diff --git a/CHANGELOG.md b/CHANGELOG.md index cd03581..1308bb5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,427 +1,24 @@ ---- -title: Changelog ---- +# Changelog -v0.1.7 (2020-11-03) -=================== +## [0.2.0](https://www.github.com/kjappelbaum/pyepal/compare/v0.1.7...v0.2.0) (2020-11-20) -Changes -------- -- Chore: updates manuscript title. \[Brian\] +### Features -v0.1.6 (2020-11-03) -=================== +* adds residual vs fitted plotting function ([#100](https://www.github.com/kjappelbaum/pyepal/issues/100)) ([e3c17fe](https://www.github.com/kjappelbaum/pyepal/commit/e3c17fefbc2db3011964a5eee5d061506c4bb776)) -Changes -------- -- Chore: removing GPy dependency. \[Kevin M. Jablonka\] +### Documentation -v0.1.5 (2020-11-03) -=================== - -Changes -------- - -- Chore: removing GPy dependency. \[Kevin M. Jablonka\] - -v0.1.4 (2020-11-03) -=================== - -Changes -------- - -- Chore: removing GPy dependency. \[Kevin M. Jablonka\] - -v0.1.3 (2020-11-03) -=================== - -Changes -------- - -- Chore: preparing pypi release. \[Kevin M. Jablonka\] - -- Chore: fixing broken links in readme after rename. \[Kevin M. - Jablonka\] - -- Chore: renaming the package. \[Kevin M. Jablonka\] - - BREAKING CHANGE - -- Chore: preparing release to pypi. \[Kevin M. Jablonka\] - -- Chore: remove pypi instructions due to clashing name. \[Kevin M. - Jablonka\] - -Other ------ - -- Merge branch \'master\' of github.com:kjappelbaum/PyPAL. \[Kevin M. - Jablonka\] - -v0.1.2 (2020-11-03) -=================== - -Changes -------- - -- Chore: preparing release to pypi. \[Kevin M. Jablonka\] -- Chore: bug in the postBuild script was a space. \[Kevin M. - Jablonka\] -- Chore: remove space in postBuild script. \[Kevin M. Jablonka\] -- Chore: for binder we need to install pypal. \[Kevin M. Jablonka\] -- Chore: updated configs for readthedocs and binder. \[Kevin M. - Jablonka\] -- Chore: making readthedocs ready. \[Kevin M. Jablonka\] - -Docs ----- - -- Docs: move doc links to readthedocs. \[Kevin M. Jablonka\] - -v0.1 (2020-10-25) -================= - -New ---- - -- Feat: Implemented first version of PALGBDT (\#75) \[Kevin Jablonka\] - - feat: started implementation of PALGBDT - - added framework for class - - added helper function to construct model tuples - - chore: implemented input validation for LGBMRegressor - - docs: example of quantile regression - - chore: API docs for PALGBDT, added validation for - interquartile_scaler - - chore: drop n_jobs support for palgbdt -- Feat: implemented kwargs for filtering based on the coefficient of - variation, closes \#58. \[Kevin M. Jablonka\] -- Feat: added new example notebook, closes \#30 (\#61) \[Kevin - Jablonka\] -- Feat: warning for too low variance, closes \#45 and \#50. \[Kevin M. - Jablonka\] -- Feat: implementing cross validation routine to address \#45 (\#49) - \[Kevin Jablonka\] -- Feat: Adding plotting subpackage (\#48) \[Kevin Jablonka\] - - feat: addressing \#23 - - feat: addressing \#23 - - fix: normalizing histogram, closes \#35 - - chore: used scaled uncertain for plot -- Feat: added uncertainty wts property (\#42) \[Kevin Jablonka\] -- Feat: Implement mulitprocessing support for GPy and sklearn (\#41) - \[Kevin Jablonka\] - - feat: first multiprocessing implementation for sklearn, \#36 - - feat: first multiprocessing implementation for GPy and added - note in docs, \#36 - - fix: more restarts for sklearn - - chore: fix random seed for tests -- Feat: Batch sampling (\#33) \[Kevin Jablonka\] - - we decided to update the mask array with the sampled points only - in