Joss paper edit #143
Joss paper edit #143
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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
![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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How to, in general terms, fix the problem:
Add a permissions block to the workflow or job to explicitly restrict the GITHUB_TOKEN permissions just to what is needed. If no write access is necessary, set to contents: read.
Best way to fix the problem without changing existing functionality:
Insert a permissions: block with contents: read immediately after the workflow name: and before the on: key (i.e., applying it at the workflow level). This ensures that all jobs in the workflow receive only read permission on contents, following the principle of least privilege. No further modifications to jobs or steps are required.
What needs changing:
- Edit
.github/workflows/draft-pdf.yml - Add a
permissions:block at the root level withcontents: read
| @@ -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
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.
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Edited the title and
Summarysection, first paragraph, adding description of statistical framework per reviewer's request