feat: Clarify FhirData setter behavior with explicit replace parameter and transition to uv

.github/workflows/ci.yml

@@ -10,30 +10,34 @@ on:
     branches: [ "main" ]
     types: [opened, synchronize, reopened, ready_for_review]
 
+
 jobs:
   test:
     if: github.event.pull_request.draft == false
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
-        poetry-version: [1.8.2]
+        python-version: ["3.10", "3.11"]
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository
         uses: actions/checkout@v3
-      - name: "Setup Python, Poetry and Dependencies"
-        uses: packetcoders/action-setup-cache-python-poetry@main
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
         with:
-          python-version: ${{matrix.python-version}}
-          poetry-version: ${{matrix.poetry-version}}
-      - name: Install package
-        run: |
-          poetry install --no-interaction
+          version: "latest"
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --all-extras --dev
+
       - name: Lint with Ruff
         run: |
-          poetry run ruff format
-          poetry run ruff check
+          uv run ruff format
+          uv run ruff check
         continue-on-error: true
+
       - name: Run tests
-        run: |
-          poetry run pytest
+        run: uv run pytest

.github/workflows/publish.yml

@@ -12,18 +12,20 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        enable-cache: true
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.11"  # Use a version compatible with >=3.8,<3.12
-    - name: Install Poetry
-      uses: snok/install-poetry@v1
-      with:
-        version: 1.8.2  # Match local version
+        python-version: "3.11"
     - name: Bump version
-      run: poetry version $(git describe --tags --abbrev=0)
+      run: |
+        VERSION=$(git describe --tags --abbrev=0)
+        uvx --from=toml-cli toml set --toml-path=pyproject.toml project.version "${VERSION#v}"
     - name: Build a binary wheel and a source tarball
-      run: poetry build
+      run: uv build
     - name: Store the distribution packages
       uses: actions/upload-artifact@v4
       with:

CONTRIBUTING.md

@@ -32,15 +32,15 @@ We believe that every contribution, big or small, makes a difference. Thank you
 
 ## How to Contribute Code
 
-This project uses `poetry` for dependency management. For more information see the [poetry documentation](https://python-poetry.org/docs/).
+This project uses `uv` for dependency management. For more information see the [uv documentation](https://docs.astral.sh/uv/).
 
 1. Fork the repository to your own GitHub account. For more details check out [github documentation](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo).
 
 2. Clone the forked repository to your local machine.
 
-3. Run `poetry install --with dev` to install all the necessary development dependencies.
+3. Run `uv sync --all-extras --dev` to install all the necessary development dependencies.
 
-4. Try running `poetry run pytest` to check that all is working as expected.
+4. Try running `uv run pytest` to check that all is working as expected.
 
 5. Create a new branch for your feature or bugfix.
 
@@ -72,12 +72,12 @@ This project uses `poetry` for dependency management. For more information see t
 
 We use `Mkdocs` for our documentation site. To download the dependencies for documentation, run:
 ```shell
-poetry install --with docs
+uv sync --group docs
 ```
 
 To preview the docs page in development:
 ```shell
-poetry run mkdocs serve
+uv run mkdocs serve
 ```
 #### Writing Clear Documentation
 

healthchain/cli.py

@@ -4,7 +4,7 @@
 
 def run_file(filename):
     try:
-        result = subprocess.run(["poetry", "run", "python", filename], check=True)
+        result = subprocess.run(["uv", "run", "python", filename], check=True)
         print(result.stdout)
     except subprocess.CalledProcessError as e:
         print(f"An error occurred while trying to run the file: {e}")

healthchain/io/containers/document.py

@@ -318,36 +318,102 @@ def problem_list(self) -> List[Condition]:
         return self.get_resources("Condition")
 
