Release/0.11.0 #141
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Release/0.11.0 #141
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Merge of Master into dev after v0.10.0
Co-authored-by: philip_pilgerstorfer <philip.pilgerstorfer!@quantumblack.com>
Co-authored-by: philip_pilgerstorfer <philip.pilgerstorfer!@quantumblack.com>
* Fix linting issues * Remove str from @pytest.mark.parametrize in TestDAGClassifier due to conflict when checking fro non-numeric columns
* Fix broken URLs for release notes and user guide * Add name into contributors list * Add a release note for documentation fix
* Check index type using is_integer() * Update RELEASE.md
* trying to reporduce the hanging error * first iteration to handle splitted graph by do-intervention. tests needed * reverted to develop as only commented * added functions docstrings and typing * first attempt at tests * fixing tests * flake * Speed up _create_node_functions by taking the first element using next() * Use next(iter(x)) to get the first element * first iterations to address PR comments and discussion: adds default marginals and returns upstream marginal from default ones rather than nans * removing nan import * setting default marginal with query() * lint changes * removed jupyter notebook file from git * lint changes * latest modifications * added my info and fix updates * fisrt attempt pr comment to avoid duplicate call to obtain parents of node * PR comment: avoide duplicate call to get node parents * fixing lint * Refactor _remove_disconnected_nodes() and tidy up codes and docstrings * Add edge one by one (instead of constructing edge list) to make graph construction faster * Linting * last PR comments * Shift add_node() inside the loop for _remove_disconnected_node Co-authored-by: oentaryorj <oentaryorj@gmail.com>
* NoTears as ScoreSolver * refactor continuous solver * adding attribute to access weight matrix * refactoring continuous solver * Adding fit_lasso method * add data_gen_continuous.py and tests (#38) * add data_gen.py * rename * wrap SM * move data_gen_continous, create test * more coverage * test fixes * move discrete sem to another file * node list dupe check test * ValueError tests * replace dag and sem functions with Ben's verions * add Ben's tests * fix fstring * to_numpy_array coverage * Ben's comments * remove unreachable ValueError for coverage * remove unused fixture * remove redundant test * remove extensions Co-Authored-By: Ben Horsburgh <Ben.Horsburgh@quantumblack.com> * docstring Co-Authored-By: Ben Horsburgh <Ben.Horsburgh@quantumblack.com> * docstring Co-Authored-By: Ben Horsburgh <Ben.Horsburgh@quantumblack.com> * docs Co-Authored-By: Ben Horsburgh <Ben.Horsburgh@quantumblack.com> * doc Co-Authored-By: Ben Horsburgh <Ben.Horsburgh@quantumblack.com> * rename file, g_dag rename to sm * add new tests for equal weights * docstring * steve docstring, leq fix * steve comments + docstrings Co-authored-by: Ben Horsburgh <Ben.Horsburgh@quantumblack.com> * Adding check input and removing some inner functions * Removing attribute original_ndarray * Aligning from pandas with new implementation * Adding tests for fit_lasso * More tests for lasso * wrapping tabu params in a dict * Aligning tests with new tabu params * Aligning from_pandas with new tabu_params * Adding fit_intercept option to _fit method * Adding scaling option * fixing lasso tests * Adding a test for fit_intercept * scaling option only with mean * Correction in lasso bounds * Fix typos * Remove duplicated bounds function * adding comments * add torch files from xunzheng * add from_numpy_torch function that works like from_numpy_lasso * lint * add requirements * add debug functionality * add visual debug test * add license * allow running as main for viz, comments * move to contrib * make multi layer work a bit better * add comment for multi layer * use polynomial dag constraint for better speed comparison * revert unnecessary changes to keep PR lean * revert unnecessary changes to keep PR lean * revert unnecessary changes to keep PR lean * fixes * refactor * Integrated tests * Checkpoint * Refactoring * Finished initial refactoring * All tests passed * Cleaning * Git add testing * Get adjacency matrix * Done cleaning * Revert change to original notears * Revert change to original structuremodel * Revert change to pylintrc * Undo deletion * Apply suggestions from Zain Co-authored-by: Zain Patel <zain.patel@quantumblack.com> * Addressed Zain comments * Migrated from_numpy * Delete contrib test * Migrated w_threshold * Some linting * Change to None * Undo deletion * List comprehension * Refactoring scipy and remove scipy optimiser * Refactoring * Refactoring * Refactoring complete * change from np to torch tensor * More refactoring * Remove hnew equal to None * Refactor again and remove commented line * Minor change * change to params * Addressing Philip's comment * Add property * Add fc2 property weights * Change to weights * Docstring * Linting * Linting completed * Add gpu code * Add gpu to from_numpy and from_pandas * cuda 0 run out of memory * Debugging * put 5 * debugging gpu * shift to inner loop * debugging not in place * Use cada instead of to * Support both interfaces * Benchmarking gpu * Minor fix * correct import path for test * change gpu from 5 to 1 * Debugging * Debugging * Experimenting * Linting * Remove hidden layer and gpu * Linting * Testing and linting * Correct pytorch to torch * Add init zeros * Change weight threshold to 0.25 * Revert requirements.txt * Update release.md * Address coments * Corrected release.md * fc1 to adjacency * Fix linting issues * Add Cython into test_requirements.txt * Update cython version in test_requirements.txt * Pytorch NOTEARS extension - GPU (#64) * Add gpu * Fix CUDA checking * Shift use_gpu argument into constructor and update test_pytorch_notears.py * Send DAG layer to device and fix linting issues * Tidy up * Fix linting Co-authored-by: oentaryorj <oentaryorj@gmail.com> * Remove pytorch from extras_require in setup.py as this is already included in requirements.txt * Update +mdlp-discretization version in test_requirements.txt * Add logging.info to indicate pytorch backend * Linting * User {} in place of dict() to meet the linting requirements * Use {} in place of dict() to meet the linting requirements Co-authored-by: Ben Horsburgh <Ben.Horsburgh@quantumblack.com> Co-authored-by: LiseDiagneQB <60981366+LiseDiagneQB@users.noreply.github.com> Co-authored-by: Casey Juanxi Li <50737712+caseyliqb@users.noreply.github.com> Co-authored-by: qbphilip <philip.pilgerstorfer@quantumblack.com> Co-authored-by: Steve Ler <Steve.Ler@quantumblack.com> Co-authored-by: stevelersl <55385183+SteveLerQB@users.noreply.github.com> Co-authored-by: Zain Patel <zain.patel@quantumblack.com>
* Speed up query by caching baseline marginals * Update type hint in inference.py * Refactor query() and _single_query(); handle invalid observations type * Fix type hint for observations argument in query() and _single_query()
* Add Expectation Maximisation (EM) algorithm implementation * Massively scale up E-step by converting multiindexed pandas dataframe into dict of dict * Add a tutorial on latent variable model based on EM algorithm * Add test cases for the EM algorithm and ensure 100% test coverage * Update sklearn tutorials * Add note on EM algorithm into RELEASE.md * Reorganise .dot and .jpg files under docs/source/03_tutorial/supporting_files folder * Fix link in plotting tutorial * Exclude docs/source/03_tutorial from end-of-file check * Update doc_requirements.txt * Add DOT to JPG conversion steps into build-docs.sh
* Developed add_cpd function for bn * Change docstring * Add more tests * Fix python 3.5 * Change into pandas dataframe * Modify test * Update causalnex/network/network.py Co-Authored-By: Zain Patel <52913697+ZainPatelQB@users.noreply.github.com> * Remove list * Update version to 0.11.0 * Tweat RELEASE.md * Exclude docs/source/03_tutorial from large files checking in .pre-commit-config.yaml * Merge latest codes from develop branch and resolve conflicts * Revert test_network_model.py * Revert 04_sklearn_tutorial.ipynb Co-authored-by: Zain Patel <52913697+ZainPatelQB@users.noreply.github.com> Co-authored-by: oentaryorj <oentaryorj@gmail.com>
…atting (#179) * Convert .format() to f-string * Remove redundant str() and create a variable for ', '.join()
…\end{align} into EM formula (#178)
* fix: doc_requirements.txt to reduce vulnerabilities The following vulnerabilities are fixed by pinning transitive dependencies: - https://snyk.io/vuln/SNYK-PYTHON-SPHINX-570772 - https://snyk.io/vuln/SNYK-PYTHON-SPHINX-570773 * Update sphinx requirements.txt * Adjust conf.py and breadcrumbs.html accordingly * Remove setting _dummy * Restore _dummy Co-authored-by: snyk-bot <snyk-bot@snyk.io> Co-authored-by: oentaryorj <oentaryorj@gmail.com> Co-authored-by: Richard Oentaryo <oentaryorj@users.noreply.github.com>
* Add example for structure model exporting in first causalnex tutorial * Add a release note for the exporting example
Co-authored-by: Richard Oentaryo <oentaryorj@users.noreply.github.com>
* Fix broken tutorial link in README.md * Replace latex math mode $$ with $ in latent variable tutorial * Revert README.md
…al (#184) * Fix broken tutorial link in README.md * Remove tables for images, as this may cause incorrect image referencing in the final readthedocs
Thank you for the contribution!
