survivalist 0.0.0__tar.gz

survivalist-0.0.0/LICENSE

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+The Clear BSD License
+
+Copyright (c) [2019-2024] [Thierry Moudiki]
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted (subject to the limitations in the disclaimer
+below) provided that the following conditions are met:
+
+     * Redistributions of source code must retain the above copyright notice,
+     this list of conditions and the following disclaimer.
+
+     * Redistributions in binary form must reproduce the above copyright
+     notice, this list of conditions and the following disclaimer in the
+     documentation and/or other materials provided with the distribution.
+
+     * Neither the name of the copyright holder nor the names of its
+     contributors may be used to endorse or promote products derived from this
+     software without specific prior written permission.
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
+IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

survivalist-0.0.0/MANIFEST.in

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+# by default, the source distribution includes everything that is under version control
+
+prune doc/_build
+prune doc/api/generated
+prune .binder
+prune .github
+prune ci
+exclude appveyor.yml .codecov.yml .pre-commit-config.yaml .readthedocs.yaml .zenodo.json
+
+global-exclude __pycache__
+global-exclude .ipynb_checkpoints
+global-exclude .git*
+# Cython generated files
+global-exclude _*.c
+global-exclude _*.cpp
+global-exclude *.py[oc]
+global-exclude *.bak
+global-exclude *.swp
+global-exclude *~

survivalist-0.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: survivalist
+Version: 0.0.0
+Summary: Survival analysis built on top of scikit-learn
+Author-email: "T. Moudiki" <thierry.moudiki@gmail.com>
+License: The Clear BSD License
+        
+        Copyright (c) [2019-2024] [Thierry Moudiki]
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted (subject to the limitations in the disclaimer
+        below) provided that the following conditions are met:
+        
+             * Redistributions of source code must retain the above copyright notice,
+             this list of conditions and the following disclaimer.
+        
+             * Redistributions in binary form must reproduce the above copyright
+             notice, this list of conditions and the following disclaimer in the
+             documentation and/or other materials provided with the distribution.
+        
+             * Neither the name of the copyright holder nor the names of its
+             contributors may be used to endorse or promote products derived from this
+             software without specific prior written permission.
+        
+        NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+        THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+        CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+        LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+        PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
+        CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+        EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+        PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+        BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
+        IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+        ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+        POSSIBILITY OF SUCH DAMAGE.
+Project-URL: Homepage, https://techtonique.github.io/survivalist
+Project-URL: Documentation, https://techtonique.github.io/survivalist
+Project-URL: Source Code, https://github.com/Techtonique/survivalist
+Project-URL: Bug Tracker, https://github.com/Techtonique/survivalist/issues
+Project-URL: Release Notes, https://github.com/Techtonique/survivalist/releases
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX
+Classifier: Programming Language :: C++
+Classifier: Programming Language :: Cython
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Software Development
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ecos
+Requires-Dist: joblib
+Requires-Dist: numexpr
+Requires-Dist: numpy
+Requires-Dist: osqp!=0.6.0,!=0.6.1
+Requires-Dist: pandas>=1.4.0
+Requires-Dist: scipy>=1.3.2
+Requires-Dist: scikit-learn<1.6,>=1.4.0
+Requires-Dist: nnetsauce
+Provides-Extra: dev
+Requires-Dist: black[jupyter]; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: Cython>=3.0.10; extra == "dev"
+Requires-Dist: packaging; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: setuptools-scm>=8; extra == "dev"
+Requires-Dist: tomli; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: ipython!=8.7.0; extra == "docs"
+Requires-Dist: nbsphinx>=0.9.2; extra == "docs"
+Requires-Dist: docutils; extra == "docs"
+Requires-Dist: setuptools-scm; extra == "docs"
+Requires-Dist: sphinx~=7.3.7; extra == "docs"
+Requires-Dist: pydata-sphinx-theme~=0.15.2; extra == "docs"
+Requires-Dist: sphinxcontrib-spelling; extra == "docs"
+Requires-Dist: sphinx-design~=0.5.0; extra == "docs"
+Requires-Dist: sphinx-copybutton~=0.5.2; extra == "docs"
+Provides-Extra: nbval
+Requires-Dist: ipykernel; extra == "nbval"
+Requires-Dist: ipython!=8.7.0; extra == "nbval"
+Requires-Dist: matplotlib~=3.9.0; extra == "nbval"
+Requires-Dist: nbformat; extra == "nbval"
+Requires-Dist: nbval>=0.10.0; extra == "nbval"
+Requires-Dist: seaborn~=0.13.2; extra == "nbval"
+
+# survivalist

