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Lammps Support #348

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Lammps Support #348

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Commits on Feb 5, 2024

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  2. Update formatting

    jaclark5 committed Feb 5, 2024
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  4. Add input for mbar

    jaclark5 committed Feb 5, 2024
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  5. Remove print

    jaclark5 committed Feb 5, 2024
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  6. Bug fix file outputs

    jaclark5 committed Feb 5, 2024
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  7. Bug fix file format

    jaclark5 committed 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

  1. Add abs to nblocks calc

    jaclark5 committed Feb 22, 2024
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  2. Bug fix, nblocks

    jaclark5 committed Feb 22, 2024
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Commits on Mar 13, 2024

  1. Add calculation of beta based on lammps units

    Add generation of u_nk and dHdl from linearly related dependencies
    jaclark5 committed Mar 13, 2024
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  2. Update module docstring

    jaclark5 committed Mar 13, 2024
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  3. Add name to author list

    jaclark5 committed Mar 13, 2024
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  4. Added to changelog

    jaclark5 committed Mar 13, 2024
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  5. Update docs

    jaclark5 committed Mar 13, 2024
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  6. Run Black

    jaclark5 committed Mar 13, 2024
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Commits on Jul 24, 2024

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  5. Update changelog

    jaclark5 committed Jul 24, 2024
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  7. Run Black

    jaclark5 committed Jul 24, 2024
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Commits on Aug 21, 2024

  1. Add ensemble support

    jaclark5 committed 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 3, 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

  1. 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]>
    jaclark5 and orbeckst committed Sep 19, 2024
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  2. Added to changelog

    jaclark5 committed Sep 19, 2024
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  3. 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 <[email protected]>
    2 people authored and jaclark5 committed Sep 19, 2024
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  4. add JOSS paper as preferred citation to CITATION

    - inferred DOI from proof
    - assume final acceptance in 2024...
    orbeckst authored and jaclark5 committed Sep 19, 2024
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  6. 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 authored and jaclark5 committed Sep 19, 2024
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  7. updated CHANGES and AUTHORS for 2.3.3

    - CHANGES: bump to 2.3.3
    - add reminder to AUTHORS to also update CITATION.cff
    orbeckst authored and jaclark5 committed Sep 19, 2024
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  8. 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
    orbeckst authored and jaclark5 committed Sep 19, 2024
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  9. add @jaclark5 to AUTHORS and CITATION.cff

    AUTHORS entry had been forgotten in PR alchemistry#381
    orbeckst authored and jaclark5 committed Sep 19, 2024
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  10. 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
    jaclark5 committed Sep 19, 2024
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  11. black-formatted files

    orbeckst authored and jaclark5 committed Sep 19, 2024
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  12. 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
    orbeckst authored and jaclark5 committed Sep 19, 2024
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  13. house-keeping

    - gitignore _version
    - ignore commits for blame that contain black-reformatting
      (in particular we forgot to include alchemistry#280)
    orbeckst authored and jaclark5 committed Sep 19, 2024
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  14. 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)
    orbeckst authored and jaclark5 committed Sep 19, 2024
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  15. [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)
    orbeckst authored and jaclark5 committed Sep 19, 2024
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  16. Update version

    jaclark5 committed Sep 19, 2024
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  18. Formatting

    jaclark5 committed Sep 19, 2024
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  19. FutureWarning

    jaclark5 committed Sep 19, 2024
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Commits on Sep 24, 2024

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Commits on Oct 22, 2024

  1. Add names, bug fix dHdl

    jaclark5 committed 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

  1. Add testing

    jaclark5 committed Nov 17, 2024
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