ISARIC data schema integration

[sr-murthy]

• New ISARIC data schema lib. supporting transformations of raw custom clinical datasets into ISARIC data schema form via ADTL.
• Transformations of ISARIC data schema-compliant data to VERTEX style project inputs expected by VERTEX for the dashboard (insight panels).
• A Sphinx guide to using the lib.

Plus some other unrelated but useful improvements including:

• Some doctests (in utils) (Doctests #27).
• Update contributing guide.
• Switch to an src-style package layout (Switch to src-style package layout #30).
• Use pytest fixtures for static test data (pytest fixtures #31).

PR RTD site.

[codecov]

Codecov Report

❌ Patch coverage is 77.58621% with 13 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/isaricanalytics/isaric_data_schema.py	65.71%	12 Missing ⚠️
src/isaricanalytics/isaric_transformations.py	95.45%	1 Missing ⚠️

Files with missing lines	Coverage Δ
src/isaricanalytics/__init__.py	100.00% <100.00%> (ø)
src/isaricanalytics/analytics.py	11.33% <ø> (ø)
src/isaricanalytics/logging/logger.py	89.47% <ø> (ø)
src/isaricanalytics/redcap_data.py	11.72% <ø> (ø)
src/isaricanalytics/utils.py	93.75% <ø> (ø)
src/isaricanalytics/visualisation.py	60.00% <ø> (ø)
src/isaricanalytics/isaric_transformations.py	95.45% <95.45%> (ø)
src/isaricanalytics/isaric_data_schema.py	65.71% <65.71%> (ø)

🚀 New features to boost your workflow:

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

[read-the-docs-community]

Documentation build overview

📚 IsaricAnalytics | 🛠️ Build #34973748 | 📁 Comparing 3a97bbb against latest (e2be39f)

  🔍 Preview build  

37 files changed · + 19 added · ± 15 modified · - 3 deleted

+ Added

• sg_execution_times.html
• sources/citing-isaric-analytics.html
• sources/isaric-data-schema.html
• _modules/isaricanalytics/isaric_data_schema.html
• _modules/isaricanalytics/isaric_transformations.html
• sources/isaricanalytics/isaric-data-schema.html
• sources/isaricanalytics/isaric-transformations.html
• sources/isaricanalytics/redcap-data.html
• sources/visualisation/bar.html
• sources/visualisation/bar_line.html
• and 9 more...

± Modified

• genindex.html
• index.html
• py-modindex.html
• _modules/index.html
• sources/analytics.html
• sources/api-reference.html
• sources/contributing.html
• sources/redcap-data.html
• _modules/isaricanalytics/analytics.html
• _modules/isaricanalytics/redcap_data.html
• and 5 more...

- Deleted

• sources/visualisation.html
• sources/isaricanalytics/redcap_data.html
• _modules/scipy/stats/_mannwhitneyu.html

[sr-murthy]

@alasdairwilson Please review, if you have time.

This is back in development again because of additional requirements, and will be resubmitted when it is ready.