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Misc. improvements, unit tests and mypy proofing #85

Merged
merged 39 commits into from
Jun 26, 2024
Merged

Misc. improvements, unit tests and mypy proofing #85

merged 39 commits into from
Jun 26, 2024

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kedhammar
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kedhammar added 30 commits May 30, 2024 13:40
@kedhammar
add tests
bc23fde
@kedhammar
reorganize dirs, add testcase
5a8cac6
@kedhammar
bugfix
656d710
@kedhammar
add lots of tests
9bd123c
@kedhammar
improve docs
d7a8a14
@kedhammar
add tests and safeguard
4eefaad
@kedhammar
add __pycache__ to .gitignore and alphabetize it
64263e0
@kedhammar
add gha for running pytest
071324d
@kedhammar
add pytest to dev requirements
d4938f7
@kedhammar
cleanup wip
9474946
@kedhammar
annotation, variable access and naming
8a84737
@kedhammar
rename testdir and start adding fabricated testdata for explore
84db62e
@kedhammar
add dissected .paf for useful reference
1fb87be
@kedhammar
improve docs
68b851b
@kedhammar
add simple test case for minimap2
15dd424
@kedhammar
ruff
c847dde
@kedhammar
fix introduced bug by argument reversal and update test
a75ac3d
@kedhammar
more tests
c2442a9
@kedhammar
add type annotation
d6c89e9
@kedhammar
ruff
2fe7f0d
@kedhammar
test wip
4baa2ff
@kedhammar
new testdata subset, new test
e71ccee
@kedhammar
improve docs
a8c335c
@kedhammar
docs
1dd81b7
@kedhammar
improve readability and documentation
b22a430
@kedhammar
add more tests and update testdata constructors
0611efe
@kedhammar
separate attribute type declaration and instantiation of class
8dfac77
@kedhammar
don't dump output in testdata folder
3b4e003
@kedhammar
typo
588b335
@kedhammar
type annotation
1231513
@kedhammar kedhammar requested a review from remiolsen June 12, 2024 12:24
@kedhammar kedhammar added the enhancement New feature or request label Jun 12, 2024
@kedhammar kedhammar requested a review from alneberg June 14, 2024 14:44
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I think it looks good! Let me know when it's not in draft mode.

@kedhammar kedhammar marked this pull request as ready for review June 18, 2024 13:58
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Still need to fix CI-errors, but code is ready for review.

@kedhammar kedhammar requested a review from alneberg June 18, 2024 13:58
alneberg
alneberg approved these changes Jun 25, 2024
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👍 according to previous comment.

remiolsen
remiolsen previously requested changes Jun 26, 2024
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This is very nice work.

tests/test_anglerfish/test_demux/test_demux.py Show resolved Hide resolved
@kedhammar kedhammar dismissed remiolsen’s stale review June 26, 2024 11:55

Requested changes will be adressed in future PR.

remiolsen
remiolsen approved these changes Jun 26, 2024
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Re-reviewing this as approved since requested changes is invalidated by another PR.

@kedhammar kedhammar merged commit ec25bfe into NationalGenomicsInfrastructure:master Jun 26, 2024
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@kedhammar kedhammar deleted the ake-dev branch June 26, 2024 11:56
kedhammar referenced this pull request in kedhammar/anglerfish Jul 2, 2024
@kedhammar
limit scope of tests https://github.com/remiolsen/anglerfish/pull/85#…
337a20a 
…discussion_r1654331636
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@remiolsen remiolsen remiolsen approved these changes

@alneberg alneberg alneberg approved these changes

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3 participants
@kedhammar @alneberg @remiolsen