diff --git a/.readthedocs.yml b/.readthedocs.yml index 115637a..3a7e5af 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,13 +1,13 @@ -version: 2 -formats: - - pdf +version: "2" + +build: + os: "ubuntu-22.04" + tools: + python: "3.10" + python: - version: 3.8 install: - requirements: docs/requirements.txt - - method: setuptools - path: . + sphinx: - builder: html - configuration: docs/conf.py - fail_on_warning: false \ No newline at end of file + configuration: docs/source/conf.py \ No newline at end of file diff --git a/docs/ImputationKernel.rst b/docs/ImputationKernel.rst deleted file mode 100644 index 3ce15e4..0000000 --- a/docs/ImputationKernel.rst +++ /dev/null @@ -1,12 +0,0 @@ -ImputationKernel -================ - -.. currentmodule:: miceforest - -ImputationKernel ----------------- - -.. autosummary:: - :toctree: ik/ - - ImputationKernel diff --git a/docs/ImputedData.rst b/docs/ImputedData.rst deleted file mode 100644 index bae57bc..0000000 --- a/docs/ImputedData.rst +++ /dev/null @@ -1,12 +0,0 @@ -ImputedData -=========== - -.. currentmodule:: miceforest - -ImputedData ------------ - -.. autosummary:: - :toctree: id/ - - ImputedData diff --git a/docs/Makefile b/docs/Makefile index 8845def..d4bb2cb 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -3,9 +3,9 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS ?=-vvv +SPHINXOPTS ?= SPHINXBUILD ?= sphinx-build -SOURCEDIR = ../miceforest +SOURCEDIR = . BUILDDIR = _build # Put it first so that "make" without argument is like "make help". diff --git a/docs/MeanMatchScheme.rst b/docs/MeanMatchScheme.rst deleted file mode 100644 index 96c80f4..0000000 --- a/docs/MeanMatchScheme.rst +++ /dev/null @@ -1,12 +0,0 @@ -MeanMatchScheme -================ - -.. currentmodule:: miceforest - -MeanMatchScheme ----------------- - -.. autosummary:: - :toctree: mms/ - - MeanMatchScheme diff --git a/docs/_static/themes.css b/docs/_static/themes.css deleted file mode 100644 index 9a9a1a0..0000000 --- a/docs/_static/themes.css +++ /dev/null @@ -1,3 +0,0 @@ -.wy-nav-content { -max-width: none; -} \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index baecc96..dc5a447 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,113 +1,27 @@ # Configuration file for the Sphinx documentation builder. # -# This file only contains a selection of the most common options. For a full -# list see the documentation: +# For the full list of built-in configuration values, see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html -# -- Path setup -------------------------------------------------------------- - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -import os -import sys -import sphinx -from sphinx.errors import VersionRequirementError - -sys.path.insert(0, os.path.abspath("..")) - - # -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -project = "miceforest" -copyright = "2021, Samuel Von Wilson" -author = "Samuel Von Wilson" - -# The full version, including alpha/beta/rc tags -release = "2021-08-21" - -# If your documentation needs a minimal Sphinx version, state it here. -needs_sphinx = "4.2.0" # Due to sphinx.ext.napoleon, autodoc_typehints -if needs_sphinx > sphinx.__version__: - message = f"This project needs at least Sphinx v{needs_sphinx}" - raise VersionRequirementError(message) +project = 'miceforest' +copyright = '2024, Samuel Von Wilson' +author = 'Samuel Von Wilson' # -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [ - "sphinx.ext.autodoc", - "sphinx.ext.autosummary", - "sphinx.ext.todo", - "sphinx.ext.viewcode", - "sphinx.ext.napoleon", -] - -autodoc_default_flags = ["members", "inherited-members", "show-inheritance"] -autodoc_default_options = { - "members": True, - "inherited-members": True, - "show-inheritance": True, -} - -# mock out modules -autodoc_mock_imports = [ - "matplotlib", - "seaborn", - "numpy", - "pandas", - "scipy", - "scikit-learn", - "lightgbm", -] +extensions = ["myst_parser"] -master_doc = "index" +templates_path = ['_templates'] +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] -# hide type hints in API docs -autodoc_typehints = "none" - -# Only the class' docstring