diff --git a/.binder/postBuild b/.binder/postBuild new file mode 100755 index 0000000..c8dc1b4 --- /dev/null +++ b/.binder/postBuild @@ -0,0 +1,20 @@ +#!/bin/bash +set -ex +curl -LsSf https://pixi.sh/install.sh | bash +export PATH="$HOME/.pixi/bin:$PATH" + +pixi_packages="$(NO_COLOR= pixi list --explicit --no-install | awk 'NR > 1 {print $1}')" +if [[ -n "$pixi_packages" ]]; then + pixi global install $pixi_packages +fi +export PYTHONHASHSEED="0" +pixi clean cache --yes + +uv export \ + --extra jupyter \ + --extra notebooks \ + > requirements.txt +uv pip install \ + --requirement requirements.txt \ + --system +uv cache clean diff --git a/.binder/runtime.txt b/.binder/runtime.txt new file mode 100644 index 0000000..d2aca3a --- /dev/null +++ b/.binder/runtime.txt @@ -0,0 +1 @@ +python-3.12 diff --git a/.cspell.json b/.cspell.json index ca9b221..a163559 100644 --- a/.cspell.json +++ b/.cspell.json @@ -35,8 +35,7 @@ ".readthedocs.yml", ".vscode/*", "docs/conf.py", - "pyproject.toml", - "tox.ini" + "pyproject.toml" ], "language": "en-US", "overrides": [ @@ -89,6 +88,7 @@ "Mikhasenko", "NumPy", "parametrizations", + "Pixi", "plotly", "pyplot", "QRules", @@ -172,6 +172,7 @@ "iframe", "imag", "infty", + "installkernel", "ioff", "iplt", "ipykernel", @@ -242,6 +243,7 @@ "pycode", "pyfunc", "pygments", + "pyproject", "pytest", "quadpy", "rankdir", @@ -283,6 +285,7 @@ "unbinned", "unnormalized", "unsrt", + "venv", "viridis", "vmax", "vmin", diff --git a/.editorconfig b/.editorconfig index 5c33e7e..674376f 100644 --- a/.editorconfig +++ b/.editorconfig @@ -15,3 +15,6 @@ indent_size = 4 [LICENSE] indent_size = unset + +[uv.lock] +indent_size = 4 diff --git a/.envrc b/.envrc index e1d415a..c682fb0 100644 --- a/.envrc +++ b/.envrc @@ -1,10 +1,4 @@ -if [ -e .venv ]; then - source .venv/bin/activate -elif [ -e venv ]; then - source venv/bin/activate -elif [ -e .pixi ]; then - watch_file pixi.lock - eval "$(pixi shell-hook)" -else - layout anaconda -fi +watch_file pixi.lock +eval "$(pixi shell-hook)" +uv sync --all-extras --quiet +source .venv/bin/activate diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml deleted file mode 100644 index cc29e8f..0000000 --- a/.github/release-drafter.yml +++ /dev/null @@ -1,39 +0,0 @@ -name-template: ComPWA Technical Reports $NEXT_PATCH_VERSION -tag-template: $NEXT_PATCH_VERSION - -references: - - main - - epic/* - -categories: - - title: ✨ New features - label: ✨ Feature - - title: ⚠️ Enhancements and optimizations - label: ⚙️ Enhancement - - title: ⚠️ API changes - label: ⚠️ Interface - - title: ⚠️ Changes that may affect behavior - label: ❗ Behavior - - title: 🐛 Bug fixes - label: 🐛 Bug - - title: 📝 Documentation - label: 📝 Docs - - title: 🔨 Maintenance - label: 🔨 Maintenance - - title: 🖱️ Developer Experience - label: 🖱️ DX - -change-template: "- $TITLE (#$NUMBER)" - -replacers: - - search: /([A-Z]+!?:\s*)(.*)/g - replace: $2 - -sort-direction: ascending - -template: | - _See all documentation for this version [here](https://report.rtfd.io/en/$NEXT_PATCH_VERSION)._ - - $CHANGES - - _The full changelog as commits can be found [here](https://github.com/ComPWA/report/compare/$PREVIOUS_TAG...$NEXT_PATCH_VERSION)._ diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml deleted file mode 100644 index 678aa9b..0000000 --- a/.github/workflows/cd.yml +++ /dev/null @@ -1,16 +0,0 @@ -name: CD - -on: - release: - types: - - prereleased - - released - -jobs: - milestone: - if: startsWith(github.ref, 'refs/tags') - uses: ComPWA/actions/.github/workflows/close-milestone.yml@v1 - push: - if: startsWith(github.ref, 'refs/tags') && !github.event.release.prerelease - secrets: inherit - uses: ComPWA/actions/.github/workflows/push-to-version-branches.yml@v1 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 42616bb..1920091 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,19 +28,15 @@ on: jobs: doc: - uses: ComPWA/actions/.github/workflows/ci-docs.yml@v1 + uses: ComPWA/actions/.github/workflows/ci-docs.yml@v2 permissions: pages: write id-token: write with: - apt-packages: graphviz gh-pages: true - python-version: "3.12" specific-pip-packages: ${{ inputs.specific-pip-packages }} style: if: inputs.specific-pip-packages == '' secrets: token: ${{ secrets.PAT }} - uses: ComPWA/actions/.github/workflows/pre-commit.yml@v1 - with: - python-version: "3.12" + uses: ComPWA/actions/.github/workflows/pre-commit.yml@v2 diff --git a/.github/workflows/clean-caches.yml b/.github/workflows/clean-caches.yml index a66c407..7986e0c 100644 --- a/.github/workflows/clean-caches.yml +++ b/.github/workflows/clean-caches.yml @@ -14,9 +14,9 @@ on: jobs: cleanup: name: Remove caches - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: - - uses: ComPWA/actions/clean-caches@v1 + - uses: ComPWA/actions/clean-caches@v2 with: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} ref: ${{ inputs.ref }} diff --git a/.github/workflows/lock.yml b/.github/workflows/lock.yml new file mode 100644 index 0000000..583333d --- /dev/null +++ b/.github/workflows/lock.yml @@ -0,0 +1,24 @@ +name: Update + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: |- + ${{ github.ref != format('refs/heads/{0}', github.event.repository.default_branch) }} + +on: + pull_request: + branches: + - main + - epic/* + paths: + - .pre-commit-config.yaml + - Manifest.toml + - pixi.lock + - uv.lock + workflow_dispatch: + +jobs: + lock: + uses: ComPWA/actions/.github/workflows/lock.yml@v2 + secrets: + token: ${{ secrets.PAT }} diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml index d843c24..ded993c 100644 --- a/.github/workflows/notebooks.yml +++ b/.github/workflows/notebooks.yml @@ -11,34 +11,16 @@ on: jobs: pytest: name: Test all notebooks - runs-on: ubuntu-20.04 + runs-on: ubuntu-24.04 steps: - uses: actions/checkout@v4 - - uses: actions/cache@v4 - with: - key: | - ${{ github.workflow }}-${{ github.job }}-${{ runner.os }}-${{ hashFiles('.constraints/py3.*.txt', 'setup.cfg') }} - path: | - .pytest_cache - ~/.cache/pip/ - uses: actions/setup-python@v5 with: - python-version: "3.9" - - name: Install dependencies - run: | - sudo apt-get -y install graphviz - pip install .[test] - - run: | - function run-nbmake() { - set +e - pytest --nbmake ${{ github.event.inputs.notebook-selector }} - error_code=$? - set -e - echo "Pytest returned error code $error_code" - case $error_code in - 0|5) return 0;; - *) return $error_code;; - esac - } - run-nbmake - # cspell:ignore esac + python-version: "3.12" + - uses: astral-sh/setup-uv@v3 + with: + enable-cache: true + - name: Install graphviz + run: sudo apt-get -y install graphviz + - name: Run all notebooks + run: uv run --extra test pytest ${{ github.event.inputs.notebook-selector }} diff --git a/.github/workflows/pr-linting.yml b/.github/workflows/pr-linting.yml index 0fab841..44dc9e4 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@v1 + uses: ComPWA/actions/.github/workflows/pr-linting.yml@v2 diff --git a/.github/workflows/release-drafter.yml b/.github/workflows/release-drafter.yml deleted file mode 100644 index 5234093..0000000 --- a/.github/workflows/release-drafter.yml +++ /dev/null @@ -1,16 +0,0 @@ -name: Release Drafter - -on: - push: - branches: - - main - - epic/* - workflow_dispatch: - -jobs: - update_release_draft: - runs-on: ubuntu-22.04 - steps: - - uses: release-drafter/release-drafter@v6 - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.gitignore b/.gitignore index 555f993..c7bf960 100644 --- a/.gitignore +++ b/.gitignore @@ -21,7 +21,6 @@ version.py # Temporary files *.pyc -*condaenv.* .coverage .coverage.* .ipynb_checkpoints/ @@ -38,7 +37,6 @@ prof/ .pixi/ .tox/ *venv/ -pixi.lock pyvenv*/ # Settings @@ -53,6 +51,5 @@ pyvenv*/ !.readthedocs.yml !.vscode/*.json !codecov.yml -!environment.yml !pyrightconfig.json .jupyter_ystore.db diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index cd09839..820c9a6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,9 +1,9 @@ ci: - autoupdate_commit_msg: "MAINT: autoupdate pre-commit hooks" + autoupdate_commit_msg: "MAINT: update lock files" autoupdate_schedule: quarterly skip: - - pin-nb-requirements - pyright + - uv-lock repos: - repo: meta @@ -12,16 +12,15 @@ repos: - id: check-useless-excludes - repo: https://github.com/ComPWA/policy - rev: 0.4.1 + rev: 0.5.3 hooks: - id: check-dev-files args: - - --doc-apt-packages=graphviz - - --dev-python-version=3.12 - --github-pages - --imports-on-top - - --no-prettierrc + - --no-cd - --no-pypi + - --package-manager=pixi+uv - --repo-name=report - --repo-title=ComPWA Technical Reports - id: colab-toc-visible @@ -56,8 +55,27 @@ repos: metadata.varInspector metadata.vscode + - repo: https://github.com/nbQA-dev/nbQA + rev: 1.8.7 + hooks: + - id: nbqa-isort + args: [--float-to-top] + exclude: >- + (?x)^( + docs/001/index\.ipynb| + docs/002/index\.ipynb| + docs/003/index\.ipynb| + docs/008/index\.ipynb| + docs/013/index\.ipynb| + docs/018/index\.ipynb| + docs/020/index\.ipynb| + docs/026/index\.ipynb| + docs/027/index\.ipynb| + docs/028/index\.ipynb + )$ + - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.8 + rev: v0.7.1 hooks: - id: ruff args: [--fix] @@ -66,7 +84,7 @@ repos: types_or: [python, pyi, jupyter] - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v5.0.0 hooks: - id: check-ast - id: check-case-conflict @@ -103,7 +121,7 @@ repos: exclude: (?x)^(.*/Manifest\.toml|.*/Project\.toml)$ - repo: https://github.com/streetsidesoftware/cspell-cli - rev: v8.13.3 + rev: v8.15.2 hooks: - id: cspell @@ -128,38 +146,12 @@ repos: docs/_static/favicon.ico )$ - - repo: https://github.com/nbQA-dev/nbQA - rev: 1.8.7 - hooks: - - id: nbqa-isort - args: [--float-to-top] - exclude: >- - (?x)^( - docs/001\.ipynb| - docs/002\.ipynb| - docs/003\.ipynb| - docs/008\.ipynb| - docs/013\.ipynb| - docs/018\.ipynb| - docs/020\.ipynb| - docs/026\.ipynb| - docs/027\.ipynb| - docs/028\.ipynb - )$ - - - repo: local + - repo: https://github.com/ComPWA/pyright-pre-commit + rev: v1.1.386 hooks: - - id: pin-nb-requirements - name: Check whether notebook contains a pip install line - description: - Specify which packages to install specifically in order to run - this notebook. - entry: python3 .pre-commit/pin_nb_requirements.py - language: system - types: - - jupyter + - id: pyright - - repo: https://github.com/ComPWA/mirrors-pyright - rev: v1.1.382 + - repo: https://github.com/astral-sh/uv-pre-commit + rev: 0.4.26 hooks: - - id: pyright + - id: uv-lock diff --git a/.pre-commit/pin_nb_requirements.py b/.pre-commit/pin_nb_requirements.py deleted file mode 100644 index 48ce1ee..0000000 --- a/.pre-commit/pin_nb_requirements.py +++ /dev/null @@ -1,255 +0,0 @@ -"""Enforce adding a pip install statement in the notebook. - -In `github.com/ComPWA/report `_, notebooks should -specify which package versions should be used to run the notebook. This hook checks -whether a notebook has such install statements and whether they comply with the expected -formatting. -""" -# cspell:ignore oneline precommit - -from __future__ import annotations - -import argparse -import re -import sys -from functools import lru_cache -from textwrap import dedent -from typing import TYPE_CHECKING, Callable, TypeVar - -import attr -import nbformat -from nbformat import NotebookNode - -if TYPE_CHECKING: - from collections.abc import Sequence - -if sys.version_info >= (3, 10): - from typing import ParamSpec -else: - from typing_extensions import ParamSpec - -__EXPECTED_PIP_INSTALL_LINE = "%pip install -q" - - -def main(argv: Sequence[str] | None = None) -> int: - parser = argparse.ArgumentParser(__doc__) - parser.add_argument("filenames", nargs="*", help="Filenames to check.") - args = parser.parse_args(argv) - - errors: list[PrecommitError] = [] - for filename in args.filenames: - try: - check_pinned_requirements(filename) - except PrecommitError as exception: # noqa: PERF203 - errors.append(exception) - if errors: - for error in errors: - error_msg = "\n ".join(error.args) - print(error_msg) # noqa: T201 - return 1 - return 0 - - -def check_pinned_requirements(filename: str) -> None: - notebook = load_notebook(filename) - if not __has_python_kernel(notebook): - return - for cell_id, cell in enumerate(notebook["cells"]): - if cell["cell_type"] != "code": - continue - source = __to_oneline(cell["source"]) - pip_requirements = extract_pip_requirements(source) - if pip_requirements is None: - continue - executor = Executor() - executor(_check_pip_requirements, filename, pip_requirements) - executor(_format_pip_requirements, filename, source, notebook, cell_id) - executor(_update_metadata, filename, cell["metadata"], notebook) - executor.finalize() - return - msg = ( - f'Notebook "{filename}" does not contain a pip install cell of the form' - f" {__EXPECTED_PIP_INSTALL_LINE} some-package==0.1.0 package2==3.2" - ) - raise PrecommitError(msg) - - -def __has_python_kernel(notebook: dict) -> bool: - # cspell:ignore kernelspec - metadata = notebook.get("metadata", {}) - kernel_specification = metadata.get("kernelspec", {}) - kernel_language = kernel_specification.get("language", "") - return "python" in kernel_language - - -@lru_cache(maxsize=1) -def __to_oneline(source: str) -> str: - src_lines = source.split("\n") - return "".join(s.rstrip().rstrip("\\") for s in src_lines) - - -@lru_cache(maxsize=1) -def extract_pip_requirements(source: str) -> list[str] | None: - r"""Check if the source in a cell is a pip install statement. - - >>> extract_pip_requirements("Not a pip install statement") - >>> extract_pip_requirements("pip install") - [] - >>> extract_pip_requirements("pip3 install attrs") - ['attrs'] - >>> extract_pip_requirements("pip3 install -q attrs") - ['attrs'] - >>> extract_pip_requirements("pip3 install attrs &> /dev/null") - ['attrs'] - >>> extract_pip_requirements("%pip install attrs numpy==1.24.4 ") - ['attrs', 'numpy==1.24.4'] - >>> extract_pip_requirements("!python3 -mpip install sympy") - ['sympy'] - >>> extract_pip_requirements(''' - ... python3 -m pip install \ - ... attrs numpy \ - ... sympy \ - ... tensorflow - ... ''') - ['attrs', 'numpy', 'sympy', 'tensorflow'] - """ - # cspell:ignore mpip - matches = re.match( - r"[%\!]?\s*(python3?\s+-m\s*)?pip3?\s+install\s*(-q)?(.*?)(&?>\s*/dev/null)?