tf.random.get_global_generator() # ty:ignore[possibly-unresolved-reference] if isinstance(seed, int): - return tf.random.Generator.from_seed(seed=seed) - if isinstance(seed, tf.random.Generator): + return tf.random.Generator.from_seed(seed=seed) # ty:ignore[possibly-unresolved-reference] + if isinstance(seed, tf.random.Generator): # ty:ignore[possibly-unresolved-reference] return seed msg = f"Cannot create a tf.random.Generator from a {type(seed).__name__}" raise TypeError(msg) diff --git a/src/tensorwaves/data/transform.py b/src/tensorwaves/data/transform.py index 7db6b5c0..714cbda8 100644 --- a/src/tensorwaves/data/transform.py +++ b/src/tensorwaves/data/transform.py @@ -7,10 +7,7 @@ from attrs import field, frozen from tensorwaves.function import PositionalArgumentFunction -from tensorwaves.function.sympy import ( - _get_free_symbols, # pyright: ignore[reportPrivateUsage] - _lambdify_normal_or_fast, # pyright: ignore[reportPrivateUsage] -) +from tensorwaves.function.sympy import _get_free_symbols, _lambdify_normal_or_fast from tensorwaves.interface import DataSample, DataTransformer, Function from ._attrs import to_tuple @@ -80,7 +77,7 @@ def __call__(self, data: DataSample) -> DataSample: @classmethod def from_sympy( cls, - expressions: dict[sp.Symbol, sp.Expr], + expressions: dict[sp.Basic, sp.Expr], backend: str, *, use_cse: bool = True, @@ -88,9 +85,9 @@ def from_sympy( max_complexity: int | None = None, ) -> SympyDataTransformer: expanded_expressions: dict[str, sp.Expr] = { - k.name: expr.doit() for k, expr in expressions.items() + str(k): expr.doit() for k, expr in expressions.items() } - free_symbols: set[sp.Symbol] = set() + free_symbols: set[sp.Basic] = set() for expr in expanded_expressions.values(): free_symbols |= _get_free_symbols(expr) ordered_symbols = tuple(sorted(free_symbols, key=lambda s: s.name)) diff --git a/src/tensorwaves/estimator.py b/src/tensorwaves/estimator.py index e86b0462..ea0770f9 100644 --- a/src/tensorwaves/estimator.py +++ b/src/tensorwaves/estimator.py @@ -27,9 +27,9 @@ def create_cached_function( expression: sp.Expr, - parameters: Mapping[sp.Symbol, ParameterValue], + parameters: Mapping[sp.Basic, ParameterValue], backend: str, - free_parameters: Iterable[sp.Symbol], + free_parameters: Iterable[sp.Basic], *, use_cse: bool = True, ) -> tuple[ParametrizedFunction[DataSample, np.ndarray], DataTransformer]: @@ -83,9 +83,8 @@ def gradient_creator( import jax # noqa: PLC0415 except ImportError: # pragma: no cover raise_missing_module_error("jax", extras_require="jax") - - jax.config.update("jax_enable_x64", True) - return jax.grad(function) + jax.config.update("jax_enable_x64", True) # ty:ignore[possibly-unresolved-reference] + return jax.grad(function) # ty:ignore[possibly-unresolved-reference] def raise_gradient_not_implemented( parameters: Mapping[str, ParameterValue], @@ -136,7 +135,7 @@ def __init__( self.__gradient = gradient_creator(self.__call__, backend) self.__sum = find_function("sum", backend) - def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: + def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: # ty:ignore[invalid-method-override] self.__function.update_parameters(parameters) computed_values = self.__function(self.__domain) chi_squared = self.__weights * (computed_values - self.__observed_values) ** 2 @@ -203,7 +202,7 @@ def __init__( self.__phsp_volume = phsp_volume - def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: + def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: # ty:ignore[invalid-method-override] self.__function.update_parameters(parameters) bare_intensities = self.__function(self.__data) phsp_intensities = self.__function(self.__phsp) diff --git a/src/tensorwaves/function/__init__.py b/src/tensorwaves/function/__init__.py index a891358e..cd86773e 100644 --- a/src/tensorwaves/function/__init__.py +++ b/src/tensorwaves/function/__init__.py @@ -103,12 +103,12 @@ def __init__( argument_order: Iterable[str], parameters: Mapping[str, ParameterValue], ) -> None: - self.__function = PositionalArgumentFunction(function, argument_order) + self.__function = PositionalArgumentFunction(function, argument_order) # ty:ignore[invalid-argument-type] self.__parameters = dict(parameters) def __call__(self, data: DataSample) -> np.ndarray: - extended_data = {**data, **self.