Merge branch 'main' into main

Author: chapman20j

.github/pull_request_template.md

@@ -1,14 +1,19 @@
-Resolves #\<issue_number_goes_here\>
+# What does this PR do?
 
-<!--- Please check [issues](https://github.com/jax-ml/bonsai/issues) for any pending model implementations. Consider opening issue if none exists. -->
+<!--
 
-**Reference**
-<!--- Link to the reference implementation, research paper, and GitHub issue. -->
+Pease read the following carefully so we can make sure your PR is merged
+easily.
 
-**Checklist**
-<!--- Please make sure all checkboxes are ticked before submitting this PR for review. -->
+Replace this text block with a description of the change and which issue it
+fixes (if applicable). Please also include relevant motivation/context.
+-->
+
+Fixes # (issue)
 
-- [ ] I have read the **[Contribution Guidelines](https://github.com/jax-ml/bonsai/blob/main/CONTRIBUTING.md#contributing-a-model)** and used [pre-commit hooks](https://github.com/jax-ml/bonsai/blob/main/CONTRIBUTING.md#linting-and-type-checking) to format this commit.
-- [ ] I have added all the necessary **unit tests** for my change. (`run_model.py` for model usage, `test_outputs.py` and/or `model_validation_colab.ipynb` for quality).
-- [ ] **(If using an LLM)** I have carefully reviewed and removed all **superfluous comments** or unneeded, commented-out code. Only necessary and functional code remains.
+
+**Checklist**
+- [ ] I have read the **[Contribution Guidelines](https://github.com/jax-ml/bonsai/blob/main/CONTRIBUTING.md)** and used [pre-commit hooks](https://github.com/jax-ml/bonsai/blob/main/CONTRIBUTING.md#linting-and-type-checking) to format and squash so that this PR has 1 commit typically.
+- [ ] I have added all the necessary **unit tests** for my change (`run_model.py`, `test_outputs.py`, and/or `model_validation_colab.ipynb`).
+- [ ] **(Code Quality)** I have reviewed the code and removed all superfluous comments or LLM-generated boilerplate. Only functional, necessary code remains.
 - [ ] I have signed the **[Contributor License Agreement (CLA)](https://cla.developers.google.com/about)**.

CONTRIBUTING.md

@@ -32,7 +32,7 @@ Follow these steps to contribute code:
    For more information, please see [Bonsai Pull Request checklist](#bonsai-pull-request-checklist).
 
 2. Fork the Bonsai repository by clicking the **Fork** button on the
-   [repository page](http://www.github.com/jax-ml/bonsai). This creates
+   [repository page](https://www.github.com/jax-ml/bonsai). This creates
    a copy of the Bonsai repository in your own account.
 
 3. `pip` installing your fork from source. This allows you to modify the code
@@ -125,6 +125,20 @@ Alternatively, manually run a pre-commit hook.
 pre-commit run --all-files
 ```
 
+### Single-change commits and pull requests
+
+We follow [jax's convention](https://docs.jax.dev/en/latest/contributing.html#single-change-commits-and-pull-requests) in single-change commits in pull requests.
+A git commit ought to be a self-contained, single change with a descriptive
+message. This helps with review and with identifying or reverting changes if
+issues are uncovered later on.
+
+**Pull requests typically comprise a single git commit.** (In some cases, for
+instance for large refactors or internal rewrites, they may contain several.)
+In preparing a pull request for review, you may need to squash together
+multiple commits. We ask that you do this prior to sending the PR for review if
+possible. The `git rebase -i` command might be useful to this end.
+
+
 ## Contributing a model
 
 We welcome contribution of new models that may be beneficial for the JAX community