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Jan 12, 2021
* improve to check for transfomer coverage * improve coverage test * paramterize coverage test * find pipeline classes on the basis of _BaseComposition * define UNSUPPORTED_SKLEARN_PACKAGES; skip cov. tests * add KNNImputerDF * add simple test for imputers * improved imputer support + add a test case * correctly support NaN fields in IterativeImputer * remove old "not for client use" comments * make sklearndf tests run again with scikit-learn 0.21 * implement LGBMClassifierDF alongside LGBMRegressorDF * update introductory documentation for sklearndf module * validate that all BaseEstimatorDF implementations subclass BaseEstimator * make definition of Module type more specific * Replace references to _BaseEstimatorWrapperDF with BaseEstimatorDF * Blend properties root_estimator & delegate_estimator to native_estimator * Improve type variable definition for T_DelegateLearner * invoke super().__init__() in base estimator wrapper * tweak BaseEstimatorDF API and update the docstrings * update type hinting in df_estimator * remove "Base" prefix from the names of most abstract sklearndf classes * update introductory documentation of module sklearndf * update docstrings and type hints for LearnerDF * Update wording in class docstrings of sklearndf base classes * unify terminology for inputs, outputs, and observations * update docstrings for TransformerDF * document return value for LearnerDF.predict * update docstrings for RegressorDF * update API and docstrings for ClassifierDF * update docstrings in _wrapper.py * update docstring for LearnerDF.score() * set version to 1.3.0rc1 * make sklearndf imputers work again for scikit-learn v0.21 * rename BaseEstimatorDF.root_estimator to native_estimator * use TypeVar to annotate missing _BaseImputer (avoids exception) * fix reference to scikit-learn version in a comment * move PyCharm settings to separate settings repository * rename gamma.sklearndf to sklearndf: all tests pass * no longer export T_Self in package common.fit * rename string/comment references to gamma.… to new facet counterparts * update setup.py and set version to 1.0 * move LGBMClassifier to sklearndf.classification.extra … from sklearndf.regression.extra * set to 1.0.0 * remove punch * un-ignore local PyCharm settings in git project repo * add PyCharm module definitions * flatten structure of 'pytools' module, eliminating 'common' sub-package * remove references to custom test data * add first version of Makefile & recipe for sklearndf * small bugfix in Makefile variable * mark /dist as excluded to prevent scanning * CONDA: update conda build path to replace spaces * added __all__ * added __all__ * added __all__ * added __all__ * added __all__ * added __all__ * added __all__ * added __all__ * start sphinx doc * start sphinx doc * start sphinx doc * start sphinx doc * Set up CI with Azure Pipelines [skip ci] * CI/CD: adds local pip installation to account for pytools dependency * CI/CD: adds pytest.ini and setup.cfg for coverage reports * CI/CD: update meta.yaml to take local path * CI/CD: udpates azure-pipelines.yml to build conda package * CI/CD: add coverage reports to azure-pipelines.yml * CI/CD: fix indent error * CI/CD: builds conda package dependency instead of pip install * CI/CD: clean up azure pipeline * DOCS: remove --implicit-namespace flag from Makefile * DOCS: add BCG copyright * CI/CD: divide azure-pipelines.yml into two dependent stages * CI/CD: update conda-build dependency * CI/CD: update minimum FACET_V_PYTHON_BUILD to v3.6 * CI/CD: build package only for sklearndf * CI/CD: update sklearn versions for sklearndf package build * CI/CD: update sklearn versions for sklearndf package build * CI/CD: update sklearn versions for sklearndf package build * CI/CD: update meta.yaml for new pytools version * CI/CD: update meta.yaml for new pytools version * CI/CD: update azure-pipelines.yml * CI/CD: update PYTHONPATHS in azure-pipelines.yml * CI/CD: update PYTHONPATHS in azure-pipelines.yml * CI/CD: checkout pytools * CI/CD: update test matrix * CI/CD: add less strict sklearn minimum dependency * CI/CD: lower max dependencies * CI/CD: lower max dependencies * using rst file instead * updates to doc layout * updates to doc layout * updates to doc layout * updates to doc layout * new readme using rst * place for images * API layout * contributions layout * tutorial layout * faq layout * getting started layout * script for notebook transforms * updating API layout * adding tutorial to examples layout * revised sklearn tutorial * BUILD: change to