Merge branch 'main' into JOSS

Author: kameronton

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug Report
+about: Report a reproducible bug
+labels: bug
+---
+
+## Description
+
+A clear description of what the bug is.
+
+## Steps to Reproduce
+
+```python
+# Minimal reproducible example
+```
+
+## Expected Behavior
+
+What you expected to happen.
+
+## Actual Behavior
+
+What actually happened. Include the full traceback if applicable.
+
+## Environment
+
+- OS:
+- Python version:
+- JAX version (`python -c "import jax; print(jax.__version__)"`):
+- BordAX version / commit:

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature Request
+about: Propose a new feature or improvement
+labels: enhancement
+---
+
+## Problem
+
+What problem does this solve? What are you trying to do that is currently difficult or impossible?
+
+## Proposed Solution
+
+Describe what you'd like to see added or changed.
+
+## Alternatives Considered
+
+Any alternative approaches you've thought about.
+
+## Additional Context
+
+Any other context, references, or examples that might help.

.github/pull_request_template.md

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+## Summary
+
+Brief description of what this PR does.
+
+Closes #<!-- issue number -->
+
+## Changes
+
+- 
+
+## Checklist
+
+- [ ] Tests added or updated for new behavior
+- [ ] All fast tests pass: `uv run pytest tests/ -m "not slow" -v`
+- [ ] Code formatted with `black`
+- [ ] Documentation updated if needed

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: uv sync --extra dev
+
+      - name: Run tests
+        run: uv run pytest tests/ -m "not slow" --cov=bordax --cov-report=xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/docs.yml

@@ -0,0 +1,23 @@
+name: Docs
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: uv sync --extra docs
+
+      - name: Deploy to GitHub Pages
+        run: uv run mkdocs gh-deploy --force

.github/workflows/draft-pdf.yml

@@ -1,24 +1,31 @@
 name: Draft PDF
-on: [push]
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - paper.md
+      - paper.bib
+  pull_request:
+    paths:
+      - paper.md
+      - paper.bib
 
 jobs:
   paper:
     runs-on: ubuntu-latest
     name: Paper Draft
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+      - 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: 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: paper.pdf

CODE_OF_CONDUCT.md

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+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at [INSERT CONTACT METHOD]. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 2.1, available at [https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at [https://www.contributor-covenant.org/faq][FAQ]. Translations are available at [https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

CONTRIBUTING.md

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+# Contributing to BordAX
+
+Thank you for your interest in contributing to BordAX!
+
+## Reporting Bugs
+
+Please [open a GitHub Issue](https://github.com/SynthesisLab/bordax/issues/new/choose) using the **Bug Report** template. Include:
+
+- A minimal reproducible example
+- Your environment (OS, Python version, JAX version)
+- The full error traceback
+
+## Asking Questions
+
+Open a [GitHub Issue](https://github.com/SynthesisLab/bordax/issues/new/choose) using the **Question** label.
+
+## Proposing Changes
+
+For non-trivial changes, open an Issue to discuss the idea before writing code. For small fixes (typos, documentation), you can go straight to a pull request.
+
+## Development Setup
+
+**Requirements**: Python 3.11+, [uv](https://docs.astral.sh/uv/)
+
+```bash
+git clone https://github.com/SynthesisLab/bordax.git
+cd bordax
+uv sync
+```
+
+Verify the setup:
+
+```bash
+uv run pytest tests/ -m "not slow" -v
+```
+
+## Code Style
+
+- Format with [black](https://github.com/psf/black): `uv run black .`
+- Use type hints throughout
+
+## Running Tests
+
+```bash
+# Fast tests (run before every commit)
+uv run pytest tests/ -m "not slow" -v
+
+# Full suite including slow learning tests
+uv run pytest tests/ -v
+```
+
+New code should come with tests.
+
+## Submitting a Pull Request
+
+1. Fork the repository and create a branch from `main`
+2. Make your changes with tests
+3. Ensure all fast tests pass: `uv run pytest tests/ -m "not slow"`
+4. Open a pull request against `main` — fill out the PR template
+
+## Code of Conduct
+
+This project follows the [Contributor Covenant Code of Conduct](CODE_OF_CONDUCT.md). By participating, you agree to uphold it.