diff --git a/README.md b/README.md index 9d426eda6..50d5fc367 100644 --- a/README.md +++ b/README.md @@ -9,16 +9,18 @@ scikit-tree scikit-tree is a scikit-learn compatible API for building state-of-the-art decision trees. These include unsupervised trees, oblique trees, uncertainty trees, quantile trees and causal trees. +Tree-models have withstood the test of time, and are consistently used for modern-day data science and machine learning applications. They especially perform well when there are limited samples for a problem and are flexible learners that can be applied to a wide variety of different settings, such as tabular, images, time-series, genomics, EEG data and more. + We welcome contributions for modern tree-based algorithms. We use Cython to achieve fast C/C++ speeds, while abiding by a scikit-learn compatible (tested) API. Moreover, our Cython internals are easily extensible because they follow the internal Cython API of scikit-learn as well. -**Dependency on a fork of scikit-learn** +**Submodule dependency on a fork of scikit-learn** Due to the current state of scikit-learn's internal Cython code for trees, we have to instead leverage a maintained fork of scikit-learn at https://github.com/neurodata/scikit-learn, where specifically, the `fork` branch is used to build and install this repo. We keep that fork well-maintained and up-to-date with respect to the main sklearn repo. The only difference is the refactoring of the `tree/` submodule. This fork is used internally under the namespace ``sktree._lib.sklearn``. It is necessary to use this fork for anything related to: - `RandomForest*` - `ExtraTrees*` - or any importable items from the `tree/` submodule, whether it is a Cython or Python object -If you are developing for scikit-tree, we will always depend on the most up-to-date commit of `https://github.com/neurodata/scikit-learn/submodule` as a submodule within scikit-tee. This branch is consistently maintained for changes upstream that occur in the scikit-learn tree submodule. This ensures that our fork maintains consistency and robustness due to bug fixes and improvements upstream. +If you are developing for scikit-tree, we will always depend on the most up-to-date commit of `https://github.com/neurodata/scikit-learn/submodulev2` as a submodule within scikit-tee. This branch is consistently maintained for changes upstream that occur in the scikit-learn tree submodule. This ensures that our fork maintains consistency and robustness due to bug fixes and improvements upstream. Documentation ============= @@ -43,7 +45,7 @@ We minimally require: * Python (>=3.8) * numpy * scipy - * scikit-learn + * scikit-learn >= 1.3 Building locally with Meson (RECOMMENDED) ----------------------------------------- @@ -55,9 +57,6 @@ Make sure you have the necessary packages installed # you may need these optional dependencies to build scikit-learn locally conda install -c conda-forge joblib threadpoolctl pytest compilers llvm-openmp - # (caution only if you know what you're doing) or if you're a developer and need some latest changes on the fork: - pip install scikit-learn-tree@git+https://git@github.com/neurodata/scikit-learn.git@fork - We use the ``spin`` CLI to abstract away build details: # run the build using Meson/Ninja diff --git a/build_requirements.txt b/build_requirements.txt index ed570a12c..b18d3ce9f 100644 --- a/build_requirements.txt +++ b/build_requirements.txt @@ -3,7 +3,7 @@ meson-python cython ninja numpy -scikit-learn@git+https://git@github.com/scikit-learn/scikit-learn +scikit-learn>=1.3 click rich-click doit diff --git a/doc_requirements.txt b/doc_requirements.txt index c83ed1d46..0b7c3944b 100644 --- a/doc_requirements.txt +++ b/doc_requirements.txt @@ -11,4 +11,5 @@ ipython nbsphinx memory_profiler pandas -seaborn \ No newline at end of file +seaborn +joblib \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index d40c5344a..ba4745870 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -168,6 +168,7 @@ "pipeline.Pipeline": "sklearn.pipeline.Pipeline", # "sklearn_fork.inspection.permutation_importance": "sklearn.inspection.permutation_importance", } + numpydoc_xref_ignore = { "of", "or", @@ -218,6 +219,7 @@ "n_features_z", "n_neighbors", "one", + "joblib.parallel_backend", } # validation @@ -254,7 +256,7 @@ # -- intersphinx ------------------------------------------------------------- intersphinx_mapping = { - "python": ("https://docs.python.org/3", None), + "python": ("https://docs.python.org/{.major}".format(sys.version_info), None), "numpy": ("https://numpy.org/devdocs", None), "scipy": ("https://scipy.github.io/devdocs", None), "sklearn": ("https://scikit-learn.org/dev", None), diff --git a/poetry.lock b/poetry.lock index 03d9d5008..c6b1fc0b3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. 