Closed flongford closed 4 years ago
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@@ Coverage Diff @@
## master #27 +/- ##
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Coverage ? 98.7%
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Files ? 65
Lines ? 2170
Branches ? 138
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Hits ? 2142
Misses ? 16
Partials ? 12
Impacted Files | Coverage Δ | |
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...tion_listeners/hpc_writer/tests/test_hpc_writer.py | 100% <ø> (ø) |
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force_gromacs/chemicals/i_fragment.py | 100% <ø> (ø) |
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force_gromacs/core/i_process.py | 100% <100%> (ø) |
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...romacs/commands/tests/test_base_gromacs_command.py | 100% <100%> (ø) |
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...ders/tests/test_base_gromacs_simulation_builder.py | 100% <100%> (ø) |
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...macs/data_sources/fragment/fragment_data_source.py | 100% <100%> (ø) |
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force_gromacs/commands/gromacs_commands.py | 100% <100%> (ø) |
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...es/simulation/tests/test_simulation_data_source.py | 100% <100%> (ø) |
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...omacs/simulation_builders/gromacs_topology_data.py | 100% <100%> (ø) |
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force_gromacs/io/tests/test_file_tree_builder.py | 100% <100%> (ø) |
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... and 31 more |
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Out of curiosity, what is the difference between a GromacsPipeline and a BDSS workflow in evaluation mode?
They are similar, in that they chain together command line calls using subprocess
. There's a lot of overlap between the BaseGromacsCommand
and SubprocessWorkflow
classes actually - we could probably end up refactoring the BaseProcess
class if it is useful elsewhere.
The GromacsPipeline
just has some extra functionalities ability to stack together multiple command line calls, and also output a bash script capable of performing the same operations.
This PR approaches #26
It introduces new classes that lay the foundation for how chemical and simulation concepts are handled within the BDSS.
Includes contributions from #14 , #28
Change log:
Modules
New:
force_gromacs.chemicals
: contains data frame objects describing chemical entities such as molecular fragments and moleculesforce_gromacs.simulation_builders
: contains classes that are used to constructBasePipeline
objects to run a simulationUpdated:
force_gromacs.pipeline
-->force_gromacs.pipelines
: containsBasePipeline
objects that stack a sequence of command line programsforce_gromacs.core
: now contains fundamental classes required for calling command line programs usingsubprocess
libraryClasses
New:
BasePipeline
IFragment
FileRegistry
: generic class to hold formatting instructions for simulation input / output filesGromacsFileRegistry
: subclass ofFileRegistry
that also holds example formatted file names for a given prefixGromacsTopologyData
: container class for all topology related files and objects in a simulation (defining type and numerical of each molecular fragment in a simulation and their forcefields)Renamed:
Fragment
-->GromacsFragment
BaseGromacsProcess
-->BaseProcess
IBaseProcess
-->IProcess
GromacsFileTreeBuilder
-->FileTreeBuilder