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base repository: alchemistry/alchemlyb
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base: 2.0.1
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head repository: alchemistry/alchemlyb
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compare: 2.1.0
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  • 9 commits
  • 31 files changed
  • 3 contributors

Commits on Apr 17, 2023

  1. warn and document changed behavior for dir in ABFE pipeline (PR #312)

    - fix #311 
    - In PR #310 (v2.0.1) we changed the behavior of the dir kwarg in ABFE: glob patterns are now part of
       the prefix kwar. This API change should not have been included in a patch release but because it 
       came very soon after 2.0.0, we kept it. This PR explicitly issues a warning when a glob pattern is
       used so that subsequent failures (ValueError) are easier to understand.
    - add warning if glob pattern `*` is used in `dir`
    - add test
    - updated docs
    - update CHANGES
    xiki-tempula authored Apr 17, 2023
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Commits on Jun 1, 2023

  1. avoid crash in alchemlyb.visualisation.plot_convergence with NaN (#319)

    - fix #318
    - only plot final error estimate in  alchemlyb.visualisation.plot_convergence if it is not NaN
    
    Co-authored-by: Zhiyi Wu <zwu@exscientia.co.uk>
    xiki-tempula and xiki-tempula authored Jun 1, 2023
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  2. parquet parser for dataframe serialisation (#317)

    * update
    
    * update
    
    * Update docs/parsing.rst
    
    Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
    
    * Update src/alchemlyb/parsing/parquet.py
    
    Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
    
    * Update src/alchemlyb/parsing/parquet.py
    
    Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
    
    * Update src/alchemlyb/parsing/parquet.py
    
    Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
    
    * update
    
    * update
    
    ---------
    
    Co-authored-by: William (Zhiyi) Wu <zwu@exscientia.co.uk>
    Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
    3 people authored Jun 1, 2023
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Commits on Jun 6, 2023

  1. Use loguru (#303)

    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * Update docs/miscellaneous/logging.rst
    
    ---------
    
    Co-authored-by: Zhiyi Wu <zwu@exscientia.co.uk>
    Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
    3 people authored Jun 6, 2023
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  2. Enable MBAR to do bootstrap error estimation (#322)

    * Auto stash before checking out "upstream/301-using-loguru"
    
    * update
    
    * update
    
    * add test
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    ---------
    
    Co-authored-by: Zhiyi Wu <zwu@exscientia.co.uk>
    xiki-tempula and xiki-tempula authored Jun 6, 2023
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Commits on Jun 8, 2023

  1. Correct the old style logging. (#324)

    * fix #323 
    * change all logger messages to use logguru (f-string) syntax
    * update CHANGES
    
    ---------
    
    Co-authored-by: William (Zhiyi) Wu <zwu@exscientia.co.uk>
    xiki-tempula and xiki-tempula authored Jun 8, 2023
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Commits on Jun 12, 2023

  1. The statistical inefficiency is logged at the debug level (#325)

    - close #295 
    - log SI (at DEBUG)
    - updated docs
    - updated CHANGES
    
    ---------
    
    Co-authored-by: Zhiyi Wu <zwu@exscientia.co.uk>
    xiki-tempula and xiki-tempula authored Jun 12, 2023
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Commits on Jun 22, 2023

  1. ValueError will be raised if concatenated amber output file has been …

    …ingested (#326)
    
    * update
    
    * update
    
    * update
    
    ---------
    
    Co-authored-by: Zhiyi Wu <zwu@exscientia.co.uk>
    xiki-tempula and xiki-tempula authored Jun 22, 2023
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  2. Finalize CHANGES

    xiki-tempula authored Jun 22, 2023
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