$", - __to_oneline(source).strip(), - ) - if matches is None: - return None - packages = matches.group(3).split(" ") - packages = [p.strip() for p in packages] - return [p for p in packages if p] - - -def _check_pip_requirements(filename: str, requirements: list[str]) -> None: - if len(requirements) == 0: - msg = f'At least one dependency required in install cell of "{filename}"' - raise PrecommitError(msg) - for req in requirements: - req = req.strip() - if not req: - continue - if "git+" in req: - continue - unpinned_requirements = [] - for req in requirements: - if req.startswith("git+"): - continue - if any(equal_sign in req for equal_sign in ["==", "~="]): - continue - package = req.split("<")[0].split(">")[0].strip() - unpinned_requirements.append(package) - if unpinned_requirements: - msg = ( - f'Install cell in notebook "{filename}" contains requirements without' - "pinning (== or ~=):" - ) - for req in unpinned_requirements: - msg += f"\n - {req}" - msg_unformatted = f""" - Get the currently installed versions with: - - python3 -m pip freeze | grep -iE '{"|".join(sorted(unpinned_requirements))}' - """ - msg += dedent(msg_unformatted) - raise PrecommitError(msg) - - -def _format_pip_requirements( - filename: str, install_statement: str, notebook: NotebookNode, cell_id: int -) -> None: - requirements = extract_pip_requirements(install_statement) - if requirements is None: - return - git_requirements = {r for r in requirements if r.startswith("git+")} - pip_requirements = set(requirements) - git_requirements - pip_requirements = {r.lower().replace("_", "-") for r in pip_requirements} - pip_requirements = [__wrap_quotation_marks(r) for r in pip_requirements] - sorted_requirements = sorted(pip_requirements, key=__key) + sorted(git_requirements) - expected = f"{__EXPECTED_PIP_INSTALL_LINE} {' '.join(sorted_requirements)}" - if install_statement != expected: - notebook["cells"][cell_id]["source"] = expected - nbformat.write(notebook, filename) - msg = f'Ordered and formatted pip install cell in "{filename}"' - raise PrecommitError(msg) - - -def __wrap_quotation_marks(requirement: str) -> str: - if "[" in requirement and not requirement.startswith("'"): - return f"'{requirement}'" - return requirement - - -def __key(requirement: str) -> str: - return requirement.replace("'", "", 1).lower() - - -def _update_metadata(filename: str, metadata: dict, notebook: NotebookNode) -> None: - updated_metadata = False - jupyter_metadata = metadata.get("jupyter") - if jupyter_metadata is not None and jupyter_metadata.get("source_hidden"): - if len(jupyter_metadata) == 1: - metadata.pop("jupyter") - else: - jupyter_metadata.pop("source_hidden") - updated_metadata = True - tags = set(metadata.get("tags", [])) - expected_tags = {"remove-cell"} - if expected_tags != tags: - metadata["tags"] = sorted(expected_tags) - updated_metadata = True - if updated_metadata: - nbformat.write(notebook, filename) - msg = f'Updated metadata of pip install cell in notebook "{filename}"' - raise PrecommitError(msg) - - -def load_notebook(path: str) -> NotebookNode: - return nbformat.read(path, as_version=nbformat.NO_CONVERT) - - -T = TypeVar("T") -P = ParamSpec("P") - - -@attr.s(on_setattr=attr.setters.frozen) -class Executor: - # https://github.com/ComPWA/policy/blob/359331f/src/compwa_policy/utilities/executor.py - error_messages: list[str] = attr.ib(factory=list, init=False) - - def __call__( - self, function: Callable[P, T], *args: P.args, **kwargs: P.kwargs - ) -> T | None: - """Execute a function and collect any `.PrecommitError` exceptions.""" - try: - result = function(*args, **kwargs) - except PrecommitError as exception: - error_message = str("\n".join(exception.args)) - self.error_messages.append(error_message) - return None - else: - return result - - def finalize(self, exception: bool = True) -> int: - error_msg = self.merge_messages() - if error_msg: - if exception: - raise PrecommitError(error_msg) - print(error_msg) # noqa: T201 - return 1 - return 0 - - def merge_messages(self) -> str: - stripped_messages = (s.strip() for s in self.error_messages) - return "\n--------------------\n".join(stripped_messages) - - -class PrecommitError(RuntimeError): ... - - -if __name__ == "__main__": - raise SystemExit(main()) diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..e4fba21 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.12 diff --git a/.readthedocs.yml b/.readthedocs.yml index 9e27fca..c1d08b3 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,22 +1,19 @@ version: 2 -sphinx: - builder: html - configuration: docs/conf.py - fail_on_warning: true - -formats: - - htmlzip - build: - os: ubuntu-22.04 - apt_packages: - - graphviz + os: ubuntu-24.04 tools: python: "3.12" - jobs: - pre_install: - - ./docs/install-julia-on-rtd.sh - post_install: - - python -m pip install 'uv>=0.2.0' - - python -m uv pip install -e .[doc] + commands: + - |- + export PIXI_HOME=$READTHEDOCS_VIRTUALENV_PATH + curl -fsSL https://pixi.sh/install.sh | bash + export UV_LINK_MODE=copy + pixi run \ + uv run \ + --extra doc \ + --locked \ + --with tox \ + tox -e doc + mkdir -p $READTHEDOCS_OUTPUT + mv docs/_build/html $READTHEDOCS_OUTPUT diff --git a/.vscode/settings.json b/.vscode/settings.json index c31fb3d..16d1bd7 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -59,8 +59,9 @@ "ruff.importStrategy": "fromEnvironment", "ruff.organizeImports": true, "search.exclude": { + "**/pixi.lock": true, "**/tests/**/__init__.py": true, - ".constraints/*.txt": true + "**/uv.lock": true }, "telemetry.telemetryLevel": "off" } diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 97f0665..80210d0 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,5 +1,44 @@ # How to contribute? -[![Open in Visual Studio Code](https://img.shields.io/badge/vscode-open-blue?logo=visualstudiocode)](https://open.vscode.dev/ComPWA/report) +[![Open in Visual Studio Code](https://img.shields.io/badge/vscode-open-blue?logo=visualstudiocode)](https://github.dev/ComPWA/report) -This repository is part of the [ComPWA Organization](https://github.com/ComPWA). For more information about how to contribute to the packages, go to **[compwa.github.io/develop](https://compwa.github.io/develop)**! +> [!TIP] +> This package is part of the [ComPWA Organization](https://github.com/ComPWA). For more information about how to contribute to the packages, go to **[compwa.github.io/develop](https://compwa.github.io/develop)**! + +To contribute to the project, you need to install the package in a virtual environment. This can be done best with [`uv`](https://docs.astral.sh/uv) (see installation instructions [here](https://docs.astral.sh/uv/getting-started/installation)). For this, you first need to get the source code with [Git](https://git-scm.com): + +```shell +git clone https://github.com/ComPWA/report +cd report +``` + +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). + +```shell +uv sync +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 +``` + +and [`pre-commit install`](https://pre-commit.com/#3-install-the-git-hook-scripts) **once**: + +```shell +pre-commit install --install-hooks +``` + +In addition, it may be handy to install `tox`: + +```shell +uv tool install tox --with tox-uv +``` + +If the repository provides a Tox configuration under [`pyproject.toml`](./pyproject.toml), you can see which jobs it defines with: + +```shell +tox list +``` diff --git a/README.md b/README.md index 6a2c9f9..26abbb9 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,9 @@ [![Binder](https://static.mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ComPWA/report/main) [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ComPWA/report/blob/main) [![Open in Visual Studio Code](https://img.shields.io/badge/vscode-open-blue?logo=visualstudiocode)](https://open.vscode.dev/ComPWA/report) + +[![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) +[![Pixi Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json)](https://pixi.sh) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/ComPWA/report/main.svg)](https://results.pre-commit.ci/latest/github/ComPWA/report/main) [![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) diff --git a/docs/000.ipynb b/docs/000/index.ipynb similarity index 99% rename from docs/000.ipynb rename to docs/000/index.ipynb index ffecc30..dd6bb71 100644 --- a/docs/000.ipynb +++ b/docs/000/index.ipynb @@ -888,7 +888,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "A solution to this is presented in {ref}`001:Handle for JAX`." + "A solution to this is presented in {ref}`001/index:Handle for JAX`." ] } ], diff --git a/docs/000/pyproject.toml b/docs/000/pyproject.toml new file mode 100644 index 0000000..ccc8e51 --- /dev/null +++ b/docs/000/pyproject.toml @@ -0,0 +1,17 @@ +[tool.ruff] +preview = true + +[tool.ruff.lint] +ignore = [ + "ANN001", + "ANN201", + "COM812", + "CPY001", + "D", + "ISC001", + "T201", +] +select = ["ALL"] + +[tool.ruff.lint.flake8-builtins] +builtins-ignorelist = ["display"] diff --git a/docs/001.ipynb b/docs/001/index.ipynb similarity index 92% rename from docs/001.ipynb rename to docs/001/index.ipynb index 4515d33..72489fe 100644 --- a/docs/001.ipynb +++ b/docs/001/index.ipynb @@ -36,19 +36,6 @@ "" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q black==21.5b2 jax==0.4.28 jaxlib==0.4.28 numpy~=1.26.4 sympy==1.8" - ] - }, { "cell_type": "code", "execution_count": null, @@ -82,7 +69,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "As noted in [TR-000](000.ipynb), it's hard to lambdify a {func}`sympy.sqrt ` to {doc}`JAX `. One possible way out is to define a custom class that derives from {class}`sympy.Expr ` and {doc}`overwrite its printer methods `." + "As noted in [TR-000](../000/index.ipynb), it's hard to lambdify a {func}`sympy.sqrt ` to {doc}`JAX `. One possible way out is to define a custom class that derives from {class}`sympy.Expr ` and {doc}`overwrite its printer methods `." ] }, { @@ -342,7 +329,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Just as noted in {ref}`000:Complex square root` though, {mod}`numpy.emath` is not provided by the NumPy API of {doc}`JAX `. As discussed there, we can at most decorate the {mod}`numpy.emath` version with {func}`jax.jit` and work with static arguments only:" + "Just as noted in {ref}`000/index:Complex square root` though, {mod}`numpy.emath` is not provided by the NumPy API of {doc}`JAX `. As discussed there, we can at most decorate the {mod}`numpy.emath` version with {func}`jax.jit` and work with static arguments only:" ] }, { @@ -414,7 +401,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "As concluded in {ref}`000:Conditional square root`, the alternative to lambdify to {mod}`numpy.emath` is to lambdify to {func}`numpy.select`. This has some caveats, though, like that you should not use `__dict__`. Worse, JAX is not immediately supported as backend. Fortunately, we now know how to overwrite lambdify methods.\n", + "As concluded in {ref}`000/index:Conditional square root`, the alternative to lambdify to {mod}`numpy.emath` is to lambdify to {func}`numpy.select`. This has some caveats, though, like that you should not use `__dict__`. Worse, JAX is not immediately supported as backend. Fortunately, we now know how to overwrite lambdify methods.\n", "\n", "An additional tool we need now is to {doc}`define a new printer class ` for JAX, so that we can also define a special rendering method for `ComplexSqrt` in the case of JAX. Most of its printing methods should be the same as that of SymPy's `NumPyPrinter`, the rest we can overwrite:" ] @@ -446,8 +433,7 @@ " arg = expr.args[0]\n", " x = self._print(arg)\n", " return (\n", - " f\"select([less({x}, 0), True], [1j * sqrt(-{x}), sqrt({x})],\"\n", - " \" default=nan,)\"\n", + " f\"select([less({x}, 0), True], [1j * sqrt(-{x}), sqrt({x})], default=nan,)\"\n", " )" ] }, @@ -687,9 +673,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/001/pyproject.toml b/docs/001/pyproject.toml new file mode 100644 index 0000000..9feaecd --- /dev/null +++ b/docs/001/pyproject.toml @@ -0,0 +1,34 @@ +[project] +dependencies = [ + "black", + "jax", + "matplotlib", + "sympy", +] +name = "technical-report" +requires-python = "~=3.12.0" +version = "0.1.0" + +[tool.ruff] +preview 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+156,7 @@ }, "outputs": [], "source": [ - "output_file = Path(\"002/f0(980)-graph\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "graphviz.Source(dot).render(output_file, format=\"svg\");" + "graphviz.Source(dot).render(\"f0(980)-graph\", format=\"svg\");" ] }, { @@ -376,9 +373,7 @@ }, "outputs": [], "source": [ - "output_file = Path(\"002/collapsed-expression-tree\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "graphviz.Source(dot).render(output_file, format=\"svg\");" + "graphviz.Source(dot).render(\"collapsed-expression-tree\", format=\"svg\");" ] }, { @@ -443,9 +438,7 @@ }, "outputs": [], "source": [ - "output_file = Path(\"002/simple-expression-tree\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "graphviz.Source(dot).render(output_file, format=\"svg\");" + "graphviz.Source(dot).render(\"simple-expression-tree\", format=\"svg\");" ] }, { @@ -475,7 +468,7 @@ "source": [ ":::{margin}\n", "\n", - "We store the time with {mod}`timeit` for section {ref}`002:Arbitrary expressions`.\n", + "We store the time with {mod}`timeit` for section {ref}`002/index:Arbitrary expressions`.\n", "\n", ":::" ] @@ -678,7 +671,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "{ref}`Recall <002:Component structure>` what amplitude module expressed in its amplitude components looks like:" + "{ref}`Recall <002/index:Component structure>` what amplitude module expressed in its amplitude components looks like:" ] }, { @@ -857,9 +850,7 @@ }, "outputs": [], "source": [ - "output_file = Path(\"002/histogram-m12.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file);" + "fig.savefig(\"histogram-m12.svg\");" ] }, { @@ -1006,7 +997,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The problem with {ref}`002:Test with data` is that it requires a {obj}`~ampform.helicity.HelicityModel`. In {mod}`tensorwaves`, we want to work with general {class}`sympy.Expr `s though (see [`SympyModel`](https://tensorwaves.readthedocs.io/en/0.2.7/api/tensorwaves.model.html#tensorwaves.model.SympyModel)), where we don't have sub-{attr}`ampform.helicity.HelicityModel.components` available.\n", + "The problem with {ref}`002/index:Test with data` is that it requires a {obj}`~ampform.helicity.HelicityModel`. In {mod}`tensorwaves`, we want to work with general {class}`sympy.Expr `s though (see [`SympyModel`](https://tensorwaves.readthedocs.io/en/0.2.7/api/tensorwaves.model.html#tensorwaves.model.SympyModel)), where we don't have sub-{attr}`ampform.helicity.HelicityModel.components` available.\n", "\n", "Instead, we have to split up the lambdifying in a more general way that can handle arbitrary {class}`sympy.core.expr.Expr`s. For that we need:\n", "\n", @@ -1390,9 +1381,7 @@ }, "outputs": [], "source": [ - "output_file = Path(\"002/runtime-vs-operations.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file);" + "fig.savefig(\"runtime-vs-operations.svg\");" ] }, { @@ -1570,7 +1559,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "And indeed, this is **much faster** than {ref}`002:Approach 1: Generator` (it's even possible to parallelize this for loop):" + "And indeed, this is **much faster** than {ref}`002/index:Approach 1: Generator` (it's even possible to parallelize this for loop):" ] }, { @@ -1708,7 +1697,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "We can use the same input values as in {ref}`002:Test with data` to check that the resulting lambdified expression results in the same output." + "We can use the same input values as in {ref}`002/index:Test with data` to check that the resulting lambdified expression results in the same output." ] }, { @@ -1867,9 +1856,7 @@ }, "outputs": [], "source": [ - "output_file = Path(\"002/f0-graph\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "graphviz.Source(dot).render(output_file, format=\"svg\");" + "graphviz.Source(dot).render(\"f0-graph\", format=\"svg\");" ] }, { @@ -1883,7 +1870,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This makes it clear that the functions defined in {ref}`002:Arbitrary expressions` results in a huge speed-up!" + "This makes it clear that the functions defined in {ref}`002/index:Arbitrary expressions` results in a huge speed-up!" ] }, { diff --git a/docs/002/pyproject.toml b/docs/002/pyproject.toml new file mode 100644 index 0000000..2364d02 --- /dev/null +++ b/docs/002/pyproject.toml @@ -0,0 +1,23 @@ +[tool.ruff] +preview = true + +[tool.ruff.lint] +ignore = [ + "ANN002", + "ANN20", + "ARG001", + "COM812", + "CPY001", + "D", + "DOC201", + "E501", + "F404", + "G004", + "ISC001", + "PD901", + "PLR2004", + "S101", + "T201", + "TCH003", +] +select = ["ALL"] diff --git a/docs/003.ipynb b/docs/003/index.ipynb similarity index 93% rename from docs/003.ipynb rename to docs/003/index.ipynb index 39a1812..2193394 100644 --- a/docs/003.ipynb +++ b/docs/003/index.ipynb @@ -35,19 +35,6 @@ "# Chew-Mandelstam" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q ampform==0.14.10 black==23.12.1 mpl-interactions~=0.24.2 scipy==1.12.0" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -74,10 +61,8 @@ "%config InlineBackend.figure_formats = ['svg']\n", "\n", "import inspect\n", - "import os\n", "import warnings\n", "from functools import partial\n", - "from pathlib import Path\n", "from typing import Any\n", "\n", "import black\n", @@ -105,30 +90,6 @@ "PDG = qrules.load_pdg()" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "cellView": "form", - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "# @title\n", - "if \"COLAB_RELEASE_TAG\" in os.environ:\n", - " import subprocess\n", - "\n", - " from google.colab import output\n", - "\n", - " output.enable_custom_widget_manager()\n", - " subprocess.run(\"pip install -q ipympl\".split(), check=False)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -454,20 +415,21 @@ "ylim = (-1, +1)\n", "y_factor = 16 * np.pi\n", "controls = iplt.axvline(\n", - " lambda *args, **kwargs: (kwargs[\"m1\"] + kwargs[\"m2\"]) ** 2,\n", + " lambda *args, **kwargs: (kwargs[\"m1\"].value + kwargs[\"m2\"].value) ** 2,\n", " **sliders,\n", " ax=ax1,\n", " **threshold_style,\n", ")\n", "iplt.axvline(\n", - " lambda *args, **kwargs: (kwargs[\"m1\"] + kwargs[\"m2\"]) ** 2,\n", + " lambda *args, **kwargs: (kwargs[\"m1\"].value + kwargs[\"m2\"].value) ** 2,\n", " controls=controls,\n", " ax=ax2,\n", " **threshold_style,\n", ")\n", + "to_values = lambda kwargs: {k: v.value for k, v in kwargs.items()}\n", "iplt.plot(\n", " plot_domain,\n", - " lambda *args, **kwargs: (y_factor * 1j * rho_func(*args, **kwargs)).real,\n", + " lambda *args, **kwargs: (y_factor * 1j * rho_func(*args, **to_values(kwargs))).real,\n", " controls=controls,\n", " ylim=ylim,\n", " xlim=xlim,\n", @@ -477,7 +439,7 @@ ")\n", "iplt.plot(\n", " plot_domain,\n", - " lambda *args, **kwargs: (y_factor * 1j * rho_func(*args, **kwargs)).imag,\n", + " lambda *args, **kwargs: (y_factor * 1j * rho_func(*args, **to_values(kwargs))).imag,\n", " controls=controls,\n", " ylim=ylim,\n", " xlim=xlim,\n", @@ -488,7 +450,7 @@ "\n", "iplt.plot(\n", " plot_domain,\n", - " lambda *args, **kwargs: y_factor * cm_func(*args, **kwargs).real,\n", + " lambda *args, **kwargs: y_factor * cm_func(*args, **to_values(kwargs)).real,\n", " controls=controls,\n", " ylim=ylim,\n", " xlim=xlim,\n", @@ -498,7 +460,7 @@ ")\n", "iplt.plot(\n", " plot_domain,\n", - " lambda *args, **kwargs: y_factor * cm_func(*args, **kwargs).imag,\n", + " lambda *args, **kwargs: y_factor * cm_func(*args, **to_values(kwargs)).imag,\n", " controls=controls,\n", " ylim=ylim,\n", " xlim=xlim,\n", @@ -519,9 +481,7 @@ "ax1.set_title(R\"Complex phase space factor $\\rho$\")\n", "ax2.set_title(\"Chew-Mandelstam $S$-wave ($L=0$)\")\n", "\n", - "output_file = Path(\"003/chew-mandelstam-s-wave.