Use lower-direct resolution and create groups to factorize dep lower bounds

[ValerianRey]

No description provided.

[ValerianRey]

/opencode:Plan please explain what went wrong (why the CI doesn't pass). Can we salvage this or is it a dead end?

[opencode-agent]

The CI is failing because pyproject.toml contains invalid syntax in [project.optional-dependencies].

What went wrong

The PR places {include-group = "_xxx"} entries inside [project.optional-dependencies]:

[project.optional-dependencies]
quadprog_projector = [
    {include-group = "_numpy"},
    {include-group = "_quadprog"},
    ...
]

This is not allowed. The include-group syntax is defined in PEP 735 and is only valid inside [dependency-groups]. [project.optional-dependencies] (defined by PEP 621) must contain standard PEP 508 dependency specifier strings like "numpy>=1.21.2".

When uv pip install -e '.[full]' runs, uv parses pyproject.toml to resolve the full extra. Because full transitively references quadprog_projector, nash_mtl, cagrad, and fairgrad — all of which contain invalid {include-group = ...} entries — uv fails with a pyproject.toml parsing/validation error before it even starts installing packages.

Every job that installs an extra (which is most of them: tests, build-doc, code-quality) hits this error.

Can we salvage this?

Yes, but not in its current form. You have two practical paths:

Option 1: Partial salvage (minimal change)
Keep the [dependency-groups] table with the underscore-prefixed groups and the nested include-group references — that part is valid and works. But expand [project.optional-dependencies] back to explicit dependency strings. For example:

[project.optional-dependencies]
quadprog_projector = [
    "numpy>=1.21.2",
    "quadprog>=0.1.9, != 0.1.10",
    "qpsolvers>=1.0.1",
]

You lose the cross-table factorization, but the CI works again with uv pip install -e '.[full]'.

Option 2: Full refactor to uv sync
Stop using uv pip install -e '.[...]' entirely and switch the workflow to uv sync --extra full --group test (etc.). uv sync natively handles both extras and dependency groups together. However, this requires committing a uv.lock file and restructuring the CI around uv's project interface rather than its pip-compatible interface. That's a bigger change than this PR currently makes.

Recommendation

Go with Option 1 for this PR. It preserves the useful dependency-group factorization for CI while keeping the project's published extras standards-compliant. Option 2 is a valid future direction but is a separate architectural decision.

opencode session  |  github run

[ValerianRey]

@PierreQuinton apparently it's not possible to refer to dependency groups in optional dependencies. So we can't really improve on that matter.