PY: consolidate python-r4 and python-us-core into python-r4-us-core

.github/workflows/sdk-tests.yml

@@ -91,19 +91,6 @@ jobs:
           export AIDBOX_LICENSE_ID="${{ secrets.AIDBOX_LICENSE_ID }}"
           make test-python-sdk
 
-      - name: Repository contains actual python-sdk version
-        run: |
-          diff_result=$(git diff --exit-code --name-only examples/python/fhir_types || true)
-
-          if [ -z "$diff_result" ]; then
-            echo "✅ Generated SDK is identical to the one stored in repository."
-          else
-            echo "❌ Generated SDK differs from the one stored in repository."
-            echo "Differences:"
-            git diff examples/python/fhir_types
-            exit 1
-          fi
-
   test-python-fhirpy-sdk:
     runs-on: ubuntu-latest
 
@@ -138,7 +125,7 @@ jobs:
             exit 1
           fi
 
-  test-python-us-core-example:
+  test-python-r4-us-core-example:
     runs-on: ubuntu-latest
 
     steps:
@@ -155,7 +142,20 @@ jobs:
         run: bun install --frozen-lockfile
 
       - name: Run tests
-        run: make test-python-us-core-example
+        run: make test-python-r4-us-core-example
+
+      - name: Repository contains actual python-sdk version
+        run: |
+          diff_result=$(git diff --exit-code --name-only examples/python-r4-us-core/fhir_types || true)
+
+          if [ -z "$diff_result" ]; then
+            echo "✅ Generated SDK is identical to the one stored in repository."
+          else
+            echo "❌ Generated SDK differs from the one stored in repository."
+            echo "Differences:"
+            git diff examples/python-r4-us-core/fhir_types
+            exit 1
+          fi
 
   test-typescript-custom-packages-example:
     runs-on: ubuntu-latest

Makefile

@@ -10,9 +10,9 @@ VERSION = $(shell cat package.json | grep version | sed -E 's/ *"version": "//'
 	test-on-the-fly-example test-on-the-fly-norge-r4 test-on-the-fly-kbv-r4 test-on-the-fly-ccda \
 	test-typescript-r4-us-core-example test-typescript-custom-packages-example \
 	test-mustache-java-r4-example \
-	test-csharp-sdk generate-python-sdk generate-python-sdk-fhirpy generate-python-us-core-sdk \
-	python-test-setup python-fhirpy-test-setup python-us-core-test-setup \
-	test-python-sdk test-python-fhirpy-sdk test-python-us-core-example
+	test-csharp-sdk generate-python-r4-us-core-sdk generate-python-sdk-fhirpy \
+	python-r4-us-core-test-setup python-fhirpy-test-setup \
+	test-python-sdk test-python-fhirpy-sdk test-python-r4-us-core-example
 
 all: test test-multi-package test-typescript-r4-us-core-example test-typescript-custom-packages-example lint-unsafe test-all-example-generation
 
@@ -56,9 +56,8 @@ test-all-example-generation: test-other-example-generation
 	bun run examples/csharp/generate.ts
 	bun run examples/typescript-custom-packages/generate.ts
 	bun run examples/mustache/mustache-java-r4-gen.ts
-	bun run examples/python-r4/generate.ts
+	bun run examples/python-r4-us-core/generate.ts
 	bun run examples/python-fhirpy/generate.ts
-	bun run examples/python-us-core/generate.ts
 	bun run examples/typescript-r4-us-core/generate.ts
 
 test-other-example-generation: test-on-the-fly-example
@@ -102,25 +101,20 @@ test-csharp-sdk: typecheck prepare-aidbox-runme
 	cd examples/csharp && dotnet test
 
 PYTHON=python3.13
-PYTHON_EXAMPLE=./examples/python-r4
+PYTHON_R4_US_CORE_EXAMPLE=./examples/python-r4-us-core
 PYTHON_FHIRPY_EXAMPLE=./examples/python-fhirpy
-PYTHON_US_CORE_EXAMPLE=./examples/python-us-core
 
