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Lammps Support #348
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Lammps Support #348
Commits on Feb 5, 2024
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Commits on Feb 7, 2024
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Commits on Feb 20, 2024
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Commits on Feb 22, 2024
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Commits on Mar 13, 2024
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Add calculation of beta based on lammps units
Add generation of u_nk and dHdl from linearly related dependencies
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Commits on Jul 24, 2024
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Commits on Aug 21, 2024
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Commits on Aug 23, 2024
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Commits on Aug 30, 2024
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Commits on Sep 5, 2024
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Commits on Sep 13, 2024
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Commits on Sep 19, 2024
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Moving average (alchemistry#381)
* 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 <[email protected]>
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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 <[email protected]>
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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 alchemistry#356
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add @jaclark5 to AUTHORS and CITATION.cff
AUTHORS entry had been forgotten in PR alchemistry#381
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Resolve bug in bar_model.delta_f_ creation (alchemistry#397)
* fix bug introduced in PR alchemistry#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 alchemistry#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 alchemistry#280)
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make repo title identical to JOSS paper title (alchemistry#404)
- close alchemistry#402 - use same title in CITATION.cff for paper and project (required for the JOSS paper publication alchemistry#71) - added DOI for preferred citation in note because that is the only hint that shows up on zenodo)
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[doc] tutorial: use alchemlyb.concat (alchemistry#399)
replace `pandas.concat()` with `alchemlyb.concat()` in the tutorial (given that we explicitly tell users to use it)
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Commits on Sep 24, 2024
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Commits on Oct 22, 2024
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Commits on Nov 12, 2024
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Commits on Nov 15, 2024
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Commits on Nov 17, 2024
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