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base repository: alchemistry/alchemlyb
base: 2.3.2
head repository: alchemistry/alchemlyb
compare: 2.4.0
- 16 commits
- 34 files changed
- 4 contributors
Commits on Sep 4, 2024
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fixed one remaining wrong date in CHANGES (#391)
- fix #388 - corrected remaining wrong date to be MM/DD/YYYY format - make format clearer in top message - reformatting (line length, spaces)
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Commits on Sep 13, 2024
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- generated with https://bit.ly/cffinit - authors and order from AUTHORS - affiliations and ORCID from JOSS paper - emails from paper or individuals Co-authored-by: David L. Dotson <dotsdl@gmail.com>
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add JOSS paper as preferred citation to CITATION
- inferred DOI from proof - assume final acceptance in 2024...
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inserted additional JOSS paper authors in software author list
- added David Mobley @davidlmobley (original conception and design of alchemlyb) - added Michael Shirts @mrshirts (original conception and design of alchemlyb)
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updated CHANGES and AUTHORS for 2.3.3
- CHANGES: bump to 2.3.3 - add reminder to AUTHORS to also update CITATION.cff
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add authors to CITATION who had NOT been in AUTHORS
Added all authors that were mentioned in the Acknowledgements of the JOSS paper but were not in AUTHORS - Wei-Tse Hsu @wehs7661 (2020) for code clean-up in a732380 - Jan Janssen @jan-janssen (2022) for creating the conda-forge package - Shujie Fan @VOD555 (2022) for initial code for fractional equilibration time - Helmut Carter @helmutcarter (2024) for doc fix in #356
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Commits on Sep 14, 2024
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* Add moving_average function for visualization and convergence testing * Update versionadded * Run Black * Bug fix bar_.py states * Update Changelog * Update the docs * Add tests * Formatting to align with Black * Update tests * Refactor moving_average to align with forward_backward_convergence function * Update tests * Update test_convergence and lambda tests in convergence.moving_average * Adjust convergence.py and tests for codecoverage * black * Update moving_average to block_average for more accurate descriptive name * Address reviewer comments * Update test to align with changed handling of dfs of different length in block_average * Remove incorrect popagation of error in BAR * Add tests and error catch for ill constructed BAR input, u_nk * black * Updated version comments --------- Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
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Commits on Sep 15, 2024
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Commits on Sep 16, 2024
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add @jaclark5 to AUTHORS and CITATION.cff
AUTHORS entry had been forgotten in PR #381
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Merge pull request #395 from alchemistry/add-ciff
* add CITATION.cff file * close #394 * add all AUTHORS with ORCIDs and affiliation (as far as they are confirmed); order based on AUTHORS * add alchemlyb PIs * add contributors that were listed in JOSS paper acknowledgements (PR #328) but had NOT been listed in AUTHORS (inserted in chronological order) * only add emails for maintainers/PIs * add Software Heritage Identifier * add paper citation section for MBAR, decorrelation, and preliminary citation for JOSS paper #71 * add one new contributor (from recent PR #381) to AUTHORS and CITATIONS.cff
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Commits on Sep 17, 2024
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Resolve bug in bar_model.delta_f_ creation (#397)
* fix bug introduced in PR #381: there was a change to creating the delta_f_ matrix, which resulted in the columns and indices being tuples that were in the wrong order for single lambda computations. * ensure that columns are in the correct order by explicitly sorting * add a test for the delta_f_ columns
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replace setup.py,cfg with pyproject.toml
- fix #385 - use pyproject.toml instead of setup.py (note: may need to change README for PyPi to exclude banners) - remove versioneer and use versioningit (use alchemlyb.__version__ directly where the version is needed, e.g., for sphinx docs) - updated CHANGES for 2.4.0
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- gitignore _version - ignore commits for blame that contain black-reformatting (in particular we forgot to include #280)
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Merge pull request #398 from alchemistry/prep-release-2.4.0
prepare release 2.4.0 (for #396)
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