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Add workflow for version check and release; add CHANGELOG.md; remove …
…ignoring README.md when packaging; update README.md
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,66 @@ | ||
| name: Publish release | ||
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| on: | ||
| push: | ||
| tags: | ||
| - v[0-9]+.[0-9]+.[0-9]+* | ||
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| jobs: | ||
| version_check: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| sparse-checkout: | | ||
| README.md | ||
| sparse-checkout-cone-mode: false | ||
| fetch-tags: true | ||
| token: ${{ secrets.GITHUB_TOKEN }} | ||
| ref: master | ||
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| - name: Capture version in README.md | ||
| id: file | ||
| run: | | ||
| repo_name=$(basename "$GITHUB_REPOSITORY") | ||
| cap=$(grep -oP "${repo_name}-v\K\d\.\d\.\d[^\s]*" README.md) | ||
| echo "version=$cap" >> "$GITHUB_OUTPUT" | ||
| echo "repo_name=$repo_name" >> "$GITHUB_OUTPUT" | ||
| - name: Capture version in latest tag | ||
| id: tag | ||
| run: echo "version=$(git tag --sort=committerdate -l "v*" | tail -n1 | sed 's/^v//')" >> "$GITHUB_OUTPUT" | ||
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| - name: Substitute version in README.md | ||
| id: sub | ||
| if: ${{ steps.file.outputs.version != steps.tag.outputs.version }} | ||
| run: sed -i 's/${{ steps.file.outputs.repo_name}}-${{ steps.file.outputs.version }}/${{ steps.file.outputs.repo_name}}-${{ steps.tag.outputs.version }}/g' README.md | ||
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| - name: Push changes | ||
| if: steps.sub.conclusion == 'success' | ||
| run: | | ||
| git config author.name Cheng-Hung Tsai | ||
| git config author.email chenghung.tsai@email.ucr.edu | ||
| git config committer.name GitHub Actions | ||
| git config committer.email actions@github.com | ||
| git add README.md | ||
| git commit -m "Update version in README.md" | ||
| git tag --annotate v${{ steps.tag.outputs.version }} -m "Version bump to v${{ steps.tag.outputs.version }}" --force | ||
| git push | ||
| git push --tags --force | ||
| publish_release: | ||
| runs-on: ubuntu-latest | ||
| needs: version_check | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| ref: master | ||
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| - name: Release | ||
| uses: docker://antonyurchenko/git-release:v5 | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| with: | ||
| args: build/*.zip |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| # Changelog | ||
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| All notable changes to this project will be documented in this file. | ||
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| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), | ||
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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| ## [Unreleased] | ||
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| ## [2.0.0-beta] - 2023-11/14 | ||
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| ### Added | ||
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| - Check for duplicated sample names. | ||
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| - Report problematic cds sequences. | ||
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| - Use checkpoint file to save the hmmsearch results to prevent rerunning the search process when adding/removing samples. | ||
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| ### Changed | ||
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| - Use ClipKIT to replace the self-defined function for trimming off the sites that display poor phylogenetic signal. | ||
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| - Move the MSA concatenate function from align module to tree module. Users who want to try different tree building strategy won't have to rerun the align module again. | ||
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| - Replace the VeryFastTree with FastTree for stability. | ||
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| ### Fixed | ||
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| - Fix the bug caused by translation from cds sequences with invalid length. | ||
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| - Fix the bug caused by inconsistent MSA output extension. | ||
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| - Fix the bug that the trimming function always return peptide MSA if the sequence has no site being trimmed. | ||
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| - Fix the Python logger issue. | ||
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| ## [2.0.0-alpha] - 2023/10/04 | ||
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| ### Added | ||
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| - Add Download module to download the conserved markerset HMM profiles from BUSCO v5 dataset. | ||
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| - Add align module which driven by pyhmmer to perform hmmsearch and hmmalign against the BUSCO markerset. | ||
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| - Add tree module to visualize the resulting phylogenetic tree. | ||
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| - Implement back-translation to convert the peptide MSA results to DNA counterpart when receiving coding sequence fasta as inputs. | ||
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| [2.0.0-beta]: https://github.com/stajichlab/PHYling/compare/v2.0.0-beta...v2.0.0-alpha | ||
| [2.0.0-alpha]: https://github.com/stajichlab/PHYling/releases/tag/v2.0.0-alpha |
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