[WIP] Fail fast if prepare fails in external engines
#1118
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The `prepare` command in external engines can be used to, e.g, create input for a given trajectory. For example, in Gromacs, this runs the grompp command to incorporate snapshot-independent information in the mdp with the specific trr snapshot. Previously, there was no catch for an error in `prepare`. This meant that the engine would try to run the trajetory, and, not finding required files, would fail with the unhelpful message "engine died unexpectedly." This PR provides a clearer error message in the case that the `prepare` step fails. It provides a specific error for the Gromacs engine, and a generic error for any engine that returns a non-zero result code from `prepare`, but which hasn't already raised the error.
prepare fails in external enginesprepare fails in external engines
Codecov Report
@@ Coverage Diff @@
## master #1118 +/- ##
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- Coverage 81.75% 81.75% -0.01%
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Files 142 142
Lines 15612 15614 +2
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+ Hits 12764 12765 +1
- Misses 2848 2849 +1
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The
preparecommand in external engines can be used to, e.g, create input for a given trajectory. For example, in Gromacs, this runs the grompp command to incorporate snapshot-independent information in the mdp with the specific trr snapshot.Previously, there was no catch for an error in
prepare. This meant that the engine would try to run the trajetory, and, not finding required files, would fail with the unhelpful message "engine died unexpectedly." This PR provides a clearer error message in the case that thepreparestep fails.It provides a specific error for the Gromacs engine, and a generic error for any engine that returns a non-zero result code from
prepare, but which hasn't already raised the error.EDIT: Waiting on some test coverage here, although the actual gmx is outside our normal coverage since we don't install gmx in the test env. That said, I think we need some mechanism for also testing gmx integration in CI. I think there was no official conda-forge package when we first started with gmx integration, but there is now. (We have tests that test the integration, but they skip if there's no
gmxin the$PATH.)