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + "fig.savefig(\"chew-mandelstam-s-wave.svg\")\n", "plt.show()" ] }, @@ -737,7 +697,7 @@ "metadata": {}, "source": [ ":::{note}\n", - "Integrals can be expressed symbolically with SymPy, with some caveats. See {ref}`016:SymPy integral`.\n", + "Integrals can be expressed symbolically with SymPy, with some caveats. See {ref}`016/index:SymPy integral`.\n", ":::" ] }, @@ -745,7 +705,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "As discussed in [TR-016](016.ipynb), {func}`scipy.integrate.quad` cannot integrate over complex-valued functions, but {func}`scipy.integrate.quad_vec` can. For comparison, we now compute this integral for a few values of $L>0$:" + "As discussed in [TR-016](../016/index.ipynb), {func}`scipy.integrate.quad` cannot integrate over complex-valued functions, but {func}`scipy.integrate.quad_vec` can. For comparison, we now compute this integral for a few values of $L>0$:" ] }, { @@ -795,7 +755,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Finally, as can be seen from Eq. {eq}`dispersion-integral`, the resulting values from the integral have to be shifted with a factor $\\frac{s-s_{\\mathrm{thr}_a}}{\\pi}$ to get $\\Sigma_a$. We also scale the values with $16\\pi$ so that it can be compared with the plot generated in {ref}`003:S-wave`." + "Finally, as can be seen from Eq. {eq}`dispersion-integral`, the resulting values from the integral have to be shifted with a factor $\\frac{s-s_{\\mathrm{thr}_a}}{\\pi}$ to get $\\Sigma_a$. We also scale the values with $16\\pi$ so that it can be compared with the plot generated in {ref}`003/index:S-wave`." ] }, { @@ -831,7 +791,7 @@ " tight_layout=True,\n", ")\n", "fig.suptitle(f\"Dispersion integrals for $m_1={m1_val:.2f}, m_2={m2_val:.2f}$\")\n", - "for ax, l_val in zip(axes, l_values):\n", + "for ax, l_val in zip(axes, l_values, strict=True):\n", " ax.axhline(0, linewidth=0.5, c=\"black\")\n", " ax.axvline(s_thr_val, **threshold_style)\n", " ax.plot(s_domain, sigma_scaled[l_val].real, **real_style)\n", @@ -841,10 +801,7 @@ "axes[-1].set_xlabel(\"$s$ (GeV$^2$)\")\n", "axes[0].legend()\n", "\n", - "\n", - "output_file = Path(\"003/chew-mandelstam-l-non-zero.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + "fig.savefig(\"chew-mandelstam-l-non-zero.svg\")\n", "plt.show()" ] }, @@ -866,7 +823,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In the following, we attempt to implement Equation {eq}`dispersion-integral` using {ref}`016:SymPy integral`." + "In the following, we attempt to implement Equation {eq}`dispersion-integral` using {ref}`016/index:SymPy integral`." ] }, { @@ -1106,7 +1063,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Note that the dispersion integral for $L=0$ indeed reproduces the same shape as in {ref}`003:S-wave`!" + "Note that the dispersion integral for $L=0$ indeed reproduces the same shape as in {ref}`003/index:S-wave`!" ] }, { @@ -1148,9 +1105,7 @@ "ax1.legend()\n", "fig.tight_layout()\n", "\n", - "output_file = Path(\"003/symbolic-chew-mandelstam.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + "fig.savefig(\"symbolic-chew-mandelstam.svg\")\n", "plt.show()" ] }, @@ -1167,9 +1122,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { 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\"READTHEDOCS\"}.intersection(os.environ)" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "cellView": "form", - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "# @title\n", - "if \"COLAB_RELEASE_TAG\" in os.environ:\n", - " import subprocess\n", - "\n", - " from google.colab import output\n", - "\n", - " output.enable_custom_widget_manager()\n", - " subprocess.run(\"pip install -q ipympl\".split(), check=False)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -268,8 +230,7 @@ "if STATIC_WEB_PAGE:\n", " from IPython.display import Image\n", "\n", - " output_file = Path(\"004/3D-plot.png\")\n", - " output_file.parent.mkdir(exist_ok=True)\n", + " output_file = \"3D-plot.png\"\n", " plt.savefig(output_file)\n", " display(Image(output_file))" ] @@ -347,8 +308,7 @@ "if STATIC_WEB_PAGE:\n", " from IPython.display import Image\n", "\n", - " output_file = Path(\"004/interactive-locator.png\")\n", - " output_file.parent.mkdir(exist_ok=True)\n", + " output_file = \"interactive-locator.png\"\n", " plt.savefig(output_file)\n", " display(Image(output_file))" ] @@ -551,8 +511,7 @@ "if STATIC_WEB_PAGE:\n", " from IPython.display import SVG\n", "\n", - " output_file = Path(\"004/physical-vs-unphysical.svg\")\n", - " output_file.parent.mkdir(exist_ok=True)\n", + " output_file = \"physical-vs-unphysical.svg\"\n", " plt.savefig(output_file)\n", " display(SVG(output_file))" ] @@ -563,9 +522,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/004/pyproject.toml b/docs/004/pyproject.toml new file mode 100644 index 0000000..e589b33 --- /dev/null +++ b/docs/004/pyproject.toml @@ -0,0 +1,37 @@ +[project] +dependencies = [ + "ampform~=0.14.10", + 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We here describe only the version that is **not Lorentz-invariant**, because it is simplest and allows us to check whether the case $n_R=1, n=1$ (single resonance, single channel) reduces to a Breit-Wigner function. We followed the physics as described by {pdg-review}`Resonances` and {cite}`Chung:1995dx,petersPartialWaveAnalysis2004,meyerMatrixTutorial2008`. For the Lorentz-invariant version, see [TR-009](009.ipynb).\n", + "This report investigates how to implement $K$-matrix dynamics with {doc}`SymPy `. We here describe only the version that is **not Lorentz-invariant**, because it is simplest and allows us to check whether the case $n_R=1, n=1$ (single resonance, single channel) reduces to a Breit-Wigner function. We followed the physics as described by {pdg-review}`Resonances` and {cite}`Chung:1995dx,petersPartialWaveAnalysis2004,meyerMatrixTutorial2008`. For the Lorentz-invariant version, see [TR-009](../009/index.ipynb).\n", "\n", "A brief overview of the origin of the $\\boldsymbol{K}$-matrix is given first. This overview follows {cite}`Chung:1995dx`, but skips over quite a few details, as this is only an attempt to provide some context of what is going on." ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q ampform==0.11.* mpl-interactions~=0.24.2" - ] - }, { "cell_type": "code", "execution_count": null, @@ -100,30 +87,6 @@ "warnings.filterwarnings(\"ignore\")" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "cellView": "form", - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "# @title\n", - "if \"COLAB_RELEASE_TAG\" in os.environ:\n", - " import subprocess\n", - "\n", - " from google.colab import output\n", - "\n", - " output.enable_custom_widget_manager()\n", - " subprocess.run(\"pip install -q ipympl\".split(), check=False)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -202,9 +165,9 @@ }, "outputs": [], "source": [ - "output_file = Path(\"005/two-body-scattering\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "graph.render(output_file, format=\"svg\");" + "output_file = Path(\"two-body-scattering\")\n", + "graph.render(output_file, format=\"svg\")\n", + "output_file.unlink()" ] }, { @@ -286,7 +249,7 @@ "source": [ "The challenge is to generate a correct parametrization for an arbitrary **number of coupled channels $n$** and an arbitrary **number of resonances $n_R$**. Our approach is to construct an $n \\times n$ {obj}`sympy.Matrix ` with {class}`~sympy.core.symbol.Symbol`s as its elements. We then use substitute these {class}`~sympy.core.symbol.Symbol`s with certain parametrizations using {meth}`~sympy.core.basic.Basic.subs`. In order to generate symbols for $n_R$ resonances and $n$ channels, we use {doc}`indexed symbols `.\n", "\n", - "This approach is less elegant and (theoretically) slower than using {class}`~sympy.matrices.expressions.MatrixSymbol`s. That approach is explored in [TR-007](007.ipynb)." + "This approach is less elegant and (theoretically) slower than using {class}`~sympy.matrices.expressions.MatrixSymbol`s. That approach is explored in [TR-007](../007/index.ipynb)." ] }, { @@ -762,7 +725,7 @@ "\n", ":::{margin}\n", "\n", - "[TR-008](008.ipynb) explains the need for {func}`symplot.substitute_indexed_symbols`.\n", + "[TR-008](../008/index.ipynb) explains the need for {func}`symplot.substitute_indexed_symbols`.\n", "\n", ":::" ] @@ -865,6 +828,7 @@ " # 2D plot\n", " def plot(channel: int):\n", " def wrapped(*args, **kwargs) -> sp.Expr:\n", + " kwargs = {k: v.value for k, v in kwargs.items()}\n", " kwargs[\"i\"] = channel\n", " return np.abs(np_expr(*args, **kwargs)) ** 2\n", "\n", @@ -888,7 +852,7 @@ " for name in controls.params:\n", " if not name.startswith(\"m\"):\n", " continue\n", - " iplt.axvline(controls[name], ax=ax_2d, **mass_line_style)\n", + " iplt.axvline(sliders[name].value, ax=ax_2d, **mass_line_style)\n", "\n", " # 3D plot\n", " color_mesh = None\n", @@ -1031,9 +995,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": 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true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "# @title\n", - "if \"COLAB_RELEASE_TAG\" in os.environ:\n", - " import subprocess\n", - "\n", - " from google.colab import output\n", - "\n", - " output.enable_custom_widget_manager()\n", - " subprocess.run(\"pip install -q ipympl\".split(), check=False)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -534,7 +497,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - ":::{seealso} {doc}`/023`\n", + ":::{seealso} {doc}`/023/index`\n", ":::" ] } @@ -544,9 +507,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/006/pyproject.toml b/docs/006/pyproject.toml new file mode 100644 index 0000000..ea18106 --- /dev/null +++ b/docs/006/pyproject.toml @@ -0,0 +1,39 @@ +[project] +dependencies = [ + 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In that report, the $\\boldsymbol{K}$ was constructed with a {obj}`sympy.Matrix `, but it might be more elegant to work with {class}`~sympy.matrices.expressions.MatrixSymbol`s.\n", + "This report is a sequel to [TR-005](../005/index.ipynb). In that report, the $\\boldsymbol{K}$ was constructed with a {obj}`sympy.Matrix `, but it might be more elegant to work with {class}`~sympy.matrices.expressions.MatrixSymbol`s.\n", "+++\n", "WIP\n", ":::\n", @@ -34,19 +34,6 @@ "# `MatrixSymbol`s" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q sympy==1.9" - ] - }, { "cell_type": "code", "execution_count": null, @@ -172,9 +159,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/007/pyproject.toml b/docs/007/pyproject.toml new file mode 100644 index 0000000..f7811be --- /dev/null +++ b/docs/007/pyproject.toml @@ -0,0 +1,24 @@ +[project] +dependencies = [ + "sympy", +] +name = "technical-report" +requires-python = "~=3.12.0" +version = "0.1.0" + +[tool.ruff] +preview = true + +[tool.ruff.lint] +ignore = [ + "COM812", + "CPY001", + "D", + "ISC001", +] +select = ["ALL"] + +[tool.ruff.lint.flake8-builtins] +builtins-ignorelist = ["display"] + +[tool.uv.workspace] diff --git a/docs/007/uv.lock b/docs/007/uv.lock new file mode 100644 index 0000000..0837024 --- /dev/null +++ b/docs/007/uv.lock @@ -0,0 +1,34 @@ +version = 1 +requires-python = ">=3.12.0, <3.13" + +[[package]] +name = "mpmath" +version = "1.3.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/e0/47/dd32fa426cc72114383ac549964eecb20ecfd886d1e5ccf5340b55b02f57/mpmath-1.3.0.tar.gz", hash = "sha256:7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f", size = 508106 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/43/e3/7d92a15f894aa0c9c4b49b8ee9ac9850d6e63b03c9c32c0367a13ae62209/mpmath-1.3.0-py3-none-any.whl", hash = "sha256:a0b2b9fe80bbcd81a6647ff13108738cfb482d481d826cc0e02f5b35e5c88d2c", size = 536198 }, +] + +[[package]] +name = "sympy" +version = "1.13.3" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "mpmath" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/11/8a/5a7fd6284fa8caac23a26c9ddf9c30485a48169344b4bd3b0f02fef1890f/sympy-1.13.3.tar.gz", hash = "sha256:b27fd2c6530e0ab39e275fc9b683895367e51d5da91baa8d3d64db2565fec4d9", size = 7533196 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/99/ff/c87e0622b1dadea79d2fb0b25ade9ed98954c9033722eb707053d310d4f3/sympy-1.13.3-py3-none-any.whl", hash = "sha256:54612cf55a62755ee71824ce692986f23c88ffa77207b30c1368eda4a7060f73", size = 6189483 }, +] + +[[package]] +name = "technical-report" +version = "0.1.0" +source = { virtual = "." } +dependencies = [ + { name = "sympy" }, +] + +[package.metadata] +requires-dist = [{ name = "sympy" }] diff --git a/docs/008.ipynb b/docs/008/index.ipynb similarity index 91% rename from docs/008.ipynb rename to docs/008/index.ipynb index 1085ea7..131e691 100644 --- a/docs/008.ipynb +++ b/docs/008/index.ipynb @@ -34,24 +34,11 @@ "# `Indexed` free symbols" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q sympy==1.8" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ - "In [TR-005](005.ipynb), we made use of {doc}`indexed symbols ` to create a $\\boldsymbol{K}$-matrix. The problem with that approach is that {class}`~sympy.tensor.indexed.IndexedBase` and their resulting {class}`~sympy.tensor.indexed.Indexed` instances when taking indices behave strangely in an expression tree.\n", + "In [TR-005](../005/index.ipynb), we made use of {doc}`indexed symbols ` to create a $\\boldsymbol{K}$-matrix. The problem with that approach is that {class}`~sympy.tensor.indexed.IndexedBase` and their resulting {class}`~sympy.tensor.indexed.Indexed` instances when taking indices behave strangely in an expression tree.\n", "\n", "The following {class}`~sympy.core.expr.Expr` uses a {class}`~sympy.core.symbol.Symbol` and a elements in {class}`~sympy.tensor.indexed.IndexedBase`s (an {class}`~sympy.tensor.indexed.Indexed` instance):" ] @@ -249,9 +236,9 @@ }, "keep_output": true, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/008/pyproject.toml b/docs/008/pyproject.toml new file mode 100644 index 0000000..697fcc9 --- /dev/null +++ b/docs/008/pyproject.toml @@ -0,0 +1,22 @@ +[project] +dependencies = [ + "graphviz", + "sympy", +] +name = "technical-report" +requires-python = "~=3.12.0" +version = "0.1.0" + +[tool.ruff] +preview = true + +[tool.ruff.lint] +ignore = [ + "COM812", + "CPY001", + "D", + "ISC001", +] +select = ["ALL"] + +[tool.uv.workspace] diff --git a/docs/008/uv.lock b/docs/008/uv.lock new file mode 100644 index 0000000..b441b41 --- /dev/null +++ b/docs/008/uv.lock @@ -0,0 +1,47 @@ +version = 1 +requires-python = ">=3.12.0, <3.13" + +[[package]] +name = "graphviz" +version = "0.20.3" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/fa/83/5a40d19b8347f017e417710907f824915fba411a9befd092e52746b63e9f/graphviz-0.20.3.zip", hash = "sha256:09d6bc81e6a9fa392e7ba52135a9d49f1ed62526f96499325930e87ca1b5925d", size = 256455 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/00/be/d59db2d1d52697c6adc9eacaf50e8965b6345cc143f671e1ed068818d5cf/graphviz-0.20.3-py3-none-any.whl", hash = "sha256:81f848f2904515d8cd359cc611faba817598d2feaac4027b266aa3eda7b3dde5", size = 47126 }, +] + +[[package]] +name = "mpmath" +version = "1.3.