is inserted. -autoclass_content = "class" - -# Generate autosummary pages. -autosummary_generate = [ - "ImputationKernel.rst", - "ImputedData.rst", - "utils.rst", - "MeanMatchScheme.rst", -] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] # -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -html_theme = "sphinx_rtd_theme" - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -html_theme_options = { - "includehidden": False, - "logo_only": True, -} - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ["_static"] - - -def setup(app): - app.add_css_file("themes.css") +html_theme = 'alabaster' +html_static_path = ['_static'] diff --git a/docs/id/miceforest.ImputedData.rst b/docs/id/miceforest.ImputedData.rst deleted file mode 100644 index 3bde8c4..0000000 --- a/docs/id/miceforest.ImputedData.rst +++ /dev/null @@ -1,30 +0,0 @@ -miceforest.ImputedData -====================== - -.. currentmodule:: miceforest - -.. autoclass:: ImputedData - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ImputedData.__init__ - ~ImputedData.complete_data - ~ImputedData.dataset_count - ~ImputedData.get_correlations - ~ImputedData.get_means - ~ImputedData.iteration_count - ~ImputedData.plot_correlations - ~ImputedData.plot_imputed_distributions - ~ImputedData.plot_mean_convergence - - - - - - \ No newline at end of file diff --git a/docs/ik/miceforest.ImputationKernel.rst b/docs/ik/miceforest.ImputationKernel.rst deleted file mode 100644 index 44e0ea2..0000000 --- a/docs/ik/miceforest.ImputationKernel.rst +++ /dev/null @@ -1,45 +0,0 @@ -miceforest.ImputationKernel -=========================== - -.. currentmodule:: miceforest - -.. autoclass:: ImputationKernel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ImputationKernel.__init__ - ~ImputationKernel.append - ~ImputationKernel.compile_candidate_preds - ~ImputationKernel.complete_data - ~ImputationKernel.dataset_count - ~ImputationKernel.delete_candidate_preds - ~ImputationKernel.fit - ~ImputationKernel.get_correlations - ~ImputationKernel.get_feature_importance - ~ImputationKernel.get_means - ~ImputationKernel.get_model - ~ImputationKernel.get_raw_prediction - ~ImputationKernel.impute_new_data - ~ImputationKernel.iteration_count - ~ImputationKernel.mice - ~ImputationKernel.plot_correlations - ~ImputationKernel.plot_feature_importance - ~ImputationKernel.plot_imputed_distributions - ~ImputationKernel.plot_mean_convergence - ~ImputationKernel.save_kernel - ~ImputationKernel.start_logging - ~ImputationKernel.stop_logging - ~ImputationKernel.transform - ~ImputationKernel.tune_parameters - - - - - - \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index 604fefb..5d33055 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,40 +1,17 @@ .. miceforest documentation master file, created by - sphinx-quickstart on Tue Dec 28 11:24:49 2021. + sphinx-quickstart on Sat Jul 27 20:34:30 2024. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. image:: ./logo/icon_small.png - :align: right - :width: 250 - :alt: miceforest logo. +miceforest documentation +======================== -Welcome to miceforest's documentation! -====================================== +Add your content using ``reStructuredText`` syntax. See the +`reStructuredText `_ +documentation for details. -``miceforest`` imputes missing data using LightGBM in an iterative method known as Multiple Imputation by Chained Equations (MICE). It was designed to be: - -* **Fast** - * Uses lightgbm as a backend - * Has efficient mean matching solutions. - * Can utilize GPU training -* **Flexible** - * Can impute pandas dataframes and numpy arrays - * Handles categorical data automatically - * Fits into a sklearn pipeline - * User can customize every aspect of the imputation process -* **Production Ready** - * Can impute new, unseen datasets very quickly - * Kernels are efficiently compressed during saving and loading - * Data can be imputed in place to save memory - * Can build models on non-missing data - -There are very extensive `beginner `_ and `advanced `_ tutorials on the github readme. Below is a table of contents for the topics covered: .. toctree:: - :maxdepth: 