survivalist-0.0.0/README.md

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+# survivalist

survivalist-0.0.0/pyproject.toml

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+[build-system]
+requires = [
+    "setuptools>=64",
+    "setuptools-scm>=8",
+    "packaging",
+    # same as scikit-learn
+    "Cython>=3.0.10",
+    # building against numpy 2.x is compatible with numpy 1.x
+    "numpy>=2.0.0",
+
+    # scikit-learn requirements
+    "scikit-learn~=1.4.0; python_version<='3.12'",
+    "scikit-learn~=1.5.0; python_version=='3.13'",
+    "scikit-learn; python_version>'3.13'",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "survivalist"
+description = "Survival analysis built on top of scikit-learn"
+readme = "README.md"
+authors = [
+    {name = "T. Moudiki", email = "thierry.moudiki@gmail.com"}
+]
+license = {file = "LICENSE"}
+requires-python = ">=3.10"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Programming Language :: C++",
+    "Programming Language :: Cython",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Software Development",
+    "Topic :: Scientific/Engineering"
+]
+dependencies = [
+    "ecos",
+    "joblib",
+    "numexpr",
+    "numpy",
+    "osqp !=0.6.0,!=0.6.1",
+    "pandas >=1.4.0",
+    "scipy >=1.3.2",
+    "scikit-learn >=1.4.0,<1.6",
+    "nnetsauce"
+]
+dynamic = ["version"]
+
+[project.urls]
+"Homepage" = "https://techtonique.github.io/survivalist"
+"Documentation" = "https://techtonique.github.io/survivalist"
+"Source Code" = "https://github.com/Techtonique/survivalist"
+"Bug Tracker" = "https://github.com/Techtonique/survivalist/issues"
+"Release Notes" = "https://github.com/Techtonique/survivalist/releases"
+
+[project.optional-dependencies]
+dev = [
+    "black[jupyter]",
+    "build",
+    "coverage",
+    "Cython >=3.0.10",
+    "packaging",
+    "pre-commit",
+    "pytest",
+    "ruff",
+    "setuptools-scm >=8",
+    "tomli",
+    "tox",
+]
+
+# This file purposely does not contain libraries that depend on C modules.
+# See https://docs.readthedocs.io/en/latest/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
+docs = [
+    "ipython !=8.7.0",
+    "nbsphinx>=0.9.2",
+    "docutils",
+    "setuptools-scm",
+    "sphinx ~=7.3.7",
+    "pydata-sphinx-theme ~=0.15.2",
+    "sphinxcontrib-spelling",
+    "sphinx-design ~=0.5.0",
+    "sphinx-copybutton ~=0.5.2",
+]
+
+nbval = [
+    "ipykernel",
+    "ipython!=8.7.0",
+    "matplotlib~=3.9.0",
+    "nbformat",
+    "nbval>=0.10.0",
+    "seaborn~=0.13.2",
+]
+
+[tool.setuptools]
+include-package-data = false
+
+[tool.setuptools.packages.find]
+include = ["survivalist*"]
+namespaces = false
+
+[tool.setuptools.package-data]
+"survivalist.datasets" = ["data/*.arff"]
+
+[tool.black]
+line-length = 120
+target-version = ["py310"]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "--strict-markers"