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/e0/47/dd32fa426cc72114383ac549964eecb20ecfd886d1e5ccf5340b55b02f57/mpmath-1.3.0.tar.gz", hash = "sha256:7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f", size = 508106 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/43/e3/7d92a15f894aa0c9c4b49b8ee9ac9850d6e63b03c9c32c0367a13ae62209/mpmath-1.3.0-py3-none-any.whl", hash = "sha256:a0b2b9fe80bbcd81a6647ff13108738cfb482d481d826cc0e02f5b35e5c88d2c", size = 536198 }, +] + +[[package]] +name = "sympy" +version = "1.13.3" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "mpmath" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/11/8a/5a7fd6284fa8caac23a26c9ddf9c30485a48169344b4bd3b0f02fef1890f/sympy-1.13.3.tar.gz", hash = "sha256:b27fd2c6530e0ab39e275fc9b683895367e51d5da91baa8d3d64db2565fec4d9", size = 7533196 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/99/ff/c87e0622b1dadea79d2fb0b25ade9ed98954c9033722eb707053d310d4f3/sympy-1.13.3-py3-none-any.whl", hash = "sha256:54612cf55a62755ee71824ce692986f23c88ffa77207b30c1368eda4a7060f73", size = 6189483 }, +] + +[[package]] +name = "technical-report" +version = "0.1.0" +source = { virtual = "." } +dependencies = [ + { name = "graphviz" }, + { name = "sympy" }, +] + +[package.metadata] +requires-dist = [ + { name = "graphviz" }, + { name = "sympy" }, +] diff --git a/docs/009.ipynb b/docs/009/index.ipynb similarity index 95% rename from docs/009.ipynb rename to docs/009/index.ipynb index 8702e39..f4cdf01 100644 --- a/docs/009.ipynb +++ b/docs/009/index.ipynb @@ -23,7 +23,7 @@ ":::{card} Symbolic expressions for Lorentz-invariant K-matrix\n", "TR-009\n", "^^^\n", - "This report is a sequel to [TR-005](005.ipynb).\n", + "This report is a sequel to [TR-005](../005/index.ipynb).\n", "+++\n", "✅ [ampform#120](https://github.com/ComPWA/ampform/issues/120)\n", ":::\n", @@ -37,19 +37,6 @@ "# Lorentz-invariant K-matrix" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q ampform==0.10.5 mpl-interactions~=0.24.2 sympy==1.8" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -96,7 +83,7 @@ "\\boldsymbol{K} = \\sqrt{\\boldsymbol{\\rho^\\dagger}} \\; \\boldsymbol{\\hat{K}} \\sqrt{\\boldsymbol{\\rho}}\n", "$$ (covariant-K-matrix)\n", "\n", - "with (compare Eq. {eq}`T-in-terms-of-K` in [TR-005](005.ipynb)):\n", + "with (compare Eq. {eq}`T-in-terms-of-K` in [TR-005](../005/index.ipynb)):\n", "\n", "$$\n", "\\boldsymbol{\\hat{T}} = \\boldsymbol{\\hat{K}}(\\boldsymbol{I} - i\\boldsymbol{\\rho}\\boldsymbol{\\hat{K}})^{-1}\n", @@ -108,9 +95,9 @@ "K_{ij} = \\sum_R \\frac{g_{R,i}(m)g_{R,j}(m)}{\\left(m_R^2-m^2\\right)\\sqrt{\\rho_i\\rho_j}}\n", "$$ (covariant parametrization)\n", "\n", - "Compare this with Eq. {eq}`K-matrix-parametrization` in [TR-005](005.ipynb).\n", + "Compare this with Eq. {eq}`K-matrix-parametrization` in [TR-005](../005/index.ipynb).\n", "\n", - "In addition, one often uses an \"energy dependent\" [`coupled_width()`](https://ampform.readthedocs.io/en/0.10.5/api/ampform.dynamics.html#ampform.dynamics.coupled_width) $\\Gamma_R(m)$ instead of a fixed width $\\Gamma_R$ as done in [TR-005](005.ipynb)." + "In addition, one often uses an \"energy dependent\" [`coupled_width()`](https://ampform.readthedocs.io/en/0.10.5/api/ampform.dynamics.html#ampform.dynamics.coupled_width) $\\Gamma_R(m)$ instead of a fixed width $\\Gamma_R$ as done in [TR-005](../005/index.ipynb)." ] }, { @@ -155,30 +142,6 @@ "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "cellView": "form", - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "# @title\n", - "if \"COLAB_RELEASE_TAG\" in os.environ:\n", - " import subprocess\n", - "\n", - " from google.colab import output\n", - "\n", - " output.enable_custom_widget_manager()\n", - " subprocess.run(\"pip install -q ipympl\".split(), check=False)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -396,7 +359,7 @@ "source": [ ":::{note}\n", "\n", - "In `PhaseSpaceFactor`, we used {class}`~ampform.dynamics.phasespace.PhaseSpaceFactorComplex` instead of {class}`~ampform.dynamics.phasespace.PhaseSpaceFactor`, meaning that we choose the _positive_ square root when values under the square root are negative. The only reason for doing this is, so that there is output in the figure under {ref}`009:Visualization`. The choice for which square root to choose has to do with analyticity (see [TR-004](004.ipynb)) and choosing which Riemann sheet to connect to. This issue is ignored in this report.\n", + "In `PhaseSpaceFactor`, we used {class}`~ampform.dynamics.phasespace.PhaseSpaceFactorComplex` instead of {class}`~ampform.dynamics.phasespace.PhaseSpaceFactor`, meaning that we choose the _positive_ square root when values under the square root are negative. The only reason for doing this is, so that there is output in the figure under {ref}`009/index:Visualization`. The choice for which square root to choose has to do with analyticity (see [TR-004](../004/index.ipynb)) and choosing which Riemann sheet to connect to. This issue is ignored in this report.\n", "\n", ":::" ] @@ -412,7 +375,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The implementation is quite similar to {ref}`that of TR-005 <005:Generalization>`, with the only difference being additional $\\boldsymbol{\\rho}$-matrix and the insertion of coupled width. Don't forget to convert back to $\\boldsymbol{T}$ from $\\boldsymbol{\\hat{T}}$ with Eq. {eq}`covariant-T-matrix`." + "The implementation is quite similar to {ref}`that of TR-005 <005/index:Generalization>`, with the only difference being additional $\\boldsymbol{\\rho}$-matrix and the insertion of coupled width. Don't forget to convert back to $\\boldsymbol{T}$ from $\\boldsymbol{\\hat{T}}$ with Eq. {eq}`covariant-T-matrix`." ] }, { @@ -657,7 +620,7 @@ "source": [ ":::{margin}\n", "\n", - "[TR-008](008.ipynb) explains the need for {func}`symplot.substitute_indexed_symbols`.\n", + "[TR-008](../008/index.ipynb) explains the need for {func}`symplot.substitute_indexed_symbols`.\n", "\n", ":::" ] @@ -1007,9 +970,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/009/pyproject.toml b/docs/009/pyproject.toml new file mode 100644 index 0000000..059c746 --- /dev/null +++ b/docs/009/pyproject.toml @@ -0,0 +1,40 @@ +[project] +dependencies = [ + "ampform~=0.10.5", + "ipympl", + "ipywidgets", + "matplotlib", + "mpl-interactions", +] +name = "technical-report" +requires-python = "~=3.9.0" +version = 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mpl-interactions~=0.24.2 sympy==1.8" - ] - }, { "cell_type": "code", "execution_count": null, @@ -97,30 +84,6 @@ "STATIC_WEB_PAGE = {\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "cellView": "form", - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "# @title\n", - "if \"COLAB_RELEASE_TAG\" in os.environ:\n", - " import subprocess\n", - "\n", - " from google.colab import output\n", - "\n", - " output.enable_custom_widget_manager()\n", - " subprocess.run(\"pip install -q ipympl\".split(), check=False)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -136,7 +99,7 @@ ] }, "source": [ - "As described in [TR-005](005.ipynb), the $\\boldsymbol{K}$-matrix describes **scattering processes** of the type $cd \\to ab$. The $P$-vector approach is one of two generalizations for **production processes** of the type $c \\to ab$. For more details on this approach, {cite}`Chung:1995dx` refers to {cite}`Aitchison:1972ay`.\n", + "As described in [TR-005](../005/index.ipynb), the $\\boldsymbol{K}$-matrix describes **scattering processes** of the type $cd \\to ab$. The $P$-vector approach is one of two generalizations for **production processes** of the type $c \\to ab$. For more details on this approach, {cite}`Chung:1995dx` refers to {cite}`Aitchison:1972ay`.\n", "\n", "If we take the production vector $P$ to be:\n", "\n", @@ -166,7 +129,7 @@ "$$ (K-hat in terms of K)\n", "\n", "\n", - "Just like with the residue functions in [TR-005](005.ipynb) and [TR-009](009.ipynb), $\\beta$ is often expressed in terms of resonance mass and 'width':\n", + "Just like with the residue functions in [TR-005](../005/index.ipynb) and [TR-009](../009/index.ipynb), $\\beta$ is often expressed in terms of resonance mass and 'width':\n", "\n", "$$\n", "\\beta^0_R = \\beta_R\\sqrt{m_R\\Gamma^0_R}\n", @@ -747,9 +710,9 @@ }, "keep_output": true, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/010/pyproject.toml b/docs/010/pyproject.toml new file mode 100644 index 0000000..0330bda --- /dev/null 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and boosts in a class so with a nice LaTeX printer. {ref}`Later on <011:Define lambdification>`, a NumPy printer method will be defined externally for each of them." + "First, wrap rotations and boosts in a class so with a nice LaTeX printer. {ref}`Later on <011/index:Define lambdification>`, a NumPy printer method will be defined externally for each of them." ] }, { @@ -1075,7 +1072,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Note that the four classes like `FourMomentumX` expect an `ArraySymbol` as input. This requires [sympy/sympy#22265](https://github.com/sympy/sympy/issues/22265). This allows lambdifying the above expressions to valid NumPy code. Let's compare this with the existing implementation using the {ref}`011:Test sample`:" + "Note that the four classes like `FourMomentumX` expect an `ArraySymbol` as input. This requires [sympy/sympy#22265](https://github.com/sympy/sympy/issues/22265). This allows lambdifying the above expressions to valid NumPy code. Let's compare this with the existing implementation using the {ref}`011/index:Test sample`:" ] }, { @@ -4573,7 +4570,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Finally, what's left is to compare computed data with the {ref}`011:Test sample`. Here's a little comparison function that can be called for each angle:" + "Finally, what's left is to compare computed data with the {ref}`011/index:Test sample`. Here's a little comparison function that can be called for each angle:" ] }, { diff --git a/docs/011/pyproject.toml b/docs/011/pyproject.toml new file mode 100644 index 0000000..13569be --- /dev/null +++ b/docs/011/pyproject.toml @@ -0,0 +1,30 @@ +[tool.ruff] +preview = true + +[tool.ruff.lint] +ignore = [ + "ANN00", + "ANN20", + "ARG001", + "ARG002", + "COM812", + "CPY001", + "D", + "E501", + "F404", + "F821", + "ISC001", + "N802", + "N806", + "PLC2701", + "PLR2004", + "PLR6301", + "PYI034", + "S101", + "SLF001", + "T201", +] +select = ["ALL"] + +[tool.ruff.lint.flake8-builtins] +builtins-ignorelist = ["display"] diff --git a/docs/012.ipynb b/docs/012/index.ipynb similarity index 95% rename from docs/012.ipynb rename to docs/012/index.ipynb index 7d3b8e1..a21b24d 100644 --- a/docs/012.ipynb +++ b/docs/012/index.ipynb @@ -23,7 +23,7 @@ "^^^\n", "[ampform#198](https://github.com/ComPWA/ampform/issues/198) makes it easier to generate expressions for kinematic variables that are not contained in the [`HelicityModel.expression`](https://ampform.readthedocs.io/en/0.12.1/api/ampform.helicity.html#ampform.helicity.HelicityModel.expression). In TensorWaves, this results in a [`DataSample`](https://tensorwaves.readthedocs.io/en/0.4.x/api/tensorwaves.interface.html#tensorwaves.interface.DataSample) with more keys.\n", "\n", - "A question was raised whether this affects the duration of fits. This report shows that this is not the case (see {ref}`012:Conclusion`).\n", + "A question was raised whether this affects the duration of fits. This report shows that this is not the case (see {ref}`012/index:Conclusion`).\n", ":::\n", "::::" ] @@ -35,27 +35,6 @@ "# Extended `DataSample` performance" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Note: you may need to restart the kernel to use updated packages.\n" - ] - } - ], - "source": [ - "%pip install -q ampform==0.12.6 'tensorwaves[jax,pwa]==0.4.8'" - ] - }, { "cell_type": "code", "execution_count": null, @@ -349,9 +328,9 @@ }, "keep_output": true, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/012/pyproject.toml b/docs/012/pyproject.toml new file mode 100644 index 0000000..345dadc --- /dev/null +++ b/docs/012/pyproject.toml @@ -0,0 +1,23 @@ 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"+++\n", "WIP\n", ":::\n", @@ -36,19 +36,6 @@ "# Spin alignment with data" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q ampform==0.13.3 'qrules[viz]==0.9.7' 'tensorwaves[jax,pwa]==0.4.8'" - ] - }, { "cell_type": "code", "execution_count": null, @@ -205,10 +192,9 @@ "for i, t in enumerate(reaction.transitions[:: n // 3]):\n", " dot = qrules.io.asdot([t], collapse_graphs=True, size=3.5)\n", " graph = graphviz.Source(dot)\n", - " output_file = Path(f\"013/graph{i}\")\n", - " output_file.parent.mkdir(exist_ok=True)\n", + " output_file = Path(f\"graph{i}\")\n", " graph.render(output_file, format=\"svg\")\n", - " output_file.unlink(missing_ok=True)\n", + " output_file.unlink()\n", " display(graph)" ] }, @@ -620,9 +606,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": 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"tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q 'qrules[viz]==0.9.7' sympy==1.9 git+https://github.com/ComPWA/ampform@3ed3ed5" - ] - }, { "cell_type": "code", "execution_count": null, @@ -326,7 +313,7 @@ " def evaluate(self) -> sp.Expr:\n", " indices = dict(self.indices)\n", " return sum(\n", - " self.expression.subs(zip(indices, combi))\n", + " self.expression.subs(zip(indices, combi, strict=True))\n", " for combi in itertools.product(*indices.values())\n", " )\n", "\n", @@ -378,7 +365,7 @@ " if len(values) <= 1:\n", " return False\n", " sorted_values = sorted(values)\n", - " for val, next_val in zip(sorted_values, sorted_values[1:]):\n", + " for val, next_val in itertools.pairwise(sorted_values):\n", " difference = float(next_val - val)\n", " if difference != 1.0:\n", " return False\n", @@ -1236,7 +1223,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Dynamics pose a challenge that is similar to {ref}`014:Inserting coefficients` in that we have to introduce expressions that are dependent on spin. Still, as can be seen from the available attributes on a [`TwoBodyKinematicVariableSet`](https://ampform.readthedocs.io/en/0.12.3/api/ampform.dynamics.builder.html#ampform.dynamics.builder.TwoBodyKinematicVariableSet) (which serves as input to [`ResonanceDynamicsBuilder`](https://ampform.readthedocs.io/en/0.12.3/api/ampform.dynamics.builder.html#ampform.dynamics.builder.ResonanceDynamicsBuilder)s), dynamics (currently) cannot depend on helicities.\n", + "Dynamics pose a challenge that is similar to {ref}`014/index:Inserting coefficients` in that we have to introduce expressions that are dependent on spin. Still, as can be seen from the available attributes on a [`TwoBodyKinematicVariableSet`](https://ampform.readthedocs.io/en/0.12.3/api/ampform.dynamics.builder.html#ampform.dynamics.builder.TwoBodyKinematicVariableSet) (which serves as input to [`ResonanceDynamicsBuilder`](https://ampform.readthedocs.io/en/0.12.3/api/ampform.dynamics.builder.html#ampform.dynamics.builder.ResonanceDynamicsBuilder)s), dynamics (currently) cannot depend on helicities.\n", "\n", "What may become a problem are $LS$-combinations. So far we have only considered a [`ReactionInfo`](https://qrules.readthedocs.io/en/0.9.6/api/qrules.transition.html#qrules.transition.ReactionInfo) that was created with `formalism=\"helicity\"`, but we also have to sum over $LS$-combinations when using `formalism=\"canonical-helicity\"`. This is particularly important when using dynamics with form factors, which depend on [`angular_momentum`](https://ampform.readthedocs.io/en/0.12.3/api/ampform.dynamics.builder.html#ampform.dynamics.builder.TwoBodyKinematicVariableSet.angular_momentum).\n", "\n", @@ -1416,7 +1403,7 @@ "sum_expr = symplot.substitute_indexed_symbols(sum_expr)\n", "sum_expr = remove_coefficients(sum_expr)\n", "assert sum_expr.free_symbols == expr.free_symbols\n", - "for intensity1, intensity2 in zip(sum_expr.args, expr.args):\n", + "for intensity1, intensity2 in zip(sum_expr.args, expr.args, strict=True):\n", " # Annoyingly, Abs is rewritten with conjugates when using PoolSum...\n", " amp1 = intensity1.args[0]\n", " amp2 = intensity2.rewrite(sp.conjugate).args[0]\n", @@ -1676,9 +1663,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { 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+wheels = [ + { url = "https://files.pythonhosted.org/packages/21/02/88b65cc394961a60c43c70517066b6b679738caf78506a5da7b88ffcb643/widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71", size = 2335872 }, +] diff --git a/docs/015.ipynb b/docs/015/index.ipynb similarity index 98% rename from docs/015.ipynb rename to docs/015/index.ipynb index 3de2508..58dd18e 100644 --- a/docs/015.ipynb +++ b/docs/015/index.ipynb @@ -21,7 +21,7 @@ ":::{card} Spin alignment implementation\n", "TR-015\n", "^^^\n", - "This report has been implemented through [ampform#245](https://github.com/ComPWA/ampform/pull/245). For details on how to use it, see [this notebook](https://ampform.readthedocs.io/en/0.13.3/usage/helicity/spin-alignment.html). See also [TR-013](013.ipynb) and [TR-014](014.ipynb).