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GROMOS11 Reader #4292

Merged
merged 49 commits into from
Dec 17, 2023
Merged

GROMOS11 Reader #4292

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7dfc569
Basic implementation of a GROMOS11 reader.
JoStoe Jul 18, 2023
446c2a0
Optimization of GROMOS11 trajectory reader
JoStoe Jul 18, 2023
a95c9fa
Code cleanup and optimizations
JoStoe Sep 13, 2023
dfdb45f
Reformat code to be PEP8 compliant
JoStoe Sep 14, 2023
e1867ba
Documentation
JoStoe Sep 15, 2023
c2ddedb
Adds pytests, better PEP8 compliance and GROMOS11 reader optimizations
JoStoe Sep 15, 2023
b842ba9
Authors and Changelog
JoStoe Sep 15, 2023
4ef672b
Added further tests and changed assert_almost_equal for assert_allclose
JoStoe Sep 18, 2023
cfd6b39
Update comments and documentation of GROMOS11 reader
JoStoe Sep 18, 2023
ef76854
Documentation and code clean-up
JoStoe Sep 18, 2023
81ba585
Increase and optimize test coverage
JoStoe Sep 18, 2023
8186650
Adds numbers of Github issue und pull request to CHANGELOG
JoStoe Sep 18, 2023
859b49c
fix of datafile regression
JoStoe Sep 18, 2023
3bb16b5
fix of datafile regression
JoStoe Sep 18, 2023
3b68f20
Allows frames to start with any block; adds general documentation
JoStoe Nov 13, 2023
7796846
Update GROMOS testing files & script
JoStoe Nov 13, 2023
9f123ed
Add test-trajectory for data without GENBOX and TIMESTEP
JoStoe Nov 13, 2023
7dd51fe
Change how to loop through Gromos trajectories and other Gromos reade…
JoStoe Nov 13, 2023
960f3cd
Gromos11 pytesting check for some edgecases and warnings
JoStoe Nov 14, 2023
bcbbefa
Gromos11 reader documentation and bugfixes
JoStoe Nov 14, 2023
93bc53f
Fix merge conflicts in changelog
JoStoe Nov 14, 2023
64fac25
Merge branch 'MDAnalysis:develop' into GROMOS11_Reader
JoStoe Nov 14, 2023
61a0561
Fixes PEP 8 issues
JoStoe Nov 14, 2023
c2197b1
Updated documentation und non-supported block types
JoStoe Nov 14, 2023
680ae2f
Make sure that only blocknames without any additional text get
JoStoe Nov 16, 2023
abed227
Complies with #4334 and removes ts arg from _read_next_timestep
JoStoe Nov 16, 2023
ef7238b
Removes unused import of warnings
JoStoe Nov 16, 2023
bc69032
Fixes compression detection when trj suffix is used.
JoStoe Nov 16, 2023
6eaaeac
Removes unwanted print() from code
JoStoe Nov 16, 2023
604bd53
fix reST
JoStoe Nov 16, 2023
780a46a
TRC: Documentation and straight forward change requests from review
JoStoe Dec 1, 2023
fddb54b
GROMOS11: Update testsuite as requestet by review
JoStoe Dec 1, 2023
827eecb
GROMOS11: Changes requested by reviewers, pathlib instead of os
JoStoe Dec 1, 2023
9fca76a
gromos11 reader: Adds support for triclinic boxes
JoStoe Dec 9, 2023
41c1a59
gromos11: Make formatting flake8 compatible
JoStoe Dec 9, 2023
487ca3f
GROMOS11: Allows to disable unit conversion and adds testing of empty…
JoStoe Dec 9, 2023
b313696
GROMOS11: Exchange NotImplementedError for ValueError
JoStoe Dec 10, 2023
92084e0
GROMOS11: Changes to correctly trigger exceptions during the creation…
JoStoe Dec 10, 2023
e612526
GROMOS11: Changes how state of line 3 and 4 in GENBOX are evaluated
JoStoe Dec 10, 2023
c4374cd
GROMOS11: Use class-variables
JoStoe Dec 10, 2023
f0982a9
GROMOS11: Add files to test_multiprocessing.py
JoStoe Dec 10, 2023
a88b3bf
Changes order of changelog for GROMOS11 addition to put newest on top
JoStoe Dec 10, 2023
40a1ad2
Fix merge conflicts in AUTHORS and CHANGELOG
JoStoe Dec 13, 2023
8b5beb5
GROMOS11: Fix typos, remove unnecessary functions
JoStoe Dec 16, 2023
ede2202
GROMOS11: Change attribute compression to compressed
JoStoe Dec 16, 2023
7c624ac
Reset AUTHORS and CHANGELOG to the latest status of develop to fix me…
JoStoe Dec 16, 2023
7ab5d0a
Merge branch 'MDAnalysis:develop' into GROMOS11_Reader
JoStoe Dec 16, 2023
1691782
Add to AUTHORS and CHANGELOG
JoStoe Dec 16, 2023
3e666a8
Add github handle to CHANGELOG
JoStoe Dec 17, 2023
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1 change: 1 addition & 0 deletions package/AUTHORS
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Original file line number Diff line number Diff line change
Expand Up @@ -227,6 +227,7 @@ Chronological list of authors
- Geongi Moon
- Sumit Gupta
- Heet Vekariya
- Johannes Stöckelmaier

External code
-------------
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4 changes: 3 additions & 1 deletion package/CHANGELOG
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Expand Up @@ -15,7 +15,8 @@ The rules for this file:

-------------------------------------------------------------------------------
??/??/?? IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith,
richardjgowers, lilyminium, ALescoulie, hmacdope, HeetVekariya
richardjgowers, lilyminium, ALescoulie, hmacdope, HeetVekariya,
JoStoe

* 2.7.0

Expand All @@ -34,6 +35,7 @@ Fixes
* Fix atom charge reading in PDBQT parser (Issue #4282, PR #4283)

Enhancements
* Added a reader for GROMOS11 TRC trajectories (PR #4292 , Issue #4291)
* Document the usage of NoDataError in its docstring (Issue #3901, PR #4359)
* Refactor c_distances backend to have a cython .pxd header and expose in
libmdanalysis (Issue #4315, PR #4324)
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