diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b194cdec..81537c29 100644 --- a/.github/workflows/ci.yml +++ b/.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 diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index c87e141f..26bf158a 100644 --- a/.github/workflows/publish.yml +++ b/.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: diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 730ed2b3..01365de4 100644 --- a/CONTRIBUTING.md +++ b/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 diff --git a/healthchain/cli.py b/healthchain/cli.py index 292b55bf..bf4577c6 100644 --- a/healthchain/cli.py +++ b/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}") diff --git a/healthchain/io/containers/document.py b/healthchain/io/containers/document.py index 8ee1dfd5..81f09d2b 100644 --- a/healthchain/io/containers/document.py +++ b/healthchain/io/containers/document.py @@ -318,10 +318,32 @@ 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]: @@ -329,12 +351,34 @@ def medication_list(self) -> List[MedicationStatement]: 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]: @@ -342,12 +386,34 @@ def allergy_list(self) -> List[AllergyIntolerance]: 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.""" diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 45ca8487..00000000 --- a/poetry.lock +++ /dev/null @@ -1,3472 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. - 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