\n", + "This report has been implemented through [ampform#245](https://github.com/ComPWA/ampform/pull/245). For details on how to use it, see [this notebook](https://ampform.readthedocs.io/en/0.13.3/usage/helicity/spin-alignment.html). See also [TR-013](../013/index.ipynb) and [TR-014](../014/index.ipynb).\n", "+++\n", "✅ [ampform#245](https://github.com/ComPWA/ampform/pull/245)\n", ":::\n", @@ -35,19 +35,6 @@ "# Spin alignment implementation" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q ampform==0.13.3 'qrules[viz]==0.9.7' sympy==1.10" - ] - }, { "cell_type": "code", "execution_count": null, @@ -372,7 +359,7 @@ "![](https://user-images.githubusercontent.com/29308176/164992512-f99faee9-2ca2-415c-975d-07ce16326914.svg)\n", "![](https://user-images.githubusercontent.com/29308176/164992514-d4c01c7c-7d2b-4842-8005-a8559523d001.svg)\n", "\n", - "The dashed edges and bars above the state IDs indicate \"opposite helicity\" states. The helicity of an **opposite helicity state** gets a minus sign in the Wigner-$D$ function for a two-body state as formulated by {external+ampform-0.14.x:func}`.formulate_wigner_d` (see {ref}`015:Helicity formalism`) and therefore needs to be defined consistently. AmpForm does this with {external+ampform-0.14.x:func}`.is_opposite_helicity_state`.\n", + "The dashed edges and bars above the state IDs indicate \"opposite helicity\" states. The helicity of an **opposite helicity state** gets a minus sign in the Wigner-$D$ function for a two-body state as formulated by {external+ampform-0.14.x:func}`.formulate_wigner_d` (see {ref}`015/index:Helicity formalism`) and therefore needs to be defined consistently. AmpForm does this with {external+ampform-0.14.x:func}`.is_opposite_helicity_state`.\n", "\n", "Opposite helicity states are also of importance in the spin alignment procedure sketched by {cite}`Marangotto:2019ucc`. The Wigner-$D$ functions that appear in Equations (45) and (46) from {cite}`Marangotto:2019ucc`, operate on the spin of the final state, but the angles in the Wigner-$D$ function are taken from the sibling state:" ] @@ -1350,7 +1337,7 @@ "metadata": {}, "source": [ ":::{tip}\n", - "A test with a larger data distribution is being developed in [TR-013](./013.ipynb).\n", + "A test with a larger data distribution is being developed in [TR-013](../013/index.ipynb).\n", ":::" ] }, @@ -1545,7 +1532,7 @@ "\n", ":::{note}\n", "\n", - "The {obj}`~numpy.nan` values above come from the fact that the inverse boost on a boost results in negative values under the square root of $\\gamma=\\sqrt{1-\\beta^2}$. This can be ignored, because the Wigner rotation is simply omitted when formulating the chain of rotation matrices, as noted in {ref}`015:Compute Wigner rotation angles`.\n", + "The {obj}`~numpy.nan` values above come from the fact that the inverse boost on a boost results in negative values under the square root of $\\gamma=\\sqrt{1-\\beta^2}$. This can be ignored, because the Wigner rotation is simply omitted when formulating the chain of rotation matrices, as noted in {ref}`015/index:Compute Wigner rotation angles`.\n", "\n", ":::" ] @@ -1624,9 +1611,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/015/pyproject.toml b/docs/015/pyproject.toml new file mode 100644 index 0000000..67db4f7 --- /dev/null +++ b/docs/015/pyproject.toml @@ -0,0 +1,28 @@ +[project] +dependencies = [ + "ampform[viz]~=0.13.3", + "numpy~=1.0", +] +name = "technical-report" +requires-python = "~=3.12.0" +version = "0.1.0" + +[tool.ruff] +preview = true + +[tool.ruff.lint] +ignore = [ + "ANN00", + "ANN201", + "COM812", + "CPY001", + "D", + "FBT001", + "ISC001", +] +select = ["ALL"] + +[tool.ruff.lint.flake8-builtins] +builtins-ignorelist = 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integral" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q ampform==0.14.10 black==23.12.1 scipy==1.12.0 sympy==1.12" - ] - }, { "cell_type": "code", "execution_count": null, @@ -269,7 +256,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The dispersion integral from Eq. {eq}`dispersion-integral` in **[TR-003](003.ipynb)** features a variable $s$ that is an argument to the function $\\Sigma_a$. This becomes a challenge when $s$ gets vectorized (in this case: gets an event-wise {obj}`numpy.array` of invariant masses). It seems that [`quad_vec()`](#quad_vec) can handle this well though." + "The dispersion integral from Eq. {eq}`dispersion-integral` in **[TR-003](../003/index.ipynb)** features a variable $s$ that is an argument to the function $\\Sigma_a$. This becomes a challenge when $s$ gets vectorized (in this case: gets an event-wise {obj}`numpy.array` of invariant masses). It seems that [`quad_vec()`](#quad_vec) can handle this well though." ] }, { @@ -301,7 +288,7 @@ "We now attempt to design [SymPy](https://docs.sympy.org) expression classes that correctly {func}`~sympy.utilities.lambdify.lambdify` using this **vectorized** numerical integral for handles complex values. Note that this integral expression class derives from {class}`sympy.Integral ` and that:\n", "\n", "1. overwrites its {meth}`~sympy.core.basic.Basic.doit` method, so that the integral cannot be evaluated by SymPy,\n", - "2. provides a custom NumPy printer method (see **[TR-001](001.ipynb)**) that lambdifies this expression node to [`quadpy.quad()`](https://github.com/sigma-py/quadpy),\n", + "2. provides a custom NumPy printer method (see **[TR-001](../001/index.ipynb)**) that lambdifies this expression node to [`quadpy.quad()`](https://github.com/sigma-py/quadpy),\n", "4. adds class variables that allow configuring [`quad_vec()`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.quad_vec.html),\n", "5. dummifies the integration variable in case it is not a valid Python variable name." ] @@ -477,7 +464,7 @@ "metadata": {}, "source": [ ":::{tip}\n", - "See how this integral expression class is applied to the phase space factor in **[TR-003](003.ipynb)**.\n", + "See how this integral expression class is applied to the phase space factor in **[TR-003](../003/index.ipynb)**.\n", ":::" ] } @@ -487,9 +474,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/016/pyproject.toml b/docs/016/pyproject.toml new file mode 100644 index 0000000..ac52709 --- /dev/null +++ b/docs/016/pyproject.toml @@ -0,0 +1,33 @@ +[project] +dependencies = [ + "ampform", + "black", + "matplotlib", + "scipy", + "sympy", +] +name = "technical-report" +requires-python = "~=3.12.0" +version = "0.1.0" + +[tool.ruff] +preview = true + +[tool.ruff.lint] +ignore = [ + "ANN00", + "ANN20", + "ARG002", + "C408", + "COM812", + "CPY001", + "D", + "ISC001", + "PLC2701", +] +select = ["ALL"] + +[tool.ruff.lint.flake8-self] +ignore-names = ["_print"] + +[tool.uv.workspace] diff --git 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InlineBackend.figure_formats = ['svg']" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "cellView": "form", - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "# @title\n", - "if \"COLAB_RELEASE_TAG\" in os.environ:\n", - " import subprocess\n", - "\n", - " from google.colab import output\n", - "\n", - " output.enable_custom_widget_manager()\n", - " subprocess.run(\"pip install -q ipympl\".split(), check=False)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -747,9 +709,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/017/pyproject.toml b/docs/017/pyproject.toml new file mode 100644 index 0000000..e0eb7cf --- /dev/null +++ b/docs/017/pyproject.toml @@ -0,0 +1,41 @@ +[project] 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rename to docs/018/index.ipynb index dec0198..ba7b998 100644 --- a/docs/018.ipynb +++ b/docs/018/index.ipynb @@ -35,19 +35,6 @@ "# Importance sampling" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q ampform==0.14.0 'qrules[viz]==0.9.7' scipy==1.8.0 sympy==1.10.1 'tensorwaves[jax,pwa]==0.4.8'" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -124,9 +111,9 @@ "import graphviz\n", "\n", "src = qrules.io.asdot(reaction, collapse_graphs=True)\n", - "output_file = Path(\"018/graph\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "_ = graphviz.Source(src).render(output_file, format=\"svg\")" + "output_file = Path(\"graph\")\n", + "graphviz.Source(src).render(output_file, format=\"svg\")\n", + "output_file.unlink()" ] }, { @@ -255,9 +242,7 @@ "mesh = ax.pcolormesh(X, Y, Z)\n", "c_bar = plt.colorbar(mesh, ax=ax)\n", "c_bar.ax.set_ylabel(bar_title)\n", - "output_file = Path(\"018/TFPhaseSpaceGenerator.png\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + "fig.savefig(\"TFPhaseSpaceGenerator.png\")\n", "plt.ion()\n", "plt.close(fig)" ] @@ -364,9 +349,7 @@ "\n", "plot_distribution_and_weights(unweighted_phsp, phsp_weights)\n", "plt.gcf().suptitle(\"TFWeightedPhaseSpaceGenerator sample\")\n", - "output_file = Path(\"018/TFWeightedPhaseSpaceGenerator.png\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "plt.savefig(output_file)\n", + "plt.savefig(\"TFWeightedPhaseSpaceGenerator.png\")\n", "plt.show()" ] }, @@ -463,9 +446,7 @@ "mesh = ax.pcolormesh(X, Y, Z)\n", "c_bar = plt.colorbar(mesh, ax=ax)\n", "c_bar.ax.set_ylabel(\"intensity\")\n", - "output_file = Path(\"018/intensity-distribution.png\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + "fig.savefig(\"intensity-distribution.png\")\n", "plt.ion()\n", "plt.close(fig)" ] @@ -518,9 +499,7 @@ "source": [ "plot_distribution_and_weights(importance_phsp, importance_weights)\n", "plt.gcf().suptitle(\"Importance-sampled phase space distribution\")\n", - "output_file = Path(\"018/importance-sampling.png\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "plt.savefig(output_file)\n", + "plt.savefig(\"importance-sampling.png\")\n", "plt.show()" ] }, @@ -580,9 +559,7 @@ "mesh = ax.pcolormesh(X, Y, Z)\n", "c_bar = plt.colorbar(mesh, ax=ax)\n", "c_bar.ax.set_ylabel(R\"new intensity $\\times$ importance weight\")\n", - "output_file = Path(\"018/importance-sampling-after-modification.png\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + "fig.savefig(\"importance-sampling-after-modification.png\")\n", "plt.ion()\n", "plt.close(fig)" ] @@ -600,9 +577,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, 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In this case, we activate the environment defined by the file [`019/Project.toml`](./019/Project.toml) and instantiate it so that the exact versions of the dependencies as defined in [`019/Manifest.toml`](./019/Manifest.toml) are installed." + "It's also possible to work with a local [environment](https://pkgdocs.julialang.org/v1/environments) from the notebook. In this case, we activate the environment defined by the file [`Project.toml`](./Project.toml) and instantiate it so that the exact versions of the dependencies as defined in [`Manifest.toml`](./Manifest.toml) are installed." ] }, { @@ -164,7 +164,7 @@ "outputs": [], "source": [ "using Pkg\n", - "Pkg.activate(joinpath(@__DIR__, \"019\"))\n", + "Pkg.activate(@__DIR__))\n", "Pkg.instantiate()" ] }, @@ -217,8 +217,7 @@ "end\n", " \n", "img = mandelbrot()\n", - "mkpath(\"019\")\n", - "save(\"019/mandelbrot_image.png\", img)" + "save(\"mandelbrot_image.png\", img)" ] }, { diff --git a/docs/020.ipynb b/docs/020/index.ipynb similarity index 98% rename from docs/020.ipynb rename to docs/020/index.ipynb index 5f1f909..8122d2b 100644 --- a/docs/020.ipynb +++ b/docs/020/index.ipynb @@ -37,19 +37,6 @@ "# Amplitude analysis with zfit" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q 'ampform[viz]~=0.14.1' hepstats~=0.6.0 pandas~=1.4.2 sympy~=1.10.1 'tensorwaves[jax,pwa]~=0.4.8' zfit~=0.10.0" - ] - }, { "cell_type": "code", "execution_count": null, @@ -428,7 +415,7 @@ " density=True,\n", ")\n", "ax.set_xlabel(\"$m$ [GeV]\")\n", - "for p, color in zip(resonances, colors):\n", + "for p, color in zip(resonances, colors, strict=True):\n", " ax.axvline(x=p.mass, linestyle=\"dotted\", label=p.name, color=color)\n", "ax.legend()\n", "plt.show()" @@ -585,7 +572,7 @@ "\n", "def indicate_masses(ax):\n", " ax.set_xlabel(\"$m$ [GeV]\")\n", - " for color, resonance in zip(colors, resonances):\n", + " for color, resonance in zip(colors, resonances, strict=True):\n", " ax.axvline(\n", " x=resonance.mass,\n", " linestyle=\"dotted\",\n", @@ -883,7 +870,10 @@ " \"\"\"tensorwaves intensity normalized over the *norm* dataset.\"\"\"\n", " super().__init__(obs, params, name)\n", " self.intensity = intensity\n", - " norm = {ob: jnp.asarray(ar) for ob, ar in zip(self.obs, z.unstack_x(norm))}\n", + " norm = {\n", + " ob: jnp.asarray(ar)\n", + " for ob, ar in zip(self.obs, z.unstack_x(norm), strict=True)\n", + " }\n", " self.norm_sample = norm\n", "\n", " @supports(norm=True)\n", @@ -897,7 +887,9 @@ " })\n", "\n", " # converting the data to a dict for tensorwaves\n", - " data = {ob: jnp.asarray(ar) for ob, ar in zip(self.obs, z.unstack_x(x))}\n", + " data = {\n", + " ob: jnp.asarray(ar) for ob, ar in zip(self.obs, z.unstack_x(x), strict=True)\n", + " }\n", "\n", " non_normalized_pdf = self.intensity(data)\n", " # this is not really needed, but can be useful for e.g. sampling with `pdf(..., norm_range=False)`\n", @@ -1311,7 +1303,7 @@ "def one_minus_cl_plot(x, pvalues, alpha=None, ax=None):\n", " if alpha is None:\n", " alpha = [0.32]\n", - " if isinstance(alpha, (float, int)):\n", + " if isinstance(alpha, float | int):\n", " alpha = [alpha]\n", " if ax is None:\n", " ax = plt.gca()\n", @@ -1353,9 +1345,9 @@ "toc_visible": true }, "kernelspec": { - 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-q ampform==0.14.4 qrules==0.9.7 sympy==1.11.1 'tensorwaves[jax]==0.4.8'" - ] - }, { "cell_type": "code", "execution_count": null, @@ -80,7 +67,6 @@ "import itertools\n", "import logging\n", "import os\n", - "from pathlib import Path\n", "from typing import TYPE_CHECKING\n", "\n", "import jax.numpy as jnp\n", @@ -152,30 +138,6 @@ "sp.Indexed._latex = _print_Indexed_latex" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "cellView": "form", - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "# @title\n", - "if \"COLAB_RELEASE_TAG\" in os.environ:\n", - " import subprocess\n", - "\n", - " from google.colab import output\n", - "\n", - " output.enable_custom_widget_manager()\n", - " subprocess.run(\"pip install -q ipympl\".split(), check=False)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -1361,7 +1323,7 @@ "source": [ "### Intensity expression\n", "\n", - "Incoherent sum of the amplitudes defined by {ref}`021:Aligned amplitude`:" + "Incoherent sum of the amplitudes defined by {ref}`021/index:Aligned amplitude`:" ] }, { @@ -1405,9 +1367,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Remaining {attr}`~sympy.core.basic.Basic.free_symbols` are indeed the specific amplitudes as defined by {ref}`021:Decay chain amplitudes`:\n", + "Remaining {attr}`~sympy.core.basic.Basic.free_symbols` are indeed the specific amplitudes as defined by {ref}`021/index:Decay chain amplitudes`:\n", "\n", - "The specific amplitudes from {ref}`021:Decay chain amplitudes` need to be formulated for each value of $\\nu, \\lambda$, so that they can be substituted in the top expression:" + "The specific amplitudes from {ref}`021/index:Decay chain amplitudes` need to be formulated for each value of $\\nu, \\lambda$, so that they can be substituted in the top expression:" ] }, { @@ -1717,7 +1679,7 @@ "source": [ "### Phase space\n", "\n", - "The $\\Lambda_c^+ \\to p K \\pi$ kinematics is fully described by two dynamic variables, $m_{K\\pi}$ and $m_{pK}$ (see {doc}`/017`). The third Mandelstam variable can be computed from the other two and the masses of the initial and final state:" + "The $\\Lambda_c^+ \\to p K \\pi$ kinematics is fully described by two dynamic variables, $m_{K\\pi}$ and $m_{pK}$ (see {doc}`/017/index`). The third Mandelstam variable can be computed from the other two and the masses of the initial and final state:" ] }, { @@ -1863,9 +1825,7 @@ "total_intensities = intensity_func(phsp)\n", "mesh = ax.pcolormesh(X, Y, total_intensities, norm=LogNorm())\n", "fig.colorbar(mesh, ax=ax, fraction=0.05, pad=0.02)\n", - "output_file = Path(\"021/intensity-distribution.png\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file, dpi=200)\n", + "fig.savefig(\"intensity-distribution.png\", dpi=200)\n", "plt.show()" ] }, @@ -1943,9 +1903,7 @@ "set_ylim_to_zero(ax1)\n", "set_ylim_to_zero(ax2)\n", "ax2.legend()\n", - "output_file = Path(\"021/intensity-projections.