From 1f022735492e0b2073f0f774c68aff1bfcc8adbc Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 18 Oct 2024 15:14:35 +0200 Subject: [PATCH] DX: define developer environment with `uv` (#24) Co-authored-by: GitHub --- .binder/postBuild | 12 + .binder/runtime.txt | 1 + .editorconfig | 5 +- .envrc | 3 +- .github/release-drafter.yml | 37 - .github/workflows/cd.yml | 16 - .github/workflows/ci.yml | 4 +- .github/workflows/clean-caches.yml | 4 +- .github/workflows/lock.yml | 22 + .github/workflows/pr-linting.yml | 2 +- .github/workflows/release-drafter.yml | 16 - .gitignore | 1 - .pre-commit-config.yaml | 56 +- .python-version | 1 + .vscode/extensions.json | 1 + .vscode/settings.json | 3 + README.md | 1 + docs/conf.py | 4 +- docs/visualize-jax-benchmark.ipynb | 2 - environment.yml | 10 - pyproject.toml | 132 +- scripts/visualize_jax_benchmark.py | 2 - tox.ini | 125 -- uv.lock | 2985 +++++++++++++++++++++++++ 24 files changed, 3174 insertions(+), 271 deletions(-) create mode 100755 .binder/postBuild create mode 100644 .binder/runtime.txt delete mode 100644 .github/release-drafter.yml delete mode 100644 .github/workflows/cd.yml create mode 100644 .github/workflows/lock.yml delete mode 100644 .github/workflows/release-drafter.yml create mode 100644 .python-version delete mode 100644 environment.yml delete mode 100644 tox.ini create mode 100644 uv.lock diff --git a/.binder/postBuild b/.binder/postBuild new file mode 100755 index 0000000..7119564 --- /dev/null +++ b/.binder/postBuild @@ -0,0 +1,12 @@ +#!/bin/bash +set -ex +curl -LsSf https://astral.sh/uv/install.sh | sh +source $HOME/.cargo/env +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/.editorconfig b/.editorconfig index 1d00b13..1184338 100644 --- a/.editorconfig +++ b/.editorconfig @@ -6,8 +6,11 @@ indent_style = space insert_final_newline = true trim_trailing_whitespace = true +[*.ipynb] +indent_size = unset + [*.{py,toml}] indent_size = 4 -[setup.cfg] +[uv.lock] indent_size = 4 diff --git a/.envrc b/.envrc index cce3aa5..41fd2ca 100644 --- a/.envrc +++ b/.envrc @@ -1 +1,2 @@ -layout anaconda +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 33a8fd0..0000000 --- a/.github/release-drafter.yml +++ /dev/null @@ -1,37 +0,0 @@ -name-template: benchmarks $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: | - $CHANGES - - _The full changelog as commits can be found [here](https://github.com/ComPWA/ComPWA benchmarks/compare/$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 2708cfa..1920091 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,7 +28,7 @@ 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 @@ -39,4 +39,4 @@ jobs: if: inputs.specific-pip-packages == '' secrets: token: ${{ secrets.PAT }} - uses: ComPWA/actions/.github/workflows/pre-commit.yml@v1 + 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..6a13858 --- /dev/null +++ b/.github/workflows/lock.yml @@ -0,0 +1,22 @@ +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 + - uv.lock + workflow_dispatch: + +jobs: + lock: + uses: ComPWA/actions/.github/workflows/lock.yml@v2 + secrets: + token: ${{ secrets.PAT }} 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 d94452f..bc30fec 100644 --- a/.gitignore +++ b/.gitignore @@ -16,7 +16,6 @@ version.py # Temporary files *.pyc -*condaenv.* .coverage .coverage.