From a5304546756520f8f6a1bafa0eee178fa6e3d628 Mon Sep 17 00:00:00 2001 From: Rocco Meli Date: Fri, 5 Apr 2024 23:53:00 +0200 Subject: [PATCH] Version 0.7.0 (#116) * add details on NotImplementedError exceptions * changelog * remove versioneer * changelog * fix warning * fix tests with pytest 8 * update changelog * update ci * add setuptools for python 12 * setuptools in ci * use miniconda, conda is missing from macos-14 * miniforge * fixes * mamba * bump min python version * update changelog * Update build system to flit_core * Add entry to changelog * Update CHANGELOG.md * Delete .gitattributes * Delete .lgtm.yml * Update CHANGELOG.md * Add functionality to select backend (#107) * Documentation and CLI for backend selection (#112) * Add rustworkx backend (#111) * Update graph.py to support set_backend function I also made a fuction to see the available backends and get the current backend * Apply private _available_backends suggestions from code review This commit contains the suggested changes regarding making the available_backends variable private, and refactoring the get_available_backends method to available_backends Co-authored-by: Rocco Meli * Print warning when backend is already set + make sure we use _available_backends everywhere where possible * remove reliance on environment variables * make _validate_backend function print warning when a certain backend isn't installed * Use precommit hooks add __all__ back refactor _alias_backendDict to _alias_to_backend * Update ValueError message Co-authored-by: Rocco Meli * Don't return the backend when setting it Co-authored-by: Rocco Meli * Add dummy function to make mypy happy remove __all__ assignment * fist play with rustworkx backend * add documentation for backend selection * add cli backend selection * cleanup * changelog * apply @Jnelen suggestion and add warning filter * make molecule test also more robust * add rx to ci * add rustworkx to all backends tests * add back graphtool * add rx to test all backends and add verbose mode * Update test_molecule.py --------- Co-authored-by: jnelen Co-authored-by: Jochem Nelen <78348388+Jnelen@users.noreply.github.com> * Update .readthedocs.yml (#114) * Update .readthedocs.yml * rm duplicate key * prepare release 0.7.0 --------- Co-authored-by: Thomas Kluyver Co-authored-by: Jochem Nelen <78348388+Jnelen@users.noreply.github.com> Co-authored-by: jnelen --- .gitattributes | 1 - .github/workflows/flake8.yml | 5 +- .github/workflows/mypy.yml | 5 +- .github/workflows/pre-commit.yml | 2 +- .github/workflows/pytest.yml | 20 +- .lgtm.yml | 10 - .pre-commit-config.yaml | 1 + .readthedocs.yml | 10 +- CHANGELOG.md | 32 + CITATION.cff | 5 +- MANIFEST.in | 1 - README.md | 65 +- devtools/conda-envs/spyrmsd-all.yaml | 1 + devtools/conda-envs/spyrmsd-docs.yaml | 1 + .../conda-envs/spyrmsd-test-obabel-gt.yaml | 1 + .../conda-envs/spyrmsd-test-obabel-nx.yaml | 1 + .../conda-envs/spyrmsd-test-obabel-rx.yaml | 26 + .../conda-envs/spyrmsd-test-rdkit-all.yaml | 29 + .../conda-envs/spyrmsd-test-rdkit-gt.yaml | 1 + .../conda-envs/spyrmsd-test-rdkit-nx.yaml | 1 + .../conda-envs/spyrmsd-test-rdkit-rx.yaml | 27 + devtools/conda-envs/spyrmsd.yaml | 3 +- docs/source/conf.py | 2 +- docs/source/tutorials/tutorial.ipynb | 103 +- docs/source/tutorials/tutorial.rst | 62 +- pyproject.toml | 6 +- setup.cfg | 11 - setup.py | 7 +- spyrmsd/__init__.py | 12 +- spyrmsd/__main__.py | 20 + spyrmsd/_version.py | 693 ----- spyrmsd/graph.py | 210 +- spyrmsd/graphs/rx.py | 190 ++ spyrmsd/molecule.py | 18 +- spyrmsd/optional/__init__.py | 7 - spyrmsd/optional/rdkit.py | 16 +- tests/conftest.py | 1 + tests/test_benchmarks.py | 1 - tests/test_graph.py | 52 +- tests/test_molecule.py | 41 +- versioneer.py | 2264 ----------------- 41 files changed, 858 insertions(+), 3106 deletions(-) delete mode 100644 .gitattributes delete mode 100644 .lgtm.yml create mode 100644 devtools/conda-envs/spyrmsd-test-obabel-rx.yaml create mode 100644 devtools/conda-envs/spyrmsd-test-rdkit-all.yaml create mode 100644 devtools/conda-envs/spyrmsd-test-rdkit-rx.yaml delete mode 100644 spyrmsd/_version.py create mode 100644 spyrmsd/graphs/rx.py delete mode 100644 versioneer.py diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 1a56faa..0000000 --- a/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -spyrmsd/_version.py export-subst diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml index e36e007..f28604e 100644 --- a/.github/workflows/flake8.yml +++ b/.github/workflows/flake8.yml @@ -13,7 +13,7 @@ jobs: strategy: matrix: - python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v3 @@ -24,7 +24,8 @@ jobs: - name: Install Dependencies run: | python -m pip install --upgrade pip - pip install flake8 + python -m pip install setuptools + python -m pip install flake8 - name: Install package run: | python setup.py develop --no-deps diff --git a/.github/workflows/mypy.yml b/.github/workflows/mypy.yml index 5a46ad4..23fda8a 100644 --- a/.github/workflows/mypy.yml +++ b/.github/workflows/mypy.yml @@ -13,7 +13,7 @@ jobs: strategy: matrix: - python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v3 @@ -24,7 +24,8 @@ jobs: - name: Install Dependencies run: | python -m pip install --upgrade pip - pip install mypy + python -m pip install setuptools + python -m pip install mypy - name: Install Types run: | python -m pip install types-requests diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 905f464..30941ce 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -12,7 +12,7 @@ jobs: strategy: matrix: - python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v3 diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 89b612e..6dc9e06 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -24,14 +24,17 @@ jobs: strategy: matrix: os: [macOS-latest, ubuntu-latest, windows-latest] - python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11", "3.12"] chemlib: [obabel, rdkit] - graphlib: [nx, gt] + graphlib: [nx, gt, rx, all] exclude: # graph-tools does not work on Windows - {os: "windows-latest", graphlib: "gt"} - # FIXME: Keeps failing in CI for unknown reasons during miniconda setup - - {os: "ubuntu-latest", graphlib: "gt", chemlib: "rdkit", python-version: "3.7"} + - {os: "windows-latest", graphlib: "all"} + - {graphlib: "all", chemlib: "obabel"} + include: + - {os: "macOS-14", graphlib: "gt", chemlib: "obabel", python-version: "3.12"} + - {os: "macOS-14", graphlib: "nx", chemlib: "rdkit", python-version: "3.12"} steps: - uses: actions/checkout@v3 @@ -43,12 +46,14 @@ jobs: df -h ulimit -a - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: python-version: ${{ matrix.python-version }} environment-file: devtools/conda-envs/spyrmsd-test-${{ matrix.chemlib }}-${{ matrix.graphlib }}.yaml - channels: conda-forge,defaults + miniforge-version: "latest" activate-environment: spyrmsd + miniforge-variant: Mambaforge + use-mamba: true auto-update-conda: true auto-activate-base: false show-channel-urls: true @@ -56,7 +61,8 @@ jobs: - name: Install run: | python -m pip install . --no-deps - conda list + mamba info + mamba list - name: Test run: | diff --git a/.lgtm.yml b/.lgtm.yml deleted file mode 100644 index 5419265..0000000 --- a/.lgtm.yml +++ /dev/null @@ -1,10 +0,0 @@ -extraction: - python: - python_setup: - version: 3 -path_classifiers: - library: - - versioneer.py - - devtools/* - generated: - - spyrmsd/_version.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 176a260..6da5c7c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -25,6 +25,7 @@ repos: rev: 5.12.0 hooks: - id: isort + args: ["--profile", "black"] - repo: https://github.com/pre-commit/mirrors-mypy rev: v1.5.1 hooks: diff --git a/.readthedocs.yml b/.readthedocs.yml index 91db81d..bed6774 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,16 +1,20 @@ -# .readthedocs.yml -# Read the Docs configuration file +# Read the Docs configuration file for Sphinx projects # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details version: 2 +build: + os: ubuntu-22.04 + tools: + python: "mambaforge-22.9" + sphinx: builder: html configuration: docs/source/conf.py formats: - - epub - pdf + - epub conda: environment: devtools/conda-envs/spyrmsd-docs.yaml diff --git a/CHANGELOG.md b/CHANGELOG.md index 315d2ef..67f0996 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,38 @@ ------------------------------------------------------------------------------ +## Version 0.7.0 + +Date: 05/04/2024 +Contributors: @RMeli, @takluyver, @Jnelen + +### Added + +* Support for `rustworkx` graph library [PR 111 | @RMeli] +* Functionality to manually select the backend from CLI [PR #108 | @RMeli] +* Functionality to manually select the backend [PR #107 | @Jnelen] +* Python `3.12` to CI [PR #102 | @RMeli] +* macOS M1 (`macoOS-14`) to CI [PR #102 | @RMeli] + +### Changed + +* Molecular graphs cache to cache by backend [PR #107 | @Jnelen] +* Python build system to use flit_core directly [PR #103 | @takluyver] +* Minimum version of Python to `3.9` (to reduce CI matrix) [PR #102 | @RMeli] + +### Fixed + +* Failing tests with `pytest=8.0.0` [PR #101 | @RMeli] + +### Improved + +* Messages for `NotImplementedError` exceptions [PR #90 | @RMeli] + +### Removed + +* `.gitattributes` and `.lgtm.yaml` stale files +* `versioneer` [PR #91 | @RMeli] + ## Version 0.6.0 Date: 08/09/2023 diff --git a/CITATION.cff b/CITATION.cff index d1d1a7c..07a57a1 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -4,8 +4,11 @@ authors: - family-names: "Meli" given-names: "Rocco" orcid: "https://orcid.org/0000-0002-2845-3410" +- family-names: "Nelen" + given-names: "Jochem" + orcid: "https://orcid.org/0000-0002-9970-4950" title: "spyrmsd" -version: 0.6.0 +version: 0.7.0 doi: 10.5281/zenodo.3631876 date-released: 2021-06-21 url: "https://github.com/RMeli/spyrmsd" diff --git a/MANIFEST.in b/MANIFEST.in index f872f73..4cf5bf7 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,6 +1,5 @@ include LICENSE include MANIFEST.in -include versioneer.py graft spyrmsd global-exclude *.py[cod] __pycache__ *.so diff --git a/README.md b/README.md index 701a1e6..e2e5bb8 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ [![Documentation Status](https://readthedocs.org/projects/spyrmsd/badge/?version=develop)](https://spyrmsd.readthedocs.io/en/develop/?badge=develop) [![License](https://img.shields.io/github/license/RMeli/pyrmsd?color=%2333BBFF)](https://opensource.org/licenses/MIT) -[![PyPI](https://img.shields.io/badge/PyPI-v0.6.0%20-ff69b4)](https://pypi.org/project/spyrmsd/) +[![PyPI](https://img.shields.io/badge/PyPI-v0.7.0%20-ff69b4)](https://pypi.org/project/spyrmsd/) [![Conda Version](https://img.shields.io/conda/vn/conda-forge/spyrmsd.svg)](https://anaconda.org/conda-forge/spyrmsd) [![J. Cheminform.](https://img.shields.io/badge/J.