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Fix missing names in ExternalMDSnapshot - #908

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dwhswenson merged 3 commits into
openpathsampling:masterfrom
dwhswenson:fix_ext_snapshot_missing
Mar 20, 2020
Merged

dwhswenson merged 3 commits into
openpathsampling:masterfrom
dwhswenson:fix_ext_snapshot_missing

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@dwhswenson

@dwhswenson dwhswenson commented Mar 9, 2020 •

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ExternalMDSnapshot was moved to a different file, and didn't get all its module-level names redefined. Bug uncovered by @jasperdenduijf in #907.

Right now, this still requires tests (tests added!). We're missing coverage on the lines that caused that part of the issue in #907, so we should have tests covering those lines.

@sefalkner

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Tested this on my Gromacs TPS setup that also had these occasional Errors (#907) after some 10-30 mc cycles, now runs smooth for > 300 cycles.

In general I thought about contributing to the docs for the gromacs engine. For a new user it is unclear that setting n_frames_max to the gromacs nsteps option is crucial as there is little documentation about it.

@dwhswenson

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Tested this on my Gromacs TPS setup that also had these occasional Errors (#907) after some 10-30 mc cycles, now runs smooth for > 300 cycles.

Thanks for the confirmation that this fixes -- I'll make finishing this PR a priority, but things are a little bit busy for the next week. (Out-of-town guests.)

In general I thought about contributing to the docs for the gromacs engine. For a new user it is unclear that setting n_frames_max to the gromacs nsteps option is crucial as there is little documentation about it.

Please do! Improvements to the docs are always welcome. External engines (such as Gromacs) are newer, and neither the code nor the docs have had as much stress testing, so the help is appreciated.

That said, you might wait until, say, Monday. I've been working on a branch to improve a few things in the Gromacs engine docs -- docstrings and, especially, the example notebooks -- so it might be easier to build on that than to write (possibly conflicting) changes. I'll try to make a PR of that very soon.

@dwhswenson dwhswenson added this to the 1.3 milestone Mar 18, 2020
@jasperdenduijf

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This might be an obvious question, but once I've installed openpathsampling, how do I pull these commits and add them to my current PATH?

@dwhswenson

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@jasperdenduijf : I think most of what you want is described at http://openpathsampling.org/latest/developers/install_developers.html (after getting the dev install script with the curl command at http://openpathsampling.org/latest/install.html#developer-install-with-conda). The quickest way to do a bugfix test install is under the heading "Quick bugfix/developer installation" in the first link. That creates a separate conda environment for the bugfix version of OPS. For this specific branch, you'd use remote dwhswenson and branch fix_ext_snapshot_missing (in place of experimental_feature in the docs).

Assuming the tests that I just added pass, then I expect this will be merged to master tomorrow evening or Saturday morning. It will be included in the 1.3 release, which I hope to release early next week.

@dwhswenson

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Tests pass; I'll leave this open for comment for at least 24 hours before merging. I will merge no earlier than Friday 20 March, 14:00 GMT (15:00 my local).

This PR involves adding some missing imports and then adding tests to improve our test coverage, so I can't imagine anything here is controversial.

@dwhswenson dwhswenson changed the title [WIP] Fix missing names in ExternalMDSnapshot Fix missing names in ExternalMDSnapshot Mar 19, 2020

@sroet sroet left a comment

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LGTM, have a question about one line in the test: whether or not it is leftover debug statements or an actual test of the existence of an attribute.

Comment thread openpathsampling/tests/test_external_snapshots.py Outdated
@dwhswenson
dwhswenson merged commit 6e48b62 into openpathsampling:master Mar 20, 2020
@dwhswenson dwhswenson mentioned this pull request Sep 26, 2020
@dwhswenson
dwhswenson deleted the fix_ext_snapshot_missing branch January 17, 2021 11:54
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4 participants