Fix COBRA install: add scikit-learn dependency + revamp install docs (#391)

[marouenbg]

Fixes #391.

Problem

A user following the documented install (git clone → cd netZooPy → pip3 install -e .) could not run COBRA.

netZooPy/cobra/cobra.py imports from sklearn.linear_model import LinearRegression, Lasso, but setup.py did not list scikit-learn in install_requires (it was only in requirements.txt). Because netZooPy/__init__.py eagerly runs from netZooPy import cobra, a clean pip install -e . left import netZooPy itself broken with ModuleNotFoundError: No module named 'sklearn', not just COBRA.

Separately, the reporter's No module named 'netZooPy.cobra' / (unknown location) errors come from an environment pitfall: running Python from the clone's parent directory (or a Jupyter/VS Code kernel that isn't the install env) makes the cloned netZooPy folder resolve as an empty namespace package that shadows the installed one.

Changes

• setup.py: add scikit-learn to install_requires (the substantive fix).
• README.md: keep it minimal — only adds from netZooPy.cobra import cobra to the usage example.
• docs/install/index.md: revamp the install guide —
  • sync the dependency list with setup.py (was missing h5py, joblib, statsmodels, scikit-learn, click, tables, torch) and note pip installs them automatically; document CuPy as the optional GPU dependency;
  • recommend a virtual environment;
  • expand the Troubleshooting section to cover both failure modes above.

Troubleshooting content lives in the install guide (where users look) rather than the README.

Verification

• Clean python -m venv + pip install -e . now auto-installs scikit-learn; import netZooPy and from netZooPy.cobra import cobra both succeed; cobra() runs in nnls and MLE modes.
• tests/test_cobra.py passes.
• Audited every submodule's module-load-time imports: scikit-learn was the only undeclared hard dependency. cupy is correctly optional (lazy, GPU-only); patsy is guaranteed via statsmodels.

🤖 Generated with Claude Code

[katehoffshutta]

Hi @marouenbg, we have added a requirement that all claude/AI code is human reviewed. The changes to setup.py and README.md are straightforward. Can you confirm the changes to docs/install/index.md look good to you? I am testing them on my end as well but prefer the author of the PR to also take a look.

[marouenbg]

Yes all good on my side. Index is just docs not code.

…

On Tue, Aug 11, 2026, 3:34 PM katehoffshutta ***@***.***> wrote: *katehoffshutta* left a comment (netZoo/netZooPy#392) <#392 (comment)> Hi @marouenbg <https://github.com/marouenbg>, we have added a requirement that all claude/AI code is human reviewed. The changes to setup.py and README.md are straightforward. Can you confirm the changes to docs/install/index.md look good to you? I am testing them on my end as well but prefer the author of the PR to also take a look. — Reply to this email directly, view it on GitHub <#392?email_source=notifications&email_token=AB4MINFMDFN57ROJTZ7Q6NT5JNYM7A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRVG44TANRXGM42M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-5257906739>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4MINFZSTF5BFGNYOVNF7L5JNYM7AVCNFSNUABFKJSXA33TNF2G64TZHMYTSMJXHAZDGOJTHNEXG43VMU5TINRTGUYTIMJRGQ2KC5QC> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AB4MINBYBOKSZ5ZCDTNCTJT5JNYM7A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRVG44TANRXGM42M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android <https://github.com/notifications/mobile/android/AB4MING67XFRR7U42MEKK4T5JNYM7A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRVG44TANRXGM42M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.***>

[katehoffshutta]

Does the troubleshooting advice and suggested code for environments look good to you, though?

[marouenbg]

Yes, I reviewed the PR before pushing.

…

On Tue, Aug 11, 2026, 3:42 PM katehoffshutta ***@***.***> wrote: *katehoffshutta* left a comment (netZoo/netZooPy#392) <#392 (comment)> Does the troubleshooting advice and suggested code for environments look good to you, though? — Reply to this email directly, view it on GitHub <#392?email_source=notifications&email_token=AB4MINGDVBXYPZZA46BHFST5JNZI5A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRVG44TQNBRGE42M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-5257984119>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4MINF5HBQXAU446R7FNB35JNZI5AVCNFSNUABFKJSXA33TNF2G64TZHMYTSMJXHAZDGOJTHNEXG43VMU5TINRTGUYTIMJRGQ2KC5QC> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AB4MINHR54EXV4QZCR6REJL5JNZI5A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRVG44TQNBRGE42M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android <https://github.com/notifications/mobile/android/AB4MINDPTA2637EFVZO7IJD5JNZI5A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRVG44TQNBRGE42M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.***>

[katehoffshutta]

Awesome, thanks!

[marouenbg]

https://x.com/DustinTownsend/status/2087113602306064471