-generate-python-sdk:
-	$(TYPECHECK) --project examples/python-r4/tsconfig.json
-	bun run examples/python-r4/generate.ts
+generate-python-r4-us-core-sdk:
+	$(TYPECHECK) --project examples/python-r4-us-core/tsconfig.json
+	bun run examples/python-r4-us-core/generate.ts
 
 generate-python-sdk-fhirpy:
 	$(TYPECHECK) --project examples/python-fhirpy/tsconfig.json
 	bun run examples/python-fhirpy/generate.ts
 
-generate-python-us-core-sdk:
-	$(TYPECHECK) --project examples/python-us-core/tsconfig.json
-	bun run examples/python-us-core/generate.ts
-
-python-test-setup:
-	@if [ ! -d "$(PYTHON_EXAMPLE)/venv" ]; then \
-		cd $(PYTHON_EXAMPLE) && \
+python-r4-us-core-test-setup:
+	@if [ ! -d "$(PYTHON_R4_US_CORE_EXAMPLE)/venv" ]; then \
+		cd $(PYTHON_R4_US_CORE_EXAMPLE) && \
 		$(PYTHON) -m venv venv && \
 		. venv/bin/activate && \
 		pip install -r fhir_types/requirements.txt; \
@@ -135,44 +129,23 @@ python-fhirpy-test-setup:
 		pip install fhirpy; \
 	fi
 
-python-us-core-test-setup:
-	@if [ ! -d "$(PYTHON_US_CORE_EXAMPLE)/venv" ]; then \
-		cd $(PYTHON_US_CORE_EXAMPLE) && \
-		$(PYTHON) -m venv venv && \
-		. venv/bin/activate && \
-		pip install -r fhir_types/requirements.txt; \
-	fi
-
-test-python-sdk: typecheck prepare-aidbox-runme generate-python-sdk python-test-setup
-    # Run mypy in strict mode
-	cd $(PYTHON_EXAMPLE) && \
-         . venv/bin/activate && \
-         mypy --strict .
-
-	cd $(PYTHON_EXAMPLE) && \
-         . venv/bin/activate && \
-         python -m pytest test_sdk.py -v
+# Offline: mypy + profile/bundle/extension tests (no Aidbox required).
+test-python-r4-us-core-example: typecheck generate-python-r4-us-core-sdk python-r4-us-core-test-setup
+	cd $(PYTHON_R4_US_CORE_EXAMPLE) && \
+	     . venv/bin/activate && \
+	     mypy .
 
-	cd $(PYTHON_EXAMPLE) && \
-         . venv/bin/activate && \
-         python -m pytest test_raw_extension.py -v
+	cd $(PYTHON_R4_US_CORE_EXAMPLE) && \
+	     . venv/bin/activate && \
+	     python -m pytest --ignore=test_sdk.py -v
 
-	cd $(PYTHON_EXAMPLE) && \
-         . venv/bin/activate && \
-         python -m pytest test_bundle.py -v
+# Live SDK client tests via client.py (require Aidbox).
+test-python-sdk: typecheck prepare-aidbox-runme generate-python-r4-us-core-sdk python-r4-us-core-test-setup
+	cd $(PYTHON_R4_US_CORE_EXAMPLE) && \
+	     . venv/bin/activate && \
+	     python -m pytest test_sdk.py -v
 
 test-python-fhirpy-sdk: typecheck prepare-aidbox-runme generate-python-sdk-fhirpy python-fhirpy-test-setup
-    # Run mypy in strict mode
 	cd $(PYTHON_FHIRPY_EXAMPLE) && \
-       . venv/bin/activate && \
-       mypy --strict .
-
-# Profile tests are offline (no Aidbox required).
-test-python-us-core-example: typecheck generate-python-us-core-sdk python-us-core-test-setup
-	cd $(PYTHON_US_CORE_EXAMPLE) && \
-	     . venv/bin/activate && \
-	     mypy --config-file mypy.ini .
-
-	cd $(PYTHON_US_CORE_EXAMPLE) && \
-	     . venv/bin/activate && \
-	     python -m pytest -v
+	   . venv/bin/activate && \
+	   mypy .

