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Versioning #269

Merged
merged 12 commits into from
May 6, 2022
Merged

Versioning #269

merged 12 commits into from
May 6, 2022

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evanroyrees
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@evanroyrees evanroyrees commented May 6, 2022

  • 📝🎨🐍 Add autometa entrypoint (prints --version, --citation, or w/o args; commands with urls to docs and code)
  • 🎨⬆️ pin black to version 22.3.0 for .pre-commit-config.yaml hooks and within test/environment.yml
  • 🐛⬆️ Previous black version was causing failures during pre-commit hook formatting. Upgrading to v22.3.0 resolves this issue
  • 🐳 Add autometa --version when checking entrypoints in Dockerfile

One may test the autometa entrypoint by issuing the following commands:

Env setup

git clone -b versioning https://github.com/KwanLab/Autometa
cd Autometa
make create_environment
conda activate autometa
make install

Command

autometa

image

autometa --version
# or
autometa -V

image

autometa --citation
# or
autometa -C

image

PR checklist

  • This comment contains a description of changes (with reason).
  • Have you followed the pipeline conventions in the contribution docs

🎨⬆️ pin black to version 22.3.0 for .pre-commit-config.yaml hooks and within test/environment.yml
📝🎨🐍 autometa entrypoint prints version, citation, commands, urls to docs and code
🐳 Add 'autometa --version' when checking entrypoints in Dockerfile
🎨 Include autometa/validation/benchmark.py, autometa/validation/datasets.py, tests and bin in black command
@evanroyrees evanroyrees added documentation Improvements or additions to documentation enhancement New feature or request python Python related issues/code labels May 6, 2022
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github-actions bot commented May 6, 2022

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c26acca

+| ✅  62 tests passed       |+
#| ❔  34 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/autometa/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/autometa/main/nextflow_schema.json
  • schema_description - No description provided in schema for parameter: plaintext_email
  • schema_description - No description provided in schema for parameter: custom_config_version
  • schema_description - No description provided in schema for parameter: custom_config_base
  • schema_description - No description provided in schema for parameter: hostnames
  • schema_description - No description provided in schema for parameter: show_hidden_params
  • schema_description - No description provided in schema for parameter: singularity_pull_docker_container

❔ Tests ignored:

  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_exist - File is ignored: .github/workflows/branch.yml
  • files_exist - File is ignored: .github/workflows/ci.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: assets/nf-core-autometa_logo_light.png
  • files_exist - File is ignored: docs/usage.md
  • files_exist - File is ignored: docs/output.md
  • files_exist - File is ignored: docs/images/nf-core-autometa_logo.png
  • files_exist - File is ignored: docs/images/nf-core-autometa_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-autometa_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/bug_report.md
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/feature_request.md
  • nextflow_config - nextflow_config
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File does not exist: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File does not exist: assets/nf-core-autometa_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-autometa_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-autometa_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or foo
  • actions_ci - '.github/workflows/ci.yml' not found
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/Autometa/Autometa/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2022-05-06 06:20:00

🔥 Remove import 'from importlib_metadata import entry_points' in autometa/__init__.py
@codecov
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codecov bot commented May 6, 2022

Codecov Report

Merging #269 (c26acca) into dev (5002fd7) will increase coverage by 27.72%.
The diff coverage is 78.78%.

@@           Coverage Diff            @@
##           dev     #269       +/-   ##
========================================
+ Coverage     0   27.72%   +27.72%     
========================================
  Files        0       47       +47     
  Lines        0     5406     +5406     
========================================
+ Hits         0     1499     +1499     
- Misses       0     3907     +3907     
Flag Coverage Δ
unittests 27.72% <78.78%> (?)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
autometa/common/utilities.py 22.69% <ø> (ø)
autometa/taxonomy/lca.py 8.79% <0.00%> (ø)
autometa/common/kmers.py 88.02% <66.66%> (ø)
autometa/__main__.py 86.95% <86.95%> (ø)
autometa/__init__.py 100.00% <100.00%> (ø)
autometa/validation/cluster_process_docker.py 0.00% <0.00%> (ø)
autometa/binning/recursive_dbscan.py 84.80% <0.00%> (ø)
autometa/config/environ.py 19.81% <0.00%> (ø)
autometa/common/external/hmmscan.py 17.35% <0.00%> (ø)
autometa/common/external/samtools.py 71.42% <0.00%> (ø)
... and 40 more

Continue to review full report at Codecov.

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@evanroyrees evanroyrees self-assigned this May 6, 2022
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@Sidduppal Sidduppal left a comment

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Looks good to me.

@evanroyrees evanroyrees merged commit 042293d into dev May 6, 2022
@evanroyrees evanroyrees deleted the versioning branch May 6, 2022 15:58
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