     @problem_list.setter
-    def problem_list(self, conditions: List[Condition]) -> None:
-        # TODO: should make this behaviour more explicit whether it's adding or replacing
-        """Set problem list in the bundle."""
-        self.add_resources(conditions, "Condition")
+    def problem_list(self, value: Union[List[Condition], Dict[str, Any]]) -> None:
+        """
+        Set problem list in the bundle.
+
+        By default, this adds the provided conditions to any existing conditions in the bundle.
+        To replace existing conditions instead, pass a dictionary with 'resources' and 'replace' keys.
+
+        Args:
+            value: Either a list of Condition resources (adds by default) or a dict with:
+                - 'resources': List of Condition resources
+                - 'replace': bool, whether to replace existing resources (default: False)
+
+        Examples:
+            >>> # Add to existing conditions (default behavior)
+            >>> fhir.problem_list = [condition1, condition2]
+            >>> # Replace existing conditions
+            >>> fhir.problem_list = {'resources': [condition1], 'replace': True}
+        """
+        if isinstance(value, dict):
+            resources = value.get("resources", [])
+            replace = value.get("replace", False)
+        else:
+            resources = value
+            replace = False
+
+        self.add_resources(resources, "Condition", replace=replace)
 
     @property
     def medication_list(self) -> List[MedicationStatement]:
         """Get medication list from the bundle."""
         return self.get_resources("MedicationStatement")
 
     @medication_list.setter
-    def medication_list(self, medications: List[MedicationStatement]) -> None:
-        """Set medication list in the bundle.
-        Medication statements are stored as MedicationStatement resources in the bundle.
-        See: https://www.hl7.org/fhir/medicationstatement.html
+    def medication_list(
+        self, value: Union[List[MedicationStatement], Dict[str, Any]]
+    ) -> None:
         """
-        self.add_resources(medications, "MedicationStatement")
+        Set medication list in the bundle.
+
+        By default, this adds the provided medications to any existing medications in the bundle.
+        To replace existing medications instead, pass a dictionary with 'resources' and 'replace' keys.
+
+        Args:
+            value: Either a list of MedicationStatement resources (adds by default) or a dict with:
+                - 'resources': List of MedicationStatement resources
+                - 'replace': bool, whether to replace existing resources (default: False)
+
+        Examples:
+            >>> # Add to existing medications (default behavior)
+            >>> fhir.medication_list = [medication1, medication2]
+            >>> # Replace existing medications
+            >>> fhir.medication_list = {'resources': [medication1], 'replace': True}
+        """
+        if isinstance(value, dict):
+            resources = value.get("resources", [])
+            replace = value.get("replace", False)
+        else:
+            resources = value
+            replace = False
+
+        self.add_resources(resources, "MedicationStatement", replace=replace)
 
     @property
     def allergy_list(self) -> List[AllergyIntolerance]:
         """Get allergy list from the bundle."""
         return self.get_resources("AllergyIntolerance")
 
     @allergy_list.setter
-    def allergy_list(self, allergies: List[AllergyIntolerance]) -> None:
-        """Set allergy list in the bundle.
-        Allergy intolerances are stored as AllergyIntolerance resources in the bundle.
-        See: https://www.hl7.org/fhir/allergyintolerance.html
+    def allergy_list(
+        self, value: Union[List[AllergyIntolerance], Dict[str, Any]]
+    ) -> None:
         """
-        self.add_resources(allergies, "AllergyIntolerance")
+        Set allergy list in the bundle.
+
+        By default, this adds the provided allergies to any existing allergies in the bundle.
+        To replace existing allergies instead, pass a dictionary with 'resources' and 'replace' keys.
+
+        Args:
+            value: Either a list of AllergyIntolerance resources (adds by default) or a dict with:
+                - 'resources': List of AllergyIntolerance resources
+                - 'replace': bool, whether to replace existing resources (default: False)
+
+        Examples:
+            >>> # Add to existing allergies (default behavior)
+            >>> fhir.allergy_list = [allergy1, allergy2]
+            >>> # Replace existing allergies
+            >>> fhir.allergy_list = {'resources': [allergy1], 'replace': True}
+        """
+        if isinstance(value, dict):
+            resources = value.get("resources", [])
+            replace = value.get("replace", False)
+        else:
+            resources = value
+            replace = False
+
+        self.add_resources(resources, "AllergyIntolerance", replace=replace)
 
     def get_prefetch_resources(self, key: str) -> List[Any]:
         """Get resources of a specific type from the prefetch bundle."""