the [update_train_set()]{.title-ref} function, which makes - sense to me as before that the sampling didn\'t really happen. - This is, a sample without subsequent measurement does not really - help us and we do not know if only some or all objectives have - been measured - - for this reason, we implement it via [exclude_idx]{.title-ref} - in the [sample]{.title-ref} function. -- Feat: first steps to make it nan-compatible, addressing \#24. - \[Kevin M. Jablonka\] -- Feat: first steps to make it nan-compatible, addressing \#24. - \[Kevin M. Jablonka\] -- Feat: first steps to make it nan-compatible, addressing \#24. - \[Kevin M. Jablonka\] -- Feat: use the actual sampled data and not the GPR predictions. - Adressing \#7. \[Kevin\] -- Feat: added hv indicator, closes \#16. \[Kevin\] -- Feat: added sampling utils. \[Kevin\] -- Feat: renaming package, addressing \#5. \[Kevin\] -- Feat: renaming package, addressing \#5. \[Kevin\] -- Feat: renaming package, addressing \#5. \[Kevin\] -- Feat: renaming package, addressing \#5. \[Kevin\] -- Feat: renaming package, addressing \#5. \[Kevin\] -- Feat: renaming package, addressing \#5. \[Kevin\] -- Feat: renaming package, addressing \#5. \[Kevin\] -- Feat: PALCoregionalized implemented. \[Kevin\] -- Feat: implemented turn_to_maximization. \[Kevin\] -- Feat: implemented update_train_set function. \[Kevin\] -- Feat: implemented PALSklearn. \[Kevin\] -- Feat: PALGPy class. \[Kevin\] - -Changes -------- - -- Chore: fix pre-commit. \[Kevin M. Jablonka\] -- Chore: updating doc notes about pre-commit and adding notes to - readme. \[Kevin M. Jablonka\] -- Chore: license badge. \[Kevin M. Jablonka\] -- Chore: added license, closes \#60. \[Kevin M. Jablonka\] -- Chore: added license, closes \#60. \[Kevin M. Jablonka\] -- Chore: added license, closes \#60. \[Kevin M. Jablonka\] -- Chore: devops, docs, and closing \#79. \[Kevin M. Jablonka\] -- Chore: added some notebooks to create the figures in the docs. - \[Kevin - M. Jablonka\] -- Chore: updating classifiers in setup.py, closes \#73. \[Kevin M. - Jablonka\] -- Chore: implemented coefficient of variation mask. \[Kevin M. - Jablonka\] -- Chore: spelling of PyPAL in doc landing page fixed. \[Kevin M. - Jablonka\] -- Chore: adding some test for epsilon sensitivity, closes \#54 (\#64) - \[Kevin Jablonka\] -- Chore: docs example for overconfident model, fized errorbars in the - plotting functions. \[Kevin M. Jablonka\] -- Chore: tuning the plotting functions. \[Kevin M. Jablonka\] - - specify zorder - - labels lowercase -- Chore: adding more tests to address \#59. \[Kevin M. Jablonka\] -- Chore: add logger and remove print statement. \[Kevin M. Jablonka\] -- Chore: disablying cross-validation in most tests, closes \#53 (\#55) - \[Kevin Jablonka\] -- Chore: reducing restarts, fix random seed, closes \#52. \[Kevin M. - Jablonka\] -- Chore: fixing typo in prospector settings. \[Kevin M. Jablonka\] -- Chore: test with different kernel type, \#37. \[Kevin M. Jablonka\] -- Chore: allow for None option in tests. \[Kevin M. Jablonka\] -- Chore: binh-korn test with smaller beta scale. \[Kevin M. Jablonka\] -- Chore: added more binh-korn tests to address \#37. \[Kevin M. - Jablonka\] -- Chore: added more binh-korn tests to address \#37. \[Kevin M. - Jablonka\] -- Chore: added more binh-korn tests to address \#37. \[Kevin M. - Jablonka\] -- Chore: testing binh korn. \[Kevin M. Jablonka\] -- Chore: added docs to PR template, closes \#32. \[Kevin M. Jablonka\] -- Chore: updating docs \#29. \[Kevin M. Jablonka\] -- Chore: updating docs \#29. \[Kevin M. Jablonka\] -- Chore: updating docs \#29. \[Kevin M. Jablonka\] -- Chore: updating docs \#29. \[Kevin M. Jablonka\] -- Chore: updating docs \#29. \[Kevin M. Jablonka\] -- Chore: work on lvmogp on seperate branch. \[Kevin M. Jablonka\] -- Chore: added missing data tests. \[Kevin M. Jablonka\] -- Chore: adding tests for missing data. \[Kevin M. Jablonka\] -- Chore: updating missing data information in docs. \[Kevin M. - Jablonka\] -- Chore: trigger CI. \[Kevin M. Jablonka\] -- Chore: added dependabot. \[Kevin M. Jablonka\] -- Chore: adding authors, closes \#12. \[Kevin M. Jablonka\] -- Chore: pinning dependencies, closes \#3. \[Kevin M. Jablonka\] -- Chore: fixing uncertainty typos. closes \#22. \[Kevin M. Jablonka\] -- Chore: updating docs. \[Kevin\] -- Chore: updating docs. \[Kevin\] -- Chore: updating docs. \[Kevin\] -- Chore: updating docs. \[Kevin\] -- Chore: updating docs. \[Kevin\] -- Chore: updating docs. \[Kevin\] -- Chore: updating docs. \[Kevin\] -- Chore: updatings docs, changing API of samplign utilities - in - practice it is probably better to not take y in the sampling - utilities - - writing more detailed docs on how to use the code. \[Kevin\] -- Chore: updated readme. \[Kevin\] -- Chore: added test for \_replace_by_measurements. \[Kevin\] -- Chore: home logo for docs, closes \#20. \[Kevin\] -- Chore: changed sphinx themes, closes \#19 also working on testing - \#18. \[Kevin\] -- Chore: changed sphinx themes, closes \#19 also working on testing - \#18. \[Kevin\] -- Chore: added scale invariance test, closes \#17. \[Kevin\] -- Chore: updating readme. \[Kevin\] -- Chore: added test for minimization, closing \#15. \[Kevin\] -- Chore: added example notebook. \[Kevin\] -- Chore: preparing readthedocs. \[Kevin\] -- Chore: updated train data. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: docs. \[Kevin\] -- Chore: docs. \[Kevin\] -- Chore: docs. \[Kevin\] -- Chore: docs. \[Kevin\] -- Chore: reverting the addition of CI for docs. \[Kevin\] - - Maybe it is better to build locally? - - But we should anyhow serve them on GitHub pages -- Chore: trying to add CI for docs \#9. \[Kevin\] -- Chore: added docs. \[Kevin\] -- Chore: adding test cases. \[Kevin\] -- Chore: adding test cases. \[Kevin\] -- Chore: running one step test of binh korn. \[Kevin\] -- Chore: running one step test of binh korn. \[Kevin\] -- Chore: added bihn korn test function as fixture. \[Kevin\] -- Chore: updated sampling \#6. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: making stronger test cases. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: update contribution guide. \[Kevin\] -- Chore: updated readme. \[Kevin\] -- Chore: testing beta update. \[Kevin\] -- Chore: added tests. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: added tests. \[Kevin\] -- Chore: added tests. \[Kevin\] -- Chore: added tests. \[Kevin\] -- Chore: added tests. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: disabling numba for coverage report. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: updating coveragerc. \[Kevin\] -- Chore: scaled logo. \[Kevin\] -- Chore: adding tests. \[Kevin\] -- Chore: added rc file for coverage. \[Kevin\] -- Chore: added code coverage. \[Kevin\] -- Chore: adding more test cases. \[Kevin\] -- Chore: smaller logo. \[Kevin\] -- Chore: added logo placeholder. \[Kevin\] -- Chore: updating readme. \[Kevin\] -- Chore: drop Python 3.5 support due to close EOL. \[Kevin\] -- Chore: for now, skipping prospector in the CI: \[Kevin\] - - I do not want to install the dependencies in the pre-commit - workflow - - We can run prospector after