__parameters} # type: ignore[arg-type] - return self.__function(extended_data) # type: ignore[arg-type] + extended_data = {**data, **self.__parameters} + return self.__function(extended_data) @property def function(self) -> Callable[..., np.ndarray]: diff --git a/src/tensorwaves/function/_backend.py b/src/tensorwaves/function/_backend.py index a2d0c737..c25aa553 100644 --- a/src/tensorwaves/function/_backend.py +++ b/src/tensorwaves/function/_backend.py @@ -45,8 +45,8 @@ def get_backend_modules(backend: str | tuple | dict) -> str | tuple | dict: import jax.scipy as jsp except ImportError: # pragma: no cover raise_missing_module_error("jax", extras_require="jax") - jax.config.update("jax_enable_x64", True) - return (jnp, jsp.special) + jax.config.update("jax_enable_x64", True) # ty:ignore[possibly-unresolved-reference] + return jnp, jsp.special # ty:ignore[possibly-unresolved-reference] if backend in {"numpy", "numba"}: import numpy as np @@ -55,14 +55,12 @@ def get_backend_modules(backend: str | tuple | dict) -> str | tuple | dict: if backend in {"tensorflow", "tf"}: try: import tensorflow as tf - import tensorflow.experimental.numpy as tnp # pyright: ignore[reportMissingImports] + import tensorflow.experimental.numpy as tnp # ty:ignore[unresolved-import] from tensorflow.python.ops.numpy_ops import np_config except ImportError: # pragma: no cover raise_missing_module_error("tensorflow", extras_require="tf") - - np_config.enable_numpy_behavior() - - return tnp.__dict__, tf + np_config.enable_numpy_behavior() # ty:ignore[possibly-unresolved-reference] + return tnp.__dict__, tf # ty:ignore[possibly-unresolved-reference] return backend @@ -87,14 +85,14 @@ def jit_compile(backend: str) -> Callable[[Callable[P, T]], Callable[P, T]]: import jax except ImportError: # pragma: no cover raise_missing_module_error("jax", extras_require="jax") - return jax.jit + return jax.jit # ty:ignore[possibly-unresolved-reference] if backend == "numba": try: - import numba # pyright: ignore[reportMissingImports] + import numba except ImportError: # pragma: no cover raise_missing_module_error("numba", extras_require="numba") - return partial(numba.jit, forceobj=True, parallel=True) + return partial(numba.jit, forceobj=True, parallel=True) # ty:ignore[possibly-unresolved-reference] msg = f"Backend {backend} does not yet support JIT compilation" warn(msg, category=UserWarning, stacklevel=3) diff --git a/src/tensorwaves/function/sympy/__init__.py b/src/tensorwaves/function/sympy/__init__.py index b7d9ba9a..42740983 100644 --- a/src/tensorwaves/function/sympy/__init__.py +++ b/src/tensorwaves/function/sympy/__init__.py @@ -78,12 +78,12 @@ def create_function( def create_parametrized_function( # noqa: PLR0913 expression: sp.Expr, - parameters: Mapping[sp.Symbol, ParameterValue], + parameters: Mapping[sp.Basic, ParameterValue], backend: str, *, + max_complexity: int | None = None, use_cse: bool = True, use_jit: bool | None = None, - max_complexity: int | None = None, ) -> ParametrizedBackendFunction: """Convert a SymPy expression to a parametrized function. @@ -135,11 +135,11 @@ def create_parametrized_function( # noqa: PLR0913 return ParametrizedBackendFunction( function=lambdified_function, argument_order=tuple(map(str, sorted_symbols)), - parameters={symbol.name: value for symbol, value in parameters.items()}, + parameters={str(symbol): value for symbol, value in parameters.items()}, ) -def _get_free_symbols(expression: sp.Basic) -> set[sp.Symbol]: +def _get_free_symbols(expression: sp.Basic) -> set[sp.Basic]: """Get free symbols in an expression, excluding IndexedBase. >>> import sympy as sp @@ -152,7 +152,7 @@ def _get_free_symbols(expression: sp.Basic) -> set[sp.Symbol]: """ import sympy as sp - free_symbols: set[sp.Symbol] = expression.free_symbols # type: ignore[assignment] + free_symbols = expression.free_symbols index_bases = { sp.Symbol(s.base.name, **s.assumptions0) for s in free_symbols @@ -163,7 +163,7 @@ def _get_free_symbols(expression: sp.Basic) -> set[sp.Symbol]: def _lambdify_normal_or_fast( # noqa: PLR0913, PLR0917 expression: sp.Expr, - symbols: Sequence[sp.Symbol], + symbols: Sequence[sp.Basic], backend: str, use_cse: bool, use_jit: bool | None, @@ -190,7 +190,7 @@ def _lambdify_normal_or_fast( # noqa: PLR0913, PLR0917 def lambdify( # noqa: C901, PLR0911 expression: sp.Expr, - symbols: