chore: retire legacy analytics generators (#4910, #4911)

[hunterckx]

Closes #4910
Closes #4911

Notes:

• This covers deleting both the Jupyter Book reports and the Google Sheets reports
• I have not updated requirements.txt; I think that's best saved for chore: slim analytics package to the static-site core #4912
• I renamed the analytics subfolders to remove "sheets" (and moved the LungMAP one to the same level as the others, with its historical data contained directly in it)
• The individual readmes are deleted rather than being updated; the main analytics readme is updated with instructions for the static site scripts

[Copilot]

Pull request overview

Retires the legacy analytics report generators (Jupyter Book/PDF and Google Sheets notebooks) and standardizes the repo on the static-site analytics generator scripts, including some directory reshaping and updated deployment plumbing.

Changes:

• Deleted Jupyter Book report directories/files and legacy Sheets-report notebooks/readmes across analytics subfolders.
• Added/updated per-site static-site generator scripts and moved historic UA data JSONs into the new/non--sheets locations.
• Updated analytics docs and the deployment script to target the new static-site directory structure.

Reviewed changes

Copilot reviewed 34 out of 49 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
analytics/readme.md	Updates analytics docs to describe running static-site generators (and removes notebook kernel step).
analytics/lungmap/users_over_time_history.json	Adds LungMAP historic UA data in the new location.
analytics/lungmap/generate_static_site.py	Updates LungMAP static-site generator script (notably paths).
analytics/lungmap/constants.py	Adds LungMAP static-site configuration constants.
analytics/lungmap-analytics/sheets/readme.md	Removes legacy Sheets notebook instructions for LungMAP.
analytics/lungmap-analytics/sheets/generate_sheets_report.ipynb	Deletes LungMAP legacy Sheets report notebook.
analytics/lungmap-analytics/sheets/constants.py	Deletes LungMAP legacy Sheets-only constants.
analytics/lungmap-analytics/readme.md	Deletes LungMAP Jupyter Book report instructions.
analytics/lungmap-analytics/analytics_lungmap.py	Deletes LungMAP legacy Jupyter Book/python generator code.
analytics/lungmap-analytics/_toc.yml	Deletes LungMAP Jupyter Book TOC.
analytics/lungmap-analytics/_static/analytics-export.css	Deletes LungMAP Jupyter Book export CSS.
analytics/lungmap-analytics/_config.yml	Deletes LungMAP Jupyter Book config.
analytics/hca-explorer/generate_static_site.py	Adds HCA Explorer static-site generator script in the renamed folder.
analytics/hca-explorer/constants.py	Removes Sheets-only constants from HCA Explorer configuration.
analytics/hca-explorer-sheets/readme.md	Removes legacy Sheets notebook instructions for HCA Explorer.
analytics/hca-explorer-sheets/generate_sheets_report.ipynb	Deletes HCA Explorer legacy Sheets report notebook.
analytics/hca-analytics/users_over_time_history.json	Deletes HCA legacy Jupyter Book historic UA data file along with the retired directory.
analytics/hca-analytics/readme.md	Deletes HCA Jupyter Book report instructions.
analytics/hca-analytics/analytics_hca.py	Deletes HCA legacy Jupyter Book/python generator code.
analytics/hca-analytics/analytics_hca_bq.py	Deletes HCA legacy BigQuery/matplotlib reporting code.
analytics/hca-analytics/_toc.yml	Deletes HCA Jupyter Book TOC.
analytics/hca-analytics/_static/analytics-export.css	Deletes HCA Jupyter Book export CSS.
analytics/hca-analytics/_config.yml	Deletes HCA Jupyter Book config.
analytics/example/users_over_time_history.json	Deletes example legacy UA history JSON.
analytics/example/readme.md	Deletes example legacy Sheets/notebook documentation.
analytics/example/generate_sheets_report.ipynb	Deletes example legacy Sheets report notebook.
analytics/example/constants.py	Deletes example legacy Sheets constants.
analytics/deploy_sites.sh	Updates deploy script to copy built static sites from the renamed per-site folders.
analytics/anvil-explorer/utils.py	Adds AnVIL Explorer helper to fetch dataset titles for enrichment.
analytics/anvil-explorer/generate_static_site.py	Adds AnVIL Explorer static-site generator script in the renamed folder.
analytics/anvil-explorer/constants.py	Removes Sheets-only constants from AnVIL Explorer configuration.
analytics/anvil-explorer-sheets/utils.py	Deletes legacy Sheets utilities (superseded by renamed/static-site flow).
analytics/anvil-explorer-sheets/readme.md	Removes legacy Sheets notebook instructions for AnVIL Explorer.
analytics/anvil-explorer-sheets/generate_sheets_report.ipynb	Deletes AnVIL Explorer legacy Sheets report notebook.
analytics/anvil-catalog/users_over_time_history.json	Adds AnVIL Catalog historic UA data in the new location.
analytics/anvil-catalog/generate_static_site.py	Adds AnVIL Catalog static-site generator script in the renamed folder.
analytics/anvil-catalog/constants.py	Removes Sheets-only constants from AnVIL Catalog configuration.
analytics/anvil-catalog-sheets/readme.md	Removes legacy Sheets notebook instructions for AnVIL Catalog.
analytics/anvil-catalog-sheets/generate_sheets_report.ipynb	Deletes AnVIL Catalog legacy Sheets report notebook.
.gitignore	Drops ignore rule for analytics _build outputs (legacy Jupyter Book artifact).

Suppressed comments (1)

analytics/lungmap/generate_static_site.py:61

• deploy_sites.sh expects generated output under analytics/lungmap/site/, but output_dir="../../gh-pages/lungmap" writes elsewhere, so the deploy script will deploy an empty/stale site.

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[NoopDog]

@hunterckx thx ! See the suppressed comment above by copilot. It looks real.

[hunterckx]

@NoopDog See my earlier comment -- the deploy script is out-of-scope I think (but perhaps worth a ticket to address it)

[NoopDog]

@hunterckx thx — here's the review. Two inline comments below, plus two notes on files outside the diff hunks:

analytics/analytics_package/analytics/static_site/README.md — still references the pre-rename folder names (anvil-explorer-sheets, anvil-catalog-sheets, hca-explorer-sheets, lungmap-analytics/sheets) in the cd instructions (line 25) and the per-app script table (lines 59–62); anyone following the doc gets "no such file or directory". Line 29's claim that the script "writes the site to ./site/" is also wrong for the three explorer scripts, which write to ../../gh-pages/<app>.

analytics/anvil-catalog/generate_static_site.py — anvil-catalog is the odd one out: it writes to a gitignored ./site/ (via /analytics/**/site/) and appears in neither deploy_sites.sh nor gh-pages/index.html, yet the new readme section documents all four folders identically — the generated report silently goes nowhere. Pre-existing asymmetry, but if it's intentional (internal-only report) it deserves a note in the readme.

[Copilot]

Pull request overview

Copilot reviewed 35 out of 49 changed files in this pull request and generated no new comments.

Suppressed comments (1)

analytics/readme.md:34

• The local viewing instructions only work for sites generated into gh-pages/ and are incorrect for the anvil-catalog generator (which writes to anvil-catalog/site). This can confuse someone who just generated the catalog site and then follows the ../../gh-pages command.

[NoopDog]

Re-reviewed the updated branch — all review feedback addressed: deploy_sites.sh removed in favor of a committed gh-pages/index.html, the duplicate fetch logic replaced with the shared fetch_entity_title_map helper (with timeout), docs updated and the anvil-catalog exception noted. Remaining minor items (requirements.txt cleanup) are tracked in #4912. LGTM — thanks @hunterckx!