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Implement CI testing and increase testing coverage #413

Merged
merged 44 commits into from
Feb 9, 2024
Merged

Implement CI testing and increase testing coverage #413

merged 44 commits into from
Feb 9, 2024

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kedhammar
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Also discovered some bugs :)

@kedhammar
bump dev reqs
605d66c
@kedhammar
move functional tests into subdir
ed107e2
@kedhammar
move configuration of pytest to pyproject.toml and replace coverage e…
1d89ecd 
…xclusion method
@kedhammar
start building testing framework
6493113
@kedhammar
remove unused var
24eb34a
@kedhammar
update hint for checking manual coverage
d25471e
@kedhammar
wip
bcc91ea
@kedhammar
good progress
f44e48c
@kedhammar
bump file being tested to dev version
233b84a
@kedhammar
successfully instantiate run object for testing
42975cd
@kedhammar
update docs
b0c6f07
@kedhammar
fix error, 28% coverage!
d763fe7
@kedhammar
Merge remote-tracking branch 'upstream/master' into pytest-ci
742f97b
@kedhammar
update config to ignore deprecationwarnings from external packages
fc0ed3f
@kedhammar
docstring
c6db7ae
@kedhammar
move fixture to conftest file
f5ce95f
@kedhammar
wip
2aac3c4
@kedhammar
remove redundancy
36bb0ee
@kedhammar
update test
35d33a5
@kedhammar
add conditional files to created run dir
1604858
@kedhammar
remove irrelevant rows from test data
6721af6
@kedhammar
Don't fail ONT run class instantiation w. missing analysis server config
99293ae
@kedhammar
ATTN! Fix what I interpret as a bug
94999d2
@kedhammar
remove analysis server from test config and add mail mock entry
957de2b
@kedhammar
functional user run processing, continuing with qc run
e61d7e6
@kedhammar
add comment headers
1fe5081
@kedhammar
formatting
42514e2
@kedhammar
add anglerfish samplesheets dir to fixture
6e2a1fe
@kedhammar
make samplesheet glob agnostic to current year and fix bug
3fe7cc4
@kedhammar
- add anglerfish dir to config and add more options for creating test…
78967b0 
… run
@kedhammar kedhammar marked this pull request as ready for review February 7, 2024 16:19
@kedhammar
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@alneberg I marked as ready for review a bit prematurely, just gotta fix the CI-checks.

alneberg
alneberg approved these changes Feb 9, 2024
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@alneberg alneberg left a comment

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Looks good!

@kedhammar kedhammar merged commit 0a6a4b8 into SciLifeLab:master Feb 9, 2024
7 checks passed
@kedhammar kedhammar deleted the pytest-ci branch February 9, 2024 08:33
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@alneberg alneberg alneberg approved these changes

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@kedhammar @alneberg