+testpaths = ["tests"]
+filterwarnings = [
+    # Treat all warnings as errors other than the ignored ones
+    "error",
+    # distutils is deprecated in 3.10, scheduled for removal in 3.12
+    "ignore:The distutils package is deprecated:DeprecationWarning",
+    "ignore:Setuptools is replacing distutils",
+    "ignore:distutils Version classes are deprecated.*:DeprecationWarning",
+    "ignore:Jupyter is migrating its paths to use standard platformdirs:DeprecationWarning",
+    # added with pandas 2.1
+    "ignore:DataFrame.applymap has been deprecated:FutureWarning",
+    # deprecated since Pandas 2.2.0
+    "ignore:\\nPyarrow will become a required dependency of pandas in the next major release of pandas.*:DeprecationWarning",
+    # deprecated since Python 3.12
+    "ignore:datetime\\.datetime\\.utcfromtimestamp\\(\\) is deprecated and scheduled for removal in a future version.*:DeprecationWarning",
+    "ignore:ast\\.Num is deprecated and will be removed in Python 3\\.14.*:DeprecationWarning",
+    "ignore:Attribute n is deprecated and will be removed in Python 3\\.14.*:DeprecationWarning",
+    # deprecated since NumPy 1.25
+    "ignore:np\\.find_common_type is deprecated.  Please use `np\\.result_type` or `np\\.promote_types`:DeprecationWarning",
+    # deprecated since NumPy 2.0
+    "ignore:`trapz` is deprecated\\. Use `trapezoid` instead.*:DeprecationWarning",
+    # deprecated since scikit-learn 1.5
+    "ignore:'multi_class' was deprecated in version 1\\.5 and will be removed in 1\\.7.*:FutureWarning",
+]
+
+[tool.coverage.run]
+branch = true
+plugins = ["Cython.Coverage"]
+relative_files = true
+source = ["survivalist"]
+
+[tool.coverage.report]
+exclude_lines = [
+    # Have to re-enable the standard pragma
+    "pragma: no cover",
+
+    # Don't complain about missing debug-only code:
+    "def __repr__",
+    "if self\\.debug",
+
+    # Don't complain if tests don't hit defensive assertion code:
+    "raise AssertionError",
+    "raise NotImplementedError",
+
+    # Don't complain if non-runnable code isn't run:
+    "if 0:",
+    "if __name__ == .__main__.:",
+]
+ignore_errors = true
+
+omit = [
+    "tests/*",
+    "*/setup.py",
+    "*/_version.py",
+]
+
+[tool.ruff]
+extend-exclude = [
+    "doc/conf.py",
+]
+# Group violations by containing file.
+output-format = "grouped"
+line-length = 120
+target-version = "py310"
+
+[tool.ruff.lint]
+ignore = ["C408"]
+ignore-init-module-imports = true
+select = [
+    "C4",
+    "C9",
+    "E",
+    "F",
+    "I",
+    "PT",
+    "W",
+]
+
+[tool.ruff.lint.flake8-pytest-style]
+fixture-parentheses = true
+mark-parentheses = true
+parametrize-names-type = "csv"
+
+[tool.ruff.lint.mccabe]
+max-complexity = 10
+
+[tool.ruff.lint.isort]
+force-sort-within-sections = true
+known-first-party = ["survivalist"]
+
+[tool.setuptools_scm]

