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Add more module testing and upgrade to pytest #166

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merged 23 commits into from
Jul 27, 2020
+254 −175
Merged

Add more module testing and upgrade to pytest #166

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a93ad29
Added tearDown function to TestTools.
Jul 21, 2020
8d39c5d
Changed name of map2function method.
Jul 22, 2020
0db0da0
Reordered imports.
Jul 22, 2020
e461f0b
Removed tearDown method.
Jul 22, 2020
6985f33
Migrate to pytest.
Jul 23, 2020
e4766d7
Add pytest to .travis.yml.
Jul 23, 2020
249377b
Delete mpi tests.
Jul 23, 2020
d0a1b54
Add pip installation of package for pytest.
Jul 23, 2020
82d8238
Added codecov.
Jul 23, 2020
cc625e9
Update version of pytest.
Jul 23, 2020
f142f08
Update travis script.
Jul 23, 2020
39f2a92
Deprecate code coverage.
Jul 24, 2020
9845980
Remove pytest version.
Jul 24, 2020
62a8dc8
Change warn to warning.
Jul 24, 2020
2bc1ffd
Added OrthoBlastN test.
Jul 24, 2020
f9121cb
Expose auto_start method for OrthoBlastN.
Jul 24, 2020
b00ca64
Changed .ix or .loc
Jul 24, 2020
f29348a
Fixed OrthoBlastN.
Jul 24, 2020
35748d4
warn to warning.
Jul 26, 2020
d7855b1
Fixed spelling error in mygene.py
Jul 26, 2020
d2e60f8
Expanded test_multiprocess.
Jul 26, 2020
45d7a56
Light reformatting and refactoring.
Jul 26, 2020
90972d4
Light reformatting.
Jul 26, 2020
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warn to warning.
Shaurita Hutchins committed Jul 26, 2020
commit 35748d44130d6d9ac65bf761923570241dd7efd5
4 changes: 2 additions & 2 deletions OrthoEvol/utilities.py
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Original file line number Diff line number Diff line change
@@ -234,9 +234,9 @@ def get_dup_acc(self, acc_dict, gene_list, org_list):
elif orgs.count(o) != 1:
alt_genes = list(
gene for gene, org in go_list if org == o)
blastutils_log.warn(
blastutils_log.warning(
"A duplicate accession number(%s) persists across %s for %s." % (accession, o, alt_genes))
blastutils_log.warn("%s is also duplicated elsewhere." % accession)
blastutils_log.warning("%s is also duplicated elsewhere." % accession)
duplicated_dict['organisms'][o][accession] = alt_genes

# Duplicates that persist across a gene