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base repository: alchemistry/alchemlyb
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base: 1.0.0
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head repository: alchemistry/alchemlyb
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compare: 1.0.1
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  • 15 commits
  • 50 files changed
  • 3 contributors

Commits on Nov 8, 2022

  1. test on python 3.11

    - close #267
    - update setup.py metadata
    - add Python 3.11 to test matrix
    - only test lowest (3.8) and highest (3.11) python for the expensive
      Windows and macOS runners to reduce CI load and wait times.
    - use Python 3.10 for deploy environment
    orbeckst committed Nov 8, 2022
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  2. fix Python 3.10 in deploy workflow

    Must quote "3.10"!
    orbeckst authored Nov 8, 2022
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Commits on Nov 9, 2022

  1. small fixes for 1.0.1 (#266)

    * fix year in Chodera2016 reference
    * 1.0.0 CHANGES: extract() is an enhancement
    * updated package metadata: set status to 5 - production/stable
    orbeckst authored Nov 9, 2022
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Commits on Nov 14, 2022

  1. AMBER parser had a "too strict" regex to extract values (#273)

    This PR addresses issue #272.
    This issue exposed a nasty bug inside the regex pattern we used to extract sections in the amber output file.
    
    we are trying to match a sequence of type
    
    filed = int/float
    
    extracting the int/float corresponding to the field. Up till now, the pattern was
    
    fr' {field}\s+=\s+(\*+|{_FP_RE}|\d+)'
    were field was the string we want to extract the value for, and _FP_RE is defined to extract the float/int after the equal.
    
    The problem arises when the field and/or the value are not separated from the = sign by a space (as was the case in the issue). It's strange this didn't appear before!
    
    I just changed the + in \s+=\s+ to *.
    
    Thinking about it, this should not break anything else, but I can't be 100% sure and the tests should catch any "macro" problems eventually introduced with this PR.
    DrDomenicoMarson authored Nov 14, 2022
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  2. add 1.0.1 header to CHANGES

    - header
    - add @DrDomenicoMarson from PR #273
    orbeckst authored Nov 14, 2022
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Commits on Dec 5, 2022

  1. fix rtd (#277)

    - fix crashing RTD doc build readthedocs/readthedocs.org#9776
    - Use mamba with Python 3.8 on RTD
    xiki-tempula authored Dec 5, 2022
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  2. Slicing will no longer drop the NaN rows (#275)

    - Fix #274
    - removed dropping of rows with NaN in the pre-processing slicing() functions (functionality was not documented
       and lead to incorrect behavior with NAMD data) 
    - update tests
    - update CHANGES
    xiki-tempula authored Dec 5, 2022
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Commits on Dec 6, 2022

  1. Clean up the iloc in the tests (#254)

    * fix #202 
    * use `.loc` instead of `.iloc` in our tests where possible (as per our best practices)
    xiki-tempula authored Dec 6, 2022
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  2. Blackfy the code (#280)

    * black (we now use black for code formatting, see also 
       https://github.com/alchemistry/alchemlyb/wiki/Developer-Guide#style-guide )
    * ci
    * change log
    xiki-tempula authored Dec 6, 2022
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  3. evaluate data-loading fixtures at test time, not set-up and reorganize (

    #278)
    
    - fix #206 
    - speed up tests by avoiding to evaluate fixtures at test collection time
    - reorganized fixtures: fixtures that load data are now global in `conftest.py`
    - updated tests
    - updated CHANGES
    xiki-tempula authored Dec 6, 2022
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Commits on Dec 9, 2022

  1. refactor ABFE tests (#281)

    * refactor ABFE tests
    xiki-tempula authored Dec 9, 2022
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  2. Fix #276 (#282)

    * refactor ABFE tests
    
    * update
    
    * update
    
    * update
    
    * update changelog
    xiki-tempula authored Dec 9, 2022
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  3. finalized CHANGELOG

    For release 1.0.1, #279.
    
    Note that this is a patch release so any Enhancements listed are internal
    and do NOT affect user-facing code. They are only improving code quality
    and ability to maintain.
    orbeckst committed Dec 9, 2022
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Commits on Dec 10, 2022

  1. deprecate AutoMBAR (PR #285)

    - fix #284
    - Deprecate AutoMBAR (for removal in 2.0.0)
    - test DeprecationWarning
    - silence this warning otherwise
    - update docs
    - update CHANGES
    xiki-tempula authored Dec 10, 2022
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