survivalist-0.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

survivalist-0.0.0/setup.py

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+import os
+from pathlib import Path
+import shutil
+import sys
+
+from packaging import version
+from setuptools import Command, Extension, setup
+
+CYTHON_MIN_VERSION = version.parse("0.29")
+
+
+# adapted from bottleneck's setup.py
+class clean(Command):
+    user_options = [("all", "a", "")]
+
+    def initialize_options(self):
+        self.all = True
+        self.delete_dirs = []
+        self.delete_files = []
+
+        for root, dirs, files in os.walk("survivalist"):
+            root = Path(root)
+            for d in dirs:
+                if d == "__pycache__":
+                    self.delete_dirs.append(root / d)
+
+            if "__pycache__" in root.name:
+                continue
+
+            for f in (root / x for x in files):
+                ext = f.suffix
+                if ext == ".pyc" or ext == ".so":
+                    self.delete_files.append(f)
+
+                if ext in (
+                    ".c",
+                    ".cpp",
+                ):
+                    source_file = f.with_suffix(".pyx")
+                    if source_file.exists():
+                        self.delete_files.append(f)
+
+        build_path = Path("build")
+        if build_path.exists():
+            self.delete_dirs.append(build_path)
+
+    def finalize_options(self):
+        pass
+
+    def run(self):
+        for delete_dir in self.delete_dirs:
+            shutil.rmtree(delete_dir)
+        for delete_file in self.delete_files:
+            delete_file.unlink()
+
+
+EXTENSIONS = {
+    "_coxph_loss": {"sources": ["survivalist/ensemble/_coxph_loss.pyx"]},
+}
+
+
+def get_module_from_sources(sources):
+    for src_path in map(Path, sources):
+        if src_path.suffix == ".pyx":
+            return ".".join(src_path.parts[:-1] + (src_path.stem,))
+    raise ValueError(f"could not find module from sources: {sources!r}")
+
+
+def _check_cython_version():
+    message = (
+        f"Please install Cython with a version >= {CYTHON_MIN_VERSION} in order to build a scikit-learn from source."
+    )
+    try:
+        import Cython
+    except ModuleNotFoundError:
+        # Re-raise with more informative error message instead:
+        raise ModuleNotFoundError(message)
+
+    if version.parse(Cython.__version__) < CYTHON_MIN_VERSION:
+        message += f" The current version of Cython is {Cython.__version__} installed in {Cython.__path__}."
+        raise ValueError(message)
+
+
+def cythonize_extensions(extensions):
+    """Check that a recent Cython is available and cythonize extensions"""
+    _check_cython_version()
+    from Cython.Build import cythonize
+
+    # http://docs.cython.org/en/latest/src/userguide/source_files_and_compilation.html#cythonize-arguments
+    directives = {"language_level": "3"}
+    cy_cov = os.environ.get("CYTHON_COVERAGE", False)
+    macros = [("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")]
+    if cy_cov:
+        directives["linetrace"] = True
+        macros.append(("CYTHON_TRACE", "1"))
+        macros.append(("CYTHON_TRACE_NOGIL", "1"))
+
+    for ext in extensions:
+        if ext.define_macros is None:
+            ext.define_macros = macros
+        else:
+            ext.define_macros += macros
+
+    return cythonize(extensions, compiler_directives=directives)
+
+
+def get_extensions():
+    import numpy
+
+    numpy_includes = [numpy.get_include()]
+    
+    extensions = []
+    for config in EXTENSIONS.values():
+        name = get_module_from_sources(config["sources"])
+        include_dirs = numpy_includes + config.get("include_dirs", [])
+        extra_compile_args = config.get("extra_compile_args", [])
+        language = config.get("language", "c")
+        ext = Extension(
+            name=name,
+            sources=config["sources"],
+            include_dirs=include_dirs,
+            extra_compile_args=extra_compile_args,
+            language=language,
+        )
+        extensions.append(ext)
+
+    # Skip cythonization as we do not want to include the generated
+    # C/C++ files in the release tarballs as they are not necessarily
+    # forward compatible with future versions of Python for instance.
+    if "sdist" not in sys.argv and "clean" not in sys.argv:
+        extensions = cythonize_extensions(extensions)
+
+    return extensions
+
+
+if __name__ == "__main__":
+    setup(
+        ext_modules=get_extensions(),
+        cmdclass={"clean": clean},
+    )

