diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 0000000..e6b7435 --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,51 @@ + + +## Description + + + +## Related issue + + +Closes # + +## What changed + + + +- +- + +## Testing + + + +**Test environment:** + +- Dataset used: +- Key parameters: + +**Results:** + +- + +## Documentation + + +- [ ] Added/updated code comments +- [ ] Added/updated docstring +- [ ] Updated README or docs if needed +- [ ] Added example usage (if relevant) + +## Checklist + + +- [ ] My code follows the project guidelines +- [ ] Complex logic is commented +- [ ] No unnecessary files or debug code included +- [ ] My PR is targeting the `dev` branch + +## Additional notes + + + diff --git a/VERSION b/VERSION index a918a2a..ee6cdce 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.6.0 +0.6.1 diff --git a/docs/developer/git.md b/docs/developer/git.md index 68fb84f..3afbc15 100644 --- a/docs/developer/git.md +++ b/docs/developer/git.md @@ -97,44 +97,38 @@ You've done the hard work - now let's get it merged! ### PR Title and Description -Write a clear title that summarizes your change and use the PR template to provide context: +Write a clear title that summarizes your change and use the PR template to provide context. -```markdown -## What does this PR do? - -Adds a new module for detecting CRISPR-Cas systems in bacterial genomes using HMM profiles. - -## Why is this needed? - -Many users requested CRISPR detection capabilities. This addresses issue #123. - -## What changed? - -- Added `panorama/crispr/detector.py` with detection logic -- Added HMM profiles for Cas proteins -- Added unit tests (coverage: 95%) -- Updated user documentation with examples +```{important} +If your PR addresses an issue, link it! Use these keywords in your PR description: +- `Fixes #123` - Automatically closes issue when PR merges +- `Closes #123` - Same as above +- `Related to #123` - Links without closing +``` -## How to test? +### For reviewer -pytest tests/test_crispr.py -panorama detect_crispr --pangenome examples/ecoli.h5 +Before to validate the commit change, you should check the elements in the following template for reviewer. -## Related Issues +```md +## Quick Review -Closes #123 -Related to #456 +### ✅ Checks +- [ ] Code runs correctly +- [ ] Logic makes sense +- [ ] No obvious bugs +- [ ] Comments help understand the code -## Version +### 💬 Feedback + -Updated VERSION from 1.2.5 → 1.2.6 +**Status:** ✅ Approved / 🔄 Suggestions / ❌ Changes needed ``` -```{important} -If your PR addresses an issue, link it! Use these keywords in your PR description: -- `Fixes #123` - Automatically closes issue when PR merges -- `Closes #123` - Same as above -- `Related to #123` - Links without closing +```{tip} +You can add this template direclty in your saved replies (Go to your Settings->Saved replies) + +See [Using saved replies documentation](https://docs.github.com/en/get-started/writing-on-github/working-with-saved-replies/using-saved-replies) ``` ## Keeping Your Branch Updated