From 797c10e3ba0e316571e3bcfa560dc9b2912b3812 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Arnoux?= <39793176+jpjarnoux@users.noreply.github.com> Date: Thu, 16 Oct 2025 16:03:59 +0200 Subject: [PATCH 1/5] Add pull request template for contributions --- .github/pull_request_template.md | 50 ++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 .github/pull_request_template.md diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 0000000..3c92b00 --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,50 @@ + + +## 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 + +## Additional notes + + + From 8b05efc4022d28761f12e02e5a9d8ab0aecca4dc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Arnoux?= <39793176+jpjarnoux@users.noreply.github.com> Date: Thu, 16 Oct 2025 16:14:41 +0200 Subject: [PATCH 2/5] Update PR guidelines in git.md Removed outdated PR template and example content. --- docs/developer/git.md | 33 +-------------------------------- 1 file changed, 1 insertion(+), 32 deletions(-) diff --git a/docs/developer/git.md b/docs/developer/git.md index 68fb84f..cd91c37 100644 --- a/docs/developer/git.md +++ b/docs/developer/git.md @@ -97,38 +97,7 @@ 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: - -```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 - -## How to test? - -pytest tests/test_crispr.py -panorama detect_crispr --pangenome examples/ecoli.h5 - -## Related Issues - -Closes #123 -Related to #456 - -## Version - -Updated VERSION from 1.2.5 → 1.2.6 -``` +Write a clear title that summarizes your change and use the PR template to provide context. ```{important} If your PR addresses an issue, link it! Use these keywords in your PR description: From 1fd64a3d8e06f43895634291611c3c78bc2ad589 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Arnoux?= <39793176+jpjarnoux@users.noreply.github.com> Date: Thu, 16 Oct 2025 16:16:38 +0200 Subject: [PATCH 3/5] Update pull_request_template.md --- .github/pull_request_template.md | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 3c92b00..e6b7435 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -43,6 +43,7 @@ Closes # - [ ] 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 From 54b6fad282e54bfca40b1bd5c9d4256d98b639f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Arnoux?= <39793176+jpjarnoux@users.noreply.github.com> Date: Thu, 16 Oct 2025 16:24:49 +0200 Subject: [PATCH 4/5] Bump version from 0.6.0 to 0.6.1 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index a918a2a..ee6cdce 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.6.0 +0.6.1 From 679752c5218958c90d62ac3e472d6e3f18ebfebe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Arnoux?= <39793176+jpjarnoux@users.noreply.github.com> Date: Thu, 16 Oct 2025 16:42:51 +0200 Subject: [PATCH 5/5] Add review checklist template to documentation Added a review checklist template for PR validation. --- docs/developer/git.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/docs/developer/git.md b/docs/developer/git.md index cd91c37..3afbc15 100644 --- a/docs/developer/git.md +++ b/docs/developer/git.md @@ -106,6 +106,31 @@ If your PR addresses an issue, link it! Use these keywords in your PR descriptio - `Related to #123` - Links without closing ``` +### For reviewer + +Before to validate the commit change, you should check the elements in the following template for reviewer. + +```md +## Quick Review + +### ✅ Checks +- [ ] Code runs correctly +- [ ] Logic makes sense +- [ ] No obvious bugs +- [ ] Comments help understand the code + +### 💬 Feedback + + +**Status:** ✅ Approved / 🔄 Suggestions / ❌ Changes needed +``` + +```{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 While you're working on your feature, `dev` keeps moving forward. Here's how to stay in sync: