From d9e96347c9f4700dacc36a2b51be212f27a73378 Mon Sep 17 00:00:00 2001 From: Remco de Boer <29308176+redeboer@users.noreply.github.com> Date: Fri, 20 Dec 2024 15:05:52 +0100 Subject: [PATCH] MAINT: update lock files (#26) * DX: remove `files.watcherExclude` * DX: set `PYTHONHASHSEED=0` * MAINT: ignore `LOG015` in TR-002 * MAINT: implement dev environment updates * MAINT: pin link to `numpy.emath` * MAINT: remove `enable-cache` argument (defaults to true) * MAINT: rename `TCH` Ruff rules to `TC` * MAINT: sort cSpell config * MAINT: update link to Lecture 17 * MAINT: update link to `ScipyTrustConstrV1` * MAINT: update to `astral-sh/setup-uv@v5` --------- Co-authored-by: GitHub Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .binder/postBuild | 1 - .cspell.json | 142 +- .github/workflows/ci.yml | 3 - .github/workflows/notebooks.yml | 4 +- .pre-commit-config.yaml | 18 +- .vscode/extensions.json | 2 + .vscode/settings.json | 6 - docs/000/index.ipynb | 2 +- docs/001/index.ipynb | 4 +- docs/002/pyproject.toml | 3 +- docs/014/pyproject.toml | 2 +- docs/020/index.ipynb | 2 +- docs/025/index.ipynb | 2 +- docs/030/pyproject.toml | 2 +- docs/031/pyproject.toml | 2 +- docs/032/pyproject.toml | 2 +- pixi.lock | 2364 ++++++++++++------------------- pixi.toml | 3 - pyproject.toml | 2 +- uv.lock | 1096 ++++++++------ 20 files changed, 1617 insertions(+), 2045 deletions(-) diff --git a/.binder/postBuild b/.binder/postBuild index 079abb3..0374364 100755 --- a/.binder/postBuild +++ b/.binder/postBuild @@ -7,7 +7,6 @@ pixi_packages="$(NO_COLOR= pixi list --explicit --no-install | awk 'NR > 1 {prin if [[ -n "$pixi_packages" ]]; then pixi global install $pixi_packages fi -export PYTHONHASHSEED="0" pixi clean cache --yes uv export \ diff --git a/.cspell.json b/.cspell.json index a163559..ed5bc90 100644 --- a/.cspell.json +++ b/.cspell.json @@ -1,5 +1,4 @@ { - "version": "0.2", "allowCompoundWords": false, "enableFiletypes": [ "git-commit", @@ -37,80 +36,10 @@ "docs/conf.py", "pyproject.toml" ], - "language": "en-US", - "overrides": [ - { - "allowCompoundWords": true, - "filename": "**/*.jl", - "languageId": "julia" - } - ], - "words": [ - "AmpForm", - "analyticity", - "arccos", - "arctan", - "Argand", - "autograd", - "Blatt", - "Breit", - "Byckling", - "Colab", - "ComPWA", - "Dalitz", - "dummifies", - "dummify", - "eigenstates", - "Flatté", - "functools", - "GlueX", - "graphviz", - "Hankel", - "helicities", - "helicity", - "hepstats", - "Hippel", - "iminuit", - "IPython", - "JHEP", - "JPAC", - "Ketzer", - "Källén", - "lambdification", - "lambdified", - "lambdifies", - "lambdify", - "lambdifying", - "LHCb", - "lineshape", - "lineshapes", - "matplotlib", - "Mikhasenko", - "NumPy", - "parametrizations", - "Pixi", - "plotly", - "pyplot", - "QRules", - "Quigg", - "SciPy", - "sympify", - "SymPy", - "TensorWaves", - "traceback", - "unevaluatable", - "unitarity", - "unitless", - "unphysical", - "vectorize", - "Weisskopf", - "zfit" - ], "ignoreWords": [ "Kutschke", "Marangotto", "PINF", - "PYTHONHASHSEED", "Richman", "absl", "aitchison", @@ -310,5 +239,76 @@ "zlim", "zorder", "zticks" + ], + "language": "en-US", + "overrides": [ + { + "allowCompoundWords": true, + "filename": "**/*.jl", + "languageId": "julia" + } + ], + "useGitignore": true, + "version": "0.2", + "words": [ + "AmpForm", + "analyticity", + "arccos", + "arctan", + "Argand", + "autograd", + "Blatt", + "Breit", + "Byckling", + "Colab", + "ComPWA", + "Dalitz", + "dummifies", + "dummify", + "eigenstates", + "Flatté", + "functools", + "GlueX", + "graphviz", + "Hankel", + "helicities", + "helicity", + "hepstats", + "Hippel", + "iminuit", + "IPython", + "JHEP", + "JPAC", + "Ketzer", + "Källén", + "lambdification", + "lambdified", + "lambdifies", + "lambdify", + "lambdifying", + "LHCb", + "lineshape", + "lineshapes", + "matplotlib", + "Mikhasenko", + "NumPy", + "parametrizations", + "Pixi", + "plotly", + "pyplot", + "QRules", + "Quigg", + "SciPy", + "sympify", + "SymPy", + "TensorWaves", + "traceback", + "unevaluatable", + "unitarity", + "unitless", + "unphysical", + "vectorize", + "Weisskopf", + "zfit" ] } diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2c925fb..9afbc84 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -5,9 +5,6 @@ concurrency: cancel-in-progress: |- ${{ github.ref != format('refs/heads/{0}', github.event.repository.default_branch) }} -env: - PYTHONHASHSEED: "0" - on: push: branches: diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml index ded993c..d08cdaf 100644 --- a/.github/workflows/notebooks.yml +++ b/.github/workflows/notebooks.yml @@ -17,9 +17,7 @@ jobs: - uses: actions/setup-python@v5 with: python-version: "3.12" - - uses: astral-sh/setup-uv@v3 - with: - enable-cache: true + - uses: astral-sh/setup-uv@v5 - name: Install graphviz run: sudo apt-get -y install graphviz - name: Run all notebooks diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ee6624d..c32e94c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,7 +12,7 @@ repos: - id: check-useless-excludes - repo: https://github.com/ComPWA/policy - rev: 0.5.5 + rev: 0.5.8 hooks: - id: check-dev-files args: @@ -28,7 +28,7 @@ repos: - id: remove-empty-tags - repo: https://github.com/kynan/nbstripout - rev: 0.7.1 + rev: 0.8.1 hooks: - id: nbstripout args: @@ -56,7 +56,7 @@ repos: metadata.vscode - repo: https://github.com/nbQA-dev/nbQA - rev: 1.8.7 + rev: 1.9.1 hooks: - id: nbqa-isort args: [--float-to-top] @@ -75,7 +75,7 @@ repos: )$ - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.7.1 + rev: v0.8.4 hooks: - id: ruff args: [--fix] @@ -104,7 +104,7 @@ repos: - id: trailing-whitespace - repo: https://github.com/ComPWA/prettier-pre-commit - rev: v3.3.3 + rev: v3.4.2 hooks: - id: prettier @@ -114,14 +114,14 @@ repos: - id: taplo-format - repo: https://github.com/pappasam/toml-sort - rev: v0.23.1 + rev: v0.24.2 hooks: - id: toml-sort args: [--in-place] exclude: (?x)^(.*/Manifest\.toml|.*/Project\.toml)$ - repo: https://github.com/streetsidesoftware/cspell-cli - rev: v8.15.2 + rev: v8.17.0 hooks: - id: cspell @@ -147,11 +147,11 @@ repos: )$ - repo: https://github.com/ComPWA/pyright-pre-commit - rev: v1.1.386 + rev: v1.1.391 hooks: - id: pyright - repo: https://github.com/astral-sh/uv-pre-commit - rev: 0.4.28 + rev: 0.5.11 hooks: - id: uv-lock diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 3cd3f4d..dddc486 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -12,6 +12,7 @@ "mhutchie.git-graph", "ms-python.python", "ms-python.vscode-pylance", + "ms-toolsai.jupyter", "ms-toolsai.vscode-jupyter-cell-tags", "ms-vscode.live-server", "ms-vsliveshare.vsliveshare", @@ -32,6 +33,7 @@ "ms-python.isort", "ms-python.mypy-type-checker", "ms-python.pylint", + "ms-toolsai.vscode-jupyter-slideshow", "travisillig.vscode-json-stable-stringify", "tyriar.sort-lines" ] diff --git a/.vscode/settings.json b/.vscode/settings.json index 16d1bd7..e152ff8 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -33,12 +33,6 @@ "files.associations": { "**/pixi.lock": "yaml" }, - "files.watcherExclude": { - "**/*_cache/**": true, - "**/.eggs/**": true, - "**/.git/**": true, - "**/.tox/**": true - }, "git.rebaseWhenSync": true, "github-actions.workflows.pinned.workflows": [".github/workflows/ci.yml"], "gitlens.telemetry.enabled": false, diff --git a/docs/000/index.ipynb b/docs/000/index.ipynb index dd6bb71..80ea8ab 100644 --- a/docs/000/index.ipynb +++ b/docs/000/index.ipynb @@ -329,7 +329,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Unfortunately, the {mod}`jax.numpy` API does not interface to {mod}`numpy.emath`. It is possible to decorate {func}`numpy.emath.sqrt` be decorated with {func}`jax.jit`, but that **only works with static, hashable arguments**:" + "Unfortunately, the {mod}`jax.numpy` API does not interface to [`numpy.emath`](https://numpy.org/doc/2.0/reference/routines.emath.html). It is possible to decorate {func}`numpy.emath.sqrt` be decorated with {func}`jax.jit`, but that **only works with static, hashable arguments**:" ] }, { diff --git a/docs/001/index.ipynb b/docs/001/index.ipynb index 72489fe..9ebe0a3 100644 --- a/docs/001/index.ipynb +++ b/docs/001/index.ipynb @@ -329,7 +329,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "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:" + "Just as noted in {ref}`000/index:Complex square root` though, [`numpy.emath`](https://numpy.org/doc/2.0/reference/routines.emath.html) is not provided by the NumPy API of {doc}`JAX `. As discussed there, we can at most decorate the [`numpy.emath`](https://numpy.org/doc/2.0/reference/routines.emath.html) version with {func}`jax.jit` and work with static arguments only:" ] }, { @@ -401,7 +401,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "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", + "As concluded in {ref}`000/index:Conditional square root`, the alternative to lambdify to [`numpy.emath`](https://numpy.org/doc/2.0/reference/routines.emath.html) 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:" ] diff --git a/docs/002/pyproject.toml b/docs/002/pyproject.toml index 2364d02..feb5600 100644 --- a/docs/002/pyproject.toml +++ b/docs/002/pyproject.toml @@ -14,10 +14,11 @@ ignore = [ "F404", "G004", "ISC001", + "LOG015", "PD901", "PLR2004", "S101", "T201", - "TCH003", + "TC003", ] select = ["ALL"] diff --git a/docs/014/pyproject.toml b/docs/014/pyproject.toml index ba3fc37..509ebc6 100644 --- a/docs/014/pyproject.toml +++ b/docs/014/pyproject.toml @@ -29,7 +29,7 @@ ignore = [ "PYI034", "S101", "SIM108", - "TCH003", + "TC003", ] select = ["ALL"] diff --git a/docs/020/index.ipynb b/docs/020/index.ipynb index 8122d2b..0006ce4 100644 --- a/docs/020/index.ipynb +++ b/docs/020/index.ipynb @@ -1028,7 +1028,7 @@ "metadata": {}, "source": [ ":::{note}\n", - "You can also try different minimizers, like {class}`~zfit.minimizers.minimizers_scipy.ScipyTrustConstrV1`, but {class}`~zfit.minimizers.minimizer_minuit.Minuit` seems to perform best.\n", + "You can also try different minimizers, like [`ScipyTrustConstrV1`](https://zfit.readthedocs.io/en/v0.18.1/user_api/minimize/_generated/minimizers/zfit.minimize.ScipyTrustConstrV1.html), but {class}`~zfit.minimizers.minimizer_minuit.Minuit` seems to perform best.\n", ":::" ] }, diff --git a/docs/025/index.ipynb b/docs/025/index.ipynb index c088bff..7af6a6b 100644 --- a/docs/025/index.ipynb +++ b/docs/025/index.ipynb @@ -68,7 +68,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - ":::{seealso} [Lecture 17](https://compwa.github.io/strong2020-salamanca/lecture17.html) on collision theory of the [STRONG2020 HaSP School](https://indico.ific.uv.es/event/6803) by Miguel Albaladejo.\n", + ":::{seealso} [Lecture 17](https://compwa.github.io/strong2020-salamanca/lecture17/) on collision theory of the [STRONG2020 HaSP School](https://indico.ific.uv.es/event/6803) by Miguel Albaladejo.\n", "\n", ":::\n", "\n", diff --git a/docs/030/pyproject.toml b/docs/030/pyproject.toml index 433626e..d3b2545 100644 --- a/docs/030/pyproject.toml +++ b/docs/030/pyproject.toml @@ -26,7 +26,7 @@ ignore = [ "PLC2401", "PLR0913", "PLR0917", - "TCH002", + "TC002", ] select = ["ALL"] diff --git a/docs/031/pyproject.toml b/docs/031/pyproject.toml index 5ceff02..6b4614e 100644 --- a/docs/031/pyproject.toml +++ b/docs/031/pyproject.toml @@ -29,7 +29,7 @@ ignore = [ "PLR0913", "PLR0917", "S101", - "TCH002", + "TC002", ] select = ["ALL"] diff --git a/docs/032/pyproject.toml b/docs/032/pyproject.toml index f7a046f..4e37d07 100644 --- a/docs/032/pyproject.toml +++ b/docs/032/pyproject.toml @@ -28,7 +28,7 @@ ignore = [ "PLR0913", "PLR0917", "S101", - "TCH00", + "TC00", ] select = ["ALL"] diff --git a/pixi.lock b/pixi.lock index a46857f..cb1c80f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,4 +1,4 @@ -version: 5 +version: 6 environments: default: channels: @@ -10,13 +10,12 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-h04ea711_2.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hebfffa5_3.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.3-h5888daf_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.2-h3394656_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda @@ -30,8 +29,8 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda - conda: https://repo.prefix.dev/julia-forge/linux-64/julia-1.10.4-hb0f4dca_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2 - - conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.22-hb9d3cd8_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.3-h5888daf_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.23-h4ddbbb0_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda @@ -40,42 +39,39 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.6.3-hb9d3cd8_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.44-hadc24fc_0.conda - conda: 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