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into an examples gallery." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2834,7 +2421,6 @@ sphinx = ">=3" name = "sphinx-issues" version = "3.0.1" description = "A Sphinx extension for linking to your project's issue tracker" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2854,7 +2440,6 @@ tests = ["pytest (>=6.2.0)"] name = "sphinxcontrib-applehelp" version = "1.0.4" description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2870,7 +2455,6 @@ test = ["pytest"] name = "sphinxcontrib-bibtex" version = "2.5.0" description = "Sphinx extension for BibTeX style citations." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2889,7 +2473,6 @@ Sphinx = ">=2.1" name = "sphinxcontrib-devhelp" version = "1.0.2" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -2905,7 +2488,6 @@ test = ["pytest"] name = "sphinxcontrib-htmlhelp" version = "2.0.1" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2921,7 +2503,6 @@ test = ["html5lib", "pytest"] name = "sphinxcontrib-jsmath" version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -2936,7 +2517,6 @@ test = ["flake8", "mypy", "pytest"] name = "sphinxcontrib-qthelp" version = "1.0.3" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -2952,7 +2532,6 @@ test = ["pytest"] name = "sphinxcontrib-serializinghtml" version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -2968,7 +2547,6 @@ test = ["pytest"] name = "stevedore" version = "5.1.0" description = "Manage dynamic plugins for Python applications" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2983,7 +2561,6 @@ pbr = ">=2.0.0,<2.1.0 || >2.1.0" name = "termcolor" version = "2.3.0" description = "ANSI color formatting for output in terminal" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2998,7 +2575,6 @@ tests = ["pytest", "pytest-cov"] name = "threadpoolctl" version = "3.1.0" description = "threadpoolctl" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3010,7 +2586,6 @@ files = [ name = "tinycss2" version = "1.2.1" description = "A tiny CSS parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3027,21 +2602,19 @@ test = ["flake8", "isort", "pytest"] [[package]] name = "tokenize-rt" -version = "5.0.0" +version = "5.1.0" description = "A wrapper around the stdlib `tokenize` which roundtrips." -category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "tokenize_rt-5.0.0-py2.py3-none-any.whl", hash = "sha256:c67772c662c6b3dc65edf66808577968fb10badfc2042e3027196bed4daf9e5a"}, - {file = "tokenize_rt-5.0.0.tar.gz", hash = "sha256:3160bc0c3e8491312d0485171dea861fc160a240f5f5766b72a1165408d10740"}, + {file = "tokenize_rt-5.1.0-py2.py3-none-any.whl", hash = "sha256:9b7bb843e77dd6ed0be5564bfaaba200083911e0497841cd3e9235a6a9794d74"}, + {file = "tokenize_rt-5.1.0.tar.gz", hash = "sha256:08f0c2daa94c4052e53c2fcaa8e32585e6ae9bdfc800974092d031401694e002"}, ] [[package]] name = "toml" version = "0.10.2" description = "Python Library for Tom's Obvious, Minimal Language" -category = "dev" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -3053,7 +2626,6 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3065,7 +2637,6 @@ files = [ name = "tornado" version = "6.3.2" description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." -category = "dev" optional = false python-versions = ">= 3.8" files = [ @@ -3086,7 +2657,6 @@ files = [ name = "traitlets" version = "5.9.0" description = "Traitlets Python configuration system" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3100,21 +2670,19 @@ test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"] [[package]] name = "typing-extensions" -version = "4.6.3" +version = "4.7.0" description = "Backported and Experimental Type Hints for Python 3.7+" -category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "typing_extensions-4.6.3-py3-none-any.whl", hash = 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displayed width of unicode strings in a terminal" -category = "dev" optional = false python-versions = "*" files = [ @@ -3184,7 +2750,6 @@ files = [ name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "dev" optional = false python-versions = "*" files = [ @@ -3196,7 +2761,6 @@ files = [ name = "yaspin" version = "2.3.0" description = "Yet Another Terminal Spinner" -category = "dev" optional = false python-versions = ">=3.7.2,<4.0.0" files = [ @@ -3211,7 +2775,6 @@ termcolor = ">=2.2,<3.0" name = "zipp" version = "3.15.