CLI requires heavy optional dependencies (matplotlib, scipy) for basic operations

[turbomam]

Environment

• OS: Ubuntu 24 on Intel
• linkml-store version: 0.3.0rc3
• Python: 3.11

Problem

Running a basic query command requires installing analytics and scipy extras, even though the query has nothing to do with plotting or scientific computing.

Minimal reproduction

uv sync  # base install only
uv run linkml-store -d "dremio-rest://lakehouse.jgi.lbl.gov" -c mytable query -l 3 -O csv

Error:

ModuleNotFoundError: No module named 'matplotlib'

After installing --extra analytics:

ModuleNotFoundError: No module named 'scipy'

Root cause

cli.py line 28 has an unconditional import:

from linkml_store.plotting.cli import plot_cli

This import chain requires:

• matplotlib (from analytics extra)
• scipy (from scipy extra, but not included in analytics)

Additional warnings without more extras

Even after installing analytics + scipy, there are warnings unless you also install llm and map extras:

Error importing linkml_store.inference.implementations.llm_inference_engine: No module named 'llm'
Error importing linkml_store.inference.implementations.sklearn_inference_engine: No module named 'linkml_map'
Error importing linkml_store.inference.implementations.rag_inference_engine: No module named 'llm'
Error importing linkml_store.inference.implementations.rule_based_inference_engine: No module named 'linkml_map'

Current workaround

Must install 4 extras for a clean basic query:

uv sync --extra analytics --extra scipy --extra llm --extra map

Suggested fixes

1. Lazy imports for plotting and inference modules - only import when those subcommands are invoked
2. Fix analytics extra to include scipy since plotting/heatmap.py requires it
3. Silence or demote the inference engine import errors to debug level when those features aren't being used

Impact

The README shows pip install linkml-store[all] which works, but users trying to install minimal dependencies for specific use cases (e.g., just dremio-rest queries) hit confusing errors.