Fix #32: scipy>=1.15 compat + lamindb modules flag

[jkobject]

Fixes #32.

Changes

• preprocess.additional_postprocess: cast pd.Series boolean mask to numpy before indexing AnnData.X. scipy >= 1.15 dropped the implicit relaxed indexing of sparse arrays with pandas Series (see scipy/scipy@66ec333), so adata.X[adata.obs[NEWOBS] == i] raises AttributeError: 'Series' object has no attribute 'nonzero'. Casting with .to_numpy() fixes the regression and is forward-compatible.
• Docs/README: replace deprecated lamin init --schema bionty with --modules bionty (lamindb 2.1.x). Also matches the reporter's working notebook (gist).
• Bumped version to 2.1.3 so scPRINT-2 can pin to the fixed release.

Test plan

• Ran the failing snippet (additional_postprocess(adata) with a mock AnnData) on scipy 1.15 — no more AttributeError.

CC @Stfort52 — thanks for the very thorough bug report (including the scipy commit pointer).

[Copilot]

Pull request overview

Fixes a preprocessing regression with SciPy ≥ 1.15 when boolean-indexing sparse AnnData.X using a pandas Series, and updates LaminDB initialization instructions to use the newer --modules flag. Also bumps the package version for downstream pinning.

Changes:

• Cast boolean masks to NumPy arrays before indexing AnnData.X in additional_postprocess (SciPy ≥ 1.15 compatibility).
• Update docs/README LaminDB init command from deprecated --schema bionty to --modules bionty.
• Bump project version from 2.1.2 to 2.1.3.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
scdataloader/preprocess.py	Fix sparse boolean indexing by converting pandas boolean Series masks to NumPy arrays.
README.md	Update lamin init examples to use --modules bionty.
pyproject.toml	Bump project version to 2.1.3.
docs/notebooks/1_download_and_preprocess.ipynb	Update commented lamin init command to --modules bionty.
docs/index.md	Mirror README doc change for lamin init --modules bionty.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[codecov-commenter]

⚠️ Please install the to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 48.02%. Comparing base (6338665) to head (78647f9).
❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #34   +/-   ##
=======================================
  Coverage   48.02%   48.02%           
=======================================
  Files          10       10           
  Lines        1976     1976           
=======================================
  Hits          949      949           
  Misses       1027     1027           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.