README.md

@@ -118,7 +118,7 @@ See the [examples/](examples/) directory for working demonstrations:
 
 - **[typescript-r4-us-core/](examples/typescript-r4-us-core/)** - FHIR R4 core + US Core type generation with resource creation, profiles, and extensions
 - **[on-the-fly/ccda/](examples/on-the-fly/ccda/)** - C-CDA on FHIR type generation (logical models, generated on the fly)
-- **[python/](examples/python/)** - Python/Pydantic model generation with simple requests-based client
+- **[python-r4-us-core/](examples/python-r4-us-core/)** - Python/Pydantic models for FHIR R4 core + US Core profiles, with a requests-based client
 - **[python-fhirpy/](examples/python-fhirpy/)** - Python/Pydantic model generation with fhirpy async client
 - **[csharp/](examples/csharp/)** - C# class generation with namespace configuration
 - **[mustache/](examples/mustache/)** - Java generation with Mustache templates and post-generation hooks

examples/README.md

@@ -17,11 +17,10 @@ This directory contains working examples demonstrating the capabilities of Atomi
 
 ### Python Generation
 
-- **[python/](python/)** - Python/Pydantic model generation with simple requests-based client
-  - `generate.ts` - Generates Python models with configurable field formats
-  - Supports `snake_case` or `camelCase` field naming
-  - Configurable extra field validation
-  - Client implementation example: [python/client.py](python/client.py)
+- **[python-r4-us-core/](python-r4-us-core/)** - Python/Pydantic models for FHIR R4 core + US Core profiles
+  - `generate.ts` - Generates R4 models and US Core profiles in one tree; configurable `snake_case`/`camelCase` field naming and extra-field validation
+  - US Core profile classes (Patient, blood pressure, body weight) with typed accessors and race/ethnicity/birth-sex extensions
+  - Simple `requests`-based FHIR client ([python-r4-us-core/client.py](python-r4-us-core/client.py)), exercised by `test_sdk.py`
 
 - **[python-fhirpy/](python-fhirpy/)** - Python/Pydantic models with fhirpy async client
   - `generate.ts` - Generates Python models with fhirpy integration

examples/python-fhirpy/mypy.ini

@@ -1,5 +1,6 @@
 [mypy]
 python_version = 3.13
+strict = True
 disallow_untyped_defs = False
 disallow_incomplete_defs = False
 check_untyped_defs = True

examples/python-us-core/.gitignore → examples/python-r4-us-core/.gitignore

@@ -3,3 +3,4 @@ __pycache__
 .mypy_cache
 venv
 /.venv/
+fhir_types/type-schemas/

examples/python-us-core/README.md → examples/python-r4-us-core/README.md

@@ -1,28 +1,41 @@
-# Python Example
+# Python Example — FHIR R4 Core + US Core
 
-FHIR R4 type generation with Pydantic models, configurable field formats, and validation.
+Python/Pydantic model generation for FHIR R4 core **and** US Core profiles, with
+configurable field formats, validation, and a simple `requests`-based FHIR client.
+
+A single `generate.ts` pulls US Core 8.0.1 (which depends on R4 core) plus a local
+`ExampleTypedBundle` StructureDefinition, so one `fhir_types/` tree contains the base
+R4 models/profiles (`hl7_fhir_r4_core`), the US Core profiles (`hl7_fhir_us_core`), and
+the local typed-bundle profile (`example_folder_structures`).
 
