Test/add tests #114
Test/add tests #114
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note: test does not include spectra methods will have to add those/fix those later.
also do fix for toPandasDf
note: add template tests for dreamDIA but currently only DIA-NN output is tested
also minor fixes and include method for closing sqlite connection
update snapshottesting for better support with pandas for OSWDataAccess
add custom numpy snapshot extension. Add tests for MzML data access
SpectrumLoader and ChromatogramLoader are blank. GenericLoader tests the get feature methods
change filepath to relative filepath based on base .git directory so work no matter where run test from
for testing create toPandasDf() methods for TransitionGroup and TransitionGroupCollection
Also fix bugs associated with tests Note: possibly better peptide example to be chosen seems that no chromatograms selected for one of the runs
MRMPeakPicker minor updates (just to imports) since no snapshots used pyMRMPeakPicker major updates, use pandas df snapshots. Fix bugs that arose when creating tests
bug fixes, remove function _find_threshold since not used
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I believe unit test is still useful for some tests? |
I thought that pytest could also test for uniittests and it looks like it has prettier syntax? |
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Hmm - not sure! |
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Hey @jcharkow, here's the issue I raised with Syrupy developers: tophat/syrupy#861 I will leave the merging of this branch up to you |
Thank you! |
runName is the same on all systems while filename path is specific to machine meaning snapshots are not reproducible.
update ionMobility.mzML file and a pandas df file
workaround: reopen and save ionMobilityTest on the fly to make it os specific
revert ionMobilityTest.mzML to linux format so readable on ubuntu and mac. For windows use the trick previously done where re-write
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Note: there was some difficulty with tests on windows (test_MzMLDataAccess.py) because of the ionMobilityTest.mzML file not being windows compatible for OnDiscMSExperiment(). As a workaround, the file is opened as an MSExperiment() and resaved and the tests are done on the test file. See the error ran into here: |
fix gui bugs that were introduced in this PR fix test where snapshot was faulty
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@singjc is this good to merge or would you like to review this before merging? @irahorecka reviewed this and said it was good to go. |
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Some Docs still have to be updated for this since syntax has changed however the GUI looks fine |
Yes, feel free to merge when ready. |
minor updates to codebase as well with updated __repr__ for collection structs.
update snapshots - minor adjustments
fix imports so hopefully docs can build correctly. Fix typo with Pandas/Numpy SnapShotExtension classes
revert notebook to old setup because old setup works
jcharkow
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Description
Add/Update Tests
Fixes # (issue)
#112
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Pytest has been run locally on ubuntu.
Checklist:
Contents (#114)
Other
Uncategorised!