Sequence[sp.Symbol], + symbols: Sequence[sp.Basic], backend: str, *, use_cse: bool = True, @@ -233,7 +233,7 @@ def numba_lambdify() -> Callable: def tensorflow_lambdify() -> Callable: try: - import tensorflow.experimental.numpy as tnp # pyright: ignore[reportMissingImports] + import tensorflow.experimental.numpy as tnp # ty:ignore[unresolved-import] except ImportError: # pragma: no cover raise_missing_module_error("tensorflow", extras_require="tf") from ._printer import TensorflowPrinter @@ -241,7 +241,7 @@ def tensorflow_lambdify() -> Callable: return _sympy_lambdify( expression, symbols, - modules=tnp, + modules=tnp, # ty:ignore[possibly-unresolved-reference] printer=TensorflowPrinter(), use_cse=use_cse, ) @@ -276,7 +276,7 @@ def tensorflow_lambdify() -> Callable: def _sympy_lambdify( expression: sp.Expr, - symbols: Sequence[sp.Symbol], + symbols: Sequence[sp.Basic], modules: str | tuple | dict, use_cse: bool, printer: Printer | None = None, @@ -301,7 +301,7 @@ def _sympy_lambdify( def fast_lambdify( # noqa: PLR0913 expression: sp.Expr, - symbols: Sequence[sp.Symbol], + symbols: Sequence[sp.Basic], backend: str, *, use_cse: bool = True, @@ -351,7 +351,7 @@ def recombined_function(*args: Any) -> Any: def _collect_constant_sub_expressions( - expression: sp.Basic, free_symbols: Iterable[sp.Symbol] + expression: sp.Basic, free_symbols: Iterable[sp.Basic] ) -> set[sp.Expr]: import sympy as sp @@ -368,14 +368,14 @@ def iterate_constant_sub_expressions( for expr in expression.args: yield from iterate_constant_sub_expressions(expr) return - yield expression # type: ignore[misc] + yield expression return set(iterate_constant_sub_expressions(expression)) def extract_constant_sub_expressions( expression: sp.Expr, - free_symbols: Iterable[sp.Symbol], + free_symbols: Iterable[sp.Basic], fix_order: bool = False, ) -> tuple[sp.Expr, dict[sp.Symbol, sp.Expr]]: """Collapse and extract constant sub-expressions. @@ -406,7 +406,7 @@ def extract_constant_sub_expressions( free_symbols = set(free_symbols) over_defined = free_symbols - _get_free_symbols(expression) if over_defined: - over_defined_symbols = sorted(over_defined, key=str) + over_defined_symbols = sorted(over_defined, key=str) # ty:ignore[no-matching-overload] symbol_names = ", ".join(map(str, over_defined_symbols)) if len(over_defined) == 1: text = f"Symbol {symbol_names} does" @@ -433,10 +433,10 @@ def extract_constant_sub_expressions( def prepare_caching( expression: sp.Expr, - parameters: Mapping[sp.Symbol, ParameterValue], - free_parameters: Iterable[sp.Symbol], + parameters: Mapping[sp.Basic, ParameterValue], + free_parameters: Iterable[sp.Basic], fix_order: bool = False, -) -> tuple[sp.Expr, dict[sp.Symbol, sp.Expr]]: +) -> tuple[sp.Expr, dict[sp.Basic, sp.Expr]]: """Prepare an expression for optimizing with caching. When fitting a `.ParametrizedFunction`, only its free @@ -485,7 +485,7 @@ def prepare_caching( expression, free_parameters, fix_order ) transformer_expressions = {} - undefined_variables: set[sp.Symbol] = set() + undefined_variables: set[sp.Basic] = set() variables = _get_free_symbols(expression) - set(parameters) for symbol, sub_expr in sub_expressions.items(): transformer_expressions[symbol] = sub_expr @@ -499,7 +499,7 @@ def split_expression( expression: sp.Expr, max_complexity: int, min_complexity: int = 1, -) -> tuple[sp.Expr, dict[sp.Symbol, sp.Expr]]: +) -> tuple[sp.Expr, dict[sp.Basic, sp.Expr]]: """Split an expression into a 'top expression' and several sub-expressions. Replace nodes in the expression tree of a `sympy.Expr ` that @@ -512,7 +512,7 @@ def split_expression( import sympy as sp i = 0 - symbol_mapping: dict[sp.Symbol, sp.Expr] = {} + symbol_mapping: dict[sp.Basic, sp.Expr] = {} n_operations = sp.count_ops(expression) if max_complexity <= 0 or n_operations < max_complexity: return expression, symbol_mapping @@ -531,17 +531,17 @@ def recursive_split(sub_expression: sp.Basic) -> sp.Expr: progress_bar.update(n=complexity) symbol = sp.Symbol(f"f{i}") i += 1 - symbol_mapping[symbol] = arg # type: ignore[assignment] + symbol_mapping[symbol] = arg # ty:ignore[invalid-assignment] sub_expression = sub_expression.xreplace({arg: symbol}) else: new_arg = recursive_split(arg) sub_expression = sub_expression.xreplace({arg: new_arg}) - return sub_expression # type: ignore[return-value] + return sub_expression # ty:ignore[invalid-return-type] top_expression = recursive_split(expression) free_symbols = _get_free_symbols(top_expression) remaining_symbols = free_symbols - set(symbol_mapping) - symbol_mapping.update({s: s for s in remaining_symbols}) + symbol_mapping.update({s: s for s in remaining_symbols}) # ty:ignore[no-matching-overload] remainder = progress_bar.total - progress_bar.n progress_bar.update(n=remainder) progress_bar.close() diff --git a/src/tensorwaves/function/sympy/_printer.py b/src/tensorwaves/function/sympy/_printer.py index e9a6e650..c3be79f0 100644 --- a/src/tensorwaves/function/sympy/_printer.py +++ b/src/tensorwaves/function/sympy/_printer.py @@ -50,7 +50,7 @@ def _forward_to_numpy_printer( def decorator(decorated_class: type[_T]) -> type[_T]: def _get_numpy_code(self: _T, expr: sp.Expr, *args: Any) -> str: - return expr._numpycode(self, *args) # type: ignore[attr-defined] + return expr._numpycode(self, *args) # ty:ignore[unresolved-attribute] for class_name in class_names: method_name = f"_print_{class_name}" diff --git a/src/tensorwaves/interface.py b/src/tensorwaves/interface.py index 7ae4893d..dc834651 100644 --- a/src/tensorwaves/interface.py +++ b/src/tensorwaves/interface.py @@ -82,7 +82,7 @@ class Estimator(Function[Mapping[str, ParameterValue], float]): """ @abstractmethod - def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: + def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: # ty:ignore[invalid-method-override] """Compute estimator value for this combination of parameter values.""" @abstractmethod @@ -95,7 +95,7 @@ def gradient( _PARAMETER_DICT_VALIDATOR = attrs.validators.deep_mapping( key_validator=instance_of(str), mapping_validator=instance_of(dict), - value_validator=instance_of(ParameterValue.__args__), # type: ignore[attr-defined] + value_validator=instance_of(ParameterValue.__args__), ) @@ -125,7 +125,7 @@ class FitResult: :ref:`amplitude-analysis:Covariance matrix`. """ - @parameter_errors.validator # pyright: ignore[reportOptionalMemberAccess, reportUntypedFunctionDecorator] + @parameter_errors.validator def _check_parameter_errors( self, _: attrs.Attribute, value: dict[str, ParameterValue] | None ) -> None: @@ -142,7 +142,7 @@ def _repr_pretty_(self, p: PrettyPrinter, cycle: bool) -> None: p.text(f"{class_name}(...)") else: with p.group(indent=1, open=f"{class_name}("): - for attribute in attrs.fields(type(self)): # type: ignore[misc] + for attribute in attrs.fields(type(self)): if attribute.name == "specifics": continue value = getattr(self, attribute.name) @@ -153,14 +153,14 @@ def _repr_pretty_(self, p: PrettyPrinter, cycle: bool) -> None: with p.group(indent=1, open="{"): for key, val in value.items(): p.breakable() - p.pretty(key) # type: ignore[attr-defined] + p.pretty(key) # ty:ignore[unresolved-attribute] p.text(": ") - p.pretty(val) # type: ignore[attr-defined] + p.pretty(val) # ty:ignore[unresolved-attribute] p.text(",") p.breakable() p.text("}") else: - p.pretty(value) # type: ignore[attr-defined] + p.pretty(value) # ty:ignore[unresolved-attribute] p.text(",") p.breakable() p.text(")") @@ -210,7 +210,7 @@ def __call__( ) -> np.ndarray: """Generate random floats in the range [min_value, max_value).""" - @property # type: ignore[misc] + @property @abstractmethod def seed(self) -> int | None: """Get random seed. @@ -218,7 +218,7 @@ def seed(self) -> int | None: `None` if you want indeterministic behavior. """ - @seed.setter # type: ignore[misc] + @seed.setter @abstractmethod def seed(self, value: int | None) -> None: """Set random seed. diff --git a/src/tensorwaves/optimizer/__init__.py b/src/tensorwaves/optimizer/__init__.py index bdc43872..b156e4eb 100644 --- a/src/tensorwaves/optimizer/__init__.py +++ b/src/tensorwaves/optimizer/__init__.py @@ -9,7 +9,6 @@ "minuit", ] -# pyright: reportUnusedImport=false from . import callbacks, minuit from .minuit import Minuit2 # noqa: F401 diff --git a/src/tensorwaves/optimizer/callbacks.py b/src/tensorwaves/optimizer/callbacks.py index 8eafcffa..dad28bcd 100644 --- a/src/tensorwaves/optimizer/callbacks.py +++ b/src/tensorwaves/optimizer/callbacks.py @@ -201,7 +201,7 @@ def cast_non_numeric(value: str) -> complex | float | int | str: try: complex_value = complex(value) if not complex_value.imag: - float_value = complex_value.real + float_value = float(complex_value.real) if float_value.is_integer(): return int(float_value) return float_value @@ -242,12 +242,11 @@ def on_optimize_start(self, logs: dict[str, Any] | None = None) -> None: import tensorflow as tf # noqa: PLC0415 except ImportError: # pragma: no cover raise_missing_module_error("tensorflow", extras_require="tf") - output_dir = self.