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3225,5 +2788,5 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more [metadata] lock-version = "2.0" -python-versions = ">=3.8,<3.11" -content-hash = "e53759607398abeadc76ea19e0285e15f429987b649159224f1e568eb4115657" +python-versions = ">=3.8,<3.12" +content-hash = "ae84ab145110fc6dad809ebb53f6f0a58b2b7d9fd3c581c1202ae45384de48bc" diff --git a/pyproject.toml b/pyproject.toml index b39cdb2dc..4ba1b109b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,6 +17,7 @@ classifiers = [ 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9', 'Programming Language :: Python :: 3.10', + 'Programming Language :: Python :: 3.11', ] keywords = ['tree', 'oblique trees', 'manifold-learning', 'scikit-learn'] include = [ @@ -68,11 +69,11 @@ vcs = "git" files = ["sktree/__init__.py"] [tool.poetry.dependencies] -python = ">=3.8,<3.11" +python = ">=3.8,<3.12" numpy = "^1.23.0" scipy = "^1.9.0" scikit-learn = "^1.2.2" -importlib-resources = { version = "*", python = "<3.9" } +importlib-resources = { version = "*", python = "<3.10" } [tool.poetry.group.test] optional = true diff --git a/requirements.txt b/requirements.txt index 3bb6e4b79..b3de48834 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,3 @@ numpy scipy -scikit-learn@git+https://git@github.com/scikit-learn/scikit-learn +scikit-learn>=1.3 diff --git a/sktree/_lib/sklearn_fork b/sktree/_lib/sklearn_fork index 1c1ec8cff..9655d0138 160000 --- a/sktree/_lib/sklearn_fork +++ b/sktree/_lib/sklearn_fork @@ -1 +1 @@ -Subproject commit 1c1ec8cff3a181b7a86a4df8a2aeb01fa7cdbe6a +Subproject commit 9655d013870e3007d5c5a1898212a9d0eeea0968 diff --git a/sktree/ensemble/_honest_forest.py b/sktree/ensemble/_honest_forest.py index bd6a7bb49..50a80841a 100644 --- a/sktree/ensemble/_honest_forest.py +++ b/sktree/ensemble/_honest_forest.py @@ -113,7 +113,7 @@ class HonestForestClassifier(ForestClassifier): n_jobs : int, default=None The number of jobs to run in parallel. :meth:`fit`, :meth:`predict`, :meth:`decision_path` and :meth:`apply` are all parallelized over the - trees. ``None`` means 1 unless in a :obj:`joblib.parallel_backend` + trees. ``None`` means 1 unless in a `joblib.parallel_backend` context. ``-1`` means using all processors. See :term:`Glossary ` for more details. diff --git a/sktree/ensemble/_supervised_forest.py b/sktree/ensemble/_supervised_forest.py index b7f02bec1..668c1abb6 100644 --- a/sktree/ensemble/_supervised_forest.py +++ b/sktree/ensemble/_supervised_forest.py @@ -114,7 +114,7 @@ class ObliqueRandomForestClassifier(SimMatrixMixin, ForestClassifier): n_jobs : int, default=None The number of jobs to run in parallel. :meth:`fit`, :meth:`predict`, :meth:`decision_path` and :meth:`apply` are all parallelized over the - trees. ``None`` means 1 unless in a :obj:`joblib.parallel_backend` + trees. ``None`` means 1 unless in a `joblib.parallel_backend` context. ``-1`` means using all processors. See :term:`Glossary ` for more details. @@ -454,7 +454,7 @@ class ObliqueRandomForestRegressor(SimMatrixMixin, ForestRegressor): n_jobs : int, default=None The number of jobs to run in parallel. :meth:`fit`, :meth:`predict`, :meth:`decision_path` and :meth:`apply` are all parallelized over the - trees. ``None`` means 1 unless in a :obj:`joblib.parallel_backend` + trees. ``None`` means 1 unless in a `joblib.parallel_backend` context. ``-1`` means using all processors. See :term:`Glossary ` for more details. @@ -743,7 +743,7 @@ class PatchObliqueRandomForestClassifier(SimMatrixMixin, ForestClassifier): n_jobs : int, default=None The number of jobs to run in parallel. :meth:`fit`, :meth:`predict`, :meth:`decision_path` and :meth:`apply` are all parallelized over the - trees. ``None`` means 1 unless in a :obj:`joblib.parallel_backend` + trees. ``None`` means 1 unless in a `joblib.parallel_backend` context. ``-1`` means using all processors. See :term:`Glossary ` for more details. @@ -1095,7 +1095,7 @@ class PatchObliqueRandomForestRegressor(SimMatrixMixin, ForestRegressor): n_jobs : int, default=None The number of jobs to run in parallel. :meth:`fit`, :meth:`predict`, :meth:`decision_path` and :meth:`apply` are all parallelized over the - trees. ``None`` means 1 unless in a :obj:`joblib.parallel_backend` + trees. ``None`` means 1 unless in a `joblib.parallel_backend` context. ``-1`` means using all processors. See :term:`Glossary ` for more details. diff --git a/sktree/tree/_marginalize.py b/sktree/tree/_marginalize.py index df16e1c13..0f876eda6 100644 --- a/sktree/tree/_marginalize.py +++ b/sktree/tree/_marginalize.py @@ -165,7 +165,7 @@ def _apply_marginal_tree( def compute_marginal(self: BaseForest, X, S, n_repeats=10): - """Compute marginal distribution of P(S = s) for each s in X. + r"""Compute marginal distribution of P(S = s) for each s in X. Parameters ---------- @@ -194,7 +194,7 @@ def compute_marginal(self: BaseForest, X, S, n_repeats=10): def compute_conditional(self, X, S, y=None, n_repeats=10): - """Compute conditional P(Y | X, Z = z) for each X and Z. + r"""Compute conditional P(Y | X, Z = z) for each X and Z. Parameters ----------