Fix: Update macOS advanced install instructions (#306) #308
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mloning
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Jul 9, 2020
* fixed link to sktime-dl * new community contributions management * fixed link * minor changes * deleted previous estimator overview file| * further comments in PR template * typo * Update PULL_REQUEST_TEMPLATE.md * Update README.rst * fixes #221 * updated openml compile error msg * introduced our own NotFittedError, update check_is_fitted, minor updates * compiled existing estimators in ESTIMATOR_OVERVIEW ... finally * udpated setup * updated README * updated link to paper * Update README.rst * Adds ROCKET (transform only) to sktime. (#204) * Adds ROCKET (transform only) to transformers. * Update proposed ROCKET implementation and add unit test. Updates: absolute imports, remove fit_transform(...), update constructor, fit(...) and transform(...), update internal implementation, add random seed argument to constructor, move _to_numpy(...) / dataframe_to_numpy(...) to utils/data_container.py, add basic test in transformers/tests/test_Rocket.py. * Added some `np.testing.assert...` checks. * Add numba to `requirements.txt`. * Add numba to dependencies. * Increase pandas min version to 0.24 for `.to_numpy()` for `dataframe_to_numpy(...)` in `utils/data_container.py'. * Terminology change: `num_examples` to `n_instances', `num_channels` to `n_columns`, `input_length` to `n_timepoints`. * Update validation import; add default value for num_kernels parameter; add example notebook. * Update estimator overview. * Updates as requested. Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * Add Mr-SEQL time series classifier (#211) * add mrseql classifier * fix windows installation, remove files,add input checking * small fix * fix method to check multiclass * add oneversusall class * add mrseql unit test * Fix unit test * edit ESTIMATOR * format code, add docstring, edit notebook example * minor clean * Implementing tsfresh transformer (#231) * finished input checks * tsfresh feature extraction (univariate and multivariate * refactored summarise and included convert_data in utils * added tests for transformer, performed validation checks * changed example * added feature selector and example notebook * Added validation checks, removed dependencies * clean up * Delete forecasting.ipynb * restored forecasting notebook * added tsfresh as soft dependency for tests * added tsfresh as soft dependency for tests * added tsfresh as soft dependency for tests * removed efficient settings * added docstrings, fixed typo * improved setting of defaults, minor udpates * updated docstrings * added code comments * Update ESTIMATOR_OVERVIEW.md Co-authored-by: Ayushmaan <ayushmaanseth@gmail.com> * enforcing unique index * Fixed the conflicted values in TimeSeriesForestClassifier. (#233) * Update documentation of TimeSeriesForestClassifier. Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * Update build/CI (#241) * updated setup.py * updated binder * added support for python=3.8 * added support for manylinux wheels * added CI on azure DevOps * added automated release script * added automatic PyPI upload from CI services * added flake8 linting * simplified requirements file * Updated forecast API (#218) * forecasting grid-search CV * temporal cross-validation * Theta forecaster * Naive forecasters * SES forecasters * sMAPE and MASE loss * reduction meta-forecasters * detrender * TransformedTargetForecaster, * AutoARIMA * deseasonaliser * fitted param extractor * PolynomialTrendForecaster * ensemble and stacking forecaster * sklearn transformer adaptor to single series setting * boxcox transformer with bounds on lambda Co-authored-by: big-o <big-o@users.noreply.github.com> * added __init__ file for mrseql test (#249) * fixed pmdarima in-sample test error * Package refactoring (#246) * folder reorganisation * unit testing for basic API for all estimators * consistent input checks * refactored high-level into benchmarking * renamed n_trees to n_estimators * refactored transformer module * enforce PEP8 linting with flake8 * fixed warnings * updated sklearn version Co-authored-by: Patrick Rockenschaub <patrick.rockenschaub.15@ucl.ac.uk> Co-authored-by: Matthew Middlehurst <pfm15hbu@uea.ac.uk> Co-authored-by: Thach Le Nguyen <lenguyenthach141@gmail.com> Co-authored-by: angus924 <55837131+angus924@users.noreply.github.com> * Improve documentation (#238) * added all-contributors specs * added new issue template for doc improvements * updated estimator overview and contributing guidelines * updated website * updated changelog * added about page * added mission statement * added new logo * added BaseTimeSeriesForest (#268) * refactored TimeSeriesForestRegressor and TimeSeriesForestClassifier Co-authored-by: mloning <markus.loning.17@ucl.ac.uk> * Added release drafter app (#269) * added release drafter workflow * fixed release-drafter * fixed release-drafter * Update release-drafter.yml * removed release-drafter app * make tsfresh relevant feature extractor tests morerobust * Add feature importance graph to modular TSF (#250) * add feature importance graph to TSF Co-authored-by: Markus Löning <markus.loning@gmail.com> * added contributors * Add license info to files (#274) * fix speed issue for MrSEQL (#275) * update license info * Update example notebooks (#273) * Release drafter (#270) * added release drafter workflow * Added resizing transformer and tutorial for use and problem it solves (#243) * added Mo-Saif for finding bug * added Amaia as contributor * Minor fixes to documentation (#279) * bumped version to 0.4.0 * fixed azure badge link * fixed azure badge link * fixed doc deployment * excluded mrseql cython-compiled cpp file * fixed travis cmd * minor changes * minor changes * added new logo * minor change * simple typo correction (#305) Co-authored-by: Hamzah Iqbal <hamzaiqb@amazon.com> * updated install docs * Added function to convert 3d numpy array to nested pandas dataframe (#304) * Added function to convert 3d numpy array to nested pandas dataframe (issue: #298) * Added unit tests for from_3d_numpy_to_nested() and nested_to_3d_numpy() functions and fixed linting errors Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * Add doctoring for AutoARIMA (#307) * Added docstring to AutoARIMA class in Arima.py Co-authored-by: dicecko <dicecko@gmail.com> Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * Fix: Update macOS advanced install instructions (#306) (#308) * Update CONTRIBUTING.rst * chore: updated installation instructions for MacOSX Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * make knn compatible with sci-kit learn below 0.23 (#310) Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * Add example notebooks for resizing transformer (#280) * Added resizing transformer and tutorial that describes error that is caused by inequal sized time series + use of transformer Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * add github workflow to assign tasks to people commenting 'take' (#312) Co-authored-by: Hamzah Iqbal <hamzaiqb@amazon.com> * Implementation of the Temporal Dictionary Ensemble (TDE) classifier (#292) * Truncate Transformer (#315) * Added ACSF dataset. (#314) * Padding transformer (#318) Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * minor fixes: typos, broken links, updated all contributors * Example notebook for the feature_importances_ method (#319) * Create an example notebook of the feature_importances_ method * incorporate changes to the univariate example notebook * Shapedtw feature branch (#287) Co-authored-by: Vincent Nicholson (CMP) <vrq16kku@c0004.hpc.private> Co-authored-by: Vincent Nicholson (CMP) <vrq16kku@login02.hpc.private> Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * dictionary notebook speed up (#331) * minor fix to notebook * added contributors Co-authored-by: fkiraly <f.kiraly@ucl.ac.uk> Co-authored-by: angus924 <55837131+angus924@users.noreply.github.com> Co-authored-by: Thach Le Nguyen <lenguyenthach141@gmail.com> Co-authored-by: Ayushmaan <ayushmaanseth@gmail.com> Co-authored-by: Ninnart Fuengfusin <ninnart.fuengfusin@yahoo.com> Co-authored-by: big-o <big-o@users.noreply.github.com> Co-authored-by: Patrick Rockenschaub <patrick.rockenschaub.15@ucl.ac.uk> Co-authored-by: Matthew Middlehurst <pfm15hbu@uea.ac.uk> Co-authored-by: HYang1996 <44179303+HYang1996@users.noreply.github.com> Co-authored-by: Dmitriy Valetov <dmitvalet@gmail.com> Co-authored-by: hiqbal2 <10302415+hiqbal2@users.noreply.github.com> Co-authored-by: Hamzah Iqbal <hamzaiqb@amazon.com> Co-authored-by: vedazeren <63582874+vedazeren@users.noreply.github.com> Co-authored-by: btrtts <66252156+btrtts@users.noreply.github.com> Co-authored-by: dicecko <dicecko@gmail.com> Co-authored-by: sophijka <47450591+sophijka@users.noreply.github.com> Co-authored-by: Cheuk Ting Ho <cheukting.ho@gmail.com> Co-authored-by: Aaron Bostrom <a.bostrom@uea.ac.uk> Co-authored-by: BANDASAITEJAREDDY <31387911+BandaSaiTejaReddy@users.noreply.github.com> Co-authored-by: Multivin12 <36476633+Multivin12@users.noreply.github.com> Co-authored-by: Vincent Nicholson (CMP) <vrq16kku@c0004.hpc.private> Co-authored-by: Vincent Nicholson (CMP) <vrq16kku@login02.hpc.private>
mloning
added a commit
that referenced
this pull request
Aug 24, 2020
