Allow relative paths in Arkane statmech #1685
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Codecov Report
@@ Coverage Diff @@
## master #1685 +/- ##
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Coverage 41.66% 41.66%
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Files 176 176
Lines 30215 30215
Branches 6256 6256
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Hits 12588 12588
Misses 16703 16703
Partials 924 924Continue to review full report at Codecov.
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Codecov Report
@@ Coverage Diff @@
## master #1685 +/- ##
=======================================
Coverage 32.65% 32.65%
=======================================
Files 87 87
Lines 26158 26158
Branches 6874 6874
=======================================
Hits 8541 8541
+ Misses 16656 16645 -11
- Partials 961 972 +11
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@goldmanm, this PR should be relatively easy. Do you mind taking a look? (rebased on the Py3 master) |
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Will look at it today.
…On September 25, 2019 2:40:17 PM EDT, Alon Grinberg Dana ***@***.***> wrote:
@goldmanm, this PR should be relatively easy. Do you mind taking a
look? (rebased on the Py3 master)
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#1685 (comment)
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goldmanm
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Sep 26, 2019
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Motivation or Problem
Previously Arkane joined the base path of the species file with any statmech file (ESS output) path, assuming that the paths to the statmech files are relative to the species file directory.
In StatMechJob.load(),
pathis the path to the Arkane specie file, anddirectoryis the base path ofpath. When we read an ESS log file we joindirectoryand its path, e.g.:os.path.join(directory, energy.path). However, ifenergy.pathis a relative path (of the single point calculation output file), Arkane won't be able find the latter due to this path manipulation.Description of Changes
All statmech files specified by users (energy, geometry, frequency, scans) are now first checked to see if they exist, if not we relate to them as relative to
directory(and if that doesn't work, we raise an error).Testing
Added a test for absolute paths (fails on master)
Reviewer Tips
See that the code makes sense, try specifying an absolute path in a species statmech file and run on this branch (should fail on master)
(edited)