* .ipynb_checkpoints/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5633d1e..312820b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,10 +1,9 @@ ci: - autoupdate_commit_msg: "MAINT: autoupdate pre-commit hooks" + autoupdate_commit_msg: "MAINT: update lock files" autoupdate_schedule: quarterly skip: - - prettier - pyright - - taplo + - uv-lock repos: - repo: meta @@ -12,11 +11,24 @@ repos: - id: check-hooks-apply - id: check-useless-excludes + - repo: https://github.com/ComPWA/policy + rev: 0.5.0 + hooks: + - id: check-dev-files + args: + - --no-cd + - --no-pypi + - --repo-name=ComPWA benchmarks + - --repo-title=benchmarks + - id: colab-toc-visible + - id: remove-empty-tags + - repo: https://github.com/kynan/nbstripout rev: 0.7.1 hooks: - id: nbstripout args: + - --drop-empty-cells - --extra-keys - | cell.attachments @@ -39,21 +51,8 @@ repos: metadata.varInspector metadata.vscode - - repo: https://github.com/ComPWA/policy - rev: 0.3.18 - hooks: - - id: check-dev-files - args: - - --no-gitpod - - --no-prettierrc - - --no-pypi - - --repo-name=ComPWA benchmarks - - --repo-title=benchmarks - - id: colab-toc-visible - - id: remove-empty-tags - - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.6 + rev: v0.7.0 hooks: - id: ruff args: [--fix] @@ -62,7 +61,7 @@ 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 @@ -76,15 +75,15 @@ repos: - id: mixed-line-ending - id: trailing-whitespace - - repo: https://github.com/pre-commit/mirrors-prettier - rev: v4.0.0-alpha.8 + - repo: https://github.com/ComPWA/prettier-pre-commit + rev: v3.3.3 hooks: - id: prettier - - repo: https://github.com/ComPWA/mirrors-taplo - rev: v0.8.1 + - repo: https://github.com/ComPWA/taplo-pre-commit + rev: v0.9.3 hooks: - - id: taplo + - id: taplo-format - repo: https://github.com/pappasam/toml-sort rev: v0.23.1 @@ -94,7 +93,7 @@ repos: - --in-place - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: 2.7.3 + rev: 3.0.3 hooks: - id: editorconfig-checker name: editorconfig @@ -104,7 +103,12 @@ repos: .*\.py )$ - - repo: https://github.com/ComPWA/mirrors-pyright - rev: v1.1.374 + - repo: https://github.com/ComPWA/pyright-pre-commit + rev: v1.1.385 hooks: - id: pyright + + - repo: https://github.com/astral-sh/uv-pre-commit + rev: 0.4.24 + hooks: + - id: uv-lock 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/.vscode/extensions.json b/.vscode/extensions.json index dba1484..acd2394 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -7,6 +7,7 @@ "executablebookproject.myst-highlight", "github.vscode-github-actions", "github.vscode-pull-request-github", + "mhutchie.git-graph", "ms-python.python", "ms-python.vscode-pylance", "ms-vscode.live-server", diff --git a/.vscode/settings.json b/.vscode/settings.json index 6ce138b..dd0961c 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -49,5 +49,8 @@ "ruff.enable": true, "ruff.importStrategy": "fromEnvironment", "ruff.organizeImports": true, + "search.exclude": { + "**/uv.lock": true + }, "telemetry.telemetryLevel": "off" } diff --git a/README.md b/README.md index 422ca9d..1323b1b 100644 --- a/README.md +++ b/README.md @@ -2,3 +2,4 @@ [![code style: prettier](https://img.shields.io/badge/code_style-prettier-ff69b4.svg?style=flat-square)](https://github.com/prettier/prettier) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) +[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv) diff --git a/docs/conf.py b/docs/conf.py index 3227f69..32eb748 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,5 +1,3 @@ -from __future__ import annotations - from sphinx_api_relink.helpers import get_branch_name, get_execution_mode BRANCH = get_branch_name() @@ -56,7 +54,7 @@ }, { "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", }, diff --git a/docs/visualize-jax-benchmark.ipynb b/docs/visualize-jax-benchmark.ipynb index 01b0c5f..0cbf42a 100644 --- a/docs/visualize-jax-benchmark.ipynb +++ b/docs/visualize-jax-benchmark.ipynb @@ -23,8 +23,6 @@ }, "outputs": [], "source": [ - "from __future__ import annotations\n", - "\n", "from collections import defaultdict\n", "\n", "import matplotlib.pyplot as plt\n", diff --git a/environment.yml b/environment.yml deleted file mode 100644 index e04eda5..0000000 --- a/environment.yml +++ /dev/null @@ -1,10 +0,0 @@ -name: benchmarks -channels: - - defaults -dependencies: - - python==3.9.