Get the docs/, templates/analyses, and the templates_examples/csvs/ up-to-date

[crouchcd]

What

Updates the documentation, analysis templates, and template_examples/csvs files with the latest code changes

Why

Noticed an issue when trying to run the pre-commit githook. The ATACseq analysis definition still referred to a "report" field that had been removed previously. See (75535d3). The docs/ were out of date.

How

The pre-commit util was installing an out-of-date version of the schemas. I opted to skip that step and instead run the pre-commit steps manually. First, I made sure PYTHONPATH included the cidc-schemas root directory and that I didn't have any installed version of cidc-schemas in site-packages. Then I ran the python docs/generate_docs.py script followed by the ./.githooks/pre-commit script. I ran into an issue with git referencing files with different names. I opted to skip the git add and git rm steps in the pre-commit script. Instead I tracked down the problem files (ATACSEQ_Analysis.csv, plasma_template__shipment.csv, and pbmc_template__shipment.csv) and used git mv to the correct names.

Remarks

Checklist

Please include and complete the following checklist. You can mark an item as complete with the - [x] prefix:

• Tests - Added unit tests for new code, regression tests for bugs and updated the integration tests if required
• Formatting & Linting - black and flake8 have been used to ensure styling guidelines are met
• Type Annotations - All new code has been type annotated in the function signatures using type hints
• Docstrings - Docstrings have been provided for functions
• Documentation - Documentation in docs/ has be regenerated and README and CHANGELOG have been updated to explain major changes & new features
• Package version - Manually bumped the Schemas package version in cidc_schemas/__init__.py