Merge recent updates from dev branch

[thomasckng]

Summary by CodeRabbit

• Chores
  • Updated project metadata with additional links to documentation, repository, bug tracker, and changelog.
  • Reorganised dependency groups for improved clarity and added CUDA support configuration.
  • Enhanced CI workflow to consistently validate across multiple Python versions.

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request transitions the CI workflow from fixed Python 3.12 setup to a matrix-driven approach using astral-sh/setup-uv with configurable Python versions. Additionally, it restructures pyproject.toml's project URLs and optional dependency groups, separating development, documentation, and testing dependencies.

Changes

Cohort / File(s)	Summary
CI Workflow .github/workflows/CI.yml	Replaces explicit setup-python steps with matrix-driven Python version handling. Removes hard-coded 3.12 specification and consolidates dependency installation to use uv sync with configurable matrix.python-version and group-based dependencies (test instead of --all-extras --dev).
Project Configuration pyproject.toml	Restructures [project.urls] to include Homepage, Documentation, Repository, Bug Tracker, and Changelog entries. Reorganises [project.optional-dependencies] from docs/–dev groups to cuda, visualize, doc, and test groups, removing ipykernel and ipython from development tools.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~15 minutes

Possibly related PRs

• Merge recent updates from dev branch #34: Modifies the same CI workflow Python setup steps, transitioning between different approaches to Python environment configuration in the test pipeline.

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title is vague and generic, using non-descriptive phrasing that does not convey meaningful information about the specific changes in the changeset.	Replace with a more specific title that reflects the main changes, such as 'Refactor CI workflow to matrix-driven Python versions and reorganise project dependencies' or similar.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch flowMC-dev

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

.github/workflows/CI.yml (1)

43-43: Consider a leaner dependency group for pre-commit.

Line 43 installs the full test group for a lint-only job. A dedicated lint/ci group would reduce CI setup time and cache churn.

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In @.github/workflows/CI.yml at line 43, Replace the heavy "test" pre-commit
group used in the CI step (the command string "uv sync --python 3.12 --group
test") with a leaner dedicated group such as "lint" or "ci" to speed up setup;
update the CI command to "uv sync --python 3.12 --group lint" (or "ci") and
ensure the corresponding pre-commit extras group (e.g., [project.optional-deps]
lint = [...]) exists in the repository's dependency metadata so only
linting-related hooks are installed.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@pyproject.toml`:
- Around line 40-42: The pyproject.toml dependency entry uses the unsupported
extra "jax[cuda]"; update the cuda list so the JAX extras use the supported,
versioned names (e.g. replace "jax[cuda]>=0.8.2" with "jax[cuda13]>=0.8.2" or
"jax[cuda12]>=0.8.2", or include both extras if you need to support multiple
CUDA versions) so the installer pulls the correct GPU-enabled JAX wheel; modify
the entry currently named cuda = [ "jax[cuda]>=0.8.2", ] accordingly.

---

Nitpick comments:
In @.github/workflows/CI.yml:
- Line 43: Replace the heavy "test" pre-commit group used in the CI step (the
command string "uv sync --python 3.12 --group test") with a leaner dedicated
group such as "lint" or "ci" to speed up setup; update the CI command to "uv
sync --python 3.12 --group lint" (or "ci") and ensure the corresponding
pre-commit extras group (e.g., [project.optional-deps] lint = [...]) exists in
the repository's dependency metadata so only linting-related hooks are
installed.

---

ℹ️ Review info

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 3e08e3b and edfe070.

⛔ Files ignored due to path filters (1)

• uv.lock is excluded by !**/*.lock

📒 Files selected for processing (2)

• .github/workflows/CI.yml
• pyproject.toml