%20Cheminform.-10.1186%2Fs13321--020--00455--2-blue)](https://doi.org/10.1186/s13321-020-00455-2) @@ -38,7 +38,7 @@ If you find `spyrmsd` useful, please consider citing the following paper: `spyrmsd` is available on [PyPI](https://pypi.org/project/spyrmsd/) and [conda-forge](https://github.com/conda-forge/spyrmsd-feedstock) and can be easily installed from source. See [Dependencies](###Dependencies) for a description of all the dependencies. > [!NOTE] -> `spyrmsd` will install [NetworkX](https://networkx.github.io/) (multi-platform). You can install [graph-tool](https://graph-tool.skewed.de/) on macOS and Linux for higher performance. +> `spyrmsd` will install [NetworkX](https://networkx.github.io/) (multi-platform). You can install the other backends for higher performance. > [!WARNING] > If `spyrmsd` is used as a standalone tool, it is required to install either [RDKit](https://rdkit.org/) or [Open Babel](http://openbabel.org/). Neither is automatically installed with `pip` nor `conda`. @@ -71,12 +71,16 @@ pip install . The following packages are required to use `spyrmsd` as a module: -* [graph-tool](https://graph-tool.skewed.de/) or [NetworkX](https://networkx.github.io/) * [numpy](https://numpy.org/) * [scipy](https://www.scipy.org/) +One of the following graph libraries is required: +* [graph-tool] +* [NetworkX] +* [rustworkx] + > [!NOTE] -> `spyrmsd` uses [graph-tool](https://graph-tool.skewed.de/) by default but will fall back to [NetworkX](https://networkx.github.io/) if the former is not installed (e.g. on Windows). However, in order to support cross-platform installation [NetworkX](https://networkx.github.io/) is installed by default, and [graph-tool](https://graph-tool.skewed.de/) needs to be installed manually. +> `spyrmsd` uses the following priority when multiple graph libraries are present: [graph-tool], [NetworkX], [rustworkx]. *This order might change. Use `set_backend` to ensure you are always using the same backend, if needed.* However, in order to support cross-platform installation [NetworkX](https://networkx.github.io/) is installed by default, and the other graph library need to be installed manually. #### Standalone Tool @@ -89,27 +93,12 @@ Additionally, one of the following packages is required to use `spyrmsd` as a st ### Standalone Tool +`spyrmsd` provides a convenient CLI tool. See `spyrmsd`'s `--help` for the usage: + ```bash python -m spyrmsd -h ``` -```text -usage: python -m spyrmsd [-h] [-m] [-c] [--hydrogens] [-n] reference molecules [molecules ...] - -Symmetry-corrected RMSD calculations in Python. - -positional arguments: - reference Reference file - molecules Input file(s) - -optional arguments: - -h, --help show this help message and exit - -m, --minimize Minimize (fit) - -c, --center Center molecules at origin - --hydrogens Keep hydrogen atoms - -n, --nosymm No graph isomorphism -``` - ### Module ```python @@ -133,7 +122,7 @@ def rmsd( ``` > [!NOTE] -> Atomic properties (`aprops`) can be any Python object when using [NetworkX](https://networkx.github.io/), or integers, floats, or strings when using [graph-tool](https://graph-tool.skewed.de/). +> Atomic properties (`aprops`) can be any Python object when using [NetworkX] and [rustworkx], or integers, floats, or strings when using [graph-tool]. #### Symmetry-Corrected RMSD @@ -157,7 +146,31 @@ def symmrmsd( ``` > [!NOTE] -> Atomic properties (`aprops`) can be any Python object when using [NetworkX](https://networkx.github.io/), or integers, floats, or strings when using [graph-tool](https://graph-tool.skewed.de/). +> Atomic properties (`aprops`) can be any Python object when using [NetworkX] and [rustworkx], or integers, floats, or strings when using [graph-tool](https://graph-tool.skewed.de/). + +#### Select Backend + +`spyrmsd` supports the following graph libraries for the calculation of graph isomorphisms: +* [graph-tool] +* [NetworkX] +* [rustworkx] + + You can check which backend is being used with + +```python +spyrmsd.get_backend() +``` + +You can also manually select your preferred backend with + +```python +spyrmsd.set_backend("networkx") +# spyrmsd uses NetworkX +spyrmsd.set_backend("graph_tool") +# spyrmsd uses graph_tool +``` + +The available backends (which depend on the installed dependencies) are stored in `spyrmsd.available_backends`. ## Development @@ -172,7 +185,7 @@ Pre-commit `git` hooks can be installed with [pre-commit](https://pre-commit.com ## Copyright -Copyright (c) 2019-2021, Rocco Meli. +Copyright (c) 2019-2024, Rocco Meli. ## References @@ -181,3 +194,7 @@ References are tracked with [duecredit](https://github.com/duecredit/duecredit/) ### Acknowledgements Project based on the [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version `1.1`. + +[rustworkx]: https://www.rustworkx.org +[NetworkX]: https://networkx.github.io/ +[graph-tool]: https://graph-tool.skewed.de/ diff --git a/devtools/conda-envs/spyrmsd-all.yaml b/devtools/conda-envs/spyrmsd-all.yaml index c4fc680..d47e18d 100644 --- a/devtools/conda-envs/spyrmsd-all.yaml +++ b/devtools/conda-envs/spyrmsd-all.yaml @@ -7,6 +7,7 @@ dependencies: - python - pip - ipython + - setuptools # Jupyter - jupyterlab diff --git a/devtools/conda-envs/spyrmsd-docs.yaml b/devtools/conda-envs/spyrmsd-docs.yaml index aa214ed..7730ceb 100644 --- a/devtools/conda-envs/spyrmsd-docs.yaml +++ b/devtools/conda-envs/spyrmsd-docs.yaml @@ -5,6 +5,7 @@ channels: dependencies: # Base - python + - setuptools # Maths - numpy diff --git a/devtools/conda-envs/spyrmsd-test-obabel-gt.yaml b/devtools/conda-envs/spyrmsd-test-obabel-gt.yaml index 259ffa3..47476cb 100644 --- a/devtools/conda-envs/spyrmsd-test-obabel-gt.yaml +++ b/devtools/conda-envs/spyrmsd-test-obabel-gt.yaml @@ -4,6 +4,7 @@ channels: dependencies: # Base - python + - setuptools # Maths - numpy diff --git a/devtools/conda-envs/spyrmsd-test-obabel-nx.yaml b/devtools/conda-envs/spyrmsd-test-obabel-nx.yaml index 3e35486..f16ceaa 100644 --- a/devtools/conda-envs/spyrmsd-test-obabel-nx.yaml +++ b/devtools/conda-envs/spyrmsd-test-obabel-nx.yaml @@ -4,6 +4,7 @@ channels: dependencies: # Base - python + - setuptools # Maths - numpy diff --git a/devtools/conda-envs/spyrmsd-test-obabel-rx.yaml b/devtools/conda-envs/spyrmsd-test-obabel-rx.yaml new file mode 100644 index 0000000..af3cf83 --- /dev/null +++ b/devtools/conda-envs/spyrmsd-test-obabel-rx.yaml @@ -0,0 +1,26 @@ +name: spyrmsd +channels: + - conda-forge +dependencies: + # Base + - python + - setuptools + + # Maths + - numpy + - scipy + - rustworkx + + # Chemistry + - openbabel + + # Testing + - pytest + - pytest-cov + - pytest-benchmark + + # Dev + - mypy + - flake8 + - black + - codecov diff --git a/devtools/conda-envs/spyrmsd-test-rdkit-all.yaml b/devtools/conda-envs/spyrmsd-test-rdkit-all.yaml new file mode 100644 index 0000000..d1d7ced --- /dev/null +++ b/devtools/conda-envs/spyrmsd-test-rdkit-all.yaml @@ -0,0 +1,29 @@ +name: spyrmsd +channels: + - conda-forge + - rdkit +dependencies: + # Base + - python + - setuptools + + # Maths + - numpy + - scipy + - graph-tool + - networkx>=2 + - rustworkx + + # Chemistry + - rdkit + + # Testing + - pytest + - pytest-cov + - pytest-benchmark + + # Dev + - mypy + - flake8 + - black + - codecov diff --git a/devtools/conda-envs/spyrmsd-test-rdkit-gt.yaml b/devtools/conda-envs/spyrmsd-test-rdkit-gt.yaml index b35dfbc..06e9dd9 100644 --- a/devtools/conda-envs/spyrmsd-test-rdkit-gt.yaml +++ b/devtools/conda-envs/spyrmsd-test-rdkit-gt.yaml @@ -5,6 +5,7 @@ channels: dependencies: # Base - python + - setuptools # Maths - numpy diff --git a/devtools/conda-envs/spyrmsd-test-rdkit-nx.yaml b/devtools/conda-envs/spyrmsd-test-rdkit-nx.yaml index bd130ba..e35ae1b 100644 --- a/devtools/conda-envs/spyrmsd-test-rdkit-nx.yaml +++ b/devtools/conda-envs/spyrmsd-test-rdkit-nx.yaml @@ -5,6 +5,7 @@ channels: dependencies: # Base - python + - setuptools # Maths - numpy diff --git a/devtools/conda-envs/spyrmsd-test-rdkit-rx.yaml b/devtools/conda-envs/spyrmsd-test-rdkit-rx.yaml new file mode 100644 index 0000000..e752f97 --- /dev/null +++ b/devtools/conda-envs/spyrmsd-test-rdkit-rx.yaml @@ -0,0 +1,27 @@ +name: spyrmsd +channels: + - conda-forge + - rdkit +dependencies: + # Base + - python + - setuptools + + # Maths + - numpy + - scipy + - rustworkx + + # Chemistry + - rdkit + + # Testing + - pytest + - pytest-cov + - pytest-benchmark + + # Dev + - mypy + - flake8 + - black + - codecov diff --git a/devtools/conda-envs/spyrmsd.yaml b/devtools/conda-envs/spyrmsd.yaml index 5558e99..9a76a89 100644 --- a/devtools/conda-envs/spyrmsd.yaml +++ b/devtools/conda-envs/spyrmsd.yaml @@ -4,8 +4,9 @@ channels: dependencies: # Base - python + - setuptools # Maths - numpy - scipy - - graph-tool + - networkx diff --git a/docs/source/conf.py b/docs/source/conf.py index 1be2b02..eb02994 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -23,7 +23,7 @@ project = "spyrmsd" copyright = ( - "2019-2021, Rocco Meli. Project structure based on the " + "2019-2024, Rocco Meli. Project structure based on the " "Computational Molecular Science Python Cookiecutter version 1.1" ) author = "Rocco Meli" diff --git a/docs/source/tutorials/tutorial.ipynb b/docs/source/tutorials/tutorial.ipynb index 5b626ea..1cf200e 100644 --- a/docs/source/tutorials/tutorial.ipynb +++ b/docs/source/tutorials/tutorial.ipynb @@ -14,6 +14,7 @@ "metadata": {}, "outputs": [], "source": [ + "import spyrmsd\n", "from spyrmsd import io, rmsd" ] }, @@ -107,8 +108,8 @@ "output_type": "stream", "text": [ ":241: RuntimeWarning: to-Python converter for std::__1::pair already registered; second conversion method ignored.\n", - "[18:44:03] Molecule does not have explicit Hs. Consider calling AddHs()\n", - "[18:44:03] Molecule does not have explicit Hs. Consider calling AddHs()\n" + "[21:58:01] Molecule does not have explicit Hs. Consider calling AddHs()\n", + "[21:58:01] Molecule does not have explicit Hs. Consider calling AddHs()\n" ] }, { @@ -289,6 +290,102 @@ "\n", "print(RMSD)" ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Change Backend" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "`spyrmsd` supports multiple backends. You see which backends are available by looking at the `available_backends` attribute:" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['graph_tool', 'networkx']" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "spyrmsd.available_backends" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The available backends are a subset of the supported backends. Only the backends that are installed will be available." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "You can check the current backend with" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'graph_tool'" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "spyrmsd.get_backend()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "You can switch the backend using" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'networkx'" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "spyrmsd.set_backend(\"networkx\")\n", + "spyrmsd.get_backend()" + ] } ], "metadata": { @@ -307,7 +404,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.4" + "version": "3.11.8" } }, "nbformat": 4, diff --git a/docs/source/tutorials/tutorial.rst b/docs/source/tutorials/tutorial.rst index 10dcfb6..0c37d23 100644 --- a/docs/source/tutorials/tutorial.rst +++ b/docs/source/tutorials/tutorial.rst @@ -3,6 +3,7 @@ Tutorial .. code:: ipython3 + import spyrmsd from spyrmsd import io, rmsd OpenBabel or RDKit @@ -68,8 +69,8 @@ constructors. .. parsed-literal:: :241: RuntimeWarning: to-Python converter for std::__1::pair already registered; second conversion method ignored. - [18:44:03] Molecule does not have explicit Hs. Consider calling AddHs() - [18:44:03] Molecule does not have explicit Hs. Consider calling AddHs() + [21:58:01] Molecule does not have explicit Hs. Consider calling AddHs() + [21:58:01] Molecule does not have explicit Hs. Consider calling AddHs() @@ -95,7 +96,7 @@ Hydrogen atoms can be removed with the ``strip()`` function: mol.strip() Symmetry-Corrected RMSD ------------------------ +~~~~~~~~~~~~~~~~~~~~~~~ ``spyrmsd`` only needs atomic coordinates, atomic number and the molecular adjacency matrix to compute the standard RMSD with @@ -137,7 +138,7 @@ reference molecule and all other molecules: Minimum RMSD -~~~~~~~~~~~~ +------------ We can also compute the minimum RMSD obtained by superimposing the molecular structures: @@ -160,3 +161,56 @@ molecular structures: .. parsed-literal:: [1.2012368667355435, 1.0533413220699535, 1.153253104575529, 1.036542688936588, 0.8407673221224187, 1.1758143217869736, 0.7817315189656655, 1.0933314311267845, 1.0260767175206462, 0.9586369647000478] + + + +Change Backend +~~~~~~~~~~~~~~ + +``spyrmsd`` supports multiple backends. You see which backends are +available by looking at the ``available_backends`` attribute: + +.. code:: ipython3 + + spyrmsd.available_backends + + + + +.. parsed-literal:: + + ['graph_tool', 'networkx'] + + + +The available backends are a subset of the supported backends. Only the +backends that are installed will be available. + +You can check the current backend with + +.. code:: ipython3 + + spyrmsd.get_backend() + + + + +.. parsed-literal:: + + 'graph_tool' + + + +You can switch the backend using + +.. code:: ipython3 + + spyrmsd.set_backend("networkx") + spyrmsd.get_backend() + + + + +.. parsed-literal:: + + 'networkx' diff --git a/pyproject.toml b/pyproject.toml index 2cf8457..39b18ef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [build-system] -requires = ["flit"] -build-backend = "flit.buildapi" +requires = ["flit_core >=2,<4"] +build-backend = "flit_core.buildapi" [tool.flit.metadata] module = "spyrmsd" @@ -12,5 +12,5 @@ home-page = "https://spyrmsd.readthedocs.io" classifiers = [ "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3",] -requires-python = ">=3.7" +requires-python = ">=3.9" requires = ["numpy", "scipy", "networkx>=2"] diff --git a/setup.cfg b/setup.cfg index 83818f8..680226d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -5,7 +5,6 @@ ignore = E203, E266, E501, W503 max-line-length = 88 max-complexity = 18 select = B,C,E,F,W,T4 -exclude=versioneer.py [mypy] files=spyrmsd, tests @@ -32,13 +31,3 @@ markers = omit = # Omit the tests */tests/* - # Omit generated versioneer - spyrmsd/_version.py - -[versioneer] -# Automatic version numbering scheme -VCS = git -style = pep440 -versionfile_source = spyrmsd/_version.py -versionfile_build = spyrmsd/_version.py -tag_prefix = '' diff --git a/setup.py b/setup.py index 704b420..d819573 100644 --- a/setup.py +++ b/setup.py @@ -6,8 +6,6 @@ from setuptools import find_packages, setup -import versioneer - short_description = __doc__.split("\n") try: @@ -25,8 +23,7 @@ description=short_description[0], long_description=long_description, long_description_content_type="text/markdown", - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), + version="0.7.0-dev", license="MIT", packages=find_packages(), include_package_data=True, @@ -38,5 +35,5 @@ "openbabel": ["openbabel"], }, platforms=["Linux", "Mac OS-X", "Unix", "Windows"], - python_requires=">=3.7", + python_requires=">=3.9", ) diff --git a/spyrmsd/__init__.py b/spyrmsd/__init__.py index b2e6609..b2f849b 100644 --- a/spyrmsd/__init__.py +++ b/spyrmsd/__init__.py @@ -2,13 +2,15 @@ Python RMSD tool with symmetry correction. """ -from ._version import get_versions from .due import Doi, due -versions = get_versions() -__version__ = versions["version"] -__git_revision__ = versions["full-revisionid"] -del get_versions, versions +# Make the backend related functions available from base spyrmsd +# Add noqa to avoid flake8 error +from .graph import _available_backends as available_backends # noqa: F401 +from .graph import _get_backend as get_backend # noqa: F401 +from .graph import _set_backend as set_backend # noqa: F401 + +__version__ = "0.7.0" # This will print latest Zenodo version due.cite( diff --git a/spyrmsd/__main__.py b/spyrmsd/__main__.py index b18dcac..4e8ba96 100644 --- a/spyrmsd/__main__.py +++ b/spyrmsd/__main__.py @@ -6,7 +6,9 @@ import argparse as ap import importlib.util import sys + import warnings + import spyrmsd from spyrmsd import io from spyrmsd.rmsd import rmsdwrapper @@ -25,6 +27,16 @@ parser.add_argument( "-n", "--nosymm", action="store_false", help="No graph isomorphism" ) + parser.add_argument( + "-g", + "--graph-backend", + type=str, + default=None, + help="Graph library (backend)", + ) + parser.add_argument( + "-v", "--verbose", action="store_true", help="Enable verbose mode" + ) args = parser.parse_args() @@ -49,6 +61,14 @@ print("ERROR: Molecule file(s) not found.", file=sys.stderr) exit(-1) + if args.graph_backend is not None: + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + spyrmsd.set_backend(args.graph_backend) + + if args.verbose: + print(f"Graph library: {spyrmsd.get_backend()}") + # Loop over molecules within fil RMSDlist = rmsdwrapper( ref, diff --git a/spyrmsd/_version.py b/spyrmsd/_version.py deleted file mode 100644 index d41e250..0000000 --- a/spyrmsd/_version.py +++ /dev/null @@ -1,693 +0,0 @@ -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.28 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import functools -import os -import re -import subprocess -import sys -from typing import Callable, Dict - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "$Format:%d$" - git_full = "$Format:%H$" - git_date = "$Format:%ci$" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "pep440" - cfg.tag_prefix = "" - cfg.parentdir_prefix = "None" - cfg.versionfile_source = "spyrmsd/_version.py" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen( - [command] + args, - cwd=cwd, - env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr else None), - **popen_kwargs, - ) - break - except OSError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return { - "version": dirname[len(parentdir_prefix) :], - "full-revisionid": None, - "dirty": False, - "error": None, - "date": None, - } - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print( - "Tried directories %s but none started with prefix %s" - % (str(rootdirs), parentdir_prefix) - ) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r"\d", r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix) :] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r"\d", r): - continue - if verbose: - print("picking %s" % r) - return { - "version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": None, - "date": date, - } - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return { - "version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": "no suitable tags", - "date": None, - } - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner( - GITS, - [ - "describe", - "--tags", - "--dirty", - "--always", - "--long", - "--match", - f"{tag_prefix}[[:digit:]]*", - ], - cwd=root, - ) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[: git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( - full_tag, - tag_prefix, - ) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix) :] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces): - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver): - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces): - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return { - "version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None, - } - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return { - "version": rendered, - "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], - "error": None, - "date": pieces.get("date"), - } - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split("/"): - root = os.path.dirname(root) - except NameError: - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None, - } - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", - "date": None, - } diff --git a/spyrmsd/graph.py b/spyrmsd/graph.py index 0235a25..f777eed 100644 --- a/spyrmsd/graph.py +++ b/spyrmsd/graph.py @@ -1,42 +1,184 @@ -try: - from spyrmsd.graphs.gt import ( - cycle, - graph_from_adjacency_matrix, - lattice, - match_graphs, - num_edges, - num_vertices, - vertex_property, - ) +import importlib.util +import warnings + +import numpy as np + +from spyrmsd import constants + +_supported_backends = ("graph_tool", "networkx", "rustworkx") + +_available_backends = [] +_current_backend = None + +_backend_to_alias = { + "graph_tool": ["graph_tool", "graphtool", "graph-tool", "graph tool", "gt"], + "networkx": ["networkx", "nx"], + "rustworkx": ["rustworkx", "rx"], +} + +_alias_to_backend = {} +for backend, aliases in _backend_to_alias.items(): + for alias in aliases: + _alias_to_backend[alias] = backend + + +def _dummy(*args, **kwargs): + """ + Dummy function for backend not set. + """ + raise NotImplementedError("No backend is set for spyrmsd.") + + +cycle = _dummy +graph_from_adjacency_matrix = _dummy +lattice = _dummy +match_graphs = _dummy +num_edges = _dummy +num_vertices = _dummy +vertex_property = _dummy + +# Check which supported backend is available +for backend in _supported_backends: + if importlib.util.find_spec(backend) is not None: + _available_backends.append(backend) + + +def _validate_backend(backend): + """ + Validate backend. + + Check if a backend is supported and installed (available). + + Parameters + ---------- + backend: str + Backend to validate + return: str + Standardized backend name + + Raises + ------ + ValueError + If the backend is not recognized or supported + ImportError + If the backend is not installed + + Notes + ----- + This function is case-insensitive. + """ + standardized_backend = _alias_to_backend.get(backend.lower()) + + if standardized_backend is None: + raise ValueError(f"The {backend} backend is not recognized or supported") + + if standardized_backend not in _available_backends: + raise ImportError(f"The {backend} backend doesn't seem to be installed") -except ImportError: - try: + return standardized_backend + + +def _set_backend(backend): + """ + Set backend to use for graph operations. + + Parameters + ---------- + backend: str + Backend to use + + Notes + ----- + This function sets the :code:`_current_backend` variable with a validated backend. + + This function modifies the global (module) variables. + """ + # Global (module) variables modified by this function + global _current_backend + global cycle, graph_from_adjacency_matrix, lattice, match_graphs, num_edges, num_vertices, vertex_property + + backend = _validate_backend(backend) + + # Check if we actually need to switch backends + if backend == _current_backend: + warnings.warn(f"The backend is already {backend}.") + return + + if backend == "graph_tool": + from spyrmsd.graphs.gt import cycle as gt_cycle + from spyrmsd.graphs.gt import ( + graph_from_adjacency_matrix as gt_graph_from_adjacency_matrix, + ) + from spyrmsd.graphs.gt import lattice as gt_lattice + from spyrmsd.graphs.gt import match_graphs as gt_match_graphs + from spyrmsd.graphs.gt import num_edges as gt_num_edges + from spyrmsd.graphs.gt import num_vertices as gt_num_vertices + from spyrmsd.graphs.gt import vertex_property as gt_vertex_property + + cycle = gt_cycle + graph_from_adjacency_matrix = gt_graph_from_adjacency_matrix + lattice = gt_lattice + match_graphs = gt_match_graphs + num_edges = gt_num_edges + num_vertices = gt_num_vertices + vertex_property = gt_vertex_property + + elif backend == "networkx": + from spyrmsd.graphs.nx import cycle as nx_cycle from spyrmsd.graphs.nx import ( - cycle, - graph_from_adjacency_matrix, - lattice, - match_graphs, - num_edges, - num_vertices, - vertex_property, + graph_from_adjacency_matrix as nx_graph_from_adjacency_matrix, ) - except ImportError: - raise ImportError("graph_tool or NetworkX libraries not found.") - -__all__ = [ - "graph_from_adjacency_matrix", - "match_graphs", - "vertex_property", - "num_vertices", - "num_edges", - "lattice", - "cycle", - "adjacency_matrix_from_atomic_coordinates", -] + from spyrmsd.graphs.nx import lattice as nx_lattice + from spyrmsd.graphs.nx import match_graphs as nx_match_graphs + from spyrmsd.graphs.nx import num_edges as nx_num_edges + from spyrmsd.graphs.nx import num_vertices as nx_num_vertices + from spyrmsd.graphs.nx import vertex_property as nx_vertex_property + + cycle = nx_cycle + graph_from_adjacency_matrix = nx_graph_from_adjacency_matrix + lattice = nx_lattice + match_graphs = nx_match_graphs + num_edges = nx_num_edges + num_vertices = nx_num_vertices + vertex_property = nx_vertex_property + + elif backend == "rustworkx": + from spyrmsd.graphs.rx import cycle as rx_cycle + from spyrmsd.graphs.rx import ( + graph_from_adjacency_matrix as rx_graph_from_adjacency_matrix, + ) + from spyrmsd.graphs.rx import lattice as rx_lattice + from spyrmsd.graphs.rx import match_graphs as rx_match_graphs + from spyrmsd.graphs.rx import num_edges as rx_num_edges + from spyrmsd.graphs.rx import num_vertices as rx_num_vertices + from spyrmsd.graphs.rx import vertex_property as rx_vertex_property + + cycle = rx_cycle + graph_from_adjacency_matrix = rx_graph_from_adjacency_matrix + lattice = rx_lattice + match_graphs = rx_match_graphs + num_edges = rx_num_edges + num_vertices = rx_num_vertices + vertex_property = rx_vertex_property + + _current_backend = backend + + +if len(_available_backends) == 0: + raise ImportError( + "No valid backends found. Please ensure that one of the supported backends is installed." + + f"\nSupported backends: {_supported_backends}" + ) +else: + if _current_backend is None: + _set_backend(backend=_available_backends[0]) -import numpy as np -from spyrmsd import constants +def _get_backend(): + """ + Get the current backend. + """ + return _current_backend def adjacency_matrix_from_atomic_coordinates( diff --git a/spyrmsd/graphs/rx.py b/spyrmsd/graphs/rx.py new file mode 100644 index 0000000..673293a --- /dev/null +++ b/spyrmsd/graphs/rx.py @@ -0,0 +1,190 @@ +import warnings +from typing import Any, List, Optional, Tuple, Union + +import numpy as np +import rustworkx as rx + +from spyrmsd.exceptions import NonIsomorphicGraphs +from spyrmsd.graphs._common import ( + error_non_isomorphic_graphs, + warn_disconnected_graph, + warn_no_atomic_properties, +) + + +def graph_from_adjacency_matrix( + adjacency_matrix: Union[np.ndarray, List[List[int]]], + aprops: Optional[Union[np.ndarray, List[Any]]] = None, +) -> rx.PyGraph: + """ + Graph from adjacency matrix. + + Parameters + ---------- + adjacency_matrix: Union[np.ndarray, List[List[int]]] + Adjacency matrix + aprops: Union[np.ndarray, List[Any]], optional + Atomic properties + + Returns + ------- + Graph + Molecular graph + + Notes + ----- + It the atomic numbers are passed, they are used as node attributes. + """ + + G = rx.PyGraph.from_adjacency_matrix(np.asarray(adjacency_matrix, dtype=np.float64)) + + if not rx.is_connected(G): + warnings.warn(warn_disconnected_graph) + + if aprops is not None: + for i in G.node_indices(): + G[i] = aprops[i] + + return G + + +def match_graphs(G1, G2) -> List[Tuple[List[int], List[int]]]: + """ + Compute graph isomorphisms. + + Parameters + ---------- + G1: + Graph 1 + G2: + Graph 2 + + Returns + ------- + List[Tuple[List[int],List[int]]] + All possible mappings between nodes of graph 1 and graph 2 (isomorphisms) + + Raises + ------ + NonIsomorphicGraphs + If the graphs `G1` and `G2` are not isomorphic + """ + + def match_aprops(node1, node2): + """ + Check if atomic properties for two nodes match. + """ + return node1 == node2 + + if G1[0] is None or G2[0] is None: + # Nodes without atomic number information + # No node-matching check + node_match = None + + warnings.warn(warn_no_atomic_properties) + + else: + node_match = match_aprops + + GM = rx.vf2_mapping(G1, G2, node_match) + + isomorphisms = [ + (list(isomorphism.keys()), list(isomorphism.values())) for isomorphism in GM + ] + + # Check if graphs are actually isomorphic + if len(isomorphisms) == 0: + raise NonIsomorphicGraphs(error_non_isomorphic_graphs) + + return isomorphisms + + +def vertex_property(G, vproperty: str, idx: int) -> Any: + """ + Get vertex (node) property from graph + + Parameters + ---------- + G: + Graph + vproperty: str + Vertex property name + idx: int + Vertex index + + Returns + ------- + Any + Vertex property value + """ + return G[idx] + + +def num_vertices(G) -> int: + """ + Number of vertices + + Parameters + ---------- + G: + Graph + + Returns + ------- + int + Number of vertices (nodes) + """ + return G.num_nodes() + + +def num_edges(G) -> int: + """ + Number of edges + + Parameters + ---------- + G: + Graph + + Returns + ------- + int + Number of edges + """ + return G.num_edges() + + +def lattice(n1, n2): + """ + Build 2D lattice graph + + Parameters + ---------- + n1: int + Number of nodes in dimension 1 + n2: int + Number of nodes in dimension 2 + + Returns + ------- + Graph + Lattice graph + """ + return rx.generators.grid_graph(rows=n1, cols=n2, multigraph=False) + + +def cycle(n): + """ + Build cycle graph + + Parameters + ---------- + n: int + Number of nodes + + Returns + ------- + Graph + Cycle graph + """ + return rx.generators.cycle_graph(n, multigraph=False) diff --git a/spyrmsd/molecule.py b/spyrmsd/molecule.py index 3d593a0..b2ab87c 100644 --- a/spyrmsd/molecule.py +++ b/spyrmsd/molecule.py @@ -1,5 +1,5 @@ import warnings -from typing import List, Optional, Union +from typing import Dict, List, Optional, Union import numpy as np @@ -50,7 +50,7 @@ def __init__( self.adjacency_matrix: np.ndarray = np.asarray(adjacency_matrix, dtype=int) # Molecular graph - self.G = None + self.G: Dict[str, object] = {} self.masses: Optional[List[float]] = None @@ -182,7 +182,7 @@ def strip(self) -> None: self.adjacency_matrix = self.adjacency_matrix[np.ix_(idx, idx)] # Reset molecular graph when stripping - self.G = None + self.G = {} self.stripped = True @@ -200,11 +200,13 @@ def to_graph(self): If the molecule does not have an associated adjacency matrix, a simple bond perception is used. - The molecular graph is cached. + The molecular graph is cached per backend. """ - if self.G is None: + _current_backend = graph._current_backend + + if _current_backend not in self.G.keys(): try: - self.G = graph.graph_from_adjacency_matrix( + self.G[_current_backend] = graph.graph_from_adjacency_matrix( self.adjacency_matrix, self.atomicnums ) except AttributeError: @@ -218,11 +220,11 @@ def to_graph(self): self.atomicnums, self.coordinates ) - self.G = graph.graph_from_adjacency_matrix( + self.G[_current_backend] = graph.graph_from_adjacency_matrix( self.adjacency_matrix, self.atomicnums ) - return self.G + return self.G[_current_backend] def __len__(self) -> int: """ diff --git a/spyrmsd/optional/__init__.py b/spyrmsd/optional/__init__.py index 40060b9..e69de29 100644 --- a/spyrmsd/optional/__init__.py +++ b/spyrmsd/optional/__init__.py @@ -1,7 +0,0 @@ -# Handle versioneer -from spyrmsd._version import get_versions - -versions = get_versions() -__version__ = versions["version"] -__git_revision__ = versions["full-revisionid"] -del get_versions, versions diff --git a/spyrmsd/optional/rdkit.py b/spyrmsd/optional/rdkit.py index 4d0ee9b..25bbf71 100644 --- a/spyrmsd/optional/rdkit.py +++ b/spyrmsd/optional/rdkit.py @@ -64,7 +64,9 @@ def load(fname: str): else: rdmol = _load_block_gzipped(Chem.MolFromPDBBlock, fname) else: - raise NotImplementedError + raise NotImplementedError( + f"Format '{fmt}' is currently not supported with RDKit." + ) return rdmol @@ -87,7 +89,11 @@ def loadall(fname: str): fmt = utils.molformat(fname) if fmt == "mol2": - raise NotImplementedError # See RDKit Issue #415 + error = ( + "Multiple molecules in MOL2 files are not supported. " + "See RDKit#415 (https://github.com/rdkit/rdkit/pull/415)." + ) + raise NotImplementedError(error) # See RDKit Issue #415 elif fmt == "sdf": if not gzipped: rdmols = Chem.SDMolSupplier(fname, removeHs=False) @@ -100,9 +106,11 @@ def loadall(fname: str): mols = [rdmol for rdmol in rdmols] elif fmt == "pdb": # TODO: Implement - raise NotImplementedError + raise NotImplementedError("Multiple molecules in PDB files are not supported.") else: - raise NotImplementedError + raise NotImplementedError( + f"Format '{fmt}' is currently not supported with RDKit." + ) return mols diff --git a/tests/conftest.py b/tests/conftest.py index 32e9ea0..9c04244 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -4,6 +4,7 @@ Soource: https://docs.pytest.org/en/latest/example/simple.html """ + import numpy as np import pytest diff --git a/tests/test_benchmarks.py b/tests/test_benchmarks.py index d75fa8d..6690450 100644 --- a/tests/test_benchmarks.py +++ b/tests/test_benchmarks.py @@ -19,7 +19,6 @@ def systems(): return systems -@pytest.mark.benchmark @pytest.fixture(scope="module", params=systems()) def molecules(request): system = request.param diff --git a/tests/test_graph.py b/tests/test_graph.py index 6639861..c25bf5a 100644 --- a/tests/test_graph.py +++ b/tests/test_graph.py @@ -1,8 +1,10 @@ import numpy as np import pytest +import spyrmsd from spyrmsd import constants, graph, io, molecule from spyrmsd.exceptions import NonIsomorphicGraphs +from spyrmsd.graphs import _common as gc from tests import molecules @@ -104,9 +106,7 @@ def test_graph_from_adjacency_matrix_atomicnums(rawmol, mol) -> None: ], ) def test_match_graphs_isomorphic(G1, G2) -> None: - with pytest.warns( - UserWarning, match="No atomic property information stored on nodes." - ): + with pytest.warns(UserWarning, match=gc.warn_no_atomic_properties): isomorphisms = graph.match_graphs(G1, G2) assert len(isomorphisms) != 0 @@ -121,8 +121,8 @@ def test_match_graphs_isomorphic(G1, G2) -> None: ) def test_match_graphs_not_isomorphic(G1, G2) -> None: with pytest.raises( - NonIsomorphicGraphs, match="Graphs are not isomorphic." - ), pytest.warns(UserWarning, match="No atomic number information stored on nodes."): + NonIsomorphicGraphs, match=gc.error_non_isomorphic_graphs + ), pytest.warns(UserWarning, match=gc.warn_no_atomic_properties): graph.match_graphs(G1, G2) @@ -143,14 +143,48 @@ def test_build_graph_node_features(property) -> None: assert graph.num_edges(G) == 3 +@pytest.mark.skipif( + spyrmsd.get_backend() != "graph_tool", + reason="NetworkX supports all Python objects as node properties.", +) def test_build_graph_node_features_unsupported() -> None: - pytest.importorskip( - "graph_tool", reason="NetworkX supports all Python objects as node properties." - ) - A = np.array([[0, 1, 1], [1, 0, 0], [1, 0, 1]]) property = [True, False, True] with pytest.raises(ValueError, match="Unsupported property type:"): _ = graph.graph_from_adjacency_matrix(A, property) + + +@pytest.mark.skipif( + # Run test if all supported backends are installed + not set(spyrmsd.graph._supported_backends) <= set(spyrmsd.available_backends), + reason="Not all of the required backends are installed", +) +def test_set_backend() -> None: + import graph_tool as gt + import networkx as nx + import rustworkx as rx + + A = np.array([[0, 1, 1], [1, 0, 0], [1, 0, 1]]) + + spyrmsd.set_backend("networkx") + assert spyrmsd.get_backend() == "networkx" + + Gnx = graph.graph_from_adjacency_matrix(A) + assert isinstance(Gnx, nx.Graph) + + spyrmsd.set_backend("graph-tool") + assert spyrmsd.get_backend() == "graph_tool" + + Ggt = graph.graph_from_adjacency_matrix(A) + assert isinstance(Ggt, gt.Graph) + + spyrmsd.set_backend("rustworkx") + assert spyrmsd.get_backend() == "rustworkx" + + Grx = graph.graph_from_adjacency_matrix(A) + assert isinstance(Grx, rx.PyGraph) + + with pytest.raises(ValueError, match="backend is not recognized or supported"): + spyrmsd.set_backend("unknown") diff --git a/tests/test_molecule.py b/tests/test_molecule.py index 43efda4..fde466b 100644 --- a/tests/test_molecule.py +++ b/tests/test_molecule.py @@ -6,6 +6,7 @@ import numpy as np import pytest +import spyrmsd from spyrmsd import constants, graph, io, molecule, utils from tests import molecules @@ -167,7 +168,7 @@ def test_graph_from_atomic_coordinates_perception( m = copy.deepcopy(mol) delattr(m, "adjacency_matrix") - m.G = None + m.G = {} with pytest.warns(UserWarning): # Uses automatic bond perception @@ -236,3 +237,41 @@ def test_from_rdmol(adjacency): with pytest.raises(AttributeError): # No adjacency_matrix attribute mol.adjacency_matrix + + +@pytest.mark.skipif( + # Run test if all supported backends are installed + not set(spyrmsd.graph._supported_backends) <= set(spyrmsd.available_backends), + reason="Not all of the required backends are installed", +) +@pytest.mark.parametrize( + "mol", [(molecules.benzene), (molecules.ethanol), (molecules.dialanine)] +) +def test_molecule_graph_cache(mol) -> None: + import graph_tool as gt + import networkx as nx + import rustworkx as rx + + ## Graph cache persists from previous tests, manually reset them + mol.G = {} + spyrmsd.set_backend("networkx") + mol.to_graph() + + assert isinstance(mol.G["networkx"], nx.Graph) + assert "graph_tool" not in mol.G.keys() + + spyrmsd.set_backend("graph-tool") + mol.to_graph() + + spyrmsd.set_backend("rustworkx") + mol.to_graph() + + ## Make sure all backends (still) have a cache + assert isinstance(mol.G["networkx"], nx.Graph) + assert isinstance(mol.G["graph_tool"], gt.Graph) + assert isinstance(mol.G["rustworkx"], rx.PyGraph) + + ## Strip the molecule to ensure the cache is reset + mol.strip() + + assert len(mol.G.items()) == 0 diff --git a/versioneer.py b/versioneer.py deleted file mode 100644 index 6e4d8bf..0000000 --- a/versioneer.py +++ /dev/null @@ -1,2264 +0,0 @@ -# Version: 0.28 - -"""The Versioneer - like a rocketeer, but for versions. - -The Versioneer -============== - -* like a rocketeer, but for versions! -* https://github.com/python-versioneer/python-versioneer -* Brian Warner -* License: Public Domain (Unlicense) -* Compatible with: Python 3.7, 3.8, 3.9, 3.10 and pypy3 -* [![Latest Version][pypi-image]][pypi-url] -* [![Build Status][travis-image]][travis-url] - -This is a tool for managing a recorded version number in setuptools-based -python projects. The goal is to remove the tedious and error-prone "update -the embedded version string" step from your release process. Making a new -release should be as easy as recording a new tag in your version-control -system, and maybe making new tarballs. - - -## Quick Install - -Versioneer provides two installation modes. The "classic" vendored mode installs -a copy of versioneer into your repository. The experimental build-time dependency mode -is intended to allow you to skip this step and simplify the process of upgrading. - -### Vendored mode - -* `pip install versioneer` to somewhere in your $PATH - * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is - available, so you can also use `conda install -c conda-forge versioneer` -* add a `[tool.versioneer]` section to your `pyproject.toml` or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) - * Note that you will need to add `tomli; python_version < "3.11"` to your - build-time dependencies if you use `pyproject.toml` -* run `versioneer install --vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -### Build-time dependency mode - -* `pip install versioneer` to somewhere in your $PATH - * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is - available, so you can also use `conda install -c conda-forge versioneer` -* add a `[tool.versioneer]` section to your `pyproject.toml` or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) -* add `versioneer` (with `[toml]` extra, if configuring in `pyproject.toml`) - to the `requires` key of the `build-system` table in `pyproject.toml`: - ```toml - [build-system] - requires = ["setuptools", "versioneer[toml]"] - build-backend = "setuptools.build_meta" - ``` -* run `versioneer install --no-vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -## Version Identifiers - -Source trees come from a variety of places: - -* a version-control system checkout (mostly used by developers) -* a nightly tarball, produced by build automation -* a snapshot tarball, produced by a web-based VCS browser, like github's - "tarball from tag" feature -* a release tarball, produced by "setup.py sdist", distributed through PyPI - -Within each source tree, the version identifier (either a string or a number, -this tool is format-agnostic) can come from a variety of places: - -* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows - about recent "tags" and an absolute revision-id -* the name of the directory into which the tarball was unpacked -* an expanded VCS keyword ($Id$, etc) -* a `_version.py` created by some earlier build step - -For released software, the version identifier is closely related to a VCS -tag. Some projects use tag names that include more than just the version -string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool -needs to strip the tag prefix to extract the version identifier. For -unreleased software (between tags), the version identifier should provide -enough information to help developers recreate the same tree, while also -giving them an idea of roughly how old the tree is (after version 1.2, before -version 1.3). Many VCS systems can report a description that captures this, -for example `git describe --tags --dirty --always` reports things like -"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the -0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes). - -The version identifier is used for multiple purposes: - -* to allow the module to self-identify its version: `myproject.