build: bump version to 2.0

And remove deprecated chart-review alias for upload-notes, since this
is a good time to break CLI promises.

compose.yaml

@@ -80,10 +80,6 @@ services:
   ctakes-covid:
     extends: ctakes-covid-base
     profiles:
-      # chart-review is a deprecated alias for upload-notes since Jan 2024.
-      # Remove when you feel like it.
-      - chart-review
-      - chart-review-gpu
       - covid-symptom
       - covid-symptom-gpu
       - upload-notes
@@ -93,9 +89,6 @@ services:
     extends: common-base
     image: smartonfhir/cnlp-transformers:negation-0.6.1-cpu
     profiles:
-      # chart-review is a deprecated alias for upload-notes since Jan 2024.
-      # Remove when you feel like it.
-      - chart-review
       - covid-symptom
       - upload-notes
     networks:
@@ -105,9 +98,6 @@ services:
     extends: common-base
     image: smartonfhir/cnlp-transformers:negation-0.6.1-gpu
     profiles:
-      # chart-review-gpu is a deprecated alias for upload-notes-gpu since Jan 2024.
-      # Remove when you feel like it.
-      - chart-review-gpu
       - covid-symptom-gpu
       - upload-notes-gpu
     networks:

cumulus_etl/__init__.py

@@ -1,3 +1,3 @@
 """Turns FHIR data into de-identified & aggregated records"""
 
-__version__ = "1.5.0"
+__version__ = "2.0.0"

cumulus_etl/cli.py

@@ -16,10 +16,6 @@
 class Command(enum.Enum):
     """Subcommand strings"""
 
-    # chart-review is a deprecated alias of upload-notes since Jan 2024.
-    # Keep as long as you like.
-    # It's a low-usage feature, but it's not a maintenance burden to keep this around.
-    CHART_REVIEW = "chart-review"
     CONVERT = "convert"
     ETL = "etl"
     EXPORT = "export"
@@ -65,7 +61,7 @@ async def main(argv: list[str]) -> None:
         prog += f" {subcommand}"  # to make --help look nicer
     parser = argparse.ArgumentParser(prog=prog)
 
-    if subcommand in {Command.CHART_REVIEW.value, Command.UPLOAD_NOTES.value}:
+    if subcommand == Command.UPLOAD_NOTES.value:
         run_method = upload_notes.run_upload_notes
     elif subcommand == Command.CONVERT.value:
         run_method = convert.run_convert