[Bug] Former indicium bug fixed but not in main .toml

[llegregam]

Summary

After cloning the repo, I seem to have hit the same bug as described in issue #6 .

Steps to reproduce

1. git clone https://github.com/HolobiomicsLab/Perspicacite-AI.git
2. cd Perspicacite-AI
3. uv sync

Expected behaviour

All packages be updated

Actual behaviour

(perspicacite) PS C:\Users\legregam\Documents\Perspicacite-AI> uv sync
error: Distribution not found at: file:///C:/Users/legregam/Documents/indicium

Environment

perspicacite --version  : 2.0.0
python --version        : 3.12.12
OS                      :  Windows 11
LLM provider/model      :  didn't get this far
Install method          : uv
SciLEx installed        : no

[lfnothias]

Thank you for the report, and for spotting that the earlier fix had not survived.

You are right that this is #6 regressing. Commit 940fd36 re-enabled the indicia / adapters extras together with the [tool.uv.sources] local paths, in order to restore the knowledge-graph tests. uv builds a universal lockfile, so uv lock resolves every extra whether or not it is requested; the ../indicium path is therefore required on any install, and resolution fails before the network is consulted. CI did not catch it because the test job installs with pip, which ignores [tool.uv.sources] entirely.

The three indicium packages are private and unpublished, so they cannot be declared in pyproject.toml under any mechanism. They have been removed. The RDF backend they used to pull in is public and now has its own extra:

uv sync                  # works on a fresh clone
uv sync --extra graph    # adds rdflib + pyoxigraph for the claim-graph layer

The claim-graph and export_astra MCP tools remain maintainer-only and report a clear error when indicium is absent.

To prevent a third occurrence, two guards were added: a uv-resolve CI job that runs uv lock on a clean runner, which is exactly an environment without the sibling checkouts, and a unit test rejecting local-path sources or private packages in any extra or dependency-group.

Fixed in #30. A uv sync on main should now succeed on Windows; please reopen if it does not.