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + "fig.savefig(\"intensity-projections.svg\")\n", "plt.show()" ] }, @@ -2337,12 +2295,12 @@ " children=[\n", " Tab(\n", " children=[\n", - " VBox([HBox(s) for s in zip(*pair)])\n", + " VBox([HBox(s) for s in zip(*pair, strict=True)])\n", " for pair in coupling_sliders.values()\n", " ],\n", " titles=tuple(coupling_sliders),\n", " ),\n", - " VBox([HBox([r, i]) for r, i in zip(mass_sliders, width_sliders)]),\n", + " VBox([HBox([r, i]) for r, i in zip(mass_sliders, width_sliders, strict=True)]),\n", " ],\n", " titles=(\"Couplings\", \"Masses and widths\"),\n", ")\n", @@ -2450,8 +2408,7 @@ "outputs": [], "source": [ "if STATIC_WEB_PAGE:\n", - " output_file = Path(\"021/polarimeter-field.png\")\n", - " output_file.parent.mkdir(exist_ok=True)\n", + " output_file = \"polarimeter-field.png\"\n", " plt.savefig(output_file, dpi=200)\n", " display(ui, Image(output_file))" ] @@ -2471,9 +2428,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/021/pyproject.toml b/docs/021/pyproject.toml new file mode 100644 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+name = "widgetsnbextension" +version = "4.0.13" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/56/fc/238c424fd7f4ebb25f8b1da9a934a3ad7c848286732ae04263661eb0fc03/widgetsnbextension-4.0.13.tar.gz", hash = "sha256:ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6", size = 1164730 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/21/02/88b65cc394961a60c43c70517066b6b679738caf78506a5da7b88ffcb643/widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71", size = 2335872 }, +] diff --git a/docs/022.ipynb b/docs/022/index.ipynb similarity index 93% rename from docs/022.ipynb rename to docs/022/index.ipynb index ecc9307..ec3656b 100644 --- a/docs/022.ipynb +++ b/docs/022/index.ipynb @@ -22,7 +22,7 @@ ":::{card} Polarimetry: Computing the B-matrix for Λc→pKπ\n", "TR-022\n", "^^^\n", - "The $B$-matrix forms an extension of the polarimeter vector field $\\vec\\alpha$ ([arXiv:2301.07010](https://arxiv.org/abs/2301.07010), see also [TR-021](021.ipynb)) that takes the polarization of the proton into account. See [arXiv:2302.07665](https://arxiv.org/abs/2302.07665), Eq. (B6).\n", + "The $B$-matrix forms an extension of the polarimeter vector field $\\vec\\alpha$ ([arXiv:2301.07010](https://arxiv.org/abs/2301.07010), see also [TR-021](../021/index.ipynb)) that takes the polarization of the proton into account. See [arXiv:2302.07665](https://arxiv.org/abs/2302.07665), Eq. (B6).\n", "+++\n", "✅ [compwa.github.io#196](https://github.com/ComPWA/compwa.github.io/pull/196)\n", ":::\n", @@ -36,19 +36,6 @@ "# B-matrix extension of polarimeter" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q git+https://github.com/ComPWA/polarimetry@0.0.9" - ] - }, { "cell_type": "code", "execution_count": null, @@ -216,7 +203,7 @@ "outputs": [], "source": [ "B_test = tuple(\n", - " tuple(sp.Symbol(Rf\"\\tau={τ}, \\rho={p}\") for ρ in range(4)) for τ in range(4)\n", + " tuple(sp.Symbol(Rf\"\\tau={τ}, \\rho={ρ}\") for ρ in range(4)) for τ in range(4)\n", ")\n", "B_test = sp.Matrix(B_test)\n", "B_test" @@ -447,9 +434,7 @@ "ax.set_ylabel(s2_label)\n", "ax.set_box_aspect(1)\n", "ax.pcolormesh(X, Y, B_arrays[0, 0].real)\n", - "output_file = Path(\"022/b00-is-intensity.png\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + "fig.savefig(\"b00-is-intensity.png\")\n", "plt.show()" ] }, @@ -498,11 +483,11 @@ " ax.set_box_aspect(1)\n", " if τ == 0 and ρ == 0:\n", " Z = B_arrays[τ, ρ].real\n", - " ax.set_title(f\"$B_{{{τ}{p}}}$\")\n", + " ax.set_title(f\"$B_{{{τ}{ρ}}}$\")\n", " cmap = plt.cm.viridis\n", " else:\n", " Z = B_norm[τ, ρ].real\n", - " ax.set_title(f\"$B_{{{τ}{p}}} / B_{{00}}$\")\n", + " ax.set_title(f\"$B_{{{τ}{ρ}}} / B_{{00}}$\")\n", " cmap = plt.cm.coolwarm\n", " mesh = ax.pcolormesh(X, Y, Z, cmap=cmap)\n", " cbar = fig.colorbar(mesh, ax=ax, fraction=0.047, pad=0.01)\n", @@ -517,9 +502,7 @@ " progress_bar.update()\n", "progress_bar.close()\n", "fig.tight_layout()\n", - "output_file = Path(\"022/b-matrix-elements.png\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + "fig.savefig(\"b-matrix-elements.png\")\n", "plt.show()" ] }, @@ -609,9 +592,7 @@ "ax.set_xlabel(Rf\"{s1_label}, $\\quad\\alpha_z$\")\n", "ax.set_ylabel(Rf\"{s2_label}, $\\quad\\alpha_x$\")\n", "cbar.set_label(R\"$\\left|\\vec{\\alpha}\\right|$\")\n", - "output_file = Path(\"022/alpha-field.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + "fig.savefig(\"alpha-field.svg\")\n", "plt.show()" ] }, @@ -644,9 +625,7 @@ "ax.set_xlabel(Rf\"{s1_label}, $\\quad \\beta_z = B_{{03}}$\")\n", "ax.set_ylabel(Rf\"{s2_label}, $\\quad \\beta_x = B_{{01}}$\")\n", "cbar.set_label(R\"$\\left|\\vec{\\beta}\\right|$\")\n", - "output_file = Path(\"022/beta-field.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + "fig.savefig(\"beta-field.svg\")\n", "plt.show()" ] }, @@ -703,9 +682,7 @@ "ax1.set_xlabel(s1_label)\n", "ax2.set_xlabel(s1_label)\n", "ax1.set_ylabel(s2_label)\n", - "output_file = Path(\"022/alpha-beta-comparison.png\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file)\n", + 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docs/023/index.ipynb index 009fc7c..3580587 100644 --- a/docs/023.ipynb +++ b/docs/023/index.ipynb @@ -48,24 +48,11 @@ "" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q plotly==5.18.0" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ - "This TR tests whether the HTML build of the TR notebooks supports [Plotly](https://plotly.com/python) figures. It's a follow-up to [TR-006](006.ipynb), without the interactivity of `ipywidgets`, but with the better 3D rendering of Plotly. For more info on how Plotly figures can be embedded in Sphinx HTML builds, see [this page](https://myst-nb.readthedocs.io/en/v0.17.2/render/interactive.html#plotly) of MyST-NB (particularly the remark on [`html_js_files`](https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_js_files).\n", + "This TR tests whether the HTML build of the TR notebooks supports [Plotly](https://plotly.com/python) figures. It's a follow-up to [TR-006](../006/index.ipynb), without the interactivity of `ipywidgets`, but with the better 3D rendering of Plotly. For more info on how Plotly figures can be embedded in Sphinx HTML builds, see [this page](https://myst-nb.readthedocs.io/en/v0.17.2/render/interactive.html#plotly) of MyST-NB (particularly the remark on [`html_js_files`](https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_js_files).\n", "\n", "The following example is copied from [this tutorial](https://plotly.com/python/3d-isosurface-plots)." ] @@ -108,7 +95,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - ":::{seealso} {ref}`006:Plotly with ipywidgets`\n", + ":::{seealso} {ref}`006/index:Plotly with ipywidgets`\n", ":::" ] } @@ -118,9 +105,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/023/pyproject.toml b/docs/023/pyproject.toml new file mode 100644 index 0000000..531c9ea --- /dev/null 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a/docs/024.ipynb b/docs/024/index.ipynb similarity index 98% rename from docs/024.ipynb rename to docs/024/index.ipynb index de67271..76ffefe 100644 --- a/docs/024.ipynb +++ b/docs/024/index.ipynb @@ -35,19 +35,6 @@ "# Symbolic model serialization" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q ampform==0.14.10 graphviz==0.20.1 polarimetry-lc2pkpi==0.0.10 sympy==1.12" - ] - }, { "cell_type": "code", "execution_count": null, @@ -582,7 +569,7 @@ "metadata": {}, "outputs": [], "source": [ - "exec_filename = Path(\"_static/exported_intensity_model.py\")\n", + "exec_filename = Path(\"../_static/exported_intensity_model.py\")\n", "with open(exec_filename, \"w\") as f:\n", " f.write(exec_str)" ] @@ -799,9 +786,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + 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{\"EXECUTE_NB\", \"READTHEDOCS\"}.intersection(os.environ)" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "cellView": "form", - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "# @title\n", - "if \"COLAB_RELEASE_TAG\" in os.environ:\n", - " import subprocess\n", - "\n", - " from google.colab import output\n", - "\n", - " output.enable_custom_widget_manager()\n", - " subprocess.run(\"pip install -q ipympl\".split(), check=False)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -429,8 +391,7 @@ "outputs": [], "source": [ "if STATIC_WEB_PAGE:\n", - " output_file = Path(\"025/rotated-sqrt-complex-plane.png\")\n", - " output_file.parent.mkdir(exist_ok=True)\n", + " output_file = \"rotated-sqrt-complex-plane.png\"\n", " mpl_fig.savefig(output_file, dpi=200)\n", " display(ui, Image(output_file))" ] @@ -450,9 +411,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 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This results in $2^n$ Riemann sheets for $n$ channels, each starting at the threshold $s_{thr}=(m_1+m_2)^{2}$ of the two final state particles, the so-called branching point of the respective channel going along the so-called branch cut along the real axis where the function is not uniquely defined to $+\\infty$. This choice of the direction of the brach cut is most commonly used in particle physics. The physical Riemann sheet is defined for positive imaginary part (1st quadrant of the complex plane) and the unphysical Riemann sheets are only defined for negative imaginary part (4th quadrant of the complex plane). 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docs/027.ipynb rename to docs/027/index.ipynb index a860250..a70fa07 100644 --- a/docs/027.ipynb +++ b/docs/027/index.ipynb @@ -21,7 +21,7 @@ ":::{card} Visualization of the Riemann sheets for the two-channel $T$-matrix with one pole\n", "TR-027\n", "^^^\n", - "Following **[TR-026](./026.ipynb)**, the Riemann sheets for the amplitude calculated within the $K$-matrix formalism for the two-channel case are visualized. The method of transitioning from the first physical sheet to the unphysical sheets is extended to the two dimensional case using [Eur. Phys. J. C (2023) 83:850](https://juser.fz-juelich.de/record/1017534/files/s10052-023-11953-6.pdf) in order to visualize the third and the fourth unphysical sheet.\n", + "Following **[TR-026](../026/index.ipynb)**, the Riemann sheets for the amplitude calculated within the $K$-matrix formalism for the two-channel case are visualized. The method of transitioning from the first physical sheet to the unphysical sheets is extended to the two dimensional case using [Eur. Phys. J. C (2023) 83:850](https://juser.fz-juelich.de/record/1017534/files/s10052-023-11953-6.pdf) in order to visualize the third and the fourth unphysical sheet.\n", "+++\n", "🚧 [ampform#67](https://github.com/ComPWA/ampform/issues/67)\n", ":::\n", @@ -35,19 +35,6 @@ "# Coupled channel Riemann sheets\n" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q ampform==0.15.0 plotly==5.18.0 sympy==1.12" - ] - }, { "cell_type": "code", "execution_count": null, @@ -68,7 +55,6 @@ "# @title\n", "from __future__ import annotations\n", "\n", - "import os\n", "import warnings\n", "from typing import Any\n", "\n", @@ -87,54 +73,6 @@ "warnings.filterwarnings(\"ignore\")" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "cellView": "form", - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "# @title\n", - "if \"COLAB_RELEASE_TAG\" in os.environ:\n", - " import subprocess\n", - "\n", - " from google.colab import output\n", - "\n", - " output.enable_custom_widget_manager()\n", - " subprocess.run(\"pip install -q ipympl\".split(), check=False)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "cellView": "form", - "jupyter": { - "source_hidden": true - }, - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "# @title\n", - "if \"COLAB_RELEASE_TAG\" in os.environ:\n", - " import subprocess\n", - "\n", - " from google.colab import output\n", - "\n", - " output.enable_custom_widget_manager()\n", - " subprocess.run(\"pip install -q ipympl\".split(), check=False)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -1120,9 +1058,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { 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"https://files.pythonhosted.org/packages/21/02/88b65cc394961a60c43c70517066b6b679738caf78506a5da7b88ffcb643/widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71", size = 2335872 }, +] diff --git a/docs/028.ipynb b/docs/028/index.ipynb similarity index 54% rename from docs/028.ipynb rename to docs/028/index.ipynb index cdaff9f..72b0f1b 100644 --- a/docs/028.ipynb +++ b/docs/028/index.ipynb @@ -34,19 +34,6 @@ "# PDG Python API: decay query" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q pdg==0.1.3 tqdm==4.66.5" - ] - }, { "cell_type": "code", "execution_count": null, @@ -81,8 +68,28 @@ { "cell_type": "code", "execution_count": null, - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [ + "keep_output" + ] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "{pdg.data.PdgLifetime,\n", + " pdg.data.PdgMass,\n", + " pdg.data.PdgProperty,\n", + " pdg.data.PdgWidth,\n", + " pdg.decay.PdgBranchingFraction,\n", + " pdg.particle.PdgParticleList}" + ] + }, + "execution_count": null, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "{type(obj) for obj in PDG.get_all()}" ] @@ -97,8 +104,23 @@ { "cell_type": "code", "execution_count": null, - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [ + "keep_output" + ] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "pdg.decay.PdgBranchingFraction" + ] + }, + "execution_count": null, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "jpsi_decay = PDG.get(\"M070.313/2023\")\n", "type(jpsi_decay)" @@ -107,8 +129,23 @@ { "cell_type": "code", "execution_count": null, - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [ + "keep_output" + ] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'J/psi(1S) --> rho(1700) pi --> pi+ pi- pi0'" + ] + }, + "execution_count": null, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "jpsi_decay.description" ] @@ -123,8 +160,23 @@ { "cell_type": "code", "execution_count": null, - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [ + "keep_output" + ] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "7245" + ] + }, + "execution_count": null, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "from pdg.decay import PdgBranchingFraction\n", "\n", @@ -159,10 +211,22 @@ "source_hidden": true }, "tags": [ - "hide-input" + "hide-input", + "keep_output" ] }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "7359" + ] + }, + "execution_count": null, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "def create_final_state(description: str) -> tuple[str, ...]:\n", " items = []\n", @@ -199,8 +263,23 @@ { "cell_type": "code", "execution_count": null, - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [ + "keep_output" + ] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "2194" + ] + }, + "execution_count": null, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "three_body_decays = {\n", " (initial_state, final_state)\n", @@ -213,8 +292,38 @@ { "cell_type": "code", "execution_count": null, - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [ + "keep_output" + ] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "[('B0', ('K0S', 'K0S', 'K0S')),\n", + " ('B0', ('a', 'a', 'a')),\n", + " ('B_s()0', ('a', 'a', 'a')),\n", + " ('B_s()0', ('phi', 'phi', 'phi')),\n", + " ('J/psi(1S)', ('g', 'g', 'g')),\n", + " ('J/psi(1S)', ('gamma', 'gamma', 'gamma')),\n", + " ('Upsilon(1S)', ('g', 'g', 'g')),\n", + " ('Upsilon(2S)', ('g', 'g', 'g')),\n", + " ('Upsilon(3S)', ('g', 'g', 'g')),\n", + " ('Z', ('g', 'g', 'g')),\n", + " ('Z', ('gamma', 'gamma', 'gamma')),\n", + " ('a_1(1260)', ('pi0', 'pi0', 'pi0')),\n", + " ('a_1(1640)', ('pi', 'pi', 'pi')),\n", + " ('pi_1(1600)', ('pi', 'pi', 'pi')),\n", + " ('pi_2(1670)', ('pi0', 'pi0', 'pi0')),\n", + " ('psi(2S)', ('g', 'g', 'g'))]" + ] + }, + "execution_count": null, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "equal_state_3body_decays = {\n", " (initial_state, final_state)\n", @@ -239,10 +348,26 @@ "source_hidden": true }, "tags": [ - "hide-input" + "hide-input", + "keep_output" ] }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " J/psi(1S) → g g g\n", + " J/psi(1S) → gamma gamma gamma\n", + " Upsilon(1S) → g g g\n", + " Upsilon(2S) → g