Switch to uv python tool

.dockerignore

@@ -0,0 +1,7 @@
+**/build
+.git
+**/.mypy_cache
+.venv*
+**/.pytest_cache
+**/.ruff_cache
+**/__pycache__

.github/workflows/main.yml

@@ -56,22 +56,23 @@ jobs:
         steps:
             - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-            - name: Init Python
-              uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+            - name: Install uv
+              uses: astral-sh/setup-uv@v4
               with:
+                  version: "0.5.10"
                   python-version: "3.11"
-                  cache: "pip"
+                  enable-cache: true
+
 
             - name: Install Python dependencies
               run: |
-                  python -m pip install --upgrade pip
-                  pip install -e pytest-pixl/
-                  pip install -e pixl_core/[test]
-                  pip install -e ${{ matrix.package_dir }}/[test]
+                  uv sync --all-extras --all-packages
 
             - name: Run tests and generate coverage report
               working-directory: ${{ matrix.package_dir }}
-              run: COV_CORE_SOURCE=src COV_CORE_CONFIG=.coveragerc COV_CORE_DATAFILE=.coverage.eager pytest --cov=src --cov-append --cov-report=xml --cov-report=term-missing
+              run: |
+                  source ../.venv/bin/activate
+                  COV_CORE_SOURCE=src COV_CORE_CONFIG=.coveragerc COV_CORE_DATAFILE=.coverage.eager pytest --cov=src --cov-append --cov-report=xml --cov-report=term-missing
               env:
                   ENV: test
                   AZURE_KEY_VAULT_NAME: test
@@ -91,19 +92,19 @@ jobs:
         steps:
             - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
             - uses: docker/setup-buildx-action@c47758b77c9736f4b2ef4073d4d51994fabfe349 # v3
-            - name: Init Python
-              uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+
+            - name: Install uv
+              uses: astral-sh/setup-uv@v4
               with:
+                  version: "0.5.10"
                   python-version: "3.11"
-                  cache: "pip"
+                  enable-cache: true
 
             - name: Install Python dependencies
-              # The -e option is required here due to the way the
+              # Editable install required here due to the way the
               # code determines the export directory. See issue #318.
               run: |
-                  pip install -e pytest-pixl/
-                  pip install -e pixl_core/[test]
-                  pip install -e cli/[test]
+                  uv sync --all-extras --all-packages
 
             - name: Create .secrets.env
               run: touch test/.secrets.env
@@ -129,7 +130,7 @@ jobs:
                   HASHER_API_AZ_TENANT_ID: ${{ secrets.EXPORT_AZ_TENANT_ID }}
                   HASHER_API_AZ_KEY_VAULT_NAME: ${{ secrets.EXPORT_AZ_KEY_VAULT_NAME }}
               run: |
-                  ./run-system-test.sh coverage
+                  uv run ./run-system-test.sh coverage
                   echo FINISHED SYSTEM TEST SCRIPT
 
             - name: Dump queue docker logs for debugging
@@ -183,4 +184,4 @@ jobs:
               with:
                 directory: test
               env:
-                CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+                CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

cli/pyproject.toml

@@ -25,8 +25,13 @@ dev = [
 pixl = "pixl_cli.main:cli"
 
 [build-system]
-requires = ["setuptools>=61.0"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling>=1.0.0"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+dev-mode-dirs = [
+    "src"
+]
 
 [tool.coverage.report]
 exclude_also = [

docker-compose.yml

@@ -74,8 +74,10 @@ services:
     hasher-api:
         build:
             context: .
-            dockerfile: ./docker/hasher-api/Dockerfile
+            dockerfile: ./docker/pixl-python/Dockerfile
+            target: hasher_api
             args:
+                PIXL_PACKAGE_DIR: hasher
                 <<: *build-args-common
         environment:
             <<: [*proxy-common, *pixl-common-env]
@@ -93,7 +95,6 @@ services:
         networks:
             - pixl-net
         healthcheck:
-            test: ["CMD", "curl", "-f", "http://hasher-api:8000/heart-beat"]
             interval: 10s
             timeout: 30s
             retries: 5
@@ -102,9 +103,11 @@ services:
     orthanc-anon:
         build:
             context: .
-            dockerfile: ./docker/orthanc-anon/Dockerfile
+            dockerfile: ./docker/orthanc/Dockerfile
+            target: pixl_orthanc_anon
             args:
                 <<: *build-args-common
+                ORTHANC_DIR: orthanc-anon
                 ORTHANC_CONCURRENT_JOBS: ${ORTHANC_CONCURRENT_JOBS}
         platform: linux/amd64
         command: /run/secrets
@@ -171,9 +174,11 @@ services:
     orthanc-raw:
         build:
             context: .
-            dockerfile: ./docker/orthanc-raw/Dockerfile
+            dockerfile: ./docker/orthanc/Dockerfile
+            target: pixl_orthanc_raw
             args:
                 <<: *build-args-common
+                ORTHANC_DIR: orthanc-raw
                 ORTHANC_RAW_MAXIMUM_STORAGE_SIZE: ${ORTHANC_RAW_MAXIMUM_STORAGE_SIZE}
                 ORTHANC_RAW_JOB_HISTORY_SIZE: ${ORTHANC_RAW_JOB_HISTORY_SIZE}
                 ORTHANC_CONCURRENT_JOBS: ${ORTHANC_CONCURRENT_JOBS}
@@ -249,8 +254,10 @@ services:
     export-api:
         build:
             context: .
-            dockerfile: ./docker/export-api/Dockerfile
+            dockerfile: ./docker/pixl-python/Dockerfile
+            target: export_api
             args:
+                PIXL_PACKAGE_DIR: pixl_export
                 <<: *build-args-common
         environment:
             <<:
@@ -297,8 +304,10 @@ services:
     imaging-api:
         build:
             context: .
-            dockerfile: ./docker/imaging-api/Dockerfile
+            dockerfile: ./docker/pixl-python/Dockerfile
+            target: imaging_api
             args:
+                PIXL_PACKAGE_DIR: pixl_imaging
                 <<: *build-args-common
         depends_on:
             queue:
@@ -308,7 +317,6 @@ services:
             orthanc-anon:
                 condition: service_healthy
         healthcheck:
-            test: curl -f http://0.0.0.0:8000/heart-beat
             interval: 10s
             timeout: 30s
             retries: 5