[MAINT] use uv & tox, drop python 3.9

[Remi-Gau]

• drop python 3.9
• use uv to generate requirements
• use tox to run tests
• use dependency groups

[sourcery-ai]

Reviewer's Guide

Switches the project to uv for dependency management and tox-uv based workflows, simplifying dependency specification, aligning supported Python versions and CI/Docker images, and adding a uv lockfile.

Flow diagram for dependency management with uv and tox-uv

flowchart TD
    A[Edit pyproject_toml] --> B[Compile dependencies with uv<br>uv pip compile pyproject.toml -o requirements.txt --python-version 3_11_15 --no-deps]
    B --> C[Generate requirements_txt]
    B --> D[Generate uv_lock]

    subgraph Local_Testing
        E[Run tox -e test]
        E --> F[tox_uv resolves dependency_groups test]
        F --> G[Install test dependencies via uv]
        G --> H[Run pytest with coverage]
    end

    subgraph Linting
        I[Run tox -e lint]
        I --> J[Install pre_commit]
        J --> K[Run pre_commit hooks]
    end

    subgraph CI_Pipeline
        L[GitHub Actions test_and_coverage]
        L --> M[Use tox with tox_uv]
        M --> N[Install deps via uv using uv_lock]
        N --> O[Run tests and generate coverage]
    end

Loading

File-Level Changes

Change	Details	Files
Regenerate requirements.txt using uv with a reduced, direct-dependency-only set and updated pinned versions.	Replace pip-compile header with uv pip compile header including python version and --no-deps flags. Remove transitive dependency listings, keeping only direct project dependencies with updated versions. Update specific pins for deepmreye, kaleido, pooch, pybids, rich-argparse, tqdm, and related packages.	requirements.txt
Restructure dependency configuration in pyproject.toml to use hatch dependency-groups, tighten Python version support, and remove legacy optional extras.	Add [dependency-groups] section defining dev, doc, and test groups including tox, tox-uv, and pre-commit. Remove [project.optional-dependencies] extras in favor of dependency groups and simplify docs/test configuration. Constrain requires-python to >=3.10.0,<3.12 to match supported/runtime environments. Remove Black configuration section now unused or handled elsewhere.	pyproject.toml
Refactor tox configuration to use tox-uv, centralize environment variables, and run tests via a dedicated test environment using dependency_groups.	Add tox-uv to [tox] requires so uv is used as the backend resolver/installer. Introduce [global_var] section to centralize common passenv variables including CI and color-related env vars. Define [testenv:test] that installs dependencies from the test dependency group and runs pytest with coverage. Simplify [testenv:lint] to only depend on pre-commit and remove legacy style/import-linter and update_dependencies environments that relied on pip-tools.	tox.ini
Update GitHub Actions CI to install uv, run tests via tox with tox-uv/gh-actions, and align Python matrix with supported versions.	Reduce Python test matrix to 3.10 and 3.11, dropping 3.9 in line with new requires-python constraint. Install uv using astral-sh/setup-uv and use uv tool install to install tox with tox-uv and tox-gh-actions. Replace direct pytest invocation with tox run -e test and add a step to show tox config (tox c).	.github/workflows/test_and_coverage.yml
Tune automation schedules for dependency and hook updates to run less frequently.	Change Dependabot github-actions and gitsubmodule schedules from monthly to semiannually. Change pre-commit CI autoupdate_schedule from monthly to quarterly.	.github/dependabot.yml .pre-commit-config.yaml
Align Docker image with new Python baseline and install tooling prerequisites for uv.	Update base image to python:3.11.15-slim with a new pinned digest. Extend apt-get install to include curl and ca-certificates alongside git, needed for uv tooling and HTTPS. Keep existing model directory setup intact.	Dockerfile
Add uv-generated lockfile to pin full dependency resolution.	Introduce uv.lock at repository root to capture resolved dependencies for reproducible installs.	uv.lock

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[sourcery-ai]

Hey - I've found 1 issue, and left some high level feedback:

• Removing the existing [project.optional-dependencies] extras ([dev], [doc], [docs], [style], [test], [tests]) is a breaking change for consumers that install bidsmreye[...]; consider reintroducing these extras and mapping them to the new [dependency-groups] so external workflows keep working while you migrate to uv groups internally.
• Now that [dependency-groups] are defined, you may want to use them consistently in tox.ini (e.g. have lint also pull from dev instead of spelling out pre-commit) and in any Docker/automation setup that still relies on .[test]/.[dev] installs, so there is a single source of truth for dev/test dependencies.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- Removing the existing `[project.optional-dependencies]` extras (`[dev]`, `[doc]`, `[docs]`, `[style]`, `[test]`, `[tests]`) is a breaking change for consumers that install `bidsmreye[...]`; consider reintroducing these extras and mapping them to the new `[dependency-groups]` so external workflows keep working while you migrate to uv groups internally.
- Now that `[dependency-groups]` are defined, you may want to use them consistently in `tox.ini` (e.g. have `lint` also pull from `dev` instead of spelling out `pre-commit`) and in any Docker/automation setup that still relies on `.[test]`/`.[dev]` installs, so there is a single source of truth for dev/test dependencies.

## Individual Comments

### Comment 1
<location path="tox.ini" line_range="12-21" />
<code_context>
+[global_var]
+passenv =
+    CI
+    USERNAME
+    # Pass user color preferences through
+    PY_COLORS
</code_context>
<issue_to_address>
**suggestion:** Consider also passing `USER` for non-Windows environments that don’t set `USERNAME`.

On many Linux/macOS systems only `USER` is set, so tooling that depends on the username may not work as expected with only `USERNAME` in `passenv`. Including `USER` would improve cross-platform robustness.

```suggestion
[global_var]
passenv =
    CI
    USERNAME
    USER
    # Pass user color preferences through
    PY_COLORS
    FORCE_COLOR
    NO_COLOR
    CLICOLOR
    CLICOLOR_FORCE
```
</issue_to_address>

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 81.73%. Comparing base (1bcca23) to head (07614d8).
⚠️ Report is 123 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #262      +/-   ##
==========================================
+ Coverage   79.91%   81.73%   +1.82%     
==========================================
  Files          13       16       +3     
  Lines         926     1046     +120     
  Branches      119        0     -119     
==========================================
+ Hits          740      855     +115     
- Misses        144      191      +47     
+ Partials       42        0      -42     

Flag	Coverage Δ
tests	81.73% <ø> (+1.93%)	⬆️

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