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/orthanc/Dockerfile

@@ -18,27 +18,28 @@ SHELL ["/bin/bash", "-o", "pipefail", "-e", "-u", "-x", "-c"]
 # where you get a warning when installing system-wide packages.
 RUN export DEBIAN_FRONTEND=noninteractive && \
     apt-get update && \
-    apt-get install --yes --no-install-recommends python3-venv tzdata
-RUN python3 -m venv /.venv
+    apt-get install --yes --no-install-recommends curl tzdata && \
+    apt-get autoremove --yes && apt-get clean --yes && rm -rf /var/lib/apt/lists/*
 
-# Install curl for now, but try to remove this dependency
-RUN apt-get --assume-yes install curl
+# install uv
+COPY --from=ghcr.io/astral-sh/uv:0.5.10 /uv /uvx /bin/
 
-# Install requirements before copying modules
-COPY ./pixl_core/pyproject.toml /pixl_core/pyproject.toml
-COPY ./pixl_dcmd/pyproject.toml /pixl_dcmd/pyproject.toml
-
-RUN --mount=type=cache,target=/root/.cache \
-    /.venv/bin/pip install pixl_core/ \
-    && /.venv/bin/pip install pixl_dcmd/
-
-COPY ./pixl_core/ /pixl_core
-RUN --mount=type=cache,target=/root/.cache \
-    /.venv/bin/pip install --no-cache-dir --force-reinstall --no-deps ./pixl_core
-
-COPY ./pixl_dcmd/ /pixl_dcmd
-RUN --mount=type=cache,target=/root/.cache \
-    /.venv/bin/pip install --no-cache-dir --force-reinstall --no-deps ./pixl_dcmd
+# Install our code
+# The workspace project file
+COPY pyproject.toml .
+# All pyproject.toml files referenced by the root one must exist or uv will error
+COPY ./pixl_imaging/pyproject.toml pixl_imaging/pyproject.toml
+COPY ./pixl_export/pyproject.toml pixl_export/pyproject.toml
+COPY ./cli/pyproject.toml cli/pyproject.toml
+COPY ./hasher/pyproject.toml hasher/pyproject.toml
+# prereqs for dcmd
+COPY ./pytest-pixl/ pytest-pixl/
+COPY ./pixl_core/ pixl_core/
+COPY ./pixl_dcmd/ pixl_dcmd
+RUN uv venv
+# Need --no-editable so that our packages are in
+# site-packages, so orthanc plugin manager can find them
+RUN uv sync --no-editable --package pixl-dcmd
 
 ARG ORTHANC_DIR
 COPY ./orthanc/${ORTHANC_DIR}/plugin/pixl.py /etc/orthanc/pixl.py

docker/pixl-python/Dockerfile

@@ -16,7 +16,8 @@ SHELL ["/bin/bash", "-o", "pipefail", "-e", "-u", "-x", "-c"]
 
 ARG TEST="false"
 
-RUN export DEBIAN_FRONTEND=noninteractive && \
+RUN <<EOF
+    export DEBIAN_FRONTEND=noninteractive && \
     apt-get update && \
     apt-get install --yes --no-install-recommends \
         procps \
@@ -26,30 +27,44 @@ RUN export DEBIAN_FRONTEND=noninteractive && \
         curl \
         gnupg \
         locales \
-        tzdata
-
-RUN sed -i '/en_GB.UTF-8/s/^# //g' /etc/locale.gen && locale-gen
-RUN  apt-get autoremove && apt-get clean && rm -rf /var/lib/apt/lists/*
+        tzdata && \
+    sed -i '/en_GB.UTF-8/s/^# //g' /etc/locale.gen && locale-gen && \
+    apt-get autoremove --yes && apt-get clean --yes && rm -rf /var/lib/apt/lists/*
+EOF
 
 HEALTHCHECK CMD /usr/bin/curl -f http://0.0.0.0:8000/heart-beat || exit 1
 
+# install uv
+COPY --from=ghcr.io/astral-sh/uv:0.5.10 /uv /uvx /bin/
+
 WORKDIR /app
 # specify what we're installing using build time arg
 ARG PIXL_PACKAGE_DIR
 
-# Install requirements before copying modules
-COPY ./pixl_core/pyproject.toml ./pixl_core/pyproject.toml
-COPY ./$PIXL_PACKAGE_DIR/pyproject.toml ./$PIXL_PACKAGE_DIR/pyproject.toml
-RUN pip3 install --no-cache-dir pixl_core/ \
-    && pip3 install --no-cache-dir $PIXL_PACKAGE_DIR/
+# Install our code:
+
+# COPY doesn't support a wildcard copy which also preserves directory structure,
+# so we have to specify everything separately. We could have copied everything, but
+# then every change would trigger a rebuild of all containers.
 
