diff --git a/.github/workflows/doc.yml b/.github/workflows/doc.yml new file mode 100644 index 0000000..01e16f8 --- /dev/null +++ b/.github/workflows/doc.yml @@ -0,0 +1,23 @@ +name: Documentation + +on: + - push + - pull_request + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.12" + - name: Install PDM and Nox + run: | + pip install pdm nox + + - name: Build doc + run: | + nox -s doc diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b31d5f5..fb05564 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -12,7 +12,7 @@ jobs: strategy: matrix: os: [ubuntu-latest] - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + python-version: ["3.9", "3.10", "3.11", "3.12"] include: - os: macos-latest python-version: "3.12" @@ -33,14 +33,18 @@ jobs: create-args: >- python=${{ matrix.python-version }} pip + gdal>=3.3 - name: install dependencies - run: pip install tox tox-gh-actions + run: pip install pdm nox - - name: test with tox - run: tox - env: - CONDA_EXE: mamba + - name: Build wheel + run: | + nox -s wheel + + - name: test with nox + run: | + nox --force-python ${{ matrix.python-version }} -s test - name: upload coverage reports to Codecov uses: codecov/codecov-action@v3 diff --git a/.gitignore b/.gitignore index e12a603..14841d2 100644 --- a/.gitignore +++ b/.gitignore @@ -113,3 +113,8 @@ output/ # Transonic __pythran__ __numba__ +__python__ + +# PDM +.pdm-python +.nox diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 15fd740..64c4ac9 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -28,4 +28,4 @@ Before you submit a pull request, check that it meets these guidelines: 1. The pull request should include tests. 1. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.md. -1. The pull request should work for Python 2.7 and 3.6, as well as for PyPy. Check https://travis-ci.org/martibosch/pylandstats/pull_requests and make sure that the tests pass for all supported Python versions. +1. The pull request should work for Python >=3.9, as well as for PyPy. Check https://travis-ci.org/martibosch/pylandstats/pull_requests and make sure that the tests pass for all supported Python versions. diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..0717bea --- /dev/null +++ b/Makefile @@ -0,0 +1,15 @@ + +install: + pdm sync + +lock: + pdm lock + +test: + pdm test + +build_doc: + nox -s doc -R + +test_in_nox_env: + nox -s test diff --git a/docs/changelog.md b/docs/changelog.md new file mode 120000 index 0000000..04c99a5 --- /dev/null +++ b/docs/changelog.md @@ -0,0 +1 @@ +../CHANGELOG.md \ No newline at end of file diff --git a/docs/changelog.rst b/docs/changelog.rst deleted file mode 100644 index 6336d76..0000000 --- a/docs/changelog.rst +++ /dev/null @@ -1 +0,0 @@ -.. mdinclude:: ../CHANGELOG.md diff --git a/docs/conf.py b/docs/conf.py index de8f761..b79e482 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -21,11 +21,11 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - "m2r2", "sphinx.ext.napoleon", "sphinx.ext.autodoc", "sphinx.ext.viewcode", "sphinx.ext.imgmath", + "myst_nb", ] # List of patterns, relative to source directory, that match files and @@ -56,6 +56,7 @@ "github_url": "https://github.com/martibosch/pylandstats", "twitter_url": "https://twitter.com/mortybosch", "pygment_light_style": "tango", + "navigation_with_keys": False, } # exclude patterns from sphinx-build diff --git a/docs/contributing.md b/docs/contributing.md new file mode 120000 index 0000000..44fcc63 --- /dev/null +++ b/docs/contributing.md @@ -0,0 +1 @@ +../CONTRIBUTING.md \ No newline at end of file diff --git a/docs/contributing.rst b/docs/contributing.rst deleted file mode 100644 index 4fc5016..0000000 --- a/docs/contributing.rst +++ /dev/null @@ -1 +0,0 @@ -.. mdinclude:: ../CONTRIBUTING.md diff --git a/docs/dev-install.md b/docs/dev-install.md new file mode 100644 index 0000000..698f2e0 --- /dev/null +++ b/docs/dev-install.md @@ -0,0 +1,29 @@ +# Setup a development environment + +Once [PDM] and [Nox] are installed, it is very easy to setup a development environment for +PyLandStats. On most systems, one can install PDM and Nox with [Pipx], with something like: + +```sh +python3 -m pip install pipx +python3 -m pipx ensurepath +``` + +and then in a new terminal: + +```sh +pipx install pdm +pipx install nox +``` + +Once PDM is installed, clone the PyLandStats repo and run `make` from the root +directory. This should install a dedicated local virtual environment `.venv`. +You can then activate it and run the tests. + +Note that there are few other targets in the `Makefile` useful for developers. In +particular, it is good to periodically recompute the dependencies written in +the `pdm.lock` file (with `make lock`) to check if new packages uploaded on PyPI +do not break PyLandStats. It is reasonable to do this in a dedicated PR. + +[nox]: https://nox.thea.codes +[pdm]: https://pdm-project.org +[pipx]: https://github.com/pypa/pipx diff --git a/docs/index.rst b/docs/index.rst index ac74885..8a181c9 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -18,6 +18,7 @@ Open-source library to compute landscape metrics in the Python ecosystem (NumPy, :maxdepth: 1 :caption: Development: + dev-install changelog contributing @@ -41,7 +42,6 @@ which will install PyLandStats and all of its dependencies. Alternatively, you c $ pip install pylandstats - Nevertheless, note that the `BufferAnalysis` and `SpatioTemporalBufferAnalysis` classes make use of `geopandas `_, which cannot be installed with pip. If you already have `the dependencies for geopandas `_ installed in your system, you might then install PyLandStats with the `geo` extras as in: $ pip install pylandstats[geo] @@ -49,6 +49,8 @@ Nevertheless, note that the `BufferAnalysis` and `SpatioTemporalBufferAnalysis` and you will be able to use the `BufferAnalysis` and `SpatioTemporalBufferAnalysis` classes (without having to use conda). + + Indices and tables ================== * :ref:`genindex` diff --git a/meson.build b/meson.build new file mode 100644 index 0000000..f061cc1 --- /dev/null +++ b/meson.build @@ -0,0 +1,67 @@ +project( + 'pylandstats', + 'cpp', + license: 'GPL-3.0-or-later', + meson_version: '>= 1.1.0', + default_options: [ + 'buildtype=release', + 'cpp_std=c++11', + ], +) + +# https://mesonbuild.com/Python-module.html +py_mod = import('python') +py = py_mod.find_installation('python3', pure: false) +py_dep = py.dependency() + +backend = get_option('transonic-backend') + +if backend.contains(',') + backends = backend.split(',') +else + backends = [backend] +endif + +use_pythran = backend.contains('pythran') +if use_pythran + incdir_numpy = run_command('transonic-get-include', 'numpy', check: true).stdout().strip() + inc_np = include_directories(incdir_numpy) + np_dep = declare_dependency(include_directories: inc_np) + + incdir_pythran = run_command('transonic-get-include', 'pythran', check: true).stdout().strip() + pythran = find_program('pythran', native: true) + + cpp_args_pythran = [ + '-DENABLE_PYTHON_MODULE', + '-D__PYTHRAN__=3', + '-DPYTHRAN_BLAS_NONE' + ] + + if get_option('use-xsimd') == true + # xsimd is unvendored from pythran by conda-forge, and due to a compiler + # activation bug the default /include/ may not be visible (see + # gh-15698). Hence look for xsimd explicitly. + xsimd_dep = dependency('xsimd', required: false) + pythran_dep = declare_dependency( + include_directories: incdir_pythran, + dependencies: xsimd_dep, + ) + cpp_args_pythran += ['-DUSE_XSIMD'] + else + pythran_dep = declare_dependency( + include_directories: incdir_pythran, + ) + endif + + pythran_complex_hook = get_option('pythran-complex-hook') + if pythran_complex_hook == 'os-dependent' + pythran_complex_hook = host_machine.system() == 'linux' + endif + + if get_option('native') + cpp_args_pythran += ['-march=native', '-Ofast'] + endif + +endif + +subdir('pylandstats') diff --git a/meson.options b/meson.options new file mode 100644 index 0000000..a543b9f --- /dev/null +++ b/meson.options @@ -0,0 +1,27 @@ +option( + 'transonic-backend', + type: 'string', + value: 'pythran,python,numba', + description: + 'pythran,python,numba (default), cython, numpy, numba; ' + + 'or comma separated value representing multi-backends', +) +option( + 'native', + type: 'boolean', + value: false, + description: 'Performance oriented and not portable build', +) +option( + 'use-xsimd', + type: 'boolean', + value: true, + description: 'Turns on xsimd vectorization', +) +option( + 'pythran-complex-hook', + type: 'combo', + choices: ['os-dependent', 'true', 'false'], + value: 'os-dependent', + description: 'Pythran complex_hook option', +) diff --git a/noxfile.py b/noxfile.py new file mode 100644 index 0000000..810ab01 --- /dev/null +++ b/noxfile.py @@ -0,0 +1,62 @@ +"""Task runner for the developer. + +# Usage + +``` +nox -l # list of sessions. +nox -s # execute a session +nox -k # execute some session +``` + +""" + +import os + +import nox + +os.environ.update({"PDM_IGNORE_SAVED_PYTHON": "1"}) +nox.options.reuse_existing_virtualenvs = 1 + + +@nox.session +def doc(session): + """Build the documentation in a Nox environment.""" + command = "pdm sync --clean -G doc --no-self" + session.run_install(*command.split(), external=True) + + # for documentation, we don't need the other backends + command = "pip install . -C setup-args=-Dtransonic-backend=python" + session.run_install(*command.split(), external=True) + + session.run("sphinx-build", "docs", "docs/_build") + print(f"file://{os.getcwd()}/docs/_build/index.html") + + +@nox.session +def wheel(session): + """Build the wheel.""" + session.install("build", "twine") + session.run("python", "-m", "build") + session.run("twine", "check", "dist/*") + + +@nox.session(venv_backend="mamba|micromamba|conda") +def test(session): + """Run the test in a Nox environment.""" + command = "pdm sync --clean --prod -G test --no-self" + session.run_install(*command.split(), external=True) + + # session.conda_install("gdal>=3.3", channel=["conda-forge"]) + session.install(".", "--no-deps", external=True) + + session.run( + "pytest", + "-v", + "-s", + "--cov=pylandstats", + "--cov-append", + "--cov-report=xml", + "--cov-report", + "term-missing", + "tests", + ) diff --git a/pdm.lock b/pdm.lock new file mode 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b/pylandstats/spatiotemporal.py @@ -76,13 +76,14 @@ def __init__( neighborhood_rule : {'8', '4'}, optional Neighborhood rule to determine patch adjacencies, i.e: '8' (queen's case/Moore neighborhood) or '4' (rook's case/Von Neumann neighborhood). - Ignored if the passed-in landscapes are `Landscape` instances. If no value + Ignored if the passed-in landscapes are ``Landscape`` instances. If no value is provided and the passed-in landscapes are file-like objects or paths, the default value set in `settings.DEFAULT_NEIGHBORHOOD_RULE` will be taken. landscape_kwargs : dict, optional Other keyword arguments to be passed to the instantiation of - `pylandstats.Landscape` for each element of `landscapes`. Ignored if the - elements of `landscapes` are already instances of `pylandstats.Landcape`. + ``pylandstats.Landscape`` for each element of ``landscapes``. Ignored if the + elements of ``landscapes`` are already instances of + ``pylandstats.Landcape``. """ if dates is None: dates = ["t{}".format(i) for i in range(len(landscapes))] diff --git a/pyproject.toml b/pyproject.toml index 0bd943b..08fb6e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [build-system] -requires = ["setuptools>=61.0", "wheel", "numpy", "pythran>=0.16.0", "transonic>=0.4.0"] -build-backend = "setuptools.build_meta" +requires = ["meson-python", "numpy", "pythran>=0.16.1", "transonic>=0.4.0"] +build-backend = "mesonpy" [project] name = "pylandstats" @@ -15,13 +15,12 @@ classifiers = [ "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Natural Language :: English", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", ] -requires-python = ">=3.8" +requires-python = ">=3.9" dependencies = [ "black", "dask", @@ -32,7 +31,7 @@ dependencies = [ "pandas >= 0.23", "rasterio >= 1.0.0", "scipy >= 1.0.0", - "transonic >= 0.4.0" + "transonic >= 0.6.4", ] [project.urls] @@ -40,26 +39,26 @@ Repository = "https://github.com/martibosch/pylandstats" [project.optional-dependencies] test = ["black", "coverage[toml]", "pytest", "pytest-cov", "python-dotenv", "ruff"] -dev = ["build", "commitizen", "pre-commit", "pip", "toml", "tox", "twine"] -doc = ["m2r2", "pydata-sphinx-theme", "sphinx"] [tool.setuptools.packages.find] include = ["pylandstats", "pylandstats.*"] [tool.ruff] -select = ["D", "E", "F", "I"] line-length = 88 [tool.ruff.format] docstring-code-format = true +[tool.ruff.lint] +select = ["D", "E", "F", "I"] + [tool.ruff.lint.pydocstyle] convention = "numpy" -[tool.ruff.isort] +[tool.ruff.lint.isort] known-first-party = ["pylandstats"] -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "**/__init__.py" = ["F403"] "pylandstats/landscape.py" = ["D401"] # for metric docstrings "tests/test_pylandstats.py" = ["D"] @@ -88,9 +87,34 @@ version_files = [ ] [tool.cibuildwheel] -build = ["cp38-*", "cp39-*", "cp310-*", "cp311-*", "cp312-*"] +build = ["cp39-*", "cp310-*", "cp311-*", "cp312-*"] skip = "*-musllinux_i686" [tool.codespell] ignore-words-list = "te" -skip = "CHANGELOG.md" +skip = "CHANGELOG.md,pdm.lock" + + +[tool.pdm] +distribution = true +ignore_package_warnings = ["ipython"] + +[tool.pdm.dev-dependencies] +build = [ + "meson-python", + "numpy", + "transonic>=0.6.2", + "pythran>=0.16.1", + "ninja", +] +dev = ["commitizen", "pre-commit", "toml", "ruff"] +doc = ["pydata-sphinx-theme", "sphinx", "myst-nb", "pip"] + +[tool.pdm.options] +lock = ["-G", ":all"] +# for Meson +sync = ["--clean", "--no-isolation"] +install = ["--clean", "--no-isolation"] + +[tool.pdm.scripts] +test = "pytest tests" diff --git a/setup.py b/setup.py deleted file mode 100644 index 52cf70f..0000000 --- a/setup.py +++ /dev/null @@ -1,33 +0,0 @@ -"""pylandstats setup script.""" - -import platform -from pathlib import Path - -from setuptools import setup - -# pythran imports must go AFTER setuptools imports -# See: https://github.com/pypa/setuptools/issues/309 and https://bit.ly/300HKtK -from transonic.dist import init_transonic_extensions, make_backend_files - -here = Path(__file__).parent.absolute() - -if platform.system() == "Windows": - backend = "numba" -else: - backend = "pythran" - -paths = ["pylandstats/landscape.py"] -make_backend_files([here / path for path in paths], backend=backend) - -if platform.system() == "Linux": - compile_args = ("-O3", "-DUSE_XSIMD") -else: - compile_args = ("-O3",) - -extensions = init_transonic_extensions( - "pylandstats", compile_args=compile_args, backend=backend -) - -setup( - ext_modules=extensions, -) diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 14ac429..0000000 --- a/tox.ini +++ /dev/null @@ -1,37 +0,0 @@ -[tox] -isolated_build = true -envlist = py38, py39, py310, py311, py312, lint - -[gh-actions] -python = - 3.12: py312 - 3.11: py311 - 3.10: py310 - 3.9: py39 - 3.8: py38 - -[testenv:lint] -whitelist_externals = - build - sphinx-build - twine -extras = - test - doc - dev -commands = - python -m build - sphinx-build docs docs/_build - twine check dist/* - -[testenv] -conda_deps= - gdal>=3.3 -setenv = - PYTHONPATH = {toxinidir} -whitelist_externals = - pytest -extras = - test -commands = - pytest -s --cov=pylandstats --cov-append --cov-report=xml --cov-report term-missing tests