 ## Overview
 
-This example demonstrates how to generate Python/Pydantic models from the FHIR R4 specification using the Atomic EHR Codegen toolkit. It includes:
+This example demonstrates how to generate Python/Pydantic models using the Atomic EHR
+Codegen toolkit. It includes:
 
-- Full FHIR R4 resource type definitions as Pydantic models
+- FHIR R4 resource type definitions as Pydantic models, plus base R4 profiles (bodyweight)
+- US Core profiles (Patient, blood pressure, body weight) with typed accessors and race/ethnicity/birth-sex extensions
 - Automatic validation and serialization
 - Configurable field naming conventions (snake_case or camelCase)
-- Integration with Python type checking and IDE support
-- Virtual environment setup
-- Simple FHIR server client example using `requests`
+- Integration with Python type checking (mypy) and IDE support
+- A simple FHIR server client example using `requests` (`client.py`, exercised by `test_sdk.py`)
 
 For an example using the `fhirpy` async client library, see [python-fhirpy/](../python-fhirpy/).
 
+## Tests
+
+- `test_profile_*.py` — US Core profile API (offline: no server required)
+- `test_bundle.py` / `test_raw_extension.py` — generic Bundle and extension handling (offline)
+- `test_sdk.py` — live CRUD against a FHIR server via `client.py` (requires Aidbox)
+
 ## Setup
 
 ### Python Environment
 
 1. Create virtual environment:
 
 ```bash
-cd examples/python
+cd examples/python-r4-us-core
 python3 -m venv venv
 
 # On macOS/Linux:
@@ -48,10 +61,10 @@ python --version  # Should be 3.10 or higher
 To generate Python/Pydantic types for FHIR R4:
 