* - - pip - - pip: - - -e .[dev] -variables: - PRETTIER_LEGACY_CLI: 1 diff --git a/pyproject.toml b/pyproject.toml index c83b508..2768799 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,23 +4,6 @@ requires = ["setuptools>=61.2"] [project] authors = [{name = "Common Partial Wave Analysis", email = "compwa-admin@ep1.rub.de"}] -classifiers = [ - "Development Status :: 3 - Alpha", - "Intended Audience :: Developers", - "Intended Audience :: Education", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", - "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", - "Typing :: Typed", -] dependencies = [ "matplotlib", "polarization-sensitivity @ git+https://github.com/redeboer/polarization-sensitivity@15f5ce0", @@ -30,7 +13,7 @@ description = "Benchmarks for amplitude analysis frameworks" dynamic = ["version"] license = {text = "GPLv3 or later"} name = "benchmarks" -requires-python = ">=3.9" +requires-python = ">=3.12" [project.optional-dependencies] dev = [ @@ -39,13 +22,13 @@ dev = [ "benchmarks[sty]", "benchmarks[test]", "sphinx-autobuild", - "tox >=1.9", # for skip_install, use_develop + "tox", ] doc = [ - "Sphinx >=3", - "myst-nb >=0.14", # nb_ configuration prefixes + "benchmarks[notebooks]", + "myst-nb", "myst-parser[linkify]", - "pandas", + "sphinx", "sphinx-api-relink", "sphinx-book-theme", "sphinx-codeautolink[ipython]", @@ -53,7 +36,7 @@ doc = [ "sphinx-togglebutton", ] jupyter = [ - "jupyterlab >=3.0", + "jupyterlab", "jupyterlab", "jupyterlab-code-formatter >=3.0.0", "jupyterlab-git", @@ -66,11 +49,14 @@ jupyter = [ lint = [ "ruff", ] +notebooks = [ + "pandas", +] sty = [ "benchmarks[format]", "benchmarks[lint]", "benchmarks[types]", - "pre-commit >=1.4.0", + "pre-commit-uv", "ruff", ] test = [ @@ -88,6 +74,9 @@ file = "README.md" include-package-data = false [tool.pyright] +exclude = [ + "**/.venv/", +] reportAttributeAccessIssue = false reportGeneralTypeIssues = false reportImportCycles = false @@ -137,7 +126,6 @@ testpaths = [ extend-include = ["*.ipynb"] preview = true show-fixes = true -target-version = "py39" [tool.ruff.format] docstring-code-format = true @@ -226,6 +214,98 @@ sort_first = [ "tool.setuptools", "tool.setuptools_scm", ] -sort_table_keys = true 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 = * +setenv = + PYTHONHASHSEED = 0 + +[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 + +[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 \ + --open-browser \ + --port=0 \ + --re-ignore='.*/__pycache__/.*' \ + --re-ignore='.*/.ipynb_checkpoints/.*' \ + --re-ignore='.*/.virtual_documents/.*' \ + --re-ignore='.*\\.tmp' \ + --watch docs \ + docs/ docs/_build/html +description = Set up a server to directly preview changes to the HTML pages + +[testenv:docnblive] +base = doclive +description = {[testenv:doclive]description} with cached notebook execution +setenv = + {[testenv:doclive]setenv} + EXECUTE_NB = yes + +[testenv:linkcheck] +allowlist_externals = + sphinx-build +commands = + sphinx-build \ + --builder=linkcheck \ + --show-traceback \ + docs/ docs/_build/linkcheck +description = Check external links in the documentation (requires internet connection) +setenv = + PYTHONWARNINGS = + +[testenv:nb] +allowlist_externals = + pytest +commands = + pytest --nbmake {posargs:docs} +description = Run all notebooks with