Refresh datasets page from 2.4 build and add reusable dataset stats generator - #505
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…ator Add scripts/gen_dataset_stats.py, a stdlib-only generator that reads a local CoderData build and writes a wide per-dataset counts CSV to docs/source/_static/dataset_counts.csv. Use its 2.4 output to refresh the Datasets Included overview table (sample/drug counts and modality markers), bump the version references from 2.2.0 to 2.4, and update the Figshare record link to the 2.4 article (33990850). Refs #216
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Documentation Update
#4Merge this fourth.
Refreshes the Datasets Included documentation page so its numbers reflect the
released 2.4 build, and adds a reusable script to regenerate those numbers for
future releases.
Changes:
scripts/gen_dataset_stats.py: Reads a local build'slocal/all_files_dir and writes a wide per-dataset CSV to
docs/source/_static/dataset_counts.csv. Per dataset it reports modeltype(s), unique samples, unique drugs, unique genes across omics,
experiment count, per-modality row counts, and the set of dose-response
metrics present.
docs/source/datasets_included.rst: refreshed the Datasets and Modalitiestable (sample/drug counts and modality markers) from the 2.4 build, added a
Model Type column, updated version references from 2.2.0 to 2.4, and pointed
the Figshare record to the 2.4 article (33990850).
docs/source/_static/dataset_summary_statistics.csv: display the pair countsas integers instead of floats.
docs/README.md: documented that the Datasets page counts are generated byscripts/gen_dataset_stats.pyand how to refresh them for a new release.All 18 released datasets are represented (cNF/phospho remain deferred to 2.5).
Model types are shown as they appear in the released data.
Closes #216
Another note about this PR, and #502 and PR #503: The current live docs are already refreshed and reflect the changes seen here.