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Merged
merged 9 commits into from
Apr 25, 2018
Merged

Try to get code coverage back to the top #51

merged 9 commits into from
Apr 25, 2018

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sven1103
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@sven1103 sven1103 commented Apr 20, 2018 •
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  • Rewrite pretty_date() method
  • Provide tests for pretty_date() method
  • Provide tests for remote wf queries
  • Provide tests for local wf queries

@sven1103 sven1103 added the WIP Work in progress label Apr 20, 2018
@sven1103 sven1103 self-assigned this Apr 20, 2018
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codecov-io commented Apr 20, 2018 •
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Codecov Report

Merging #51 into master will increase coverage by 13.68%.
The diff coverage is 87.5%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #51       +/-   ##
==========================================
+ Coverage   81.11%   94.8%   +13.68%     
==========================================
  Files           4       4               
  Lines         519     500       -19     
==========================================
+ Hits          421     474       +53     
+ Misses         98      26       -72
Impacted Files Coverage Δ
nf_core/list.py 84.79% <87.5%> (+36.37%) ⬆️

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@sven1103 sven1103 requested review from a team and ewels and removed request for ewels April 23, 2018 12:02
@sven1103 sven1103 removed the WIP Work in progress label Apr 23, 2018
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This is it, for now, the remaining lines are tough, need some clever mocking for that.

ewels
ewels approved these changes Apr 25, 2018
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Awesome work 👏

Sorry for the slow review!!

tests/test_list.py

rwf_ex = nf_core.list.RemoteWorkflow(remote)
rwf_ex.commit_sha = "aw3s0meh1sh"
rwf_ex.releases = [{'tag_sha': "aw3s0meh1sh"}]
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Love it 😀

@ewels ewels merged commit 013552e into nf-core:master Apr 25, 2018
edmundmiller added a commit that referenced this pull request Oct 1, 2025
@edmundmiller
feat(template): migrate to nf-core-utils plugin
2c57587 
Integrate nf-core-utils plugin v0.3.0 to replace utility subworkflows
with centralized plugin functions, following RFC proposal #51.

Major changes:
- Add nf-core-utils@0.3.0 plugin to nextflow.config
- Replace UTILS_NEXTFLOW_PIPELINE subworkflow with direct plugin calls
- Replace UTILS_NFCORE_PIPELINE subworkflow with plugin functions
- Replace UTILS_NFSCHEMA_PLUGIN subworkflow with nf-schema plugin calls
- Remove entire subworkflows/nf-core/ directory
- Update modules.json to remove nf-core subworkflows

Functions now provided by nf-core-utils plugin:
- getWorkflowVersion, dumpParametersToJSON, checkCondaChannels
- completionEmail, completionSummary, imNotification
- checkConfigProvided, checkProfileProvided
- processVersionsFromFile, workflowVersionToChannel

Functions retained in local subworkflow:
- paramsSummaryMultiqc, softwareVersionsToYAML (uses plugin functions)
- getGenomeAttribute, validateInputSamplesheet
- toolCitationText, methodsDescriptionText

Closes: #3685
Related: nf-core/proposals#51

feat(template): migrate to nf-core-utils plugin

- Add nf-core-utils@0.3.0 plugin to nextflow.config
- Replace all nf-core subworkflow imports with plugin imports
  - utils_nextflow_pipeline functions -> direct plugin calls
  - utils_nfcore_pipeline functions -> plugin/nf-core-utils
  - utils_nfschema_plugin functions -> plugin/nf-schema
- Use plugin functions for version processing:
  - processVersionsFromFile() instead of local implementation
  - workflowVersionToChannel() instead of local implementation
- Remove entire subworkflows/nf-core/ directory
- Update modules.json: empty nf-core subworkflows section
- Update test expectations for removed subworkflows

Closes #3685
edmundmiller added a commit that referenced this pull request Oct 1, 2025
@edmundmiller
feat(template): migrate to nf-core-utils plugin
e908f0a 
Integrate nf-core-utils plugin v0.3.0 to replace utility subworkflows
with centralized plugin functions, following RFC proposal #51.

Major changes:
- Add nf-core-utils@0.3.0 plugin to nextflow.config
- Replace UTILS_NEXTFLOW_PIPELINE subworkflow with direct plugin calls
- Replace UTILS_NFCORE_PIPELINE subworkflow with plugin functions
- Replace UTILS_NFSCHEMA_PLUGIN subworkflow with nf-schema plugin calls
- Remove entire subworkflows/nf-core/ directory
- Update modules.json to remove nf-core subworkflows

Functions now provided by nf-core-utils plugin:
- getWorkflowVersion, dumpParametersToJSON, checkCondaChannels
- completionEmail, completionSummary, imNotification
- checkConfigProvided, checkProfileProvided
- processVersionsFromFile, workflowVersionToChannel

Functions retained in local subworkflow:
- paramsSummaryMultiqc, softwareVersionsToYAML (uses plugin functions)
- getGenomeAttribute, validateInputSamplesheet
- toolCitationText, methodsDescriptionText

Closes: #3685
Related: nf-core/proposals#51

feat(template): migrate to nf-core-utils plugin

- Add nf-core-utils@0.3.0 plugin to nextflow.config
- Replace all nf-core subworkflow imports with plugin imports
  - utils_nextflow_pipeline functions -> direct plugin calls
  - utils_nfcore_pipeline functions -> plugin/nf-core-utils
  - utils_nfschema_plugin functions -> plugin/nf-schema
- Use plugin functions for version processing:
  - processVersionsFromFile() instead of local implementation
  - workflowVersionToChannel() instead of local implementation
- Remove entire subworkflows/nf-core/ directory
- Update modules.json: empty nf-core subworkflows section
- Update test expectations for removed subworkflows

Closes #3685
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@sven1103 @codecov-io @ewels
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