g g\n", + " Upsilon(3S) → g g g\n", + " Z → g g g\n", + " Z → gamma gamma gamma\n", + " psi(2S) → g g g\n" + ] + } + ], "source": [ "from pdg.errors import PdgAmbiguousValueError, PdgNoDataError\n", "\n", @@ -268,8 +393,36 @@ { "cell_type": "code", "execution_count": null, - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [ + "keep_output" + ] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "['a_1(1260) --> K^*(892) K',\n", + " 'a_1(1260) --> ( rho(1450) pi )(S-wave) , rho --> pi pi',\n", + " 'a_1(1260) --> f_2(1270) pi , f_2() --> pi pi',\n", + " 'a_1(1260) --> f_0(500) pi , f_0() --> pi pi',\n", + " 'a_1(1260) --> f_0(980) pi , f_0() --> pi pi',\n", + " 'a_1(1260) --> pi0 pi0 pi0',\n", + " 'a_1(1260) --> pi+ pi- pi0',\n", + " 'a_1(1260) --> ( rho(1450) pi )(D-wave) , rho --> pi pi',\n", + " 'a_1(1260) --> pi gamma',\n", + " 'a_1(1260) --> ( rho pi )(D-wave) , rho --> pi pi',\n", + " 'a_1(1260) --> 3 pi',\n", + " 'a_1(1260) --> f_0(1370) pi , f_0() --> pi pi',\n", + " 'a_1(1260) --> K K pi',\n", + " 'a_1(1260) --> ( rho pi )(S-wave) , rho --> pi pi']" + ] + }, + "execution_count": null, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "[dec for dec in decay_descriptions if dec.startswith(\"a_1(1260)\")]" ] @@ -289,10 +442,61 @@ "source_hidden": true }, "tags": [ - "hide-input" + "hide-input", + "keep_output" ] }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['J/psi(1S) --> 2(pi+ pi- pi0)',\n", + " 'J/psi(1S) --> 2(pi+ pi- pi0) eta',\n", + " 'J/psi(1S) --> 2(pi+ pi-) 3pi0',\n", + " 'J/psi(1S) --> 2(pi+ pi-) pi0',\n", + " 'J/psi(1S) --> 3(pi+ pi-) pi0',\n", + " 'J/psi(1S) --> 4(pi+ pi-) pi0',\n", + " 'J/psi(1S) --> K+ K- pi0 pi0 pi0',\n", + " 'J/psi(1S) --> K0S K+- pi-+ pi+ pi-',\n", + " 'J/psi(1S) --> K0S K+- pi-+ pi0 pi0',\n", + " 'J/psi(1S) --> K^*(892)+ K0S pi- + c.c. --> K0S K0S pi+ pi-',\n", + " 'J/psi(1S) --> K^*(892)0 K- pi+ + c.c. --> K+ K- pi+ pi-',\n", + " 'J/psi(1S) --> K_2^*(1430)0 K- pi+ + c.c. --> K+ K- pi+ pi-',\n", + " 'J/psi(1S) --> a_2(1320)+ pi- pi0 + c.c --> 2 (pi+ pi- ) pi0',\n", + " 'J/psi(1S) --> a_2(1320)0 pi+ pi- --> 2 (pi+ pi- ) pi0',\n", + " 'J/psi(1S) --> eta pi+ pi- 3 pi0',\n", + " 'J/psi(1S) --> eta pi+ pi- pi0',\n", + " 'J/psi(1S) --> gamma pi+ pi- 2pi0',\n", + " 'J/psi(1S) --> omega 3 pi0',\n", + " 'J/psi(1S) --> omega pi+ pi+ pi- pi-',\n", + " 'J/psi(1S) --> omega pi+ pi- 2pi0',\n", + " 'J/psi(1S) --> omega pi+ pi- pi0',\n", + " 'J/psi(1S) --> omega pi0 --> pi+ pi- pi0',\n", + " 'J/psi(1S) --> p pbar pi+ pi- pi0',\n", + " 'J/psi(1S) --> phi f_1(1285) --> phi pi0 f_0(980) --> phi 3pi0',\n", + " 'J/psi(1S) --> phi f_1(1285) --> phi pi0 f_0(980) --> phi pi0 pi+ pi-',\n", + " 'J/psi(1S) --> phi pi0 f_0(980) --> phi pi0 p0 pi0',\n", + " 'J/psi(1S) --> phi pi0 f_0(980) --> phi pi0 pi+ pi-',\n", + " 'J/psi(1S) --> pi+ pi- 3pi0',\n", + " 'J/psi(1S) --> pi+ pi- 4 pi0',\n", + " 'J/psi(1S) --> pi+ pi- pi0',\n", + " 'J/psi(1S) --> pi+ pi- pi0 K+ K-',\n", + " 'J/psi(1S) --> pi+ pi- pi0 pi0 eta',\n", + " 'J/psi(1S) --> rho(1450) pi --> pi+ pi- pi0',\n", + " 'J/psi(1S) --> rho(1700) pi --> pi+ pi- pi0',\n", + " 'J/psi(1S) --> rho(2150) pi --> pi+ pi- pi0',\n", + " 'J/psi(1S) --> rho+ K+ K- pi- + c.c --> K+ K- pi+ pi- pi0',\n", + " 'J/psi(1S) --> rho+ rho- pi+ pi- pi0',\n", + " 'J/psi(1S) --> rho+- pi-+ pi+ pi- 2pi0',\n", + " 'J/psi(1S) --> rho+- pi-+ pi0 pi0',\n", + " 'J/psi(1S) --> rho_3(1690) pi --> pi+ pi- pi0']" + ] + }, + "execution_count": null, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "import re\n", "\n", @@ -309,9 +513,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/028/pyproject.toml b/docs/028/pyproject.toml new file mode 100644 index 0000000..6ad9f7d --- /dev/null +++ b/docs/028/pyproject.toml @@ -0,0 +1,26 @@ +[project] +dependencies = [ + "pdg", +] +name = "technical-report" +requires-python = "~=3.12.0" +version = "0.1.0" + +[tool.ruff] +preview = true + +[tool.ruff.lint] +ignore = [ + "COM812", + "CPY001", + "D", + "F404", + "ISC001", + "PERF203", + "PLR2004", + "PLW2901", + "T201", +] +select = ["ALL"] + +[tool.uv.workspace] diff --git 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docs/030/index.ipynb index 4508c43..699b904 100644 --- a/docs/030.ipynb +++ b/docs/030/index.ipynb @@ -35,19 +35,6 @@ "# Sub-intensities of P vector" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q ampform==0.15.4 'qrules[viz]==0.10.2' sympy==1.12 'tensorwaves[jax,phsp]==0.4.12'" - ] - }, { "cell_type": "code", "execution_count": null, @@ -205,8 +192,7 @@ "source": [ "dot = qrules.io.asdot(reaction, collapse_graphs=True)\n", "graph = graphviz.Source(dot)\n", - "output_file = Path(\"030/qrules-output\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", + "output_file = Path(\"qrules-output\")\n", "graph.render(output_file, format=\"svg\")\n", "output_file.unlink()\n", "graph" @@ -415,7 +401,7 @@ "metadata": {}, "source": [ ":::{seealso}\n", - "**[TR-026](./026.ipynb)** and **[TR-027](./027.ipynb)** on analyticity and Riemann sheets.\n", + "**[TR-026](../026/index.ipynb)** and **[TR-027](../027/index.ipynb)** on analyticity and Riemann sheets.\n", ":::" ] }, @@ -552,7 +538,8 @@ " Γ0 = [sp.Symbol(Rf\"\\Gamma_{{{p.latex}}}\") for p, _ in resonances]\n", " β = [sp.Symbol(Rf\"\\beta_{{{p.latex}}}\") for p, _ in resonances]\n", " expr = sum(\n", - " (β_ * m_ * Γ0_) / (m_**2 - s - m_ * Γ0_ * ρ) for m_, Γ0_, β_ in zip(m, Γ0, β)\n", + " (β_ * m_ * Γ0_) / (m_**2 - s - m_ * Γ0_ * ρ)\n", + " for m_, Γ0_, β_ in zip(m, Γ0, β, strict=True)\n", " )\n", " for i, (resonance, _) in enumerate(resonances):\n", " PARAMETERS_BW[β[i]] = 1 + 0j\n", @@ -635,7 +622,7 @@ " s = variables.incoming_state_mass**2\n", " m = [sp.Symbol(Rf\"m_{{{p.latex}}}\") for p, _ in resonances]\n", " g = [sp.Symbol(Rf\"g_{{{p.latex}}}\") for p, _ in resonances]\n", - " expr = sum((g_**2) / (m_**2 - s) for m_, g_ in zip(m, g))\n", + " expr = sum((g_**2) / (m_**2 - s) for m_, g_ in zip(m, g, strict=True))\n", " for i, (resonance, _) in enumerate(resonances):\n", " PARAMETERS_F[m[i]] = resonance.mass\n", " PARAMETERS_F[g[i]] = 1\n", @@ -656,7 +643,7 @@ " g = [sp.Symbol(Rf\"g_{{{p.latex}}}\") for p, _ in resonances]\n", " m = [sp.Symbol(Rf\"m_{{{p.latex}}}\") for p, _ in resonances]\n", " β = [sp.Symbol(Rf\"\\beta_{{{p.latex}}}\") for p, _ in resonances]\n", - " expr = sum((g_ * β_) / (m_**2 - s) for m_, g_, β_ in zip(m, g, β))\n", + " expr = sum((g_ * β_) / (m_**2 - s) for m_, g_, β_ in zip(m, g, β, strict=True))\n", " for i, (resonance, _) in enumerate(resonances):\n", " PARAMETERS_F[β[i]] = 1 + 0j\n", " PARAMETERS_F[m[i]] = resonance.mass\n", @@ -1160,9 +1147,7 @@ "fig.legend(loc=\"upper right\")\n", "fig.tight_layout()\n", "\n", - "output_file = Path(\"030/sub-intensities.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file, bbox_inches=\"tight\")\n", + "fig.savefig(\"sub-intensities.svg\", bbox_inches=\"tight\")\n", "plt.show()" ] }, @@ -1289,8 +1274,7 @@ "\n", " ax1.legend(loc=\"upper left\")\n", "\n", - " output_file = Path(f\"030/argand-{title.lower().replace(' ', '-')}.svg\")\n", - " output_file.parent.mkdir(exist_ok=True)\n", + " output_file = f\"argand-{title.lower().replace(' ', '-')}.svg\"\n", " fig.savefig(output_file, bbox_inches=\"tight\")\n", " fig.show()" ] @@ -1459,8 +1443,7 @@ " fig.legend(bbox_to_anchor=(0.1, 0.9), loc=\"upper left\")\n", " fig.tight_layout()\n", "\n", - " output_file = Path(f\"030/phase-{title.lower().replace(' ', '-')}.svg\")\n", - " output_file.parent.mkdir(exist_ok=True)\n", + " output_file = f\"phase-{title.lower().replace(' ', '-')}.svg\"\n", " fig.savefig(output_file, bbox_inches=\"tight\")\n", " fig.show()" ] @@ -1531,9 +1514,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/030/pyproject.toml b/docs/030/pyproject.toml new file mode 100644 index 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collapse_graphs=True)\n", "graph = graphviz.Source(dot)\n", - "output_file = Path(\"031/qrules-output\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", + "output_file = Path(\"qrules-output\")\n", "graph.render(output_file, format=\"svg\")\n", "output_file.unlink()\n", "graph" @@ -432,7 +418,7 @@ "metadata": {}, "source": [ ":::{seealso}\n", - "**[TR-026](./026.ipynb)** and **[TR-027](./027.ipynb)** on analyticity and Riemann sheets.\n", + "**[TR-026](../026/index.ipynb)** and **[TR-027](../027/index.ipynb)** on analyticity and Riemann sheets.\n", ":::" ] }, @@ -569,7 +555,8 @@ " Γ0 = [sp.Symbol(Rf\"\\Gamma_{{{p.latex}}}\") for p, _ in resonances]\n", " β = [sp.Symbol(Rf\"\\beta_{{{p.latex}}}\") for p, _ in resonances]\n", " expr = sum(\n", - " (β_ * m_ * Γ0_) / (m_**2 - s - m_ * Γ0_ * ρ) for m_, Γ0_, β_ in zip(m, Γ0, β)\n", + " (β_ * m_ * Γ0_) / (m_**2 - s - m_ * Γ0_ * ρ)\n", + " for m_, Γ0_, β_ in zip(m, Γ0, β, strict=True)\n", " )\n", " for i, (resonance, _) in enumerate(resonances):\n", " PARAMETERS_BW[β[i]] = 1 + 0j\n", @@ -653,7 +640,7 @@ " s = variables.incoming_state_mass**2\n", " m = [sp.Symbol(Rf\"m_{{{p.latex}}}\") for p, _ in resonances]\n", " g = [sp.Symbol(Rf\"g_{{{p.latex}}}\") for p, _ in resonances]\n", - " expr = sum((g_**2) / (m_**2 - s) for m_, g_ in zip(m, g))\n", + " expr = sum((g_**2) / (m_**2 - s) for m_, g_ in zip(m, g, strict=True))\n", " for i, (resonance, _) in enumerate(resonances):\n", " PARAMETERS_F[m[i]] = resonance.mass\n", " PARAMETERS_F[g[i]] = 1\n", @@ -674,7 +661,7 @@ " g = [sp.Symbol(Rf\"g_{{{p.latex}}}\") for p, _ in resonances]\n", " m = [sp.Symbol(Rf\"m_{{{p.latex}}}\") for p, _ in resonances]\n", " β = [sp.Symbol(Rf\"\\beta_{{{p.latex}}}\") for p, _ in resonances]\n", - " expr = sum((g_ * β_) / (m_**2 - s) for m_, g_, β_ in zip(m, g, β))\n", + " expr = sum((g_ * β_) / (m_**2 - s) for m_, g_, β_ in zip(m, g, β, strict=True))\n", " for i, (resonance, _) in enumerate(resonances):\n", " PARAMETERS_F[β[i]] = 1 + 0j\n", " PARAMETERS_F[m[i]] = resonance.mass\n", @@ -1062,9 +1049,7 @@ "fig.legend(loc=\"upper right\")\n", "plt.tight_layout()\n", "\n", - "output_file = Path(\"031/contributions.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file, bbox_inches=\"tight\")\n", + "fig.savefig(\"contributions.svg\", bbox_inches=\"tight\")\n", "plt.show()" ] }, @@ -1105,9 +1090,7 @@ "ax.set_ylim(0, None)\n", "fig.tight_layout()\n", "\n", - "output_file = Path(\"031/weighted-phsp-f-vector.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file, bbox_inches=\"tight\")\n", + "fig.savefig(\"weighted-phsp-f-vector.svg\", bbox_inches=\"tight\")\n", "fig.show()" ] }, @@ -1183,14 +1166,12 @@ "evenly_spaced_interval = np.linspace(0, 1, num=len(mass_parameters))\n", "colors = [plt.cm.rainbow(x) for x in evenly_spaced_interval]\n", "ax.set_xlabel(\"$m$ [GeV]\")\n", - "for (k, v), color in zip(mass_parameters.items(), colors):\n", + "for (k, v), color in zip(mass_parameters.items(), colors, strict=True):\n", " ax.axvline(v, c=color, label=f\"${k}$\", ls=\"dotted\")\n", "ax.set_ylim(0, None)\n", "ax.legend()\n", "\n", - "output_file = Path(\"031/data-f-vector.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file, bbox_inches=\"tight\")\n", + "fig.savefig(\"data-f-vector.svg\", bbox_inches=\"tight\")\n", "plt.show()" ] }, @@ -1373,9 +1354,7 @@ "original_parameters_fvector = dict(intensity_func_fvector.parameters)\n", "intensity_func_fvector.update_parameters(initial_parameters_fvector)\n", "fig = compare_model(\"m_01\", data, phsp, intensity_func_fvector, intensity_func_bw)\n", - "output_file = Path(\"031/before-fit.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file, bbox_inches=\"tight\")" + "fig.savefig(\"before-fit.svg\", bbox_inches=\"tight\")" ] }, { @@ -1558,9 +1537,7 @@ "intensity_func_fvector.update_parameters(fit_result_fvector.parameter_values)\n", "intensity_func_bw.update_parameters(fit_result_bw.parameter_values)\n", "fig = compare_model(\"m_01\", data, phsp, intensity_func_fvector, intensity_func_bw)\n", - "output_file = Path(\"031/after-fit.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file, bbox_inches=\"tight\")" + "fig.savefig(\"after-fit.svg\", bbox_inches=\"tight\")" ] }, { @@ -1971,9 +1948,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/031/pyproject.toml b/docs/031/pyproject.toml new file mode 100644 index 0000000..5ceff02 --- /dev/null +++ b/docs/031/pyproject.toml @@ -0,0 +1,36 @@ +[project] +dependencies = [ + "ampform[viz]", + "matplotlib", + "pandas", + "tensorwaves[jax,pwa]", +] +name = "technical-report" +requires-python = "~=3.12.0" +version = "0.1.0" + +[tool.ruff] 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size = 23362 }, +] diff --git a/docs/032.ipynb b/docs/032/index.ipynb similarity index 97% rename from docs/032.ipynb rename to docs/032/index.ipynb index 6d39e50..689a941 100644 --- a/docs/032.ipynb +++ b/docs/032/index.ipynb @@ -35,19 +35,6 @@ "# P-vector fit comparison" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "remove-cell" - ] - }, - "outputs": [], - "source": [ - "%pip install -q ampform==0.15.4 'qrules[viz]==0.10.2' sympy==1.12 'tensorwaves[jax,phsp]==0.4.12'" - ] - }, { "cell_type": "code", "execution_count": null, @@ -227,8 +214,7 @@ "for i, reaction in enumerate(REACTIONS, 1):\n", " src = qrules.io.asdot(reaction, collapse_graphs=True)\n", " graph = graphviz.Source(src)\n", - " output_file = Path(f\"032/graph{i}\")\n", - " output_file.parent.mkdir(exist_ok=True)\n", + " output_file = Path(f\"graph{i}\")\n", " graph.render(output_file, format=\"svg\")\n", " output_file.unlink()\n", " display(graph)\n", @@ -419,7 +405,7 @@ "metadata": {}, "source": [ ":::{seealso}\n", - "**[TR-026](./026.ipynb)** and **[TR-027](./027.ipynb)** on analyticity and Riemann sheets.\n", + "**[TR-026](../026/index.ipynb)** and **[TR-027](../027/index.ipynb)** on analyticity and Riemann sheets.\n", ":::" ] }, @@ -1123,9 +1109,7 @@ "ax.legend()\n", "ax.set_ylim(0, None)\n", "\n", - "output_file = Path(\"032/weighted-phsp.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file, bbox_inches=\"tight\")\n", + "fig.savefig(\"weighted-phsp.svg\", bbox_inches=\"tight\")\n", "fig.show()" ] }, @@ -1198,9 +1182,7 @@ "ax.legend()\n", "ax.set_ylim(0, None)\n", "\n", - "output_file = Path(\"032/toy-date.svg\")\n", - "output_file.parent.mkdir(exist_ok=True)\n", - "fig.savefig(output_file, bbox_inches=\"tight\")\n", + "fig.savefig(\"toy-date.svg\", bbox_inches=\"tight\")\n", "fig.show()" ] }, @@ -1303,8 +1285,7 @@ " fig.legend()\n", " fig.tight_layout()\n", "\n", - " output_file = Path(f\"032/{title.lower().replace(' ', '-')}.svg\")\n", - " output_file.parent.mkdir(exist_ok=True)\n", + " output_file = f\"{title.lower().replace(' ', '-')}.svg\"\n", " fig.savefig(output_file, bbox_inches=\"tight\")\n", " fig.show()\n", "\n", @@ -1592,9 +1573,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git a/docs/032/pyproject.toml b/docs/032/pyproject.toml new file mode 100644 index 0000000..f7a046f --- /dev/null +++ b/docs/032/pyproject.toml @@ -0,0 +1,38 @@ +[project] +dependencies = [ + "ampform[viz]", + "matplotlib", + "tensorwaves[jax,pwa]", +] +name = "technical-report" +requires-python = "~=3.12.0" +version = "0.1.0" + +[tool.ruff] +preview = true + +[tool.ruff.lint] +ignore = [ + "ANN00", + "ANN20", + "COM812", + "CPY001", + "D", + "E501", + "E741", + "F404", + "FBT00", 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...],\n", " data2: tuple[MomentumNumpy4D, ...],\n", ") -> tuple[MomentumNumpy4D, ...]:\n", - " return tuple(concatenate_vectors((pi1, pj2)) for pi1, pj2 in zip(data1, data2))\n", + " return tuple(\n", + " concatenate_vectors((pi1, pj2)) for pi1, pj2 in zip(data1, data2, strict=True)\n", + " )\n", "\n", "\n", "def concatenate_vectors(vectors: tuple[MomentumNumpy4D]) -> MomentumNumpy4D:\n", @@ -2990,7 +2979,7 @@ " progress_bar = tqdm(desc=\"Running fit\")\n", " new_kwargs = {\n", " **toy_parameters,\n", - " **dict(zip(arg_names, args)),\n", + " **dict(zip(arg_names, args, strict=True)),\n", " }\n", " estimator_value = unbinned_nll(**new_kwargs)\n", " progress_bar.set_postfix({\"estimator\": estimator_value})\n", @@ -3436,9 +3425,9 @@ "toc_visible": true }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Pyproject Local", "language": "python", - "name": "python3" + "name": "pyproject_local_kernel" }, "language_info": { "codemirror_mode": { diff --git 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size = 23362 }, +] diff --git a/docs/_list_technical_reports.py b/docs/_list_technical_reports.py index c0e792f..021f7d4 100644 --- a/docs/_list_technical_reports.py +++ b/docs/_list_technical_reports.py @@ -1,8 +1,7 @@ from __future__ import annotations -import os import re -from os.path import dirname +from pathlib import Path from textwrap import dedent from typing import TYPE_CHECKING @@ -14,8 +13,8 @@ def main() -> int: table = _create_tr_table() - this_dir = dirname(__file__) - output_path = f"{this_dir}/_inventory.md" + this_dir = Path(__file__).parent + output_path = this_dir / "_inventory.md" with open(output_path, "w") as f: f.write(table) return 0 @@ -34,8 +33,8 @@ def _create_tr_table() -> str: tr = card_info["tr"] title = card_info["title"] details = re.sub( - r"\[([^\]]+)\]\((\./)?(\d\d\d)\.ipynb\)", - r"[\1](\3.ipynb)", + r"\[([^\]]+)\]\((\.|\.\./)?(\d\d\d)/index\.ipynb\)", + r"[\1](\3/index.ipynb)", card_info.get("details", ""), ) details = re.sub(r"(