* fixed link to sktime-dl * new community contributions management * fixed link * minor changes * deleted previous estimator overview file| * further comments in PR template * typo * Update PULL_REQUEST_TEMPLATE.md * Update README.rst * fixes #221 * updated openml compile error msg * introduced our own NotFittedError, update check_is_fitted, minor updates * compiled existing estimators in ESTIMATOR_OVERVIEW ... finally * udpated setup * updated README * updated link to paper * Update README.rst * Adds ROCKET (transform only) to sktime. (#204) * Adds ROCKET (transform only) to transformers. * Update proposed ROCKET implementation and add unit test. Updates: absolute imports, remove fit_transform(...), update constructor, fit(...) and transform(...), update internal implementation, add random seed argument to constructor, move _to_numpy(...) / dataframe_to_numpy(...) to utils/data_container.py, add basic test in transformers/tests/test_Rocket.py. * Added some `np.testing.assert...` checks. * Add numba to `requirements.txt`. * Add numba to dependencies. * Increase pandas min version to 0.24 for `.to_numpy()` for `dataframe_to_numpy(...)` in `utils/data_container.py'. * Terminology change: `num_examples` to `n_instances', `num_channels` to `n_columns`, `input_length` to `n_timepoints`. * Update validation import; add default value for num_kernels parameter; add example notebook. * Update estimator overview. * Updates as requested. Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * Add Mr-SEQL time series classifier (#211) * add mrseql classifier * fix windows installation, remove files,add input checking * small fix * fix method to check multiclass * add oneversusall class * add mrseql unit test * Fix unit test * edit ESTIMATOR * format code, add docstring, edit notebook example * minor clean * Implementing tsfresh transformer (#231) * finished input checks * tsfresh feature extraction (univariate and multivariate * refactored summarise and included convert_data in utils * added tests for transformer, performed validation checks * changed example * added feature selector and example notebook * Added validation checks, removed dependencies * clean up * Delete forecasting.ipynb * restored forecasting notebook * added tsfresh as soft dependency for tests * added tsfresh as soft dependency for tests * added tsfresh as soft dependency for tests * removed efficient settings * added docstrings, fixed typo * improved setting of defaults, minor udpates * updated docstrings * added code comments * Update ESTIMATOR_OVERVIEW.md Co-authored-by: Ayushmaan <ayushmaanseth@gmail.com> * enforcing unique index * Fixed the conflicted values in TimeSeriesForestClassifier. (#233) * Update documentation of TimeSeriesForestClassifier. Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * Update build/CI (#241) * updated setup.py * updated binder * added support for python=3.8 * added support for manylinux wheels * added CI on azure DevOps * added automated release script * added automatic PyPI upload from CI services * added flake8 linting * simplified requirements file * Updated forecast API (#218) * forecasting grid-search CV * temporal cross-validation * Theta forecaster * Naive forecasters * SES forecasters * sMAPE and MASE loss * reduction meta-forecasters * detrender * TransformedTargetForecaster, * AutoARIMA * deseasonaliser * fitted param extractor * PolynomialTrendForecaster * ensemble and stacking forecaster * sklearn transformer adaptor to single series setting * boxcox transformer with bounds on lambda Co-authored-by: big-o <big-o@users.noreply.github.com> * added __init__ file for mrseql test (#249) * fixed pmdarima in-sample test error * Package refactoring (#246) * folder reorganisation * unit testing for basic API for all estimators * consistent input checks * refactored high-level into benchmarking * renamed n_trees to n_estimators * refactored transformer module * enforce PEP8 linting with flake8 * fixed warnings * updated sklearn version Co-authored-by: Patrick Rockenschaub <patrick.rockenschaub.15@ucl.ac.uk> Co-authored-by: Matthew Middlehurst <pfm15hbu@uea.ac.uk> Co-authored-by: Thach Le Nguyen <lenguyenthach141@gmail.com> Co-authored-by: angus924 <55837131+angus924@users.noreply.github.com> * Improve documentation (#238) * added all-contributors specs * added new issue template for doc improvements * updated estimator overview and contributing guidelines * updated website * updated changelog * added about page * added mission statement * added new logo * added BaseTimeSeriesForest (#268) * refactored TimeSeriesForestRegressor and TimeSeriesForestClassifier Co-authored-by: mloning <markus.loning.17@ucl.ac.uk> * Added release drafter app (#269) * added release drafter