 ```bash
-bun run examples/python/generate.ts
+bun run examples/python-r4-us-core/generate.ts
 ```
 
-This will output to `./examples/python/fhir_types/`
+This will output to `./examples/python-r4-us-core/fhir_types/`
 
 ## Configuration
 

examples/python-us-core/fhir_types/README.md → examples/python-r4-us-core/fhir_types/README.md

@@ -39,10 +39,12 @@
 - `http://hl7.org/fhir/StructureDefinition/Appointment`
 - `http://hl7.org/fhir/StructureDefinition/AppointmentResponse`
 - `http://hl7.org/fhir/StructureDefinition/AuditEvent`
+- `http://hl7.org/fhir/StructureDefinition/BackboneElement`
 - `http://hl7.org/fhir/StructureDefinition/Basic`
 - `http://hl7.org/fhir/StructureDefinition/Binary`
 - `http://hl7.org/fhir/StructureDefinition/BiologicallyDerivedProduct`
 - `http://hl7.org/fhir/StructureDefinition/BodyStructure`
+- `http://hl7.org/fhir/StructureDefinition/Bundle`
 - `http://hl7.org/fhir/StructureDefinition/CapabilityStatement`
 - `http://hl7.org/fhir/StructureDefinition/CarePlan`
 - `http://hl7.org/fhir/StructureDefinition/CareTeam`
@@ -78,7 +80,9 @@
 - `http://hl7.org/fhir/StructureDefinition/DiagnosticReport-geneticsReferences`
 - `http://hl7.org/fhir/StructureDefinition/DocumentManifest`
 - `http://hl7.org/fhir/StructureDefinition/DocumentReference`
+- `http://hl7.org/fhir/StructureDefinition/DomainResource`
 - `http://hl7.org/fhir/StructureDefinition/EffectEvidenceSynthesis`
+- `http://hl7.org/fhir/StructureDefinition/Element`
 - `http://hl7.org/fhir/StructureDefinition/ElementDefinition`
 - `http://hl7.org/fhir/StructureDefinition/Encounter`
 - `http://hl7.org/fhir/StructureDefinition/Endpoint`
@@ -137,12 +141,14 @@
 - `http://hl7.org/fhir/StructureDefinition/MoneyQuantity`
 - `http://hl7.org/fhir/StructureDefinition/NamingSystem`
 - `http://hl7.org/fhir/StructureDefinition/NutritionOrder`
+- `http://hl7.org/fhir/StructureDefinition/Observation`
 - `http://hl7.org/fhir/StructureDefinition/ObservationDefinition`
 - `http://hl7.org/fhir/StructureDefinition/OperationDefinition`
 - `http://hl7.org/fhir/StructureDefinition/OperationOutcome`
 - `http://hl7.org/fhir/StructureDefinition/Organization`
 - `http://hl7.org/fhir/StructureDefinition/OrganizationAffiliation`
 - `http://hl7.org/fhir/StructureDefinition/Parameters`
+- `http://hl7.org/fhir/StructureDefinition/Patient`
 - `http://hl7.org/fhir/StructureDefinition/PaymentNotice`
 - `http://hl7.org/fhir/StructureDefinition/PaymentReconciliation`
 - `http://hl7.org/fhir/StructureDefinition/Person`
@@ -2581,9 +2587,6 @@
 - `urn:fhir:binding:InvestigationGroupType`
 - `urn:fhir:binding:InvoicePriceComponentType`
 - `urn:fhir:binding:InvoiceStatus`
-- `urn:fhir:binding:IssueDetails`
-- `urn:fhir:binding:IssueSeverity`
-- `urn:fhir:binding:IssueType`
 - `urn:fhir:binding:ItemDescriptionLanguage`
 - `urn:fhir:binding:Jurisdiction`
 - `urn:fhir:binding:LDLCodes`

examples/python-us-core/fhir_types/__init__.py → examples/python-r4-us-core/fhir_types/__init__.py

@@ -16,6 +16,7 @@
 from fhir_types.hl7_fhir_r4_core.observation import (
     Observation, ObservationComponent, ObservationReferenceRange
 )
+from fhir_types.hl7_fhir_r4_core.operation_outcome import OperationOutcome, OperationOutcomeIssue
 from fhir_types.hl7_fhir_r4_core.organization import Organization, OrganizationContact
 from fhir_types.hl7_fhir_r4_core.patient import (
     Patient, PatientCommunication, PatientContact, PatientLink
@@ -55,6 +56,8 @@
 Observation.model_rebuild()
 ObservationComponent.model_rebuild()
 ObservationReferenceRange.model_rebuild()
+OperationOutcome.model_rebuild()
+OperationOutcomeIssue.model_rebuild()
 Organization.model_rebuild()
 OrganizationContact.model_rebuild()
 ParameterDefinition.model_rebuild()

examples/python-r4/fhir_types/hl7_fhir_r4_core/__init__.py → examples/python-r4-us-core/fhir_types/hl7_fhir_r4_core/__init__.py

@@ -17,6 +17,7 @@
     Observation, ObservationComponent, ObservationReferenceRange
 )
 from fhir_types.hl7_fhir_r4_core.operation_outcome import OperationOutcome, OperationOutcomeIssue
+from fhir_types.hl7_fhir_r4_core.organization import Organization, OrganizationContact
 from fhir_types.hl7_fhir_r4_core.patient import (
     Patient, PatientCommunication, PatientContact, PatientLink
 )
@@ -58,6 +59,8 @@
     'ObservationReferenceRange',
     'OperationOutcome',
     'OperationOutcomeIssue',
+    'Organization',
+    'OrganizationContact',
     'ParameterDefinition',
     'Patient',
     'PatientCommunication',

examples/python-r4-us-core/fhir_types/hl7_fhir_r4_core/profiles/__init__.py

@@ -0,0 +1,19 @@
+# WARNING: This file is autogenerated by @atomic-ehr/codegen.
+# GitHub: https://github.com/atomic-ehr/codegen
+# Any manual changes made to this file may be overwritten.
+
+from .extension_birth_place import BirthPlaceExtension
+from .extension_birth_time import BirthTimeExtension
+from .extension_nationality import NationalityExtension
+from .observation_observation_bodyweight import ObservationBodyweightProfile
+from .observation_observation_vitalsigns import ObservationVitalsignsProfile
+from .extension_own_prefix import OwnPrefixExtension
+
+__all__ = [
+    'BirthPlaceExtension',
+    'BirthTimeExtension',
+    'NationalityExtension',
+    'ObservationBodyweightProfile',
+    'ObservationVitalsignsProfile',
+    'OwnPrefixExtension',
+]