-# Install our code
+# The workspace project file
+COPY pyproject.toml .
+# All pyproject.toml files referenced by the root one must exist or uv will error
+COPY ./pixl_imaging/pyproject.toml pixl_imaging/pyproject.toml
+COPY ./pixl_export/pyproject.toml pixl_export/pyproject.toml
+COPY ./pixl_dcmd/pyproject.toml pixl_dcmd/pyproject.toml
+COPY ./cli/pyproject.toml cli/pyproject.toml
+COPY ./hasher/pyproject.toml hasher/pyproject.toml
+# prereqs for all projects
+COPY ./pytest-pixl/ pytest-pixl/
 COPY ./pixl_core/ pixl_core/
-COPY ./$PIXL_PACKAGE_DIR/ .
-RUN pip install --no-cache-dir --force-reinstall --no-deps pixl_core/ \
-    --no-cache-dir --force-reinstall --no-deps . && \
-    if [ "$TEST" = "true" ]; then pip install --no-cache-dir pixl_core/[test] .[test]; fi
+# the actual thing we are building
+COPY ./$PIXL_PACKAGE_DIR/ $PIXL_PACKAGE_DIR/
+RUN uv venv
+RUN uv sync --package "$PIXL_PACKAGE_DIR"
 
+# make uvicorn etc available
+ENV PATH="/app/.venv/bin:$PATH"
 
 # Each container should be run with a different entry point
 FROM pixl_python_base AS export_api
@@ -59,4 +74,4 @@ FROM pixl_python_base AS hasher_api
 ENTRYPOINT ["uvicorn", "hasher.main:app", "--host", "0.0.0.0", "--port", "8000"]
 
 FROM pixl_python_base AS imaging_api
-ENTRYPOINT ["/app/scripts/migrate_and_run.sh"]
+ENTRYPOINT ["/app/pixl_imaging/scripts/migrate_and_run.sh"]

hasher/pyproject.toml

@@ -25,8 +25,8 @@ dev = [
 ]
 
 [build-system]
-requires = ["setuptools>=61.0"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [tool.ruff]
 extend = "../ruff.toml"

pixl_core/pyproject.toml

@@ -44,8 +44,14 @@ dev = [
 ]
 
 [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.pytest.ini_options]
 markers = ["pika"]

pixl_dcmd/pyproject.toml

@@ -16,6 +16,7 @@ dependencies = [
     "pydicom-data",
     "python-decouple==3.8",
     "requests==2.32.3",
+    "setuptools", # pydicom needs this
     "types-requests~=2.28",
 ]
 
@@ -30,8 +31,8 @@ dev = [
 ]
 
 [build-system]
-requires = ["setuptools>=61.0"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [tool.coverage.report]
 exclude_also = [

pixl_export/pyproject.toml

@@ -21,8 +21,8 @@ dev = [
 ]
 
 [build-system]
-requires = ["setuptools>=61.0"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [tool.coverage.report]
 exclude_also = [

pixl_imaging/pyproject.toml

@@ -23,8 +23,8 @@ dev = [
 ]
 
 [build-system]
-requires = ["setuptools>=61.0"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [tool.coverage.report]
 exclude_also = [

pixl_imaging/scripts/migrate_and_run.sh

@@ -17,12 +17,12 @@
 # Run migrations (unless SKIP_ALEMBIC is true) then run the app.
 
 set -eux -o pipefail
-cd /app/alembic
+cd /app/pixl_imaging/alembic
 if [ "${SKIP_ALEMBIC:-false}" = false ]; then
     echo "Running alembic migrations"
     alembic upgrade head
 else
     echo "Skipping alembic migrations"
 fi
 
-uvicorn pixl_imaging.main:app --host "0.0.0.0" --port 8000
+uvicorn pixl_imaging.main:app --host "0.0.0.0" --port 8000

pyproject.toml

@@ -0,0 +1,52 @@
+[project]
+name = "pixl"
+version = "0.2.0rc0"
+description = "Top-level PIXL project"
+readme = "README.md"
+requires-python = ">=3.9"
+