pytest + +[testenv:sty] +allowlist_externals = + pre-commit +commands = + pre-commit run {posargs} --all-files +description = Perform all linting, formatting, and spelling checks +setenv = + SKIP = pyright +""" diff --git a/scripts/visualize_jax_benchmark.py b/scripts/visualize_jax_benchmark.py index c1b529c..acd3078 100644 --- a/scripts/visualize_jax_benchmark.py +++ b/scripts/visualize_jax_benchmark.py @@ -1,7 +1,5 @@ """Visualize benchmark results from :file:`execute_jax_benchmark.py`.""" -from __future__ import annotations - import logging from collections import defaultdict from os.path import dirname diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 315892b..0000000 --- a/tox.ini +++ /dev/null @@ -1,125 +0,0 @@ -[tox] -envlist = - sty, -passenv = PYTHONPATH -skip_install = True -skip_missing_interpreters = True -skipsdist = True - -[testenv:doc] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - --keep-going \ - -TW \ - -b html \ - docs/ docs/_build/html -description = - Build documentation and API through Sphinx -passenv = * -setenv = - FORCE_COLOR = yes - PYTHONHASHSEED = 0 - -[testenv:doclive] -allowlist_externals = - sphinx-autobuild -commands = - sphinx-autobuild \ - --open-browser \ - --re-ignore .*/.ipynb_checkpoints/.* \ - --re-ignore .*/__pycache__/.* \ - --re-ignore .*\.tmp \ - --watch docs \ - docs/ docs/_build/html -description = - Set up a server to directly preview changes to the HTML pages -passenv = * -setenv = - FORCE_COLOR = yes - PYTHONHASHSEED = 0 - -[testenv:docnb] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - --keep-going \ - -TW \ - -b html \ - docs/ docs/_build/html -description = - Build documentation through Sphinx WITH output of Jupyter notebooks -passenv = * -setenv = - EXECUTE_NB = yes - FORCE_COLOR = yes - PYTHONHASHSEED = 0 - -[testenv:docnblive] -allowlist_externals = - sphinx-autobuild -commands = - sphinx-autobuild \ - --open-browser \ - --re-ignore .*/.ipynb_checkpoints/.* \ - --re-ignore .*/__pycache__/.* \ - --re-ignore .*\.tmp \ - --watch docs \ - docs/ docs/_build/html -description = - Set up a server to directly preview changes to the HTML pages -passenv = * -setenv = - EXECUTE_NB = yes - FORCE_COLOR = yes - PYTHONHASHSEED = 0 - -[testenv:docnb-force] -allowlist_externals = - sphinx-build -commands = - sphinx-build -nW --keep-going -b html docs/ docs/_build/html -description = - Execute ALL Jupyter notebooks and build documentation with Sphinx -passenv = * -setenv = - FORCE_COLOR = yes - FORCE_EXECUTE_NB = yes - PYTHONHASHSEED = 0 - -[testenv:linkcheck] -allowlist_externals = - sphinx-build -commands = - sphinx-build \ - -T \ - -b linkcheck \ - docs/ docs/_build/linkcheck -description = - Check external links in the documentation (requires internet connection) -passenv = * -setenv = - FORCE_COLOR = yes - -[testenv:nb] -allowlist_externals = - pytest -commands = - pytest --nbmake {posargs:docs} -description = - Run all notebooks with pytest -passenv = * -setenv = - PYTHONHASHSEED = 0 - -[testenv:sty] -description = - Perform all linting, formatting, and spelling checks -setenv = - SKIP = pyright -allowlist_externals = - pre-commit -commands = - pre-commit run {posargs} -a diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..3ec3755 --- /dev/null +++ b/uv.lock @@ -0,0 +1,2985 @@ +version = 1 +requires-python = ">=3.12" +resolution-markers = [ + "python_full_version < '3.13'", + "python_full_version >= '3.13'", +] + +[[package]] +name = "accessible-pygments" +version = "0.0.5" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "pygments" }, +] +sdist = { url = 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