Merge branch 'main' into milanmlft/imaging-api-readme

.github/workflows/main.yml

@@ -111,7 +111,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -e pixl_core
-          pip install -r pixl_dcmd/src/requirements.txt
+          pip install -e pixl_dcmd[test]
 
       - name: Run tests
         working-directory: pixl_dcmd

README.md

@@ -218,12 +218,7 @@ See each service's README for instructions for individual developing and testing
 For Python development we use [ruff](https://docs.astral.sh/ruff/) alongside [pytest](https://www.pytest.org/).
 There is support (sometimes through plugins) for these tools in most IDEs & editors.
 
-Before raising a PR, **run the full test suite** from the _PIXL_ directory with
-
-```bash
-bin/run-all-tests.sh
-```
-
+Before raising a PR, make sure to **run all tests** for each PIXL module
 and not just the component you have been working on as this will help us catch unintentional regressions without spending GH actions minutes :-)
 
 We run [pre-commit](https://pre-commit.com/) as part of the GitHub Actions CI. To install and run it locally, do:

docker/orthanc-anon/Dockerfile

@@ -20,8 +20,5 @@ COPY ./orthanc/orthanc-anon/plugin/tag-operations.yaml /etc/orthanc/tag-operatio
 COPY ./pixl_core/ ./pixl_core
 RUN pip3 install --no-cache-dir ./pixl_core
 
-COPY ./pixl_dcmd/src/requirements.txt .
-RUN pip3 install --no-cache-dir -r requirements.txt
-
-COPY ./pixl_dcmd/src ./pixl_dcmd
+COPY ./pixl_dcmd/ ./pixl_dcmd
 RUN pip3 install --no-cache-dir ./pixl_dcmd

pixl_dcmd/README.md

@@ -8,15 +8,7 @@ and persisting it in the PIXL postgres database.
 Install the Python dependencies with
 
 ```bash
-pip install -e ../../pixl_core/ .
-```
-
-```bash
-pip install -r requirements.txt
-```
-
-```bash
-pip install -e .
+pip install -e ../pixl_core/ .[test,dev]
 ```
 
 ## Test

pixl_dcmd/bin/run-tests.sh

@@ -18,4 +18,4 @@ BIN_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
 PACKAGE_DIR="${BIN_DIR%/*}"
 cd "$PACKAGE_DIR"
 
-pytest src/pixl_dcmd/tests
+pytest tests

pixl_dcmd/pyproject.toml

@@ -0,0 +1,42 @@
+[project]
+name = "pixl_dcmd"
+version = "0.0.2"
+authors = [
+    { name="PIXL authors" },
+]
+description = "DICOM header anonymisation functions"
+readme = "README.md"
+requires-python = "~=3.9"
+classifiers = [
+    "Programming Language :: Python :: 3"
+]
+dependencies = [
+    "arrow==1.2.3",
+    "pydicom==2.4.4",
+    "pydicom-data",
+    "logger==1.4",
+    "pyyaml==6.0",
+    "requests==2.31.0",
+    "python-decouple==3.6",
+    "types-requests~=2.28",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest==7.4.2",
+]
+dev = [
+    "mypy",
+    "pre-commit",
+    "ruff"
+]
+
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.ruff]
+extend = "./ruff.toml"
+
+[tool.ruff.extend-per-file-ignores]
+"./tests/**" = ["D100"]

pixl_dcmd/src/pixl_dcmd/tests/test_main.py → pixl_dcmd/tests/test_main.py

@@ -32,7 +32,7 @@
 def tag_scheme() -> dict:
     """Read the tag scheme from orthanc raw."""
     tag_file = (
-        pathlib.Path(__file__).parents[4]
+        pathlib.Path(__file__).parents[2]
         / "orthanc/orthanc-anon/plugin/tag-operations.yaml"
     )
     return yaml.safe_load(tag_file.read_text())
@@ -57,7 +57,7 @@ def test_image_already_exported_throws(rows_in_session, tag_scheme):
     WHEN the dicom tag scheme is applied
     THEN an exception will be thrown as
     """
-    exported_dicom = pathlib.Path(__file__).parents[4] / "test/resources/Dicom1.dcm"
+    exported_dicom = pathlib.Path(__file__).parents[2] / "test/resources/Dicom1.dcm"
     input_dataset = pydicom.dcmread(exported_dicom)
 
     with pytest.raises(sqlalchemy.exc.NoResultFound):
@@ -71,7 +71,7 @@ def test_pseudo_identifier_processing(rows_in_session, tag_scheme):
     THEN the patient identifier tag should be the mrn and accession hashed
       and the pipeline db row should now have the fake hash
     """
-    exported_dicom = pathlib.Path(__file__).parents[4] / "test/resources/Dicom2.dcm"
+    exported_dicom = pathlib.Path(__file__).parents[2] / "test/resources/Dicom2.dcm"
     input_dataset = pydicom.dcmread(exported_dicom)
 
     accession_number = "AA12345605"

pixl_pacs/src/pixl_pacs/_processing.py

@@ -66,7 +66,7 @@ async def process_message(message: Message) -> None:
 
 @dataclass
 class ImagingStudy:
-    """Dataclass for EHR unique to a patient and xray study"""
+    """Dataclass for DICOM study unique to a patient and imaging study"""
 
     message: Message