21
/ 100
Some interest. A stronger README and CI would help.
:book: Biomedical knowledge mining using GOSemSim and clusterProfiler
A low grade is a to-do list, not a judgment of your code
Most gaps here are documentation, tests, and setup, not the code itself. Closing your top 3 gaps alone would add 30 points.
See your top fixesTop fixes
Highest-impact changes first, ranked by point weight
- 1Tests18pt
Add automated tests. They prove the code works and give contributors confidence to make changes.
- 2CI/CD14pt
Add a step like `run: npm test`, `run: pytest`, or `run: tox` to your workflow file.
- 3CI/CD14pt
Add a lint step to catch style issues automatically.
- 4CI/CD14pt
Add `tsc --noEmit`, `mypy`, or `cargo check` to catch type errors before they merge.
Working through the fixes? Let every push regrade itself.
The free GitHub App rescans this repo on every push and posts the grade as a commit check, so the score climbs without coming back to rescan by hand.
Scorecard
Every check, grouped by category and sorted worst-first
Documentation
21
No install instructions found in the README (−45 pts).
→ Add a section showing how to install dependencies.
No license detected.
→ Add a LICENSE file. Without one, nobody can legally use, copy, or contribute to your code.
Contributing guidance is in the README, not a dedicated CONTRIBUTING.md (−20 pts).
→ Moving it to a CONTRIBUTING.md makes it easier to find and keeps the README focused. A dedicated file earns +47 pts base.
README is present.
Engineering
16
No tests detected anywhere in the repository.
→ Add automated tests. They prove the code works and give contributors confidence to make changes.
No linter or formatter config found.
→ Add a linter config such as .eslintrc.json, .prettierrc, ruff.toml, or .golangci.yml to enforce consistent code style.
No dependency lockfile found (−70 pts).
→ Commit the lockfile for this project's package manager so installs produce the same dependency versions everywhere.
No issue or PR templates found (−100 pts).
→ Add .github/ISSUE_TEMPLATE/ with bug_report.md and feature_request.md to guide contributors. It dramatically improves issue quality.
CI is configured (.github/workflows/publish-book.yml).
Project health
68
No dependency manifest detected at root.
→ Add a manifest (package.json, pyproject.toml, Cargo.toml, go.mod, etc.) so others can install dependencies in one command.
Repository has a description.
Actively maintained (pushed within the last month).
.gitignore present.
Repository health signals
Activity, community, and responsiveness at scan time
Activity
- -Commits (30d / 90d)
- 30Forks
- 0Releases
Community
- 25% - WeakCommunity health
- 1 bus factorlowauthor own >50% of commits
- 95Watchers
Responsiveness
- 2hMedian issue response
- 21hMedian PR merge time
- 20Open issues
Repository files39 root entries
- .githubGood: CI is configured (.github/workflows/publish-book.yml).
- cache
- datasets
- figures
- _common.R
- _quarto.yml
- .gitignoreGood: .gitignore present.
- 01-semantic-similarity.qmd
- 011-GOSemSim.qmd
- 012-DOSE-semantic-similarity.qmd
- 013-meshes-semantic-similarity.qmd
- 02-Enrichment.qmd
- 020-enrichment-algorithms-check.R
- 020-enrichment-algorithms.qmd
- 021-go.qmd
- 022-kegg.qmd
- 023-other-dbs.qmd
- 024-reactome.qmd
- 025-do-enrichment.qmd
- 026-meshes-enrichment.qmd
- 027-universal-enrichment.qmd
- 028-chipseeker.qmd
- 029-compareCluster.qmd
- appendix.qmd
- bayesian-term-selection.qmd
- clusterProfiler-diagram.R
- COVID19_GeneSets.gmt
- dplyr.qmd
- enrichplot.qmd
- FAQ.qmd
- index.qmd
- interpretation.qmd
- Makefile
- misc.qmd
- PPI.qmd
- README.mdGood: README is present.Issue: README is fairly short (−10 pts). At 400+ chars you get partial credit; 1,500+ earns the full +20 pts.Fix: Expand with a description, install steps, usage, and examples.Good: README is well structured with multiple sections.Issue: No screenshots or images in the README (−20 pts).Fix: Add a GIF, screenshot, or logo image. It is the fastest way to show what your project does.Issue: README has no code examples (−15 pts).Fix: Show a quick-start snippet so contributors can see what using your project looks like.Good: README links to a live demo or deployed app.Issue: No status badges in the README (−10 pts).Fix: Add CI/build status badges from shields.io or your CI provider to signal project health.Issue: No install instructions found in the README (−45 pts).Fix: Add a section showing how to install dependencies.Issue: No run or usage instructions found (−45 pts).Fix: Add a section showing how to start or use the project.
- references.bib
- todo.md
- utilities.qmd
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