pip dependency conflict?

[RichardBruskiewich]

ERROR: Cannot install -r requirements.txt (line 4) and kgx because these package versions have conflicting dependencies.

The conflict is caused by:
    kgx 1.5.5 depends on Click~=7.0
    black 22.1.0 depends on click>=8.0.0

KGX pulls in black with (click>=8.0.0) but also sets Click~=7.0.

To permit black to get 8.0.0, we set kgx also rather use click>=7.0.0 ?

See also issue linkml/linkml#592 and PR linkml/linkml#593.

This PR is using the patched PR 593 version of linkml in its requirements.txt. This workaround should be removed and the dependency reverted to the regular (latest) linkml release, once linkml itself is patched?

These changes (both in kgx and linkml) appear to clear the unit tests - no errors - so this click version >=7.0.0 (not pinned ~= 7.0.0?) does not seem to be a problem.

[caufieldjh]

I saw this in KG-IDG and KG-COVID-19 - the fix was to pin black==20.8b1 (though I see the upstream linkml conflict is still with click)

[RichardBruskiewich]

Hi @caufieldjh, to my knowledge, changing the click dependency to click>=7.0.0 in LinkML, KGX, BMT, etc. solves the problem. That's the current patch that's merged but may not yet be officially released. I'm not really heavily involved in releases of these projects but we can both look into that.

I'd be hesitant to pin black to a specific release, unless strictly necessary (@cmungall may corroborate this...)

I just checked: linkml release v1.1.18 has the patch. KGX only pulls in LinkML 'latest' (no release constraints). Maybe you simply need to refresh your linkml dependency?

[caufieldjh]

Upgrading to the most recent KGX (and having it use the new linkml release) fixes this in the KG projects. Thanks!