)?", "", details) @@ -46,7 +45,7 @@ def _create_tr_table() -> str: card_info.get("footer", "\n").splitlines()[0], ) src += ( - f"\n| | [TR‑{tr}]({tr}.ipynb) | {title} | {details} | {tags} |" + f"\n| | **[TR‑{tr}]({tr}/index.ipynb)** | {title} | {details} | {tags} |" f" {status} |" ) return src @@ -56,16 +55,12 @@ def _to_badge(tag: str) -> str: return f"{{bdg-info-line}}`{tag}`" -def _get_technical_report_paths() -> list[str]: - report_dir = dirname(__file__) - return [ - f"{report_dir}/{file}" - for file in sorted(os.listdir(report_dir)) - if file.endswith(".ipynb") - ] +def _get_technical_report_paths() -> list[Path]: + report_dir = Path(__file__).parent + return sorted(report_dir.glob("???/index.ipynb")) -def _get_card_info(path: str) -> dict[str, str]: +def _get_card_info(path: Path) -> dict[str, str]: notebook = _open_notebook(path) for cell in notebook["cells"]: if cell["cell_type"] != "markdown": @@ -82,14 +77,15 @@ def _get_card_info(path: str) -> dict[str, str]: if not line3.startswith("TR-"): continue return _extract_card_info(cell) + repo_dir = Path(__file__).parent.parent msg = ( - f"Technical report {path} does not contain an info card. See one of the other" - " report notebooks for what the card should look like." + f"Technical report {path.relative_to(repo_dir)} does not contain an info card." + " See one of the other report notebooks for what the card should look like." ) raise RuntimeError(msg) -def _open_notebook(path: str) -> NotebookNode: +def _open_notebook(path: Path) -> NotebookNode: return nbformat.read(path, as_version=nbformat.NO_CONVERT) diff --git a/docs/conf.py b/docs/conf.py index 5d53438..b010dbd 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -7,7 +7,6 @@ from __future__ import annotations import os -import re import shutil import subprocess # noqa: S404 import sys @@ -21,43 +20,43 @@ def get_nb_exclusion_patterns() -> list[str]: exclusions = { - "000*", - "001*", - "002*", - "003*", - "005*", - "008*", - "009*", - "010*", - "011*", - "012*", - "013*", - "014*", - "015*", - "017*", - "018*", - "019*", - "020*", - "021*", - "022*", - "030*", - "031*", - "032*", - "033*", + "000/*", + "002/*", + "011/*", } - julia_notebooks = { - "019*", - } - if shutil.which("julia") is None or "READTHEDOCS" in os.environ: + if shutil.which("julia") is None: + julia_notebooks = { + "019*", + } exclusions.update(julia_notebooks) + if "ALL_NOTEBOOKS" not in os.environ: + frozen_notebooks = { + "001/*", + "003/*", + "005/*", + "008/*", + "009/*", + "010/*", + "012/*", + "013/*", + "014/*", + "015/*", + "017/*", + "018/*", + "019/*", + "020/*", + "021/*", + "022/*", + "028/*", + "030/*", + "031/*", + "032/*", + "033/*", + } + exclusions.update(frozen_notebooks) return sorted(exclusions) -def get_remove_from_toctrees() -> list[str]: - regex = re.compile(r"\d{3}.*\.ipynb") - return sorted(p for p in os.listdir() if regex.match(p)) - - def install_ijulia() -> None: if shutil.which("julia") is None: return @@ -73,9 +72,7 @@ def install_ijulia() -> None: REPO_NAME = "report" REPO_TITLE = "ComPWA Organization" -BINDER_LINK = ( - f"https://mybinder.org/v2/gh/ComPWA/{REPO_NAME}/{BRANCH}?filepath=docs/usage" -) +BINDER_LINK = f"https://mybinder.org/v2/gh/ComPWA/{REPO_NAME}/{BRANCH}?urlpath=lab" autosectionlabel_prefix_document = True bibtex_bibfiles = ["bibliography.bib"] @@ -100,10 +97,10 @@ def install_ijulia() -> None: copyright = f"2020, {ORGANIZATION}" default_role = "py:obj" exclude_patterns = [ - "**.ipynb_checkpoints", - "*build", - "*template.md", - "tests", + "_build", + "**/.ipynb_checkpoints/", + "**/.venv/*", + "**/.virtual_documents/", ] extensions = [ "myst_nb", @@ -155,7 +152,7 @@ def install_ijulia() -> None: }, { "name": "Launch on Binder", - "url": f"https://mybinder.org/v2/gh/{ORGANIZATION}/{REPO_NAME}/{BRANCH}?filepath=docs", + "url": f"https://mybinder.org/v2/gh/{ORGANIZATION}/{REPO_NAME}/{BRANCH}?urlpath=lab", "icon": "https://mybinder.readthedocs.io/en/latest/_static/favicon.png", "type": "url", }, @@ -247,8 +244,7 @@ def install_ijulia() -> None: myst_substitutions = { "branch": BRANCH, "remark_019": ( - "Notice how a new file [`019/Project.toml`](./019/Project.toml) and " - " [`019/Manifest.toml`](./019/Manifest.toml) are automatically generated." + "Notice how a new file [`Project.toml`](./Project.toml) and [`Manifest.toml`](./Manifest.toml) are automatically generated." if get_execution_mode() != "off" else "" ), @@ -270,7 +266,7 @@ def install_ijulia() -> None: nitpicky = True primary_domain = "py" project = REPO_TITLE -remove_from_toctrees = get_remove_from_toctrees() +remove_from_toctrees = ["???/index.ipynb"] source_suffix = { ".ipynb": "myst-nb", ".md": "myst-nb", diff --git a/docs/index.md b/docs/index.md index 7a1b09e..ef8b0f7 100644 --- a/docs/index.md +++ b/docs/index.md @@ -55,7 +55,7 @@ table.on('click', 'td.details-control', function (e) { :glob: :hidden: references -0* +???/index ``` ````{dropdown} Execution times diff --git a/docs/install-julia-on-rtd.sh b/docs/install-julia-on-rtd.sh deleted file mode 100755 index a3a67a7..0000000 --- a/docs/install-julia-on-rtd.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/bash -if [ -z "$READTHEDOCS" ]; then - echo "Can only run this script on Read the Docs" - exit 1 -fi - -version=$(sed -n '3p' docs/019/Manifest.toml | cut -d'"' -f2) -major_version=${version:0:-2} -echo "Installing Julia v${version}" -filename=julia-${version}-linux-x86_64.tar.gz -wget -q https://julialang-s3.julialang.org/bin/linux/x64/${major_version}/${filename} -tar xzf ${filename} -C ~/.asdf --strip-components=1 diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 2164e0a..0000000 --- a/environment.yml +++ /dev/null @@ -1,12 +0,0 @@ -name: compwa-report -channels: - - conda-forge -dependencies: - - graphviz - - juliaup - - pip - - python==3.12.* - - pip: - - -e .[dev] -variables: - PYTHONHASHSEED: 0 diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..4b57568 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,2460 @@ +version: 5 +environments: + default: + channels: + - url: 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https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.6-hb46c0d2_0.conda + sha256: 2d4fd1ff7ee79cd954ca8e81abf11d9d49954dd1fef80f27289e2402ae9c2e09 + md5: d96942c06c3e84bfcc5efb038724a7fd + depends: + - __osx >=11.0 + - libzlib >=1.2.13,<2.0.0a0 + license: BSD-3-Clause + license_family: BSD + size: 405089 + timestamp: 1714723101397 diff --git a/pixi.toml b/pixi.toml new file mode 100644 index 0000000..06c72bb --- /dev/null +++ b/pixi.toml @@ -0,0 +1,19 @@ +[project] +channels = [ + "conda-forge", + "https://repo.prefix.dev/julia-forge", +] +name = "compwa-report" +platforms = [ + "linux-64", + "osx-64", + "osx-arm64", +] + +[activation] +env = {PYTHONHASHSEED = "0"} + +[dependencies] +graphviz = "*" +julia = {channel = "https://repo.prefix.dev/julia-forge", version = "*"} +uv = "*" diff --git a/pyproject.toml b/pyproject.toml index 7ab5b8c..33f8938 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,48 +7,27 @@ requires = [ [project] authors = [{name = "Common Partial Wave Analysis", email = "compwa-admin@ep1.rub.de"}] -classifiers = [ - "Development Status :: 4 - Beta", - "Intended Audience :: Developers", - "Intended Audience :: Education", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: Apache Software License", - "Natural Language :: English", - "Operating System :: OS Independent", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python", - "Topic :: Scientific/Engineering :: Physics", - "Topic :: Scientific/Engineering", -] -dependencies = [ - "graphviz", - "ipympl", - "matplotlib <3.9.0", # https://github.com/ComPWA/report/actions/runs/11126901008/job/30917935221?pr=1 - "numpy==1.*", -] description = "Source code for the ComPWA Organization pages" dynamic = ["version"] license = {file = "LICENSE"} maintainers = [{email = "compwa-admin@ep1.rub.de"}] -name = "compwa-org" +name = "compwa-report" requires-python = ">=3.9" [project.optional-dependencies] dev = [ - "compwa-org[doc]", - "compwa-org[jupyter]", - "compwa-org[sty]", - "compwa-org[test]", + "compwa-report[doc]", + "compwa-report[jupyter]", + "compwa-report[sty]", + "compwa-report[test]", "sphinx-autobuild", - "tox >=1.9", # for skip_install, use_develop ] doc = [ - "Sphinx >=3", - "myst-nb >=0.14", # nb_ configuration prefixes - "sphinx-api-relink >=0.0.4", + "compwa-report[notebooks]", + "myst-nb", + "nbformat", + "sphinx", + "sphinx-api-relink", "sphinx-book-theme", "sphinx-codeautolink[ipython]", "sphinx-comments", @@ -62,6 +41,7 @@ doc = [ "sphinxcontrib-bibtex >=2", ] jupyter = [ + "compwa-report[notebooks]", "jupyterlab", "jupyterlab-code-formatter >=3.0.0", "jupyterlab-git", @@ -70,19 +50,21 @@ jupyter = [ "python-lsp-ruff", "python-lsp-server[rope]", ] +notebooks = [ + "pyproject-local-kernel", +] sty = [ - "attrs", - "compwa-org[types]", - "nbformat", - "pre-commit >=1.4.0", + "compwa-report[types]", "ruff", ] test = [ - "jupyter", + "compwa-report[notebooks]", "nbmake", + "pytest-env", ] types = [ - "sphinx-api-relink >=0.0.4", + "nbformat", + "sphinx-api-relink", ] [project.readme] @@ -99,104 +81,12 @@ include-package-data = false [tool.setuptools_scm] local_scheme = "no-local-version" -version_scheme = "post-release" +version_scheme = "only-version" write_to = "version.py" [tool.isort] profile = "black" -[tool.pixi.project] -channels = ["conda-forge"] -platforms = ["linux-64"] - -[tool.pixi.activation.env] -PRETTIER_LEGACY_CLI = "1" -PYTHONHASHSEED = "0" - -[tool.pixi.dependencies] -graphviz = "*" -juliaup = "*" -python = "3.12.*" - -[tool.pixi.environments] -default = {features = [ - "dev", - "doc", - "jupyter", - "sty", - "test", - "types", -]} - -[tool.pixi.feature.dev.tasks.ci] -depends_on = ["docnb", "linkcheck", "sty"] - -[tool.pixi.feature.dev.tasks.doc] -cmd = """ -sphinx-build \ - --builder html \ - --fail-on-warning \ - --keep-going \ - --show-traceback \ - docs/ docs/_build/html -""" -env = {FORCE_COLOR = "1", PYTHONWARNINGS = "", ZFIT_DISABLE_TF_WARNINGS = "1"} - -[tool.pixi.feature.dev.tasks.doclive] -cmd = """ -sphinx-autobuild \ - --open-browser \ - --re-ignore '.*/.ipynb_checkpoints/.*' \ - --re-ignore '.*/__pycache__/.*' \ - --re-ignore '.*\\.gitignore' \ - --re-ignore 'docs/.*\\.csv' \ - --re-ignore 'docs/.*\\.gif' \ - --re-ignore 'docs/.*\\.gv' \ - --re-ignore 'docs/.*\\.inv' \ - --re-ignore 'docs/.*\\.json' \ - --re-ignore 'docs/.*\\.pickle' \ - --re-ignore 'docs/.*\\.png' \ - --re-ignore 'docs/.*\\.svg' \ - --re-ignore 'docs/.*\\.yaml' \ - --re-ignore 'docs/.*\\.yml' \ - --re-ignore 'docs/_build/.*' \ - --re-ignore docs/_static/exported_intensity_model.py \ - --watch docs \ - docs/ docs/_build/html -""" -env = {FORCE_COLOR = "1", PYTHONWARNINGS = "", ZFIT_DISABLE_TF_WARNINGS = "1"} - -[tool.pixi.feature.dev.tasks.docnb] -cmd = "pixi run doc" -env = {EXECUTE_NB = "yes", FORCE_COLOR = "1", PYTHONWARNINGS = "", TF_CPP_MIN_LOG_LEVEL = "3", ZFIT_DISABLE_TF_WARNINGS = "1"} - -[tool.pixi.feature.dev.tasks.docnb-force] -cmd = "pixi run doc" -env = {FORCE_COLOR = "1", FORCE_EXECUTE_NB = "yes", PYTHONWARNINGS = "", TF_CPP_MIN_LOG_LEVEL = "3", ZFIT_DISABLE_TF_WARNINGS = "1"} - -[tool.pixi.feature.dev.tasks.docnblive] -cmd = "pixi run doclive" -env = {EXECUTE_NB = "yes", FORCE_COLOR = "1", PYTHONWARNINGS = "", TF_CPP_MIN_LOG_LEVEL = "3", ZFIT_DISABLE_TF_WARNINGS = "1"} - -[tool.pixi.feature.dev.tasks.linkcheck] -cmd = """ -sphinx-build \ - --builder linkcheck \ - --show-traceback \ - docs/ docs/_build/linkcheck -""" -env = {FORCE_COLOR = "1"} - -[tool.pixi.feature.dev.tasks.nb] -cmd = "pytest --nbmake docs" - -[tool.pixi.feature.dev.tasks.sty] -cmd = "pre-commit run -a" -env = {SKIP = "pyright"} - -[tool.pixi.pypi-dependencies] -compwa-org = {path = ".", editable = true} - [tool.pyright] exclude = [ "**/.git", @@ -204,6 +94,7 @@ exclude = [ "**/.mypy_cache", "**/.pytest_cache", "**/.tox", + "**/.venv/", "**/__pycache__", "**/_build", "**/exported_intensity_model.py", @@ -241,10 +132,15 @@ addopts = [ "--doctest-modules", "--durations=0", "--ignore-glob=*/.ipynb_checkpoints/*", + "--ignore-glob=*/.virtual_documents/*", + "--ignore=docs/000", + "--ignore=docs/002", + "--ignore=docs/011", + "--ignore=docs/019/index.ipynb", "--ignore=docs/_static", "--ignore=docs/conf.py", + "--nbmake", "--nbmake-timeout=1200", - "-k not docs/019.ipynb", ] filterwarnings = [ "error", @@ -259,10 +155,12 @@ norecursedirs = [ "_build", ] testpaths = [ - ".pre-commit", "docs", ] +[tool.pytest_env] +EXECUTE_NB = "yes" + [tool.ruff] extend-exclude = ["exported_intensity_model.py"] extend-include = ["*.ipynb"] @@ -311,86 +209,37 @@ builtins-ignorelist = ["display"] [tool.ruff.lint.flake8-comprehensions] allow-dict-calls-with-keyword-arguments = true -[tool.ruff.lint.flake8-self] -ignore-names = [ - "_latex", - "_print", -] - [tool.ruff.lint.isort] split-on-trailing-comma = false [tool.ruff.lint.per-file-ignores] "*.ipynb" = [ - "A003", "ANN", - "B008", "B018", - "C408", "C90", "D", "E303", - "E402", "E703", - "E741", - "F404", - "N802", - "N803", "N806", - "N807", - "N815", "N816", - "PD901", - "PLC0415", - "PLC2401", "PLR09", "PLR2004", "PLW0602", "PLW0603", - "PLW2901", - "PYI034", - "RUF001", - "RUF027", "S101", - "S307", "T20", "TCH00", ] -"**/002.ipynb" = ["F821"] -"**/003.ipynb" = ["B023", "F821", "PLC2701", "S404", "S603"] -"**/004.ipynb" = ["S404", "S603"] -"**/005.ipynb" = ["F821", "S404", "S603"] -"**/006.ipynb" = ["S404", "S603"] -"**/009.ipynb" = ["FURB113", "S404", "S603"] -"**/010.ipynb" = ["FURB113", "S404", "S603"] -"**/011.ipynb" = ["F821", "PLC2701", "PLR6301"] -"**/014.ipynb" = ["PLC2701"] -"**/016.ipynb" = ["PLC2701"] -"**/017.ipynb" = ["S404", "S603"] -"**/020.ipynb" = ["F821"] -"**/021.ipynb" = ["FIX004", "I001", "S404", "S603"] -"**/022.ipynb" = ["F821", "PLC2701"] -"**/024.ipynb" = ["E731", "E741", "F821", "S102", "S307"] -"**/025.ipynb" = ["E731", "S404", "S603"] -"**/027.ipynb" = ["PLW1510", "S404", "S603"] -"**/028.ipynb" = ["PERF203"] -"**/98*.ipynb" = ["E731", "PLR6301"] "docs/*" = [ - "D", - "E402", "INP001", "S101", "S113", - "T201", ] "docs/conf.py" = [ "A001", "D100", "PLC2701", - "PLW2901", ] -"pin_nb_requirements.py" = ["INP001", "PLW2901"] -"setup.py" = ["D100"] [tool.ruff.lint.pydocstyle] convention = "google" @@ -407,3 +256,112 @@ sort_first = [ ] spaces_indent_inline_array = 4 trailing_comma_inline_array = true + +[tool.tox] +legacy_tox_ini = """ +[tox] +envlist = + docnb-force, + linkcheck, + sty, +skip_install = True +skip_missing_interpreters = True +skipsdist = True + +[testenv] +passenv = * + +[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 +passenv = * +setenv = + PYTHONWARNINGS = + TF_CPP_MIN_LOG_LEVEL = 3 + ZFIT_DISABLE_TF_WARNINGS = 1 + +[testenv:docnb] +base = doc +description = {[testenv:doc]description} with cached notebook execution +setenv = + {[testenv:doc]setenv} + EXECUTE_NB = yes + +[testenv:docnb-force] +base = doc +description = {[testenv:doc]description} with notebook execution (no cache) +setenv = + {[testenv:doc]setenv} + FORCE_EXECUTE_NB = yes + +[testenv:doclive] +allowlist_externals = + sphinx-autobuild +commands = + sphinx-autobuild \ + --ignore=docs/_build/ \ + --ignore=docs/_static/exported_intensity_model.py \ + --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='.*\\.yaml' \ + --re-ignore='.*\\.yml' \ + --watch docs \ + docs/ docs/_build/html +description = Set up a server to directly preview changes to the HTML pages +setenv = + PYTHONWARNINGS = + ZFIT_DISABLE_TF_WARNINGS = 1 + +[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) + +[testenv:nb] +allowlist_externals = + pytest +commands = + pytest {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 +setenv = + SKIP = pyright +""" diff --git a/tox.ini b/tox.ini 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