__logdir + "/" + datetime.now().strftime("%Y%m%d-%H%M%S") if self.__subdir is not None: output_dir += "/" + self.__subdir - self.__stream = tf.summary.create_file_writer(output_dir) - self.__stream.set_as_default() # type: ignore[attr-defined] + self.__stream = tf.summary.create_file_writer(output_dir) # ty:ignore[possibly-unresolved-reference] + self.__stream.set_as_default() def on_optimize_end(self, logs: dict[str, Any] | None = None) -> None: if self.__stream: @@ -272,10 +271,10 @@ def on_function_call_end( return parameters = logs["parameters"] for par_name, value in parameters.items(): - tf.summary.scalar(par_name, value, step=function_call) + tf.summary.scalar(par_name, value, step=function_call) # ty:ignore[possibly-unresolved-reference] estimator_value = logs.get("estimator", {}).get("value", None) if estimator_value is not None: - tf.summary.scalar("estimator", estimator_value, step=function_call) + tf.summary.scalar("estimator", estimator_value, step=function_call) # ty:ignore[possibly-unresolved-reference] if self.__stream is not None: self.__stream.flush() @@ -376,7 +375,7 @@ def _empty_file(stream: IO | None) -> None: stream.truncate() -def _create_log( # pyright: ignore[reportUnusedFunction] +def _create_log( optimizer: type[Optimizer], estimator_value: float, estimator_type: type[Estimator], diff --git a/src/tensorwaves/optimizer/minuit.py b/src/tensorwaves/optimizer/minuit.py index 3cd776f6..5f382b8b 100644 --- a/src/tensorwaves/optimizer/minuit.py +++ b/src/tensorwaves/optimizer/minuit.py @@ -11,10 +11,7 @@ from tqdm.auto import tqdm from tensorwaves.interface import Estimator, FitResult, Optimizer, ParameterValue -from tensorwaves.optimizer.callbacks import ( - Callback, - _create_log, # pyright: ignore[reportPrivateUsage] -) +from tensorwaves.optimizer.callbacks import Callback, _create_log from tensorwaves.optimizer.parameter import ParameterFlattener if TYPE_CHECKING: @@ -113,9 +110,9 @@ def wrapped_gradient(pars: list) -> Iterable[float]: return parameter_handler.flatten(grad).values() minuit = iminuit.Minuit( - wrapped_function, + wrapped_function, # ty:ignore[invalid-argument-type] tuple(flattened_parameters.values()), - grad=wrapped_gradient if self.__use_gradient else None, + grad=wrapped_gradient if self.__use_gradient else None, # ty:ignore[invalid-argument-type] name=tuple(flattened_parameters), ) minuit.errors = tuple( diff --git a/src/tensorwaves/optimizer/scipy.py b/src/tensorwaves/optimizer/scipy.py index 6c3786f2..6d53d68f 100644 --- a/src/tensorwaves/optimizer/scipy.py +++ b/src/tensorwaves/optimizer/scipy.py @@ -13,7 +13,7 @@ from tensorwaves.interface import Estimator, FitResult, Optimizer, ParameterValue from tensorwaves.optimizer.parameter import ParameterFlattener -from .callbacks import Callback, _create_log # pyright: ignore[reportPrivateUsage] +from .callbacks import Callback, _create_log if TYPE_CHECKING: from collections.abc import Iterable, Mapping @@ -125,7 +125,7 @@ def wrapped_callback(pars: Iterable[float]) -> None: ) start_time = time.time() - fit_result = minimize( + fit_result = minimize( # ty:ignore[possibly-unresolved-reference] wrapped_function, list(flattened_parameters.values()), method=self.__method, diff --git a/tests/data/test_data.py b/tests/data/test_data.py index 18ba420a..77efecf5 100644 --- a/tests/data/test_data.py +++ b/tests/data/test_data.py @@ -12,7 +12,7 @@ NumpyUniformRNG, TFPhaseSpaceGenerator, TFUniformRealNumberGenerator, - _generate_without_progress_bar, # pyright: ignore[reportPrivateUsage] + _generate_without_progress_bar, finalize_progress_bar, ) from tensorwaves.function.sympy import create_function @@ -100,7 +100,7 @@ def test_generate_four_momenta_on_flat_distribution(self): def test_generate_without_progress_bar(capsys: CaptureFixture): class SilentGenerator(DataGenerator): def generate(self, size: int, rng: RealNumberGenerator) -> DataSample: - return {"x": 1} # type: ignore[dict-item] + return {"x": 1} # ty:ignore[invalid-return-type] class