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base repository: alchemistry/alchemlyb
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base: 2.3.2
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head repository: alchemistry/alchemlyb
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compare: 2.4.0
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  • 16 commits
  • 34 files changed
  • 4 contributors

Commits on Sep 4, 2024

  1. 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)
    orbeckst authored Sep 4, 2024
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Commits on Sep 13, 2024

  1. initial CITATION.cff file

    - 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>
    orbeckst and dotsdl committed Sep 13, 2024
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  2. add JOSS paper as preferred citation to CITATION

    - inferred DOI from proof
    - assume final acceptance in 2024...
    orbeckst committed Sep 13, 2024
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  4. 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)
    orbeckst committed Sep 13, 2024
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  5. updated CHANGES and AUTHORS for 2.3.3

    - CHANGES: bump to 2.3.3
    - add reminder to AUTHORS to also update CITATION.cff
    orbeckst committed Sep 13, 2024
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  6. 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
    orbeckst committed Sep 13, 2024
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Commits on Sep 14, 2024

  1. Moving average (#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 <orbeckst@gmail.com>
    jaclark5 and orbeckst authored Sep 14, 2024
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Commits on Sep 15, 2024

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Commits on Sep 16, 2024

  1. add @jaclark5 to AUTHORS and CITATION.cff

    AUTHORS entry had been forgotten in PR #381
    orbeckst committed Sep 16, 2024
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  2. 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
    orbeckst authored Sep 16, 2024
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Commits on Sep 17, 2024

  1. 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
    jaclark5 authored Sep 17, 2024
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  2. black-formatted files

    orbeckst committed Sep 17, 2024
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  3. 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
    orbeckst committed Sep 17, 2024
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  4. house-keeping

    - gitignore _version
    - ignore commits for blame that contain black-reformatting
      (in particular we forgot to include #280)
    orbeckst committed Sep 17, 2024
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  5. Merge pull request #398 from alchemistry/prep-release-2.4.0

    prepare release 2.4.0 (for #396)
    orbeckst authored Sep 17, 2024
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