* Proofread latent variable tutorial end to end
* Add CITATION.cff into repository * Add missing contributors to RELEASE.md * Fix linting issues * Update name list in CITATION.cff * Add citation instruction into README.md
…ial (#187) * Consolidate all utility functions in tutorial_utils.py * Add location identification strategy into latent variable tutorial * Tweak markdown in latent variabl tutorial * Fix linting issues * Remove student-por.csv * Rename n_splits to n_cv_folds for clarity * Add copyright notice into tutorial_utils.py * Add consultation with domain experts to description of location identification strategy * Add type hints to _compute_auc_stub and _compute_auc_lv_stub * Fix get_markov_blanket in predict_using_all_nodes and add docstring to private helper functions * Simplify ValueError message in network.py * Fix get_markov_blanket() * Simplify get_markov_blanket() * Fix return typehint * Rename n_cv_folds to n_splits * Add release note for get_markov_blanket() * Revert release notes * Add a note on LV tutorial in RELEASE.md * Update RELEASE.md
* Tidy up docstrings * Fix linting * Empty commit * Update causalnex/network/network.py * Update causalnex/network/network.py Co-authored-by: Zain Patel <zain.patel@quantumblack.com>
* Consolidate all utility functions in tutorial_utils.py * Add location identification strategy into latent variable tutorial * Tweak markdown in latent variabl tutorial * Fix linting issues * Remove student-por.csv * Rename n_splits to n_cv_folds for clarity * Add copyright notice into tutorial_utils.py * Add consultation with domain experts to description of location identification strategy * Add type hints to _compute_auc_stub and _compute_auc_lv_stub * Fix get_markov_blanket in predict_using_all_nodes and add docstring to private helper functions * Simplify ValueError message in network.py * Fix get_markov_blanket() * Simplify get_markov_blanket() * Fix return typehint * Rename n_cv_folds to n_splits * Add a note on LV tutorial in RELEASE.md * Move baseline marginal initialisation into do_intervention * Restore LV tutorial from develop branch
* Update .pre-commit-config.yaml * Update config.yml * Update PULL_REQUEST_TEMPLATE.md * Update CONTRIBUTING.md * Update network.py * Update plots.py * Update test_categorical_variable_mapper.py * Update config.yml * Update .pre-commit-config.yaml * Move notice to the bottom of pull request template * Update RELEASE.md * Remove unnecessary f-string * Simplify ValueError message in network.py * Simplify ValueError message in network.py * Linting network.py * Update RELEASE.md Co-authored-by: Richard Oentaryo <oentaryorj@users.noreply.github.com>
#188) * Consolidate all utility functions in tutorial_utils.py * Add location identification strategy into latent variable tutorial * Tweak markdown in latent variabl tutorial * Fix linting issues * Remove student-por.csv * Rename n_splits to n_cv_folds for clarity * Add copyright notice into tutorial_utils.py * Add consultation with domain experts to description of location identification strategy * Add type hints to _compute_auc_stub and _compute_auc_lv_stub * Fix get_markov_blanket in predict_using_all_nodes and add docstring to private helper functions * Simplify ValueError message in network.py * Resolve linting issues * Add raises into docstring of get_markov_blanket * Update tutorial_utils.py to use StructureModel.get_markov_blanket instead * Generalise get_markov_blanket to weighted graph * Generalise get_markov_blanket to weighted graph * Add unit tests for StructureModel.get_markov_blanket() * Rename n_cv_folds to n_splits * Add release note for get_markov_blanket() * Delete get_markov_blanket in network_utils.py and update RELEASE.md accordingly * Remove bn_train_model fixture * Revert docstrings in structure/pytorch/dist_type * Revert docstrings of test scripts * Revert docstrings in the remaining test scripts * Update RELEASE.md * Update tuple type hint * Update tuple typehint
The following vulnerabilities are fixed by pinning transitive dependencies: - https://snyk.io/vuln/SNYK-PYTHON-SCIKITLEARN-1079100 Co-authored-by: snyk-bot <snyk-bot@snyk.io>
…solves #140) Co-authored-by: philip_pilgerstorfer <philip.pilgerstorfer!@quantumblack.com>
oentaryorj
approved these changes
Nov 10, 2021
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Motivation and Context
Why was this PR created?
Release new version.
Changelog:
StructureModel(cf. Error about separate graphs when learning BN #136)PyGraphvizinstallation guide under the installation prerequisitesInferenceEngineafter a do-intervention that splitsthe graph into two or more subgraphs, as per do_intervention never ends running despite simple query #45 and Issues with isolates in do-calculus #100
How has this been tested?
What testing strategies have you used?
Checklist
RELEASE.mdfileNotice
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