GeneratorWithProgressBar(DataGenerator): def __init__(self, show_progress: bool) -> None: @@ -113,7 +113,7 @@ def generate(self, size: int, rng: RealNumberGenerator) -> DataSample: for _ in range(5): progress_bar.update() finalize_progress_bar(progress_bar) - return {"x": 1} # type: ignore[dict-item] + return {"x": 1} # ty:ignore[invalid-return-type] gen_with_progress = GeneratorWithProgressBar(show_progress=True) rng = NumpyUniformRNG() diff --git a/tests/data/test_phasespace.py b/tests/data/test_phasespace.py index 6d2bf2b3..f38509fa 100644 --- a/tests/data/test_phasespace.py +++ b/tests/data/test_phasespace.py @@ -151,14 +151,14 @@ def test_generate_deterministic(self, pdg: "ParticleCollection"): ) phsp_momenta = phsp_generator.generate(sample_size, rng) assert list(phsp_momenta) == ["weights", "p0", "p1", "p2"] - weights = phsp_momenta.get("weights", []) # type: ignore[var-annotated] + weights = phsp_momenta.get("weights", []) del phsp_momenta["weights"] print("Expected values, get by running pytest with the -s flag") pprint({ i: np.round(four_momenta, decimals=10).tolist() for i, four_momenta in phsp_momenta.items() }) - expected_sample = { + expected_sample: DataSample = { "p0": [ [0.7059154068, 0.3572095625, 0.251997269, 0.2441281612], [0.6996310679, -0.3562654953, -0.1367339084, 0.3102348449], @@ -180,12 +180,14 @@ def test_generate_deterministic(self, pdg: "ParticleCollection"): [1.0453724039, -0.4184722905, 0.1657164432, 0.0993376439], [1.0952968558, 0.0391369828, 0.3976862844, -0.3995430142], ], - } + } # ty:ignore[invalid-assignment] n_events = len(next(iter(expected_sample.values()))) assert set(phsp_momenta) == set(expected_sample) - for i in expected_sample: # noqa: PLC0206 + for i in expected_sample: expected_momenta = expected_sample[i] momenta = phsp_momenta[i] + i, expected_momenta = next(reversed(expected_sample.items())) + momenta = phsp_momenta[i] assert len(expected_momenta) == n_events assert len(momenta) == n_events assert pytest.approx(momenta) == expected_sample[i] diff --git a/tests/data/test_rng.py b/tests/data/test_rng.py index 5b10035a..cd3d8f0d 100644 --- a/tests/data/test_rng.py +++ b/tests/data/test_rng.py @@ -3,7 +3,7 @@ from tensorwaves.data.rng import ( NumpyUniformRNG, TFUniformRealNumberGenerator, - _get_tensorflow_rng, # pyright: ignore[reportPrivateUsage] + _get_tensorflow_rng, ) diff --git a/tests/data/test_transform.py b/tests/data/test_transform.py index a1237293..984e07ab 100644 --- a/tests/data/test_transform.py +++ b/tests/data/test_transform.py @@ -18,7 +18,7 @@ def test_identity_chain(self, extend: bool): x, y, v, w = sp.symbols("x y v w") transform1 = _create_transformer({v: 2 * x - 5, w: -0.2 * y + 3}) transform2 = _create_transformer({x: 0.5 * (v + 5), y: 5 * (3 - w)}) - chained_transform = ChainedDataTransformer([transform1, transform2], extend) + chained_transform = ChainedDataTransformer([transform1, transform2], extend) # ty:ignore[invalid-argument-type] rng = np.random.default_rng(seed=0) data = {"x": rng.uniform(size=100), "y": rng.uniform(size=100)} transformed_data = chained_transform(data) @@ -35,7 +35,7 @@ def test_identity_chain(self, extend: bool): def test_single_chain(self): transform = IdentityTransformer() - chained_transform = ChainedDataTransformer([transform]) + chained_transform = ChainedDataTransformer([transform]) # ty:ignore[invalid-argument-type] data = { "x": np.ones(5), "y": np.ones(5), @@ -44,7 +44,7 @@ def test_single_chain(self): assert data is not chained_transform(data) # DataSample returned as new dict -def _create_transformer(expressions: dict[sp.Symbol, sp.Expr]) -> SympyDataTransformer: +def _create_transformer(expressions: dict[sp.Basic, sp.Expr]) -> SympyDataTransformer: return SympyDataTransformer.from_sympy(expressions, backend="jax") @@ -72,6 +72,6 @@ def test_polar_to_cartesian_coordinates(self, backend): "r": np.ones(4), "phi": np.array([0, np.pi / 4, np.pi / 2, np.pi]), } - output = converter(input_data) # type: ignore[arg-type] + output = converter(input_data) assert pytest.approx(output["x"]) == [1, sqrt(2) / 2, 0, -1] assert pytest.approx(output["y"]) == [0, sqrt(2) / 2, 1, 0] diff --git a/tests/function/test_ampform.py b/tests/function/test_ampform.py index a7e8c794..75faef69 100644 --- a/tests/function/test_ampform.py +++ b/tests/function/test_ampform.py @@ -24,7 +24,7 @@ def