force-h2020 / force-bdss-plugin-gromacs

Gromacs BDSS data sources, as well as a stand-alone wrappers around Gromacs tools.
MIT License
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ENH: Use EDM Gromacs 2019 Egg #23

Closed flongford closed 4 years ago

flongford commented 4 years ago

This PR approaches #21 by including the gromacs-2019.4-1 egg from EDM as a dependency. By doing so we also need to update the syntax used by each BaseGromacsCommand subclass to include the gmx executable in each generated command. Additional changes are also made to deal with Gromacs commands that were deprecated between versions 4.6.7 and 2019.4

Gromacs 2019.4 is now assumed as the default build - consequently, the PR also closes #3, #4, and #8

Change log

codecov-io commented 4 years ago

Codecov Report

Merging #23 into master will increase coverage by 3.92%. The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff            @@
##           master     #23      +/-   ##
=========================================
+ Coverage   94.88%   98.8%   +3.92%     
=========================================
  Files          35      55      +20     
  Lines         840    2012    +1172     
  Branches      101     128      +27     
=========================================
+ Hits          797    1988    +1191     
+ Misses         30      10      -20     
- Partials       13      14       +1
Impacted Files Coverage Δ
...ce_gromacs/core/tests/test_base_gromacs_command.py 100% <100%> (ø)
force_gromacs/core/base_gromacs_command.py 94.82% <100%> (+0.18%) :arrow_up:
force_gromacs/commands/gromacs_commands.py 100% <100%> (ø) :arrow_up:
...ce_gromacs/commands/tests/test_gromacs_commands.py 100% <100%> (ø)
force_gromacs/tests/dummy_classes.py 100% <0%> (ø)
...ources/molecule/tests/test_molecule_data_source.py 100% <0%> (ø)
...omacs/data_sources/molecule/tests/test_molecule.py 100% <0%> (ø)
...tion_listeners/hpc_writer/tests/test_hpc_writer.py 100% <0%> (ø)
...line/tests/test_base_gromacs_simulation_builder.py 100% <0%> (ø)
... and 15 more

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