pytest in the python_package - workflow -- Chore: updating README. \[Kevin\] -- Chore: updating README. \[Kevin\] -- Chore: updating pre-commit workflow. \[Kevin\] -- Chore: updating pre-commit workflow. \[Kevin\] -- Chore: updating pre-commit workflow. \[Kevin\] -- Chore: added CI. \[Kevin\] -- Chore: updating readme to use sklearn as example for subclassing. - \[Kevin\] -- Chore: updated acknowledgment. \[Kevin\] -- Chore: updated readme and contribution guide. \[Kevin\] -- Chore: basic framework is ready. \[Kevin\] -- Chore: developing input validation functions. \[Kevin\] -- Chore: linting. \[Kevin\] -- Chore: added issue and PR templates. \[Kevin\] -- Chore: added issue and PR templates. \[Kevin\] -- Chore: initial commit. \[Kevin\] - -Docs ----- - -- Docs: adding description of tutorials. \[Kevin M. Jablonka\] -- Docs: added some links to API docs, explain which class to use. - Closes \#78 (\#80) \[Kevin Jablonka\] -- Docs: moving notes about class implementation to developer notes. - \[Kevin M. Jablonka\] -- Docs: adding screenshots of tutorials that can be linked to - mybinder. \[Kevin M. Jablonka\] -- Docs: pypal -\> PyPAL. \[Kevin M. Jablonka\] -- Docs: rebuild docs. \[Kevin M. Jablonka\] -- Docs: pypal -\> PyPAL in text. \[Kevin M. Jablonka\] -- Docs: added note about coef_var_threshold, closes \#71. \[Kevin M. - Jablonka\] -- Docs: citation placeholder added (\#70) \[Kevin Jablonka\] - - fix: warning message for mae_variance comparison - - chore: added citation placeholder -- Docs: move beta to background. \[Kevin M. Jablonka\] -- Docs: added some first dicussion about the hyperparameters. \[Kevin - M. Jablonka\] -- Docs: added some first dicussion about the hyperparameters. \[Kevin - M. Jablonka\] -- Docs: fix typo in the list of attributes/properties. \[Kevin M. - Jablonka\] -- Docs: adding some property docs (\#57) \[Kevin Jablonka\] -- Docs: fix typo in docs. \[Kevin M. Jablonka\] -- Docs: fixing some typos, addings some notes about plotting and - plotting api docs, \#29. \[Kevin M. Jablonka\] -- Docs: updating hints about the crossvalidation. \[Kevin M. - Jablonka\] -- Docs: updating hints about the crossvalidation. \[Kevin M. - Jablonka\] -- Docs: updating hints about the crossvalidation. \[Kevin M. - Jablonka\] -- Docs: added some hints about GPR, closes \#44 (\#46) \[Kevin - Jablonka\] -- Docs: fixed typo. \[Kevin M. Jablonka\] -- Docs: fixed typo. \[Kevin M. Jablonka\] -- Docs: inline code in sphinx docs. \[Kevin M. Jablonka\] -- Docs: fix some typos in readme, rebuilt docs. \[Kevin M. Jablonka\] -- Docs: fix some typos in readme, rebuilt docs. \[Kevin M. Jablonka\] -- Docs: added docstring to the PAL classes \#40 (\#43) \[Kevin - Jablonka\] -- Docs: updating notes on beta. \[Kevin M. Jablonka\] -- Docs: adding beta influence. \[Kevin M. Jablonka\] -- Docs: adding beta influence. \[Kevin M. Jablonka\] -- Docs: adding beta influence. \[Kevin M. Jablonka\] - -Fix ---- - -- Warning message for mae_variance comparison. \[Kevin M. Jablonka\] -- Crossvalidation returned only nan due to wrong if. \[Kevin M. - Jablonka\] -- Replace nan MAE by inf. \[Kevin M. Jablonka\] -- Indices in test fixed. \[Kevin M. Jablonka\] -- Start iteration count at 1. \[Kevin M. Jablonka\] -- Fixes remaining typos for uncertainity. \[byooooo\] -- Took two times sqrt in coregionalized pal. \[Kevin\] -- Training function for PALSklearn fixed. \[Kevin\] -- Coverage command in workflow was broken. \[Kevin\] -- Pareto_classify did not for as expected \#4. \[Kevin\] -- Need GPy for the Pythonpackage workflow. \[Kevin\] -- Omit for report of coverage. \[Kevin\] -- Uncertainity region test no longer failing. \[Kevin\] -- Should also work with 3.6. \[Kevin\] -- Should also work with 3.6. \[Kevin\] -- Should also work with 3.8. \[Kevin\] -- Install package for python package workflow. \[Kevin\] -- Activating Python Package CI. \[Kevin\] -- Export SKIP env variable in the pre-commit step. \[Kevin\] -- Installing pylint for pre-commit CI workflow. \[Kevin\] - -Other ------ - -- Update docs. \[byooooo\] - -- Merge branch \'master\' of github.com:kjappelbaum/PyPAL. \[Kevin M. - Jablonka\] - -- Merge branch \'master\' of github.com:kjappelbaum/PyPAL. \[Kevin M. - Jablonka\] - -- Validate sklearn GaussianProcessRegressor and extract model from - fitted GridSearchCV/RandomizedSearchCV (\#69) \[Kevin Jablonka\] - - - fix: warning message for mae_variance comparison - - feat: first implementation of sklearn gpr validation - - feat: using new validation in PALSklearn - - chore: updating docstring of PALsklearn - - docs: rebuilding docs - -- Docs spellcheck (\#63) \[Kevin Jablonka\] - - - chore: spellcheck on landing page - - chore: updating developer notes - - docs: some spellchecking of the docs - -- Merge branch \'master\' of github.com:kjappelbaum/PyPAL. \[Kevin M. - Jablonka\] - -- Merge pull request \#31 from kjappelbaum/docs. \[Kevin Jablonka\] - - Docs - -- Add prospector, closes \#2. \[Kevin M. Jablonka\] - -- Add prospector, closes \#2. \[Kevin M. Jablonka\] - -- Add prospector, closes \#2. \[Kevin M. Jablonka\] - -- Add prospector, closes \#2. \[Kevin M. Jablonka\] - -- Merge pull request \#21 from kjappelbaum/noise_kernel. \[Kevin - Jablonka\] - - Now, using the mu and the std of the measurement - -- Gitter added, closes \#10. \[Kevin\] +* change to sphinx-books-theme ([46642f0](https://www.github.com/kjappelbaum/pyepal/commit/46642f018a321a9408e278eb28db58d55483f0d7)) +* change to sphinx-books-theme ([e66dae9](https://www.github.com/kjappelbaum/pyepal/commit/e66dae9a1e5fcfbd39e03be64c753177b2c8be0b)) +* cleanup README; add link to chemrxiv ([#85](https://www.github.com/kjappelbaum/pyepal/issues/85)) ([7c57043](https://www.github.com/kjappelbaum/pyepal/commit/7c570434f3a66766e9590263e38dde1b3040f7b8)) +* correct minor typos ([eddee97](https://www.github.com/kjappelbaum/pyepal/commit/eddee97f355dfcdbb886efc2dfa4f4829552312d)) +* fix edit button link, closes [#96](https://www.github.com/kjappelbaum/pyepal/issues/96) ([91614f5](https://www.github.com/kjappelbaum/pyepal/commit/91614f57f7d6eedadac1d54d5d7c66573876d546)) +* fix typo in readme ([6b085ba](https://www.github.com/kjappelbaum/pyepal/commit/6b085ba2a95e7405cd55b3bbfe48e4b31c676c4a)) +* fixing link to docs in readme, link tutorials to binder ([e0e78d7](https://www.github.com/kjappelbaum/pyepal/commit/e0e78d7bf29ac91a1ecc6ca239331b712dcae94f)) +* link to chemrxiv, closes [#66](https://www.github.com/kjappelbaum/pyepal/issues/66) ([d3dfb4a](https://www.github.com/kjappelbaum/pyepal/commit/d3dfb4aacd652b0ddf7115954c63fe50592fd394)) +* reorder tabs; fix minor typos; update reference title ([330cfb2](https://www.github.com/kjappelbaum/pyepal/commit/330cfb29cb1fe76922f885b55fc4cf984f8b330a)) +* reorganize badges ([c8f5f09](https://www.github.com/kjappelbaum/pyepal/commit/c8f5f09b67c99c111814c73a5c8381e7a21f3d4b)) +* shortening the links to the API docs, do not show private API ([940607f](https://www.github.com/kjappelbaum/pyepal/commit/940607ff11f096d31780959393732aed7f9b5320)) +* updated installation instructions ([6ba0ee7](https://www.github.com/kjappelbaum/pyepal/commit/6ba0ee7d2fce75bcb1ab75a2cce93febc7c2abed))