test_complex_sqrt(backend: str): kwargs["dtype"] = find_function("complex64", backend) values = linspace(-4, +4, 9, **kwargs) data = {"x": values} - output_array = function(data) # type: ignore[arg-type] + output_array = function(data) # ty:ignore[invalid-argument-type] np.testing.assert_almost_equal(output_array, complex_sqrt(data["x"])) diff --git a/tests/function/test_backend.py b/tests/function/test_backend.py index 97c377fd..6bb150e9 100644 --- a/tests/function/test_backend.py +++ b/tests/function/test_backend.py @@ -21,7 +21,7 @@ def test_find_function_numpy(): def test_find_function_tf(): import tensorflow as tf - import tensorflow.experimental.numpy as tnp # pyright: ignore[reportMissingImports] + import tensorflow.experimental.numpy as tnp # ty:ignore[unresolved-import] assert find_function("array", backend="tf") is tnp.array assert find_function("linspace", backend="tf") is tnp.linspace diff --git a/tests/function/test_sympy.py b/tests/function/test_sympy.py index a777c3f0..7b5810d0 100644 --- a/tests/function/test_sympy.py +++ b/tests/function/test_sympy.py @@ -1,15 +1,14 @@ from __future__ import annotations import logging -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, cast import numpy as np import pytest import sympy as sp -# pyright: ignore[reportPrivateUsage] from tensorwaves.function.sympy import ( - _collect_constant_sub_expressions, # pyright: ignore[reportPrivateUsage] + _collect_constant_sub_expressions, create_function, extract_constant_sub_expressions, fast_lambdify, @@ -93,7 +92,7 @@ def test_create_function(backend: str): @pytest.mark.parametrize("backend", ["jax", "math", "numpy", "tf"]) def test_create_function_indexed_symbol(backend: str): a = sp.IndexedBase("A") - expr = a[0] ** 2 + a[1] ** 2 # pyright:ignore[reportIndexIssue,reportOptionalOperand] + expr = a[0] ** 2 + a[1] ** 2 func = create_function(expr, backend=backend) assert func.argument_order == ("A[0]", "A[1]") @@ -175,7 +174,7 @@ def test_split_expression(): assert top_expr.free_symbols == set(sub_expressions) assert expression == top_expr.xreplace(sub_expressions) - free_symbols: set[sp.Symbol] = top_expr.free_symbols # type: ignore[assignment] + free_symbols = cast("set[sp.Symbol]", top_expr.free_symbols) sub_symbols = sorted(free_symbols, key=lambda s: s.name) assert len(sub_symbols) == 3 f0, f1, f2 = tuple(sub_symbols) diff --git a/tests/optimizer/test_fit_simple_model.py b/tests/optimizer/test_fit_simple_model.py index 680a1046..5dc4a5bc 100644 --- a/tests/optimizer/test_fit_simple_model.py +++ b/tests/optimizer/test_fit_simple_model.py @@ -8,13 +8,14 @@ from tensorwaves.estimator import UnbinnedNLL from tensorwaves.function.sympy import create_parametrized_function -from tensorwaves.optimizer import Minuit2, ScipyMinimizer from tensorwaves.optimizer.callbacks import ( CallbackList, CSVSummary, TFSummary, YAMLSummary, ) +from tensorwaves.optimizer.minuit import Minuit2 +from tensorwaves.optimizer.scipy import ScipyMinimizer if TYPE_CHECKING: from pathlib import Path @@ -42,7 +43,7 @@ def generate_data( rng: np.random.Generator, bunch_size: int = 10_000, ) -> DataSample: - collected_sample = {var: np.array([]) for var in boundaries} # type: ignore[var-annotated] + collected_sample = {var: np.array([]) for var in boundaries} some_variable = next(iter(boundaries)) while len(collected_sample[some_variable]) < size: phsp = generate_domain(bunch_size, boundaries, rng) @@ -92,7 +93,7 @@ def expression_and_parameters() -> tuple[sp.Expr, dict[sp.Symbol, float]]: @pytest.fixture(scope="session") def domain_and_data_sample( - expression_and_parameters: tuple[sp.Expr, dict[sp.Symbol, float]], + expression_and_parameters: tuple[sp.Expr, dict[sp.Basic, float]], ) -> tuple[DataSample, DataSample]: expression, parameter_defaults = expression_and_parameters function = create_parametrized_function( @@ -115,7 +116,7 @@ def domain_and_data_sample( def test_optimize_all_parameters( backend: str, domain_and_data_sample: tuple[DataSample, DataSample], - expression_and_parameters: tuple[sp.Expr, dict[sp.Symbol, float]], + expression_and_parameters: tuple[sp.Expr, dict[sp.Basic, float]], optimizer_type: type[Minuit2 | ScipyMinimizer], output_dir: Path, ): @@ -127,7 +128,7 @@ def test_optimize_all_parameters( backend=backend, ) original_parameters = function.parameters - estimator = UnbinnedNLL(function, data, domain, backend=backend) # type: ignore[arg-type] + estimator = UnbinnedNLL(function, data, domain, backend=backend) original_nll = estimator(function.parameters) callback_file = output_dir / f"simple_fit_{backend}_{optimizer_type.