Closed flongford closed 4 years ago
Merging #23 into master will increase coverage by
3.92%
. The diff coverage is100%
.
@@ 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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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 eachBaseGromacsCommand
subclass to include thegmx
executable in each generated command. Additional changes are also made to deal with Gromacs commands that were deprecated between versions 4.6.7 and 2019.4Gromacs 2019.4 is now assumed as the default build - consequently, the PR also closes #3, #4, and #8
Change log
gromacs-2019.4-1
egg included (fromenthought/lgpl
)BaseGromacsCommand
class has newexecutable
attribute in order to supportgmx
command syntaxGromacs_solvate
andGromacs_insert_molecules
in order to replace deprecatedgenbox
commandGromacs_select
refactored to incorporate new naming conventionGromacs_mdrun
refactored to incorporate new syntax for MPI runs