Switch the ETL to ruff

[mikix]

• Switch to ruff (first commit)
• Meet Matt halfway at 100 line width (second commit)
• Dropped pylint disable lines (third commit)

Interesting deltas with Library's ruff config:

• I dropped the ISC checks (only 3 of them and 2 of them actively conflict with the formatter - I'm just letting format handle this)
• I dropped the B (bugbear) checks - they were marked as security checks, but that's not really what bugbear is doing. And I didn't love two of the changes it wanted (B027 and B905 -- 905 I can kind of see, but 027 especially I didn't love)
• I added S (bandit) checks to get back security scanning - I'd recommend the same in Library

Checklist

• Consider if documentation (like in docs/) needs to be updated
• Consider if tests should be added

[dogversioning]

You can keep the 120 if it makes you happy, you're the boss over here.

[github-actions]

☂️ Python Coverage

current status: ❌

Overall Coverage

Lines	Covered	Coverage	Threshold	Status
3207	3105	97%	93%	🟢

New Files

No new covered files...

Modified Files

File	Coverage	Status
cumulus_etl/cli.py	100%	🟢
cumulus_etl/cli_utils.py	100%	🟢
cumulus_etl/common.py	95%	🔴
cumulus_etl/completion/init.py	100%	🟢
cumulus_etl/completion/schema.py	100%	🟢
cumulus_etl/deid/codebook.py	99%	🔴
cumulus_etl/deid/mstool.py	100%	🟢
cumulus_etl/deid/scrubber.py	100%	🟢
cumulus_etl/errors.py	100%	🟢
cumulus_etl/etl/cli.py	100%	🟢
cumulus_etl/etl/config.py	100%	🟢
cumulus_etl/etl/context.py	97%	🔴
cumulus_etl/etl/convert/cli.py	97%	🔴
cumulus_etl/etl/studies/covid_symptom/covid_ctakes.py	82%	🔴
cumulus_etl/etl/studies/covid_symptom/covid_tasks.py	89%	🔴
cumulus_etl/etl/tasks/base.py	99%	🔴
cumulus_etl/etl/tasks/basic_tasks.py	99%	🔴
cumulus_etl/etl/tasks/batching.py	100%	🟢
cumulus_etl/etl/tasks/nlp_task.py	100%	🟢
cumulus_etl/etl/tasks/task_factory.py	100%	🟢
cumulus_etl/fhir/fhir_auth.py	96%	🔴
cumulus_etl/fhir/fhir_client.py	95%	🔴
cumulus_etl/formats/base.py	100%	🟢
cumulus_etl/formats/batch.py	100%	🟢
cumulus_etl/formats/deltalake.py	92%	🔴
cumulus_etl/loaders/fhir/bulk_export.py	99%	🔴
cumulus_etl/loaders/fhir/export_log.py	100%	🟢
cumulus_etl/loaders/fhir/ndjson_loader.py	98%	🔴
cumulus_etl/loaders/i2b2/loader.py	98%	🔴
cumulus_etl/loaders/i2b2/oracle/connect.py	100%	🟢
cumulus_etl/loaders/i2b2/oracle/extract.py	96%	🔴
cumulus_etl/loaders/i2b2/oracle/query.py	86%	🔴
cumulus_etl/loaders/i2b2/transform.py	83%	🔴
cumulus_etl/nlp/init.py	100%	🟢
cumulus_etl/nlp/extract.py	100%	🟢
cumulus_etl/nlp/huggingface.py	100%	🟢
cumulus_etl/nlp/utils.py	100%	🟢
cumulus_etl/nlp/watcher.py	100%	🟢
cumulus_etl/upload_notes/cli.py	100%	🟢
cumulus_etl/upload_notes/downloader.py	100%	🟢
cumulus_etl/upload_notes/labelstudio.py	99%	🔴
cumulus_etl/upload_notes/selector.py	95%	🔴
TOTAL	97%	🔴

updated for commit: 5be339e by action🐍