1 + :maxdepth: 2 :caption: Contents: - ImputationKernel - ImputedData - MeanMatchScheme - utils diff --git a/docs/logo/icon_small.png b/docs/logo/icon_small.png deleted file mode 100644 index a4bca08..0000000 Binary files a/docs/logo/icon_small.png and /dev/null differ diff --git a/docs/mms/miceforest.MeanMatchScheme.rst b/docs/mms/miceforest.MeanMatchScheme.rst deleted file mode 100644 index 0286d7a..0000000 --- a/docs/mms/miceforest.MeanMatchScheme.rst +++ /dev/null @@ -1,29 +0,0 @@ -miceforest.MeanMatchScheme -========================== - -.. automodule:: miceforest.MeanMatchScheme - - - - - - - - - - - - .. rubric:: Classes - - .. autosummary:: - - MeanMatchScheme - - - - - - - - - diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index 606fa79..0000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,55 +0,0 @@ -alabaster==0.7.12 -atomicwrites==1.4.0 -attrs==21.2.0 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--git a/docs/utils.rst b/docs/utils.rst deleted file mode 100644 index 0ab29d8..0000000 --- a/docs/utils.rst +++ /dev/null @@ -1,13 +0,0 @@ -utils -===== - -.. currentmodule:: miceforest - -Utility Functions ------------------ - -.. autosummary:: - :toctree: utils/ - - ampute_data - load_kernel \ No newline at end of file diff --git a/docs/utils/miceforest.ampute_data.rst b/docs/utils/miceforest.ampute_data.rst deleted file mode 100644 index 99ec0c8..0000000 --- a/docs/utils/miceforest.ampute_data.rst +++ /dev/null @@ -1,6 +0,0 @@ -miceforest.ampute\_data -======================= - -.. currentmodule:: miceforest - -.. autofunction:: ampute_data \ No newline at end of file diff --git a/docs/utils/miceforest.load_kernel.rst b/docs/utils/miceforest.load_kernel.rst deleted file mode 100644 index b2c4a8a..0000000 --- a/docs/utils/miceforest.load_kernel.rst +++ /dev/null @@ -1,6 +0,0 @@ -miceforest.load\_kernel -======================= - -.. currentmodule:: miceforest - -.. autofunction:: load_kernel \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index f5f10f0..ad25435 100644 --- a/poetry.lock +++ b/poetry.lock @@ -29,6 +29,17 @@ typing_extensions = ">=4.0" dev = ["attribution (==1.7.0)", "black (==24.2.0)", "coverage[toml] (==7.4.1)", "flake8 (==7.0.0)", "flake8-bugbear (==24.2.6)", "flit (==3.9.0)", "mypy (==1.8.0)", "ufmt (==2.3.0)", "usort (==1.0.8.post1)"] docs = ["sphinx (==7.2.6)", "sphinx-mdinclude (==0.5.3)"] +[[package]] +name = "alabaster" +version = "0.7.16" +description = "A light, configurable Sphinx theme" +optional = false +python-versions = ">=3.9" +files = [ + {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, + {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, +] + [[package]] name = "anyio" version = "4.4.0" @@ -932,6 +943,17 @@ files = [ {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"}, ] +[[package]] +name = "imagesize" +version = "1.4.1" +description = "Getting image size from png/jpeg/jpeg2000/gif file" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"}, + {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"}, +] + [[package]] name = "importlib-metadata" version = "8.2.0" @@ -3416,6 +3438,17 @@ files = [ {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"}, ] +[[package]] +name = "snowballstemmer" +version = "2.2.0" +description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms." +optional = false +python-versions = "*" +files = [ + {file = 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index 4f30651..afe4ef0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [project] name = "miceforest" license = {file = "LICENSE"} -version = "6.0.0" +version = "6.0.1" description = "Multiple Imputation by Chained Equations with LightGBM" authors = [{name="Sam Von Wilson"}] readme = "README.md" @@ -40,7 +40,7 @@ packages = ['miceforest'] [tool.poetry] name = "miceforest" -version = "6.0.0" +version = "0.9000" description = "Multiple Imputation by Chained Equations with LightGBM" authors = ["Sam Von Wilson"] package-mode = true @@ -70,6 +70,7 @@ mypy = "^1.11.0" build = "^1.2.1" pytest-cov = "^5.0.0" twine = "^5.1.1" +sphinx = "^7.4.7" [tool.mypy] ignore_missing_imports = true