__version__` -* to choose a name and prefix for a 'setup.py sdist' tarball - -## Theory of Operation - -Versioneer works by adding a special `_version.py` file into your source -tree, where your `__init__.py` can import it. This `_version.py` knows how to -dynamically ask the VCS tool for version information at import time. - -`_version.py` also contains `$Revision$` markers, and the installation -process marks `_version.py` to have this marker rewritten with a tag name -during the `git archive` command. As a result, generated tarballs will -contain enough information to get the proper version. - -To allow `setup.py` to compute a version too, a `versioneer.py` is added to -the top level of your source tree, next to `setup.py` and the `setup.cfg` -that configures it. This overrides several distutils/setuptools commands to -compute the version when invoked, and changes `setup.py build` and `setup.py -sdist` to replace `_version.py` with a small static file that contains just -the generated version data. - -## Installation - -See [INSTALL.md](./INSTALL.md) for detailed installation instructions. - -## Version-String Flavors - -Code which uses Versioneer can learn about its version string at runtime by -importing `_version` from your main `__init__.py` file and running the -`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can -import the top-level `versioneer.py` and run `get_versions()`. - -Both functions return a dictionary with different flavors of version -information: - -* `['version']`: A condensed version string, rendered using the selected - style. This is the most commonly used value for the project's version - string. The default "pep440" style yields strings like `0.11`, - `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section - below for alternative styles. - -* `['full-revisionid']`: detailed revision identifier. For Git, this is the - full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". - -* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the - commit date in ISO 8601 format. This will be None if the date is not - available. - -* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that - this is only accurate if run in a VCS checkout, otherwise it is likely to - be False or None - -* `['error']`: if the version string could not be computed, this will be set - to a string describing the problem, otherwise it will be None. It may be - useful to throw an exception in setup.py if this is set, to avoid e.g. - creating tarballs with a version string of "unknown". - -Some variants are more useful than others. Including `full-revisionid` in a -bug report should allow developers to reconstruct the exact code being tested -(or indicate the presence of local changes that should be shared with the -developers). `version` is suitable for display in an "about" box or a CLI -`--version` output: it can be easily compared against release notes and lists -of bugs fixed in various releases. - -The installer adds the following text to your `__init__.py` to place a basic -version in `YOURPROJECT.__version__`: - - from ._version import get_versions - __version__ = get_versions()['version'] - del get_versions - -## Styles - -The setup.cfg `style=` configuration controls how the VCS information is -rendered into a version string. - -The default style, "pep440", produces a PEP440-compliant string, equal to the -un-prefixed tag name for actual releases, and containing an additional "local -version" section with more detail for in-between builds. For Git, this is -TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags ---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the -tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and -that this commit is two revisions ("+2") beyond the "0.11" tag. For released -software (exactly equal to a known tag), the identifier will only contain the -stripped tag, e.g. "0.11". - -Other styles are available. See [details.md](details.md) in the Versioneer -source tree for descriptions. - -## Debugging - -Versioneer tries to avoid fatal errors: if something goes wrong, it will tend -to return a version of "0+unknown". To investigate the problem, run `setup.py -version`, which will run the version-lookup code in a verbose mode, and will -display the full contents of `get_versions()` (including the `error` string, -which may help identify what went wrong). - -## Known Limitations - -Some situations are known to cause problems for Versioneer. This details the -most significant ones. More can be found on Github -[issues page](https://github.com/python-versioneer/python-versioneer/issues). - -### Subprojects - -Versioneer has limited support for source trees in which `setup.py` is not in -the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are -two common reasons why `setup.py` might not be in the root: - -* Source trees which contain multiple subprojects, such as - [Buildbot](https://github.com/buildbot/buildbot), which contains both - "master" and "slave" subprojects, each with their own `setup.py`, - `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI - distributions (and upload multiple independently-installable tarballs). -* Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other languages) in subdirectories. - -Versioneer will look for `.git` in parent directories, and most operations -should get the right version string. However `pip` and `setuptools` have bugs -and implementation details which frequently cause `pip install .` from a -subproject directory to fail to find a correct version string (so it usually -defaults to `0+unknown`). - -`pip install --editable .` should work correctly. `setup.py install` might -work too. - -Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in -some later version. - -[Bug #38](https://github.com/python-versioneer/python-versioneer/issues/38) is tracking -this issue. The discussion in -[PR #61](https://github.com/python-versioneer/python-versioneer/pull/61) describes the -issue from the Versioneer side in more detail. -[pip PR#3176](https://github.com/pypa/pip/pull/3176) and -[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve -pip to let Versioneer work correctly. - -Versioneer-0.16 and earlier only looked for a `.git` directory next to the -`setup.cfg`, so subprojects were completely unsupported with those releases. - -### Editable installs with setuptools <= 18.5 - -`setup.py develop` and `pip install --editable .` allow you to install a -project into a virtualenv once, then continue editing the source code (and -test) without re-installing after every change. - -"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a -convenient way to specify executable scripts that should be installed along -with the python package. - -These both work as expected when using modern setuptools. When using -setuptools-18.5 or earlier, however, certain operations will cause -`pkg_resources.DistributionNotFound` errors when running the entrypoint -script, which must be resolved by re-installing the package. This happens -when the install happens with one version, then the egg_info data is -regenerated while a different version is checked out. Many setup.py commands -cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into -a different virtualenv), so this can be surprising. - -[Bug #83](https://github.com/python-versioneer/python-versioneer/issues/83) describes -this one, but upgrading to a newer version of setuptools should probably -resolve it. - - -## Updating Versioneer - -To upgrade your project to a new release of Versioneer, do the following: - -* install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg` and `pyproject.toml`, if necessary, - to include any new configuration settings indicated by the release notes. - See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install --[no-]vendor` in your source tree, to replace - `SRC/_version.py` -* commit any changed files - -## Future Directions - -This tool is designed to make it easily extended to other version-control -systems: all VCS-specific components are in separate directories like -src/git/ . The top-level `versioneer.py` script is assembled from these -components by running make-versioneer.py . In the future, make-versioneer.py -will take a VCS name as an argument, and will construct a version of -`versioneer.py` that is specific to the given VCS. It might also take the -configuration arguments that are currently provided manually during -installation by editing setup.py . Alternatively, it might go the other -direction and include code from all supported VCS systems, reducing the -number of intermediate scripts. - -## Similar projects - -* [setuptools_scm](https://github.com/pypa/setuptools_scm/) - a non-vendored build-time - dependency -* [minver](https://github.com/jbweston/miniver) - a lightweight reimplementation of - versioneer -* [versioningit](https://github.com/jwodder/versioningit) - a PEP 518-based setuptools - plugin - -## License - -To make Versioneer easier to embed, all its code is dedicated to the public -domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the "Unlicense", as described in -https://unlicense.org/. - -[pypi-image]: https://img.shields.io/pypi/v/versioneer.svg -[pypi-url]: https://pypi.python.org/pypi/versioneer/ -[travis-image]: -https://img.shields.io/travis/com/python-versioneer/python-versioneer.svg -[travis-url]: https://travis-ci.com/github/python-versioneer/python-versioneer - -""" -# pylint:disable=invalid-name,import-outside-toplevel,missing-function-docstring -# pylint:disable=missing-class-docstring,too-many-branches,too-many-statements -# pylint:disable=raise-missing-from,too-many-lines,too-many-locals,import-error -# pylint:disable=too-few-public-methods,redefined-outer-name,consider-using-with -# pylint:disable=attribute-defined-outside-init,too-many-arguments - -import configparser -import errno -import functools -import json -import os -import re -import subprocess -import sys -from pathlib import Path -from typing import Callable, Dict - -have_tomllib = True -if sys.version_info >= (3, 11): - import tomllib -else: - try: - import tomli as tomllib - except ImportError: - have_tomllib = False - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_root(): - """Get the project root directory. - - We require that all commands are run from the project root, i.e. the - directory that contains setup.py, setup.cfg, and versioneer.py . - """ - root = os.path.realpath(os.path.abspath(os.getcwd())) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - # allow 'python path/to/setup.py COMMAND' - root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - err = ( - "Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND')." - ) - raise VersioneerBadRootError(err) - try: - # Certain runtime workflows (setup.py install/develop in a setuptools - # tree) execute all dependencies in a single python process, so - # "versioneer" may be imported multiple times, and python's shared - # module-import table will cache the first one. So we can't use - # os.path.dirname(__file__), as that will find whichever - # versioneer.py was first imported, even in later projects. - my_path = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(my_path)[0]) - vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir and "VERSIONEER_PEP518" not in globals(): - print( - "Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(my_path), versioneer_py) - ) - except NameError: - pass - return root - - -def get_config_from_root(root): - """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise OSError (if setup.cfg is missing), or - # configparser.NoSectionError (if it lacks a [versioneer] section), or - # configparser.NoOptionError (if it lacks "VCS="). See the docstring at - # the top of versioneer.py for instructions on writing your setup.cfg . - root = Path(root) - pyproject_toml = root / "pyproject.toml" - setup_cfg = root / "setup.cfg" - section = None - if pyproject_toml.exists() and have_tomllib: - try: - with open(pyproject_toml, "rb") as fobj: - pp = tomllib.load(fobj) - section = pp["tool"]["versioneer"] - except (tomllib.TOMLDecodeError, KeyError): - pass - if not section: - parser = configparser.ConfigParser() - with open(setup_cfg) as cfg_file: - parser.read_file(cfg_file) - parser.get("versioneer", "VCS") # raise error if missing - - section = parser["versioneer"] - - cfg = VersioneerConfig() - cfg.VCS = section["VCS"] - cfg.style = section.get("style", "") - cfg.versionfile_source = section.get("versionfile_source") - cfg.versionfile_build = section.get("versionfile_build") - cfg.tag_prefix = section.get("tag_prefix") - if cfg.tag_prefix in ("''", '""', None): - cfg.tag_prefix = "" - cfg.parentdir_prefix = section.get("parentdir_prefix") - cfg.verbose = section.get("verbose") - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -# these dictionaries contain VCS-specific tools -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - HANDLERS.setdefault(vcs, {})[method] = f - return f - - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen( - [command] + args, - cwd=cwd, - env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr else None), - **popen_kwargs, - ) - break - except OSError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -LONG_VERSION_PY[ - "git" -] = r''' -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.28 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys -from typing import Callable, Dict -import functools - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" - git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" - git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "%(STYLE)s" - cfg.tag_prefix = "%(TAG_PREFIX)s" - cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" - cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %%s" %% dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %%s" %% (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %%s (error)" %% dispcmd) - print("stdout was %%s" %% stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %%s but none started with prefix %%s" %% - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %%d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%%s', no digits" %% ",".join(refs - tags)) - if verbose: - print("likely tags: %%s" %% ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %%s" %% r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %%s not under git control" %% root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%%s'" - %% describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%%s' doesn't start with prefix '%%s'" - print(fmt %% (full_tag, tag_prefix)) - pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" - %% (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces): - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver): - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces): - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%%d.dev%%d" %% (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%%d" %% (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%%d" %% pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%%s'" %% style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} -''' - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r"\d", r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix) :] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r"\d", r): - continue - if verbose: - print("picking %s" % r) - return { - "version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": None, - "date": date, - } - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return { - "version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": "no suitable tags", - "date": None, - } - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner( - GITS, - [ - "describe", - "--tags", - "--dirty", - "--always", - "--long", - "--match", - f"{tag_prefix}[[:digit:]]*", - ], - cwd=root, - ) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[: git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( - full_tag, - tag_prefix, - ) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix) :] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def do_vcs_install(versionfile_source, ipy): - """Git-specific installation logic for Versioneer. - - For Git, this means creating/changing .gitattributes to mark _version.py - for export-subst keyword substitution. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - files = [versionfile_source] - if ipy: - files.append(ipy) - if "VERSIONEER_PEP518" not in globals(): - try: - my_path = __file__ - if my_path.endswith((".pyc", ".pyo")): - my_path = os.path.splitext(my_path)[0] + ".py" - versioneer_file = os.path.relpath(my_path) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) - present = False - try: - with open(".gitattributes", "r") as fobj: - for line in fobj: - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - break - except OSError: - pass - if not present: - with open(".gitattributes", "a+") as fobj: - fobj.write(f"{versionfile_source} export-subst\n") - files.append(".gitattributes") - run_command(GITS, ["add", "--"] + files) - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return { - "version": dirname[len(parentdir_prefix) :], - "full-revisionid": None, - "dirty": False, - "error": None, - "date": None, - } - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print( - "Tried directories %s but none started with prefix %s" - % (str(rootdirs), parentdir_prefix) - ) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.28) from -# revision-control system data, or from the parent directory name of an -# unpacked source archive. Distribution tarballs contain a pre-generated copy -# of this file. - -import json - -version_json = ''' -%s -''' # END VERSION_JSON - - -def get_versions(): - return json.loads(version_json) -""" - - -def versions_from_file(filename): - """Try to determine the version from _version.py if present.""" - try: - with open(filename) as f: - contents = f.read() - except OSError: - raise NotThisMethod("unable to read _version.py") - mo = re.search( - r"version_json = '''\n(.*)''' # END VERSION_JSON", contents, re.M | re.S - ) - if not mo: - mo = re.search( - r"version_json = '''\r\n(.*)''' # END VERSION_JSON", contents, re.M | re.S - ) - if not mo: - raise NotThisMethod("no version_json in _version.py") - return json.loads(mo.group(1)) - - -def write_to_version_file(filename, versions): - """Write the given version number to the given _version.py file.""" - os.unlink(filename) - contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": ")) - with open(filename, "w") as f: - f.write(SHORT_VERSION_PY % contents) - - print("set %s to '%s'" % (filename, versions["version"])) - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces): - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver): - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces): - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return { - "version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None, - } - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return { - "version": rendered, - "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], - "error": None, - "date": pieces.get("date"), - } - - -class VersioneerBadRootError(Exception): - """The project root directory is unknown or missing key files.""" - - -def get_versions(verbose=False): - """Get the project version from whatever source is available. - - Returns dict with two keys: 'version' and 'full'. - """ - if "versioneer" in sys.modules: - # see the discussion in cmdclass.py:get_cmdclass() - del sys.modules["versioneer"] - - root = get_root() - cfg = get_config_from_root(root) - - assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" - handlers = HANDLERS.get(cfg.VCS) - assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or cfg.verbose - assert ( - cfg.versionfile_source is not None - ), "please set versioneer.versionfile_source" - assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" - - versionfile_abs = os.path.join(root, cfg.versionfile_source) - - # extract version from first of: _version.py, VCS command (e.g. 'git - # describe'), parentdir. This is meant to work for developers using a - # source checkout, for users of a tarball created by 'setup.py sdist', - # and for users of a tarball/zipball created by 'git archive' or github's - # download-from-tag feature or the equivalent in other VCSes. - - get_keywords_f = handlers.get("get_keywords") - from_keywords_f = handlers.get("keywords") - if get_keywords_f and from_keywords_f: - try: - keywords = get_keywords_f(versionfile_abs) - ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) - if verbose: - print("got version from expanded keyword %s" % ver) - return ver - except NotThisMethod: - pass - - try: - ver = versions_from_file(versionfile_abs) - if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) - return ver - except NotThisMethod: - pass - - from_vcs_f = handlers.get("pieces_from_vcs") - if from_vcs_f: - try: - pieces = from_vcs_f(cfg.tag_prefix, root, verbose) - ver = render(pieces, cfg.style) - if verbose: - print("got version from VCS %s" % ver) - return ver - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - if verbose: - print("got version from parentdir %s" % ver) - return ver - except NotThisMethod: - pass - - if verbose: - print("unable to compute version") - - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", - "date": None, - } - - -def get_version(): - """Get the short version string for this project.""" - return get_versions()["version"] - - -def get_cmdclass(cmdclass=None): - """Get the custom setuptools subclasses used by Versioneer. - - If the package uses a different cmdclass (e.g. one from numpy), it - should be provide as an argument. - """ - if "versioneer" in