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GROMOS11 Reader #4292

Merged
merged 49 commits into from
Dec 17, 2023
Merged

GROMOS11 Reader #4292

merged 49 commits into from
Dec 17, 2023

Commits on Sep 15, 2023

  1. Basic implementation of a GROMOS11 reader.

    @JoStoe
    JoStoe committed Sep 15, 2023
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  2. Optimization of GROMOS11 trajectory reader

    @JoStoe
    JoStoe committed Sep 15, 2023
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  3. Code cleanup and optimizations

    @JoStoe
    JoStoe committed Sep 15, 2023
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  4. Reformat code to be PEP8 compliant

    @JoStoe
    JoStoe committed Sep 15, 2023
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  5. Documentation

    @JoStoe
    JoStoe committed Sep 15, 2023
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  6. Adds pytests, better PEP8 compliance and GROMOS11 reader optimizations

    @JoStoe
    JoStoe committed Sep 15, 2023
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  7. Authors and Changelog

    @JoStoe
    JoStoe committed Sep 15, 2023
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Commits on Sep 18, 2023

  1. Added further tests and changed assert_almost_equal for assert_allclose

    @JoStoe
    JoStoe committed Sep 18, 2023
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  2. Update comments and documentation of GROMOS11 reader

    @JoStoe
    JoStoe committed Sep 18, 2023
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  3. Documentation and code clean-up

    @JoStoe
    JoStoe committed Sep 18, 2023
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  4. Increase and optimize test coverage

    @JoStoe
    JoStoe committed Sep 18, 2023
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  5. Adds numbers of Github issue und pull request to CHANGELOG

    @JoStoe
    JoStoe committed Sep 18, 2023
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  6. fix of datafile regression

    @JoStoe
    JoStoe committed Sep 18, 2023
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  7. fix of datafile regression

    @JoStoe
    JoStoe committed Sep 18, 2023
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Commits on Nov 13, 2023

  1. Allows frames to start with any block; adds general documentation

    @JoStoe
    JoStoe committed Nov 13, 2023
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  2. Update GROMOS testing files & script

    @JoStoe
    JoStoe committed Nov 13, 2023
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  3. Add test-trajectory for data without GENBOX and TIMESTEP

    @JoStoe
    JoStoe committed Nov 13, 2023
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  4. Change how to loop through Gromos trajectories and other Gromos reade… 

    …r bugfixes
    @JoStoe
    JoStoe committed Nov 13, 2023
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Commits on Nov 14, 2023

  1. Gromos11 pytesting check for some edgecases and warnings

    @JoStoe
    JoStoe committed Nov 14, 2023
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  2. Gromos11 reader documentation and bugfixes

    @JoStoe
    JoStoe committed Nov 14, 2023
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  3. Fix merge conflicts in changelog

    @JoStoe
    JoStoe committed Nov 14, 2023
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  4. Merge branch 'MDAnalysis:develop' into GROMOS11_Reader

    @JoStoe
    JoStoe authored Nov 14, 2023
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  5. Fixes PEP 8 issues

    @JoStoe
    JoStoe committed Nov 14, 2023
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  6. Updated documentation und non-supported block types

    @JoStoe
    JoStoe committed Nov 14, 2023
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Commits on Nov 16, 2023

  1. Make sure that only blocknames without any additional text get 

    identified as blocknames
    @JoStoe
    JoStoe committed Nov 16, 2023
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  2. Complies with MDAnalysis#4334 and removes ts arg from _read_next_time… 

    …step
    @JoStoe
    JoStoe committed Nov 16, 2023
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  3. Removes unused import of warnings

    @JoStoe
    JoStoe committed Nov 16, 2023
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  4. Fixes compression detection when trj suffix is used.

    @JoStoe
    JoStoe committed Nov 16, 2023
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  5. Removes unwanted print() from code

    @JoStoe
    JoStoe committed Nov 16, 2023
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  6. fix reST

    @JoStoe
    JoStoe committed Nov 16, 2023
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Commits on Dec 1, 2023

  1. TRC: Documentation and straight forward change requests from review

    @JoStoe
    JoStoe committed Dec 1, 2023
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  2. GROMOS11: Update testsuite as requestet by review

    @JoStoe
    JoStoe committed Dec 1, 2023
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  3. GROMOS11: Changes requested by reviewers, pathlib instead of os

    @JoStoe
    JoStoe committed Dec 1, 2023
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Commits on Dec 9, 2023

  1. gromos11 reader: Adds support for triclinic boxes

    @JoStoe
    JoStoe committed Dec 9, 2023
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  2. gromos11: Make formatting flake8 compatible

    @JoStoe
    JoStoe committed Dec 9, 2023
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  3. GROMOS11: Allows to disable unit conversion and adds testing of empty… 

    … file
    @JoStoe
    JoStoe committed Dec 9, 2023
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Commits on Dec 10, 2023

  1. GROMOS11: Exchange NotImplementedError for ValueError

    @JoStoe
    JoStoe committed Dec 10, 2023
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  2. GROMOS11: Changes to correctly trigger exceptions during the creation… 

    … of universe
    @JoStoe
    JoStoe committed Dec 10, 2023
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  3. GROMOS11: Changes how state of line 3 and 4 in GENBOX are evaluated

    @JoStoe
    JoStoe committed Dec 10, 2023
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  4. GROMOS11: Use class-variables

    @JoStoe
    JoStoe committed Dec 10, 2023
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  5. GROMOS11: Add files to test_multiprocessing.py

    @JoStoe
    JoStoe committed Dec 10, 2023
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  6. Changes order of changelog for GROMOS11 addition to put newest on top

    @JoStoe
    JoStoe committed Dec 10, 2023
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Commits on Dec 13, 2023

  1. Fix merge conflicts in AUTHORS and CHANGELOG

    @JoStoe
    JoStoe committed Dec 13, 2023
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Commits on Dec 16, 2023

  1. GROMOS11: Fix typos, remove unnecessary functions

    @JoStoe
    JoStoe committed Dec 16, 2023
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  2. GROMOS11: Change attribute compression to compressed

    @JoStoe
    JoStoe committed Dec 16, 2023
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  3. Reset AUTHORS and CHANGELOG to the latest status of develop to fix me… 

    …rge conflicts
    @JoStoe
    JoStoe committed Dec 16, 2023
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  4. Merge branch 'MDAnalysis:develop' into GROMOS11_Reader

    @JoStoe
    JoStoe authored Dec 16, 2023
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  5. Add to AUTHORS and CHANGELOG

    @JoStoe
    JoStoe committed Dec 16, 2023
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Commits on Dec 17, 2023

  1. Add github handle to CHANGELOG

    @JoStoe
    JoStoe committed Dec 17, 2023
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