workflow * fixed release-drafter * fixed release-drafter * Update release-drafter.yml * removed release-drafter app * make tsfresh relevant feature extractor tests morerobust * Add feature importance graph to modular TSF (#250) * add feature importance graph to TSF Co-authored-by: Markus Löning <markus.loning@gmail.com> * added contributors * Add license info to files (#274) * fix speed issue for MrSEQL (#275) * update license info * Update example notebooks (#273) * Release drafter (#270) * added release drafter workflow * Added resizing transformer and tutorial for use and problem it solves (#243) * added Mo-Saif for finding bug * added Amaia as contributor * Minor fixes to documentation (#279) * bumped version to 0.4.0 * fixed azure badge link * fixed azure badge link * fixed doc deployment * excluded mrseql cython-compiled cpp file * fixed travis cmd * minor changes * minor changes * added new logo * minor change * simple typo correction (#305) Co-authored-by: Hamzah Iqbal <hamzaiqb@amazon.com> * updated install docs * Added function to convert 3d numpy array to nested pandas dataframe (#304) * Added function to convert 3d numpy array to nested pandas dataframe (issue: #298) * Added unit tests for from_3d_numpy_to_nested() and nested_to_3d_numpy() functions and fixed linting errors Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * Add doctoring for AutoARIMA (#307) * Added docstring to AutoARIMA class in Arima.py Co-authored-by: dicecko <dicecko@gmail.com> Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * Fix: Update macOS advanced install instructions (#306) (#308) * Update CONTRIBUTING.rst * chore: updated installation instructions for MacOSX Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * make knn compatible with sci-kit learn below 0.23 (#310) Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * Add example notebooks for resizing transformer (#280) * Added resizing transformer and tutorial that describes error that is caused by inequal sized time series + use of transformer Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * add github workflow to assign tasks to people commenting 'take' (#312) Co-authored-by: Hamzah Iqbal <hamzaiqb@amazon.com> * Implementation of the Temporal Dictionary Ensemble (TDE) classifier (#292) * Truncate Transformer (#315) * Added ACSF dataset. (#314) * Padding transformer (#318) Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * minor fixes: typos, broken links, updated all contributors * Example notebook for the feature_importances_ method (#319) * Create an example notebook of the feature_importances_ method * incorporate changes to the univariate example notebook * Shapedtw feature branch (#287) Co-authored-by: Vincent Nicholson (CMP) <vrq16kku@c0004.hpc.private> Co-authored-by: Vincent Nicholson (CMP) <vrq16kku@login02.hpc.private> Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * dictionary notebook speed up (#331) * minor fix to notebook * added contributors * Fixed STC Bug (#329) * added two shapelet tests to demonstrate pd/np fix. Added fix to STC to check if pd.Series and convert * fixed seeding issue in STC. Added tests for verifying correctness of STC and underlying rotf/contracted transform. * input arg checking to conform with new style * tidy up * added self.check_is_fitted() to base.py for baseclassifier linting error fix * removed shapelets from the exclusions list. Fixed various issues with the checks. Idemptoency being a particular sticking point. * fixed idemptoency issue for STC. Needed to construct pipeline in fit to avoid seeding issue. * linting error * tidy up * changed the runtime to be slightly longer when testing. so it's 10seconds, rather than 6seconds. This gives slightly less variability in contracting. Also added a 25% of the runtime of the max shapelet runtime to give some leeway on multiple runtime incase of CPU discrepancies * updated timing to be more concise * additional changes to allow config to exclude certain estimators from certain tests. * checking against wrong types in the dict * _stc tests taking too long to complete * changed shapelet transform params to ensure it finishes in a timely manner * clean ups and consistency * missed one. * missed a refactor Co-authored-by: Tony Bagnall <ajb@uea.ac.uk> * Add missing docstrings to methods (#357) * Fix instruction for checking out the dev branch from git. Old command did not work for me but the revised command does work. * (#349) Add docstring to DirectRegressionForecaster, RecursiveRegressionForecaster, DirectTimeSeriesRegressionForecaster, RecursiveTimeSeriesRegressionForecaster * (#349) Add docstring to PolynomialTrendForecaster * (#349) Add docstring to ForecastingGridSearchCV * (#349) Add docstring to FittedParamExtractor * (#349) Add docstring to Detrender * (#349) Correct docstring length (max 79 chars) * #357 Clarify FittedParamExtractor description Co-authored-by: Markus Löning <markus.loning@gmail.com> * Add docstrings to describe input variables * Correct docstring length (<79 chars Co-authored-by: Markus Löning <markus.loning@gmail.com> * Updated forecasting tutorial (#359) - Added code to demonstrate how to tune scikitl-earn regressors in sktime - And how to use the "scoring" argument of ForecastingGridSearchCV. * Add seasonal strategies to NaiveForecaster (#335) * Refactored seasonal last and implemented seasonal mean with help of sp param * Refactored seasonal last in example ipython * Added unit test for seasonal mean strategy and refactored unit test for seasonal last * Styled to pep8 conventions * Corrected unit test for seasonal mean in test_naive.py and added self.sp_ param for seasonal mean * Modified last_window when fh<sp * Styled to pep8 * Default value for sp made 1 * Implemented seasonal mean without pandas * Refactored unit test for seasonal mean * Modified documentation * Refactored unit test for seasonal mean * Refactored if condition of unit test for seasonal mean * Verified for pep8 * clean up as discussed * Modified doc string * Removed local files Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> * Add drift strategy to NaiveForecaster (#337) * Refactored seasonal last and implemented seasonal mean with help of sp param * Refactored seasonal last in example ipython * Added unit test for seasonal mean strategy and refactored unit test for seasonal last * Styled to pep8 conventions * Corrected unit test for seasonal mean in test_naive.py and added self.sp_ param for seasonal mean * Modified last_window when fh<sp * Styled to pep8 * Implemented drift strategy in naiveforecaster when data doesnot contain Nan * Added unit test for drift strategy * Default value for sp made 1 * Implemented seasonal mean without pandas * Refactored unit test for seasonal mean * Modified documentation * Refactored unit test for seasonal mean * Refactored if condition of unit test for seasonal mean * Verified for pep8 * Added drift strategy * Added unit test for drift strategy * Implemented drift strategy * Refactored drift strategy * Drift strategy implemented only when multiple values in window * Refactored params for arange method * Modified slope formula and added unit tests * Update sktime/forecasting/naive.py * Update sktime/forecasting/naive.py * Update 3 sktime/forecasting/naive.py * Update 4 sktime/forecasting/naive.py * Update 5 sktime/forecasting/naive.py * Update documentation * Added a unit test for testing window length * updated a unit test for testing window length Co-authored-by: Piyush <gade@outlook.in> Co-authored-by: Markus Löning <markus.loning.17@ucl.ac.uk> Co-authored-by: fkiraly <f.kiraly@ucl.ac.uk> Co-authored-by: angus924 <55837131+angus924@users.noreply.github.com> Co-authored-by: Thach Le Nguyen <lenguyenthach141@gmail.com> Co-authored-by: Ayushmaan <ayushmaanseth@gmail.com> Co-authored-by: Ninnart Fuengfusin <ninnart.fuengfusin@yahoo.com> Co-authored-by: big-o <big-o@users.noreply.github.com> Co-authored-by: Patrick Rockenschaub <patrick.rockenschaub.15@ucl.ac.uk> Co-authored-by: Matthew Middlehurst <pfm15hbu@uea.ac.uk> Co-authored-by: HYang1996 <44179303+HYang1996@users.noreply.github.com> Co-authored-by: Dmitriy Valetov <dmitvalet@gmail.com> Co-authored-by: hiqbal2 <10302415+hiqbal2@users.noreply.github.com> Co-authored-by: Hamzah Iqbal <hamzaiqb@amazon.com> Co-authored-by: vedazeren <63582874+vedazeren@users.noreply.github.com> Co-authored-by: btrtts <66252156+btrtts@users.noreply.github.com> Co-authored-by: dicecko <dicecko@gmail.com> Co-authored-by: sophijka <47450591+sophijka@users.noreply.github.com> Co-authored-by: Cheuk Ting Ho <cheukting.ho@gmail.com> Co-authored-by: Aaron Bostrom <a.bostrom@uea.ac.uk> Co-authored-by: BANDASAITEJAREDDY <31387911+BandaSaiTejaReddy@users.noreply.github.com> Co-authored-by: Multivin12 <36476633+Multivin12@users.noreply.github.com> Co-authored-by: Vincent Nicholson (CMP) <vrq16kku@c0004.hpc.private> Co-authored-by: Vincent Nicholson (CMP) <vrq16kku@login02.hpc.private> Co-authored-by: Aaron Bostrom <aaron.bostrom1@gmail.com> Co-authored-by: Tony Bagnall <ajb@uea.ac.uk> Co-authored-by: Alexandra Amidon <alexandra.amidon@hotmail.com> Co-authored-by: Huayi Wei <hw1103@nyu.edu> Co-authored-by: Piyush1729 <64950012+Piyush1729@users.noreply.github.com> Co-authored-by: sri1419 <65078278+sri1419@users.noreply.github.com> Co-authored-by: Piyush <gade@outlook.in>
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