sys.modules: - del sys.modules["versioneer"] - # this fixes the "python setup.py develop" case (also 'install' and - # 'easy_install .'), in which subdependencies of the main project are - # built (using setup.py bdist_egg) in the same python process. Assume - # a main project A and a dependency B, which use different versions - # of Versioneer. A's setup.py imports A's Versioneer, leaving it in - # sys.modules by the time B's setup.py is executed, causing B to run - # with the wrong versioneer. Setuptools wraps the sub-dep builds in a - # sandbox that restores sys.modules to it's pre-build state, so the - # parent is protected against the child's "import versioneer". By - # removing ourselves from sys.modules here, before the child build - # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/python-versioneer/python-versioneer/issues/52 - - cmds = {} if cmdclass is None else cmdclass.copy() - - # we add "version" to setuptools - from setuptools import Command - - class cmd_version(Command): - description = "report generated version string" - user_options = [] - boolean_options = [] - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - def run(self): - vers = get_versions(verbose=True) - print("Version: %s" % vers["version"]) - print(" full-revisionid: %s" % vers.get("full-revisionid")) - print(" dirty: %s" % vers.get("dirty")) - print(" date: %s" % vers.get("date")) - if vers["error"]: - print(" error: %s" % vers["error"]) - - cmds["version"] = cmd_version - - # we override "build_py" in setuptools - # - # most invocation pathways end up running build_py: - # distutils/build -> build_py - # distutils/install -> distutils/build ->.. - # setuptools/bdist_wheel -> distutils/install ->.. - # setuptools/bdist_egg -> distutils/install_lib -> build_py - # setuptools/install -> bdist_egg ->.. - # setuptools/develop -> ? - # pip install: - # copies source tree to a tempdir before running egg_info/etc - # if .git isn't copied too, 'git describe' will fail - # then does setup.py bdist_wheel, or sometimes setup.py install - # setup.py egg_info -> ? - - # pip install -e . and setuptool/editable_wheel will invoke build_py - # but the build_py command is not expected to copy any files. - - # we override different "build_py" commands for both environments - if "build_py" in cmds: - _build_py = cmds["build_py"] - else: - from setuptools.command.build_py import build_py as _build_py - - class cmd_build_py(_build_py): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_py.run(self) - if getattr(self, "editable_mode", False): - # During editable installs `.py` and data files are - # not copied to build_lib - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - cmds["build_py"] = cmd_build_py - - if "build_ext" in cmds: - _build_ext = cmds["build_ext"] - else: - from setuptools.command.build_ext import build_ext as _build_ext - - class cmd_build_ext(_build_ext): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_ext.run(self) - if self.inplace: - # build_ext --inplace will only build extensions in - # build/lib<..> dir with no _version.py to write to. - # As in place builds will already have a _version.py - # in the module dir, we do not need to write one. - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if not cfg.versionfile_build: - return - target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build) - if not os.path.exists(target_versionfile): - print( - f"Warning: {target_versionfile} does not exist, skipping " - "version update. This can happen if you are running build_ext " - "without first running build_py." - ) - return - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - cmds["build_ext"] = cmd_build_ext - - if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe - - # nczeczulin reports that py2exe won't like the pep440-style string - # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. - # setup(console=[{ - # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION - # "product_version": versioneer.get_version(), - # ... - - class cmd_build_exe(_build_exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _build_exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - cmds["build_exe"] = cmd_build_exe - del cmds["build_py"] - - if "py2exe" in sys.modules: # py2exe enabled? - try: - from py2exe.setuptools_buildexe import py2exe as _py2exe - except ImportError: - from py2exe.distutils_buildexe import py2exe as _py2exe - - class cmd_py2exe(_py2exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _py2exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - cmds["py2exe"] = cmd_py2exe - - # sdist farms its file list building out to egg_info - if "egg_info" in cmds: - _egg_info = cmds["egg_info"] - else: - from setuptools.command.egg_info import egg_info as _egg_info - - class cmd_egg_info(_egg_info): - def find_sources(self): - # egg_info.find_sources builds the manifest list and writes it - # in one shot - super().find_sources() - - # Modify the filelist and normalize it - root = get_root() - cfg = get_config_from_root(root) - self.filelist.append("versioneer.py") - if cfg.versionfile_source: - # There are rare cases where versionfile_source might not be - # included by default, so we must be explicit - self.filelist.append(cfg.versionfile_source) - self.filelist.sort() - self.filelist.remove_duplicates() - - # The write method is hidden in the manifest_maker instance that - # generated the filelist and was thrown away - # We will instead replicate their final normalization (to unicode, - # and POSIX-style paths) - from setuptools import unicode_utils - - normalized = [ - unicode_utils.filesys_decode(f).replace(os.sep, "/") - for f in self.filelist.files - ] - - manifest_filename = os.path.join(self.egg_info, "SOURCES.txt") - with open(manifest_filename, "w") as fobj: - fobj.write("\n".join(normalized)) - - cmds["egg_info"] = cmd_egg_info - - # we override different "sdist" commands for both environments - if "sdist" in cmds: - _sdist = cmds["sdist"] - else: - from setuptools.command.sdist import sdist as _sdist - - class cmd_sdist(_sdist): - def run(self): - versions = get_versions() - self._versioneer_generated_versions = versions - # unless we update this, the command will keep using the old - # version - self.distribution.metadata.version = versions["version"] - return _sdist.run(self) - - def make_release_tree(self, base_dir, files): - root = get_root() - cfg = get_config_from_root(root) - _sdist.make_release_tree(self, base_dir, files) - # now locate _version.py in the new base_dir directory - # (remembering that it may be a hardlink) and replace it with an - # updated value - target_versionfile = os.path.join(base_dir, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file( - target_versionfile, self._versioneer_generated_versions - ) - - cmds["sdist"] = cmd_sdist - - return cmds - - -CONFIG_ERROR = """ -setup.cfg is missing the necessary Versioneer configuration. You need -a section like: - - [versioneer] - VCS = git - style = pep440 - versionfile_source = src/myproject/_version.py - versionfile_build = myproject/_version.py - tag_prefix = - parentdir_prefix = myproject- - -You will also need to edit your setup.py to use the results: - - import versioneer - setup(version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), ...) - -Please read the docstring in ./versioneer.py for configuration instructions, -edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. -""" - -SAMPLE_CONFIG = """ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -#VCS = git -#style = pep440 -#versionfile_source = -#versionfile_build = -#tag_prefix = -#parentdir_prefix = - -""" - -OLD_SNIPPET = """ -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions -""" - -INIT_PY_SNIPPET = """ -from . import {0} -__version__ = {0}.get_versions()['version'] -""" - - -def do_setup(): - """Do main VCS-independent setup function for installing Versioneer.""" - root = get_root() - try: - cfg = get_config_from_root(root) - except (OSError, configparser.NoSectionError, configparser.NoOptionError) as e: - if isinstance(e, (OSError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", file=sys.stderr) - with open(os.path.join(root, "setup.cfg"), "a") as f: - f.write(SAMPLE_CONFIG) - print(CONFIG_ERROR, file=sys.stderr) - return 1 - - print(" creating %s" % cfg.versionfile_source) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py") - if os.path.exists(ipy): - try: - with open(ipy, "r") as f: - old = f.read() - except OSError: - old = "" - module = os.path.splitext(os.path.basename(cfg.versionfile_source))[0] - snippet = INIT_PY_SNIPPET.format(module) - if OLD_SNIPPET in old: - print(" replacing boilerplate in %s" % ipy) - with open(ipy, "w") as f: - f.write(old.replace(OLD_SNIPPET, snippet)) - elif snippet not in old: - print(" appending to %s" % ipy) - with open(ipy, "a") as f: - f.write(snippet) - else: - print(" %s unmodified" % ipy) - else: - print(" %s doesn't exist, ok" % ipy) - ipy = None - - # Make VCS-specific changes. For git, this means creating/changing - # .gitattributes to mark _version.py for export-subst keyword - # substitution. - do_vcs_install(cfg.versionfile_source, ipy) - return 0 - - -def scan_setup_py(): - """Validate the contents of setup.py against Versioneer's expectations.""" - found = set() - setters = False - errors = 0 - with open("setup.py", "r") as f: - for line in f.readlines(): - if "import versioneer" in line: - found.add("import") - if "versioneer.get_cmdclass()" in line: - found.add("cmdclass") - if "versioneer.get_version()" in line: - found.add("get_version") - if "versioneer.VCS" in line: - setters = True - if "versioneer.versionfile_source" in line: - setters = True - if len(found) != 3: - print("") - print("Your setup.py appears to be missing some important items") - print("(but I might be wrong). Please make sure it has something") - print("roughly like the following:") - print("") - print(" import versioneer") - print(" setup( version=versioneer.get_version(),") - print(" cmdclass=versioneer.get_cmdclass(), ...)") - print("") - errors += 1 - if setters: - print("You should remove lines like 'versioneer.VCS = ' and") - print("'versioneer.versionfile_source = ' . This configuration") - print("now lives in setup.cfg, and should be removed from setup.py") - print("") - errors += 1 - return errors - - -def setup_command(): - """Set up Versioneer and exit with appropriate error code.""" - errors = do_setup() - errors += scan_setup_py() - sys.exit(1 if errors else 0) - - -if __name__ == "__main__": - cmd = sys.argv[1] - if cmd == "setup": - setup_command()