Move to pyproject.toml and src-layout; stop writing _version.py.

... and update warnings filters.
hmmlearn · Sep 16, 2024 · 8ae8e7f · 8ae8e7f
1 parent 33b1a91
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diff --git a/src/_hmmc.cpp → ext/_hmmc.cpp b/src/_hmmc.cpp → ext/_hmmc.cpp
diff --git a/lib/hmmlearn/.gitignore b/lib/hmmlearn/.gitignore
diff --git a/lib/hmmlearn/__init__.py b/lib/hmmlearn/__init__.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,74 @@
+# Copyright (C) 2007-2009 Cournapeau David <cournape@gmail.com>
+#               2010 Fabian Pedregosa <fabian.pedregosa@inria.fr>
+#               2014 Gael Varoquaux
+#               2014-2016 Sergei Lebedev <superbobry@gmail.com>
+#               2018-2023 Antony Lee
+#               2023- Matthew Danielson
+
+[build-system]
+requires = [
+    "setuptools>=62",
+    "setuptools_scm[toml]>=6.2",
+    "pybind11>=2.6.0",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "hmmlearn"
+description = "Hidden Markov Models in Python with scikit-learn like API"
+readme = "README.rst"
+authors = [
+    {name = "David Cournapeau"},  # 2007-2009
+    {name = "Fabian Pedregosa"},  # 2010
+    {name = "Gael Varoquaux"},  # 2014
+    {name = "Sergei Lebedev"},  # 2014-2016
+    {name = "Antony Lee"},  # 2018-2023
+    {name = "Matthew Danielson"},  # 2023
+]
+urls = {Repository = "https://github.com/hmmlearn/hmmlearn"}
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "License :: OSI Approved :: BSD License",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Topic :: Software Development",
+    "Topic :: Scientific/Engineering",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+]
+requires-python = ">=3.8"
+dependencies = [
+    "numpy>=1.10",  # np.broadcast_to.
+    "scikit-learn>=0.16,!=0.22.0",  # check_array, check_is_fitted.
+    "scipy>=0.19",  # scipy.special.logsumexp.
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+tests = [
+    "pytest",
+]
+docs = [
+    "matplotlib",
+    "pydata_sphinx_theme",
+    "sphinx>=2.0",
+    "sphinx-gallery",
+]
+
+[tool.setuptools_scm]
+version_scheme = "post-release"
+local_scheme = "node-and-date"
+fallback_version = "0+unknown"
+
+[tool.coverage.run]
+branch = true
+source_pkgs = ["hmmlearn"]
+
+[tool.pytest.ini_options]
+addopts = "--doctest-glob=src/**/*.py --doctest-glob=*.rst"
+filterwarnings = [
+    "error",
+    "ignore::DeprecationWarning",
+    "error::DeprecationWarning:hmmlearn",
+    "ignore:underflow",
+]
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
@@ -1,84 +1,9 @@
-# Copyright (C) 2007-2009 Cournapeau David <cournape@gmail.com>
-#               2010 Fabian Pedregosa <fabian.pedregosa@inria.fr>
-#               2014 Gael Varoquaux
-#               2014-2016 Sergei Lebedev <superbobry@gmail.com>
-#               2018- Antony Lee
-
-import os
-os.environ.setdefault("SETUPTOOLS_USE_DISTUTILS", "stdlib")
-
-import setuptools
-from setuptools import Extension, find_packages, setup
-from setuptools.command.build_ext import build_ext
-
-
-class build_ext(build_ext):
-
-    def finalize_options(self):
-        from pybind11.setup_helpers import Pybind11Extension
-        self.distribution.ext_modules[:] = [Pybind11Extension(
-            "hmmlearn._hmmc", ["src/_hmmc.cpp"], cxx_std=11)]
-        super().finalize_options()
-
-    def build_extensions(self):
-        try:
-            self.compiler.compiler_so.remove("-Wstrict-prototypes")
-        except (AttributeError, ValueError):
-            pass
-        super().build_extensions()
+from pybind11.setup_helpers import Pybind11Extension
+from setuptools import setup
 
 
 setup(
-    name="hmmlearn",
-    description="Hidden Markov Models in Python with scikit-learn like API",
-    long_description=open("README.rst", encoding="utf-8").read(),
-    long_description_content_type="text/x-rst",
-    maintainer="Antony Lee",
-    url="https://github.com/hmmlearn/hmmlearn",
-    license="new BSD",
-    classifiers=[
-        "Development Status :: 3 - Alpha",
-        "License :: OSI Approved",
-        "Intended Audience :: Developers",
-        "Intended Audience :: Science/Research",
-        "Topic :: Software Development",
-        "Topic :: Scientific/Engineering",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
-    ],
-    cmdclass={"build_ext": build_ext},
-    py_modules=[],
-    packages=find_packages("lib"),
-    package_dir={"": "lib"},
-    ext_modules=[Extension("", [])],
-    package_data={},
-    python_requires=">=3.8",
-    setup_requires=[
-        "pybind11>=2.6",
-        "setuptools_scm>=3.3",  # fallback_version.
-    ],
-    use_scm_version=lambda: {  # xref __init__.py
-        "version_scheme": "post-release",
-        "local_scheme": "node-and-date",
-        "write_to": "lib/hmmlearn/_version.py",
-        "fallback_version": "0+unknown",
-    },
-    install_requires=[
-        "numpy>=1.10",  # np.broadcast_to.
-        "scikit-learn>=0.16,!=0.22.0",  # check_array, check_is_fitted.
-        "scipy>=0.19",  # scipy.special.logsumexp.
