Joss paper response to review #146
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adamKpark
commented
Jan 8, 2026
adamKpark
commented
- Readme: Added some clarifications reflecting the comments by JOSS reviewers.
- joss/*: Includes all document components used to generate the JOSS paper.
- workflow/draft-pdf: Triggers the workflow (in Action) that generates a JOSS draft pdf on commit.
Added missing comma was added that was causing the bib file test fail.
…ki D, Brown CT. 2022. Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers. bioRxiv 10.1101/2022.01.11.475838 [DOI] per JOSS reviewer request
…e example section of the main JOSS paper
…ata of a defined microbial mock community." Scientific data 3.1 (2016): 1-8.
Change title by adding "Software for" (refer to JOSS reviewer #137)
added description of what statistical framework is being referred to
readme - Added target audiences and the problem statement at the front, briefly wrote the dependencies. JOSS/paper.md - figure formatting, references from and within figures and tables, input clarifications.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #146 +/- ##
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Coverage 51.40% 51.40%
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Files 11 11
Lines 1171 1171
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Hits 602 602
Misses 569 569 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Merge branch 'main' into JOSS_paper
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
| runs-on: ubuntu-latest | ||
| name: Paper Draft | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| - name: Build draft PDF | ||
| uses: openjournals/openjournals-draft-action@master | ||
| with: | ||
| journal: joss | ||
| # This should be the path to the paper within your repo. | ||
| paper-path: joss/paper.md | ||
| - name: Upload | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: paper | ||
| # This is the output path where Pandoc will write the compiled | ||
| # PDF. Note, this should be the same directory as the input | ||
| # paper.md | ||
| path: joss/paper.pdf No newline at end of file |
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Workflow does not contain permissions Medium
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AI 12 days ago
In general, you fix this by explicitly specifying a permissions block in the workflow (either at the top level or per job) to restrict the GITHUB_TOKEN to the minimal scopes required. For this workflow, the steps only read repository contents and upload an artifact; they do not push commits, modify issues, or alter PRs. The minimal and recommended setting is therefore contents: read.
The best fix is to add a root-level permissions block, which will apply to all jobs in this workflow (currently just paper). Insert it just after the name: line and before the on: block. Set contents: read as suggested by CodeQL. No additional imports, methods, or definitions are required because this is just a YAML configuration change.
Concretely:
- Edit
.github/workflows/draft-pdf.yml. - After line 1 (
name: Draft PDF), insert:
permissions:
contents: readThis limits the GITHUB_TOKEN in this workflow to read-only access to repository contents, which is sufficient for actions/checkout and the build step.
| @@ -1,4 +1,6 @@ | ||
| name: Draft PDF | ||
| permissions: | ||
| contents: read | ||
| on: | ||
| push: | ||
| paths: |
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| - name: Build draft PDF | ||
| uses: openjournals/openjournals-draft-action@master |
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Unpinned tag for a non-immutable Action in workflow Medium
Corrected citation formatting on markdown (main body). It should be a semicolon, not a comma when listing multiple citations.
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