Skip to content

Latest commit

 

History

History
75 lines (59 loc) · 2.21 KB

CONTRIBUTING.md

File metadata and controls

75 lines (59 loc) · 2.21 KB
Raw

Contributing to Cumulus Library

Set up your dev environment

To use the same dev environment as us, you'll want to run these commands:

pip install .[dev]
pre-commit install

This will install dependencies & build tools, as well as set up an auto-formatter commit hook.

Running tests

Tests can be run with pytest like you might expect, but you'll first want to set up a fake test AWS profile.

  1. Edit ~/.aws/credentials
  2. Add a block like:
[test]
aws_access_key_id = test
aws_secret_access_key = test
  1. Then run pytest

Adding new resources

Things to keep in mind:

  • If the new resource links to Encounter, add it to the completion checking done in the Encounter code. (Though consider the effect this will have on existing encounters.)
  • Try to keep the columns in spec-order, except please move any isolated reference fields to the end, since they are not really human-readable and this makes it nicer to visually scan the table.
  • Add a self-Reference field for easier joining. For example, if you're adding a condition table, in addition to the id field, add a condition_ref field defined like: concat('Condition/', id) AS condition_ref

Rebuilding the reference SQL

We keep some reference SQL in git, to help us track unexpected changes and verify our SQL indenting. These are stored in cumulus_library/studies/*/reference_sql/

You can regenerate these yourself when you make changes to SQL:

cumulus-library generate-sql \
  --db-type duckdb \
  --database :memory: \
  --load-ndjson-dir tests/test_data/duckdb_data \
  --target core \
  --target discovery

Rebuilding the Markdown table docs

We keep some generated documentation in git, to help us keep our docs in sync with table changes. This is stored in docs/core-study-details.md

You can regenerate these yourself when you make changes to table layout:

  1. Rebuild the core study in Athena.
  2. Run generate-md against Athena:
cumulus-library generate-md --target core [database args pointing at your athena db]

Then take the contents of cumulus_library/studies/core/core_generated.md and paste them into docs/core-study-details.md (being careful to not erase any manually entered descriptions).