+    ext_modules=[
+        Pybind11Extension("hmmlearn._hmmc", ["ext/_hmmc.cpp"], cxx_std=11),
     ],
-    extras_require={
-        "tests": ["pytest"],
-        "docs": [
-            "matplotlib",
-            "pydata_sphinx_theme",
-            "sphinx>=2.0",
-            "sphinx-gallery",
-        ],
-    },
-    entry_points={
-        "console_scripts": [],
-        "gui_scripts": [],
-    },
 )
diff --git a/src/hmmlearn/__init__.py b/src/hmmlearn/__init__.py
@@ -0,0 +1,15 @@
+"""
+hmmlearn
+========
+
+``hmmlearn`` is a set of algorithms for learning and inference of
+Hidden Markov Models.
+"""
+
+import importlib.metadata
+
+
+try:
+    __version__ = importlib.metadata.version("hmmlearn")
+except ImportError:
+    __version__ = "0+unknown"
diff --git a/lib/hmmlearn/_emissions.py → src/hmmlearn/_emissions.py b/lib/hmmlearn/_emissions.py → src/hmmlearn/_emissions.py
diff --git a/lib/hmmlearn/_kl_divergence.py → src/hmmlearn/_kl_divergence.py b/lib/hmmlearn/_kl_divergence.py → src/hmmlearn/_kl_divergence.py
diff --git a/lib/hmmlearn/_utils.py → src/hmmlearn/_utils.py b/lib/hmmlearn/_utils.py → src/hmmlearn/_utils.py
diff --git a/lib/hmmlearn/base.py → src/hmmlearn/base.py b/lib/hmmlearn/base.py → src/hmmlearn/base.py
diff --git a/lib/hmmlearn/hmm.py → src/hmmlearn/hmm.py b/lib/hmmlearn/hmm.py → src/hmmlearn/hmm.py
diff --git a/lib/hmmlearn/stats.py → src/hmmlearn/stats.py b/lib/hmmlearn/stats.py → src/hmmlearn/stats.py
diff --git a/lib/hmmlearn/tests/__init__.py → src/hmmlearn/tests/__init__.py b/lib/hmmlearn/tests/__init__.py → src/hmmlearn/tests/__init__.py
diff --git a/lib/hmmlearn/tests/conftest.py → src/hmmlearn/tests/conftest.py b/lib/hmmlearn/tests/conftest.py → src/hmmlearn/tests/conftest.py
diff --git a/lib/hmmlearn/tests/test_base.py → src/hmmlearn/tests/test_base.py b/lib/hmmlearn/tests/test_base.py → src/hmmlearn/tests/test_base.py
diff --git a/lib/hmmlearn/tests/test_categorical_hmm.py → src/hmmlearn/tests/test_categorical_hmm.py b/lib/hmmlearn/tests/test_categorical_hmm.py → src/hmmlearn/tests/test_categorical_hmm.py
diff --git a/lib/hmmlearn/tests/test_gaussian_hmm.py → src/hmmlearn/tests/test_gaussian_hmm.py b/lib/hmmlearn/tests/test_gaussian_hmm.py → src/hmmlearn/tests/test_gaussian_hmm.py
diff --git a/lib/hmmlearn/tests/test_gmm_hmm.py → src/hmmlearn/tests/test_gmm_hmm.py b/lib/hmmlearn/tests/test_gmm_hmm.py → src/hmmlearn/tests/test_gmm_hmm.py
diff --git a/...learn/tests/test_gmm_hmm_multisequence.py → ...learn/tests/test_gmm_hmm_multisequence.py b/...learn/tests/test_gmm_hmm_multisequence.py → ...learn/tests/test_gmm_hmm_multisequence.py
diff --git a/lib/hmmlearn/tests/test_gmm_hmm_new.py → src/hmmlearn/tests/test_gmm_hmm_new.py b/lib/hmmlearn/tests/test_gmm_hmm_new.py → src/hmmlearn/tests/test_gmm_hmm_new.py
diff --git a/lib/hmmlearn/tests/test_kl_divergence.py → src/hmmlearn/tests/test_kl_divergence.py b/lib/hmmlearn/tests/test_kl_divergence.py → src/hmmlearn/tests/test_kl_divergence.py
diff --git a/lib/hmmlearn/tests/test_multinomial_hmm.py → src/hmmlearn/tests/test_multinomial_hmm.py b/lib/hmmlearn/tests/test_multinomial_hmm.py → src/hmmlearn/tests/test_multinomial_hmm.py
diff --git a/lib/hmmlearn/tests/test_poisson_hmm.py → src/hmmlearn/tests/test_poisson_hmm.py b/lib/hmmlearn/tests/test_poisson_hmm.py → src/hmmlearn/tests/test_poisson_hmm.py
diff --git a/lib/hmmlearn/tests/test_utils.py → src/hmmlearn/tests/test_utils.py b/lib/hmmlearn/tests/test_utils.py → src/hmmlearn/tests/test_utils.py
diff --git a/...arn/tests/test_variational_categorical.py → ...arn/tests/test_variational_categorical.py b/...arn/tests/test_variational_categorical.py → ...arn/tests/test_variational_categorical.py
diff --git a/...mlearn/tests/test_variational_gaussian.py → ...mlearn/tests/test_variational_gaussian.py b/...mlearn/tests/test_variational_gaussian.py → ...mlearn/tests/test_variational_gaussian.py
diff --git a/lib/hmmlearn/utils.py → src/hmmlearn/utils.py b/lib/hmmlearn/utils.py → src/hmmlearn/utils.py
diff --git a/lib/hmmlearn/vhmm.py → src/hmmlearn/vhmm.py b/lib/hmmlearn/vhmm.py → src/hmmlearn/vhmm.py