readme.rst in setup.py * removed m2r * removed text * removing m2r from extensions list * DOCS: update heading to sklearndf only * DOCS: add extensive contribution guide * DOCS: update matrix strategy in contribution_guide.rst * ENV: adds environment.yml for sklearndf * DOCS: update contribution_guide.rst * ENV: add dev-setup.sh for pre-commit hooks * DOCS: update env name in contribution_guide.rst * DOCS: remove redundant sphinx setup instructions * ENV: activate env in shell script * minor corrections and revisions * ENV: updates shebang line to use /sh instead of /bash * inherit learner pipeline docstrings from superclasses * document return value for method LearnerDF.fit_predict() * CI/CD: update repositories to checkout * use more meaningful names for the target variables used for unit tests (#16) * add convenience property `classes` to ClassifierDF (#17) * fix a typo in azure-pipelines.yml (#18) * Prevent sample weights from being passed to the preprocessing step of a learner pipeline (#19) * pass sample weights only to the final estimator of a 2-step pipeline * add docstring to ˋ_BaseEstimatorPipelineDF.fit()ˋ * clarify a docstring for new sample_weight behaviour Co-authored-by: Jason Bentley <Bentley.Jason@bcg.com> * update PyCharm settings (#20) * update python interpreter setting * ignore pytest cache folder * SPHINX: deactivate option show-inheritance; we generate this ourselves * SPHINX: no longer include native sklearn documentation in sklearndf docs … add references to sklearn docs instead * SPHINX: remove redundant __all__ statements from __init__.py files * DOC: tweak sklearndf class hierarchy to generate clean documentation * SPHINX: stop auto=generating API doc in the sphinx Makefiles * SPHINX: mark sphinx/build as excluded in PyCharm * SPHINX: use event callbacks from new pytools.sphinx package * DOC: apply corrections to docstrings * WRAPPER: fix typo in local variable name * fix return statement format in docstring * clarify scikit-learn error messages (#23) * catch and enhance sklearn exceptions to help locate errors in pipelines * clarify exception message for invalid ColumnTransformerDF parameters * rename classes whose names start with BaseEstimator… to Estimator… (#24) * rename classes whose names start with BaseEstimator… to Estimator… * adapt some comments to renamed class Co-authored-by: Jörg Schneider <schneider.joerg@bcg.com> * Docs/use py script for docs (#25) * used in worked example * used in worked example * used in worked example * used in worked example * so logo shows in readme * added cleanout of jupyter output to pre-commit * added getting started notebook * script for doc build * added metadata to cells for removal during transform * added metadata to cells for removal during transform * replaced by make.py * replaced my make.py * decided to retain NB output as it is minimal * also pass getting started NB to notebooks folder * updated with output * change reference to make.py * load Ames housing dataset from OpenML, rather than using a local copy Co-authored-by: Jan Ittner <ittner.jan@bcg.com> * append '_' to names of properties available only after fitting (#26) * Create LICENSE * Bugfix: rename _EstimatorPipelineDF.features_out to features_out_ (#28) * rename _EstimatorPipelineDF.features_out to features_out_ * make _EstimatorPipelineDF.fit kwargs non-positional * Bugfix: prevent duplicate occurrences of parameters in API documentation generated by sphinx (#27) * deactivate autodoc typehints option always_document_param_types * exclude notebooks folder from git: content is generated during build (#31) * reduce scope of tests in azure pipeline for develop branch (#32) * reduce scope of tests in azure pipeline for develop branch * update environment.yml * update package versions in conda build recipe * Share code for Sphinx make.py and conf.py across all repos (#30) This commit: * adds custom css and js for custom HTML styling and external link handling * replaces make.py with forwarder to pytools/sphinx/make.py (see shared config_base in pytools) and removes duplicate transform_notebook.py * updates package dependencies and ensures conda develop environment is created * This commit corrects a typo in a line of code in the tutorial notebook (#33) * bugfix: set sphinx parameters passed to set_config() (#35) * add custom `css` and `js` for custom HTML styling and external link handling * move `gamma.js` to `_static/js` * open all links in a new frame that are not known to be internal * replace make.py with forwarder to `pytools/sphinx/make.py` * remove the now duplicate `transform_notebook.py` from the sphinx scripts * move bulk of sphinx config to shared `config_base` in pytools * refactor `make.py` proxy script * add custom `css` and `js` files from within conf_base script * update package dependencies; ensure conda develop environment is created * replace `path.dirname(__file__)` with `path.dirname(path.realpath(__file__))` * bugfix: set sphinx parameters passed to `set_config()` * update conditional build logic depending on target branch and scheduling (#34) * replace wildcard imports with explicit import statements; upgrade black to v20.8b1 (#36) * replace wildcard imports with explicit import statements * upgrade black to v20.8b1 * Add code checks to the CI pipeline: isort, black, flake (#37) * add isort to pre-commit config * set CI checks (black, isort, flake8) * remove PEP8 errors, W293, E302, W291, F811, E121, W291, E126, E503, E122, E501 * clarify names of pipeline steps and jobs * add test folder to known local folders Co-authored-by: Jan Ittner <ittner.jan@bcg.com> * Update CI pipeline configuration (avoid black/flake8 conflicts; report failed unit test) (#38) * update errors ignored by flake8 to avoid conflicts with black * force pipeline to stop when a unit test fails * Remove forward slash at end of sklearndf git_url so build works on windows (#39) * Strengthen pre-commit checks (#40) * add flake8 config in pre-commit * add large file detector in pre-commit * add yaml files checker in pre-commit * update sklearndf sphinx build for new build process (#41) * update develop environment to ensure error-free documentation build * move conda_base and make to new directory sphinx/base * update sklearndf documentation for new build process * fix indentation of admonition in auto-generated rst docstring for scikit-learn estimators * align PyCharm folder exclusions with .gitignore * re-enable tutorial build * update nbsphinx to v0.7 for compatibility with nbconvert 6 * commit cell output from the jupyter notebook tutorial used in documentation * Update flake8 pre-commit to use local configs (#43) * fix a comment in function test_regression_pipeline_df (#47) * add initial gitbadges faq and correct typos (#45) This commit * adds initial gitbadge placeholders to the readme file and those needing to be updated upon release have been left blank to ensure they are noticeable for correction * adds initial material to the FAQ section of the documentation * Rename attributes 'feature_…_' to 'feature_names_…_' (#46) This commit * renames iris_target to iris_target_name * renames attributes 'feature_…_' to 'feature_names_…_' * adjusts property names of fittable classes to scikit-learn conventions * minor updates to tutorials and readme for api changes (#48) * replace deprecated imports from pandas.util.testing with pandas.testing (#50) * Add FACET team email in the sklearndf FAQ (#49) * Update PyCharm configuration, incl. newly introduced PyCharm features (#52) * Move to Python make script and link version strings (#51) * build: setup.py reference package's __version__ * build: move meta.yaml to condabuild/; reference setup.py version * build: add make.py for sklearndf package calling pytools' make script * build: remove bsd/gnu Makefile, use make.py in azure-pipelines.yml * build: add x flag to make.py * build: bugfix reference in setup.py * build: move package version to _version.py; to avoid ext. dependencies * build: name gamma_sklearndf_version __version__; load w/o ext. deps. * build: join path to version module platform independently * Fix the typo in "preprocessing" in the ReadMe (#53) * Apply ReadMe extensions from facet repo (#55) * simplify the logo banners on documentation landing pages (#56) * Feature/build/rework sklearndf build (#54) * change distribution/package name to sklearndf (#57) * update channel for conda install (#58) * minor readme updates to align formatting with facet readme (#59) * remove breaks in bullet list for proper rendering (#60) * build: set same pipeline triggers as used for pytools (#61) * update pypi and conda package build metadata (#62) * make sklearndf italic and remove index from doc build (#63) * make sklearndf italic * remove genindex * no longer include index * Bugfix/remove sgd regressor warning (#64) * bugfix add missing requirement packaging (#66) * add package badges to readme (#68) * add trove classifiers to pypi metadata (#65) * Add automatic docs deployment to GitHub Pages (#67) * add azure badge links and update conda install instructions (#69) * update notebook links for tutorials page in docs (#70) * remove local path setting from tutorial notebooks (#74) * implement flexible get started (#75) * add nb download icon (#76) * replace raw html (#78) * revise doc build documentation (#77) * GitHub release pipeline (#73) * CI/CD: Adapt release pipeline from pytools * CI/CD: Add atrifact storage to publish in release * CI/CD: Fix path for conda/tox builds * CI/CD: Use fork as target for testing release * CI/CD: Use existing target in test repo for release test (instead of triggering repo) * CI/CD: Fix path of artifacts to upload with release * CI/CD: Remove test settings * CI/CD: Reset single build to test 'max' dependencies * CI/CD: Fix format in config file * CI/CD: Use OAuth service connection to GitHub as required by Azure Pipelines * CI/CD: Let release pipeline fail when line command fails * CI/CD: Use bcg_gamma channel for conda upgrade instructions in release notes * reformat api preamble (#79) * add API landing rst to documentation guide (#80) * updates to development guidelines (#81) * fix docstrings (#82) * remove trailing backslashes in docstrings: not needed in canonical ReST * fix spelling * remove trailing backslashes in docstrings: not needed in canonical ReST (#83) * remove trailing backslashes in docstrings: not needed in canonical ReST * fix spelling * minor code tweaks to eliminate IDE warnings (#84) * Doc/tabs to spaces (#85) * Update issue templates (#86) * doc cleanup (#88) * rename type variables for methods' "self" arguments to T_Self (#89) * add 'return' after referencing an estimator method from a DF class (#90) * fix sklearn links (#91) * Bugfix/pipeline fixes (#94) * restore unconstr build (#95) * Documentation improvements (#92) * add missing documentation for sklearndf class attributes * return two redundant sub-methods that mess up the sphinx documentation * introduce @inheritdoc for class OutlierRemoverDF * improve code and docs of class OutlierRemoverDF (no functional changes) * Improve docstrings for COL_FEATURE_IN and COL_FEATURE_OUT * introduce AllTracker across all of sklearndf * remove badges * assign wrapper's module when wrapping a native sklearn estimator * assign wrapper's module when wrapping a native sklearn estimator (bugfix) * assign wrapper's module when wrapping native sklearn estimator (bugfix) * make detection of sklearn class tag lines more robust * fix incomplete cross-references * update doc_url * updates for pypi and conda package pages * updates for pypi and conda package pages * point docs to index * bump initial release version * update docstring Co-authored-by: Jason Bentley <Bentley.Jason@bcg.com> * Bugfix/python3.9 compatibility (#96) * add missing documentation for sklearndf class attributes * return two redundant sub-methods that mess up the sphinx documentation * introduce @inheritdoc for class OutlierRemoverDF * improve code and docs of class OutlierRemoverDF (no functional changes) * Improve docstrings for COL_FEATURE_IN and COL_FEATURE_OUT * introduce AllTracker across all of sklearndf * remove badges * assign wrapper's module when wrapping a native sklearn estimator * assign wrapper's module when wrapping a native sklearn estimator (bugfix) * assign wrapper's module when wrapping native sklearn estimator (bugfix) * make detection of sklearn class tag lines more robust * fix incomplete cross-references * do not pass arguments on to object.__new__() Co-authored-by: Jason Bentley <Bentley.Jason@bcg.com> * import from numpy.testing instead of sklearn.utils.testing (#98) * sklearn 0.24 currently not supported (#99) * disallow scipy >=1.6, allow pandas 1.2.*, prefer joblib 1.0.* (#100) * disallow scipy >=1.6, allow pandas 1.2.*, prefer joblib 1.0.* * set pandas to 1.1.0 in 'max' matrix test for compatibility with pytools * CI/CD: roll back joblib test dependency to 0.16 Co-authored-by: Konstantin Hemker <hemker.konstantin@bcg.com> Co-authored-by: Jörg Schneider <schneider.joerg@bcg.com> Co-authored-by: Jan Ittner <ittner.jan@bcg.com> Co-authored-by: Jörg Schneider <46053259+joerg-schneider@users.noreply.github.com> Co-authored-by: Konstantin Hemker <hemker.konstantin@bcg.com> Co-authored-by: Jason Bentley <Bentley.Jason@bcg.com> Co-authored-by: Jan Ittner <github.com@ittner.de> Co-authored-by: Kennedy Ricardo <Kennedy.Ricardo@bcg.com> Co-authored-by: Jason <jasonpben@gmail.com> Co-authored-by: mgelsm <malo.grisard@pm.me> Co-authored-by: mgelsm <grisard.malo@bcg.com> Co-authored-by: sithankanna <sithankanna@gmail.com>
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The PR removes nb download link from README as it cause a bug in the pipeline for FACET. Also replace html coded download of notebook with rst.