survivalist-0.0.0/survivalist/__init__.py

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+from importlib.metadata import PackageNotFoundError, version
+import platform
+import sys
+
+from sklearn.pipeline import Pipeline, _final_estimator_has
+from sklearn.utils.metaestimators import available_if
+
+from .util import property_available_if
+
+
+def _get_version(name):
+    try:
+        pkg_version = version(name)
+    except ImportError:
+        pkg_version = None
+    return pkg_version
+
+
+def show_versions():
+    sys_info = {
+        "Platform": platform.platform(),
+        "Python version": f"{platform.python_implementation()} {platform}",
+        "Python interpreter": sys.executable,
+    }
+
+    deps = [
+        "survivalist",
+        "scikit-learn",
+        "numpy",
+        "scipy",
+        "pandas",
+        "numexpr",
+        "ecos",
+        "osqp",
+        "joblib",
+        "matplotlib",
+        "pytest",
+        "sphinx",
+        "Cython",
+        "pip",
+        "setuptools",
+    ]
+    minwidth = max(
+        max(map(len, deps)),
+        max(map(len, sys_info.keys())),
+    )
+    fmt = "{0:<%ds}: {1}" % minwidth
+
+    print("SYSTEM")
+    print("------")
+    for name, version_string in sys_info.items():
+        print(fmt.format(name, version_string))
+
+    print("\nDEPENDENCIES")
+    print("------------")
+    for dep in deps:
+        version_string = _get_version(dep)
+        print(fmt.format(dep, version_string))
+
+
+@available_if(_final_estimator_has("predict_cumulative_hazard_function"))
+def predict_cumulative_hazard_function(self, X, **kwargs):
+    """Predict cumulative hazard function.
+
+    The cumulative hazard function for an individual
+    with feature vector :math:`x` is defined as
+
+    .. math::
+
+        H(t \\mid x) = \\exp(x^\\top \\beta) H_0(t) ,
+
+    where :math:`H_0(t)` is the baseline hazard function,
+    estimated by Breslow's estimator.
+
+    Parameters
+    ----------
+    X : array-like, shape = (n_samples, n_features)
+        Data matrix.
+
+    Returns
+    -------
+    cum_hazard : ndarray, shape = (n_samples,)
+        Predicted cumulative hazard functions.
+    """
+    Xt = X
+    for _, _, transform in self._iter(with_final=False):
+        Xt = transform.transform(Xt)
+    return self.steps[-1][-1].predict_cumulative_hazard_function(Xt, **kwargs)
+
+
+@available_if(_final_estimator_has("predict_survival_function"))
+def predict_survival_function(self, X, **kwargs):
+    """Predict survival function.
+
+    The survival function for an individual
+    with feature vector :math:`x` is defined as
+
+    .. math::
+
+        S(t \\mid x) = S_0(t)^{\\exp(x^\\top \\beta)} ,
+
+    where :math:`S_0(t)` is the baseline survival function,
+    estimated by Breslow's estimator.
+
+    Parameters
+    ----------
+    X : array-like, shape = (n_samples, n_features)
+        Data matrix.
+
+    Returns
+    -------
+    survival : ndarray, shape = (n_samples,)
+        Predicted survival functions.
+    """
+    Xt = X
+    for _, _, transform in self._iter(with_final=False):
+        Xt = transform.transform(Xt)
+    return self.steps[-1][-1].predict_survival_function(Xt, **kwargs)
+
+
+@property_available_if(_final_estimator_has("_predict_risk_score"))
+def _predict_risk_score(self):
+    return self.steps[-1][-1]._predict_risk_score
+
+
+def patch_pipeline():
+    Pipeline.predict_survival_function = predict_survival_function
+    Pipeline.predict_cumulative_hazard_function = (
+        predict_cumulative_hazard_function
+    )
+    Pipeline._predict_risk_score = _predict_risk_score
+
+
+try:
+    __version__ = version("survivalist")
+except PackageNotFoundError:  # pragma: no cover
+    # package is not installed
+    __version__ = "unknown"
+
+patch_pipeline()