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Release/v2.3.0 #52

Merged
merged 95 commits into from
Oct 25, 2024
Merged

Release/v2.3.0 #52

merged 95 commits into from
Oct 25, 2024

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ellendejong
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ALuesink and others added 30 commits July 8, 2024 16:10
@ALuesink
Merge pull request #40 from UMCUGenetics/hotfix-2.2.1
1731f99 
Hotfix 2.2.1 to develop
@ALuesink
Merge pull request #42 from UMCUGenetics/hotfix-2.2.2
d571ef0 
Hotfix 2.2.2 to develop
@ellendejong
add pandas to dockerfile
73e7f37
@ellendejong
refactor kinship: use pandas and add user friendly message if kinship…
4d22c20 
… check fails
@ellendejong
Install CustomModules as package to enable import of utils
9059f93
@ellendejong
add non_empty_existing_path to utils
658a832
@ellendejong
Move parse_ped to utils and add unit tests
0e9d1f7
@ellendejong
add utils and remove unused imports
c56a676
@ellendejong
use non_empty_existing_path in argparser
2857d93
@ellendejong
fix quote issues
3b7909f
@ellendejong
add pytest
16abdac
@ellendejong
add docstrings to check_kinship
677032f
@ellendejong
add docstring to non_empty_existing_path
0d7c4d1
@ellendejong
add docstring parse_ped
c5c9d13
@ellendejong
resolve flake8 warnings and errors.
0d10f6e
@ellendejong
Add message to output
7d0ecd7
@ellendejong
add pyproject custommodules
0e6a209
@ellendejong
Instead of using util functions, duplicate function in tool.
96f0bba
@ellendejong
add poetry project
f4b5d49
@ellendejong
Add github workflows kinship lint and test
2a7d6ac
@ellendejong
Change python version
bcffc89
@ellendejong
Add missing dependencies using poetry
407e569
@ellendejong
add dependency pytest-datadir
81ea36e
@ellendejong
Move parse_ped to utils and add unit tests
fc23da1
@ellendejong
Change import of parse_ped
9392db8
@ellendejong
Use poetry and add github workflows
224a91f
@ellendejong
remove custommodules install as package in readme
1d7f5dc
@ellendejong
remove init in custommodules
e22c2d6
@ellendejong
revert parse_ped pytest in utils, will be added to dev via another br…
79cd433 
…anch
@ellendejong
change compare_gender to required params
90c0913
ellendejong and others added 26 commits October 9, 2024 13:46
@ellendejong
Validate gender.
a7330d7
@ellendejong
Move translation of gender to dedicated function.
5519fc7
@ellendejong
Rename true and test gender. Add unit test cases for unexpected gende…
41a6890 
…rs (for example by using upper case).
@ellendejong
Rename true_gender in .nf
38c4263
@ellendejong
Rename mapping_qual to min_mapping_qual.
aa8d45f
@ellendejong
Rename compare_gender to compare_and_evaluate_gender
2335143
@ellendejong
Add docstrings
5635be9
@ellendejong
change message to 'stated gender'.
1f7699f
@ellendejong
Fix PySam object variablename to mapping_quality.
33005dd
@ellendejong
use pip3
da15079
@ellendejong
Remove setuptools.
3f4ef68
@melferink
refactor
0bd1fb1
@melferink
refactor of docstring for clarification combined with more descriptiv…
1341341 
…e param names
@melferink
codereview refactor
fed0aa0
@melferink
added comment to make astype conversion more clear
5e995ab
@ellendejong
Merge pull request #43 from UMCUGenetics/feature/refactor_kinship_pri…
12f456a 
…nt_to_write

Feature/refactor kinship print to write
@ellendejong
Merge pull request #47 from UMCUGenetics/feature/update_messages
14b3af8 
Add message to output GenderCheck
@melferink
moved astype to other function, added docstring and try/except
1a95a0d
@melferink
updated
c80fc2b
@ellendejong
Merge remote-tracking branch 'origin/develop' into feature/add_pytest…
c443f0d 
…_parse_ped
@ellendejong
Merge pull request #46 from UMCUGenetics/feature/add_pytest_parse_ped
1a2bdee 
Feature/add pytest parse ped
@ellendejong
Merge remote-tracking branch 'origin/develop' into feature/giabeval_m…
0ad0138 
…ultiqc
@ellendejong
Merge pull request #48 from UMCUGenetics/feature/giabeval_multiqc
2d4600a 
Feature/giabeval_multiqc
@ellendejong
fix checkqc test by creating a valid qc metric (all required columns)
3736ca0
@ellendejong
Merge pull request #51 from UMCUGenetics/fix/test_checkqc
297bcec 
fix checkqc test by creating a valid qc metric (all required columns)
@ellendejong
Merge remote-tracking branch 'origin/develop' into release/v2.3.0
8f25f19
@BasMonkey BasMonkey self-requested a review October 25, 2024 06:04
BasMonkey
BasMonkey approved these changes Oct 25, 2024
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All commits are reviewed. All OK!

@melferink melferink merged commit 976e215 into main Oct 25, 2024
4 checks passed
@melferink melferink deleted the release/v2.3.0 branch October 25, 2024 06:10
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@BasMonkey BasMonkey BasMonkey approved these changes

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4 participants
@ellendejong @BasMonkey @melferink @ALuesink