feat(pineapple): add gget pineapple module (#161)

[Elarwei001]

Summary

Adds a new gget pineapple module to list and download curated bio-imaging data from Pineapple.

A point worth being explicit about: Pineapple is a Rust command-line tool for image-based cell profiling — it does not expose a REST/JSON API. What it does provide (via its pineapple download command) is a curated, standardized catalog of bio-imaging datasets and pre-trained model weights, hosted on Google Drive (each resource maps to a hardcoded Google Drive file ID in the pineapple-data crate). This module mirrors that catalog and downloads the resources directly from the same Google Drive host, so users get the data without installing the Rust binary.

What it does

• List the catalog by category: segmentation (12 datasets), benchmark (13 datasets), or weights (5 pre-trained model weights). Returns names, authors, sizes (GB), licenses, filenames, and Google Drive IDs.
• Download a resource by name directly from Google Drive (handles the large-file virus-scan-warning confirmation flow).
• Available in both the Python API (gget.pineapple(...)) and the command line (gget pineapple ...).

# List the segmentation datasets
gget pineapple --category segmentation

# Download one by name
gget pineapple vicar_2021 --download --out_dir ./pineapple_data

# List pre-trained model weights
gget pineapple --category weights

import gget
gget.pineapple(category="segmentation")
gget.pineapple("vicar_2021", download=True, out_dir="./pineapple_data")

The catalog includes each dataset's original author and license so users can check usage terms (some datasets are non-commercial only).

Testing

• 10 network-free unit tests (tests/test_pineapple.py, mocked downloads) covering catalog contents/columns, filename conventions, Google Drive virus-scan-warning form parsing, and download routing. No real downloads happen in tests.
• ruff: clean on all changed files.
• Live-verified: a real Google Drive file ID from the catalog returns HTTP 200 (application/octet-stream, Content-Disposition: attachment; filename="arvidsson-2022.tar.gz"), matching the module's filename convention.
• Docs added (docs/src/en/pineapple.md + SUMMARY entry) and an updates.md bullet under Version ≥ 0.30.8.

⚠️ Note for maintainers

Because Pineapple hardcodes its dataset Google Drive file IDs in its own source (the upstream author notes this isn't ideal and may move them out of the library later), this module's catalog is a point-in-time mirror of those IDs. If upstream Pineapple adds/changes datasets, gget's catalog would need a corresponding refresh. I went with mirroring because there is no programmatic API to query — flagging this wrapper approach for your input in case you'd prefer a different strategy (e.g. fetching the registry from a maintained upstream manifest if/when one exists).

Resolves #161

Scope — download only

This module intentionally wraps only Pineapple's data-distribution layer (its pineapple download subcommand): it lets gget users list the curated bio-imaging catalog (segmentation/benchmark datasets and pre-trained model weights) and download individual resources directly from Google Drive, without installing the Pineapple Rust binary.

It deliberately does not reimplement Pineapple's image-processing functionality (process, profile, neural, measure) — extracting morphological descriptors, running self-supervised embeddings, etc. Those are the core of the Pineapple tool itself and are out of scope for gget, whose role here is data access, not image analysis. Users who want to process images should use Pineapple directly. This matches the original request (#161): a module to download bio-imaging data.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 78.94737% with 20 lines in your changes missing coverage. Please review.
✅ Project coverage is 56.92%. Comparing base (e43a804) to head (ccc6383).
⚠️ Report is 2 commits behind head on dev.

Files with missing lines	Patch %	Lines
gget/gget_pineapple.py	78.49%	20 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #245      +/-   ##
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+ Coverage   56.70%   56.92%   +0.21%     
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  Files          29       30       +1     
  Lines        9392     9487      +95     
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+ Hits         5326     5400      +74     
- Misses       4066     4087      +21     

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[Elarwei001]

Hi @lauraluebbert — I think this PR is ready for review. Quick summary:

1. Scope — download only. It wraps only Pineapple's data download (pineapple download): listing the curated catalog and downloading individual datasets/weights directly from Google Drive, no Rust binary required. It deliberately does not reimplement Pineapple's image-processing features (process, profile, neural, measure) — those stay with the Pineapple tool itself. This matches the original request in Pineapple module to download bio-imaging data #161 ("download bio-imaging data").

2. Tests. Two complementary layers: network-free unit tests covering the catalog/parsing/routing logic, plus a live data test (TestPineappleLiveAccess) that does a header-only check (no multi-GB body downloads) confirming each resource still resolves to a binary download from Google Drive with the catalog's expected filename — so CI fails loudly if an ID is repointed/removed upstream. To keep CI fast and resilient, the live test covers a representative sample (one per category + both filename conventions + both resolution paths), not all 30 IDs; if Google Drive temporarily rate-limits the request, that resource is skipped rather than failing the build.

3. Docs. Added English (docs/src/en/pineapple.md) and Spanish (docs/src/es/pineapple.md) pages, both registered in SUMMARY.md, plus an updates.md entry.
   Please Note: the Spanish page is an AI-generated translation — it would be good to have a Spanish speaker review it before merging.

Could you take a look when you have a chance? Thanks