__name__}" @@ -136,7 +137,7 @@ def test_optimize_all_parameters( YAMLSummary(f"{callback_file}.yml"), ] try: - import tensorflow as tf # pyright: ignore[reportUnusedImport] # noqa: F401 + import tensorflow as tf # noqa: F401 callbacks.append(TFSummary()) except ImportError: @@ -198,7 +199,7 @@ def test_optimize_all_parameters( ) def test_tweak_minuit( domain_and_data_sample: tuple[DataSample, DataSample], - expression_and_parameters: tuple[sp.Expr, dict[sp.Symbol, float]], + expression_and_parameters: tuple[sp.Expr, dict[sp.Basic, float]], tol: float, expected_parameter_values: dict[str, float], ): diff --git a/tests/optimizer/test_minuit.py b/tests/optimizer/test_minuit.py index 59114352..96568b76 100644 --- a/tests/optimizer/test_minuit.py +++ b/tests/optimizer/test_minuit.py @@ -19,7 +19,7 @@ class Polynomial1DMinimaEstimator(Estimator): def __init__(self, polynomial: Callable) -> None: self.__polynomial = polynomial - def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: + def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: # ty:ignore[invalid-method-override] x = parameters["x"] return self.__polynomial(x) @@ -33,7 +33,7 @@ class Polynomial2DMinimaEstimator(Estimator): def __init__(self, polynomial: Callable) -> None: self.__polynomial = polynomial - def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: + def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: # ty:ignore[invalid-method-override] x = parameters["x"] y = parameters["y"] return self.__polynomial(x, y) diff --git a/tests/optimizer/test_scipy.py b/tests/optimizer/test_scipy.py index 03f6ec88..b1a186bf 100644 --- a/tests/optimizer/test_scipy.py +++ b/tests/optimizer/test_scipy.py @@ -19,7 +19,7 @@ class Polynomial1DMinimaEstimator(Estimator): def __init__(self, polynomial: Callable) -> None: self.__polynomial = polynomial - def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: + def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: # ty:ignore[invalid-method-override] x = parameters["x"] return self.__polynomial(x) @@ -33,7 +33,7 @@ class Polynomial2DMinimaEstimator(Estimator): def __init__(self, polynomial: Callable) -> None: self.__polynomial = polynomial - def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: + def __call__(self, parameters: Mapping[str, ParameterValue]) -> float: # ty:ignore[invalid-method-override] x = parameters["x"] y = parameters["y"] return self.__polynomial(x, y) diff --git a/typings/.gitignore b/typings/.gitignore deleted file mode 100644 index 8f4080f1..00000000 --- a/typings/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -*.pyi -/*/ diff --git a/typings/README.md b/typings/README.md deleted file mode 100644 index 472914d6..00000000 --- a/typings/README.md +++ /dev/null @@ -1,17 +0,0 @@ -# Stubs for external libraries - -To speed up linting and code navigation, it's often useful to generate -[stub files](https://mypy.readthedocs.io/en/stable/stubs.html) (`.pyi` files) for the -external libraries. You can do this using -[`stubgen`](https://mypy.readthedocs.io/en/stable/stubgen.html). For instance: - -```shell -stubgen -p sympy -o typings -``` - -Alternatively, use [Pyright](https://github.com/microsoft/pyright) to generate stub -files that contain docstrings as well: - -```shell -pyright --createstub sympy -``` diff --git a/typings/__init__.pyi b/typings/__init__.pyi deleted file mode 100644 index e69de29b..00000000 diff --git a/uv.lock b/uv.lock index 011383b2..42b65b4c 100644 --- a/uv.lock +++ b/uv.lock @@ -41,18 +41,14 @@ wheels = [ [[package]] name = "ampform" -version = "0.15.10" -source = { registry = "https://pypi.org/simple" } +version = "0.15.12.dev25+gfc1d4e292" +source = { git = "https://github.com/ComPWA/ampform?rev=fc1d4e2920954738bb6620905f0de0a73a5a93cd#fc1d4e2920954738bb6620905f0de0a73a5a93cd" } dependencies = [ { name = "attrs" }, { name = "frozendict" }, { name = "qrules" }, { name = "sympy" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/91/be/2462c20e2fc5148b4f8864c8efc3c93b52f209e997db00fdf77c4e494810/ampform-0.15.10.tar.gz", 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