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Dev -> Master for v2.11 #2590

Merged
merged 586 commits into from
Dec 19, 2023
Merged

Dev -> Master for v2.11 #2590

merged 586 commits into from
Dec 19, 2023

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mashehu
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@mashehu mashehu commented Dec 19, 2023

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mashehu and others added 30 commits November 21, 2023 10:45
…ehu/tools into migrate-component-create-to-nf_test
…test

Migrate component create to nf test
linting tests requiring nf-test will be warnings instead of failures
there is never any dev tag, so let's point to dev branch
move set_wd from tests/utils.py to utils.py
MatthiasZepper and others added 23 commits December 18, 2023 18:33
Download: Add docker prefix for absolute container URIs as well.
add subworklow prefix to tag for swfs test command and fix pytest CI
This option is about to be stripped out of Nextflow itself, so we need to remove it from the nf-core template.

See nextflow-io/nextflow#4596
downgrade to python 3.11 in the tests
@mashehu mashehu requested a review from mirpedrol December 19, 2023 14:49
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codecov bot commented Dec 19, 2023

Codecov Report

Attention: 205 lines in your changes are missing coverage. Please review.

Comparison is base (314aa0b) 70.64% compared to head (26e43b5) 75.02%.
Report is 1 commits behind head on master.

❗ Current head 26e43b5 differs from pull request most recent head 7dccc13. Consider uploading reports for the commit 7dccc13 to get more accurate results

Files Patch % Lines
nf_core/subworkflows/lint/subworkflow_tests.py 64.70% 30 Missing ⚠️
nf_core/components/patch.py 79.04% 22 Missing ⚠️
nf_core/modules/lint/module_tests.py 77.10% 19 Missing ⚠️
nf_core/modules/bump_versions.py 64.00% 18 Missing ⚠️
nf_core/components/components_test.py 84.84% 15 Missing ⚠️
nf_core/schema.py 51.61% 15 Missing ⚠️
nf_core/components/components_utils.py 40.00% 12 Missing ⚠️
nf_core/utils.py 78.57% 12 Missing ⚠️
nf_core/__main__.py 82.25% 11 Missing ⚠️
nf_core/components/list.py 71.42% 8 Missing ⚠️
... and 14 more
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #2590      +/-   ##
==========================================
+ Coverage   70.64%   75.02%   +4.37%     
==========================================
  Files          87       85       -2     
  Lines        9431     9376      -55     
==========================================
+ Hits         6663     7034     +371     
+ Misses       2768     2342     -426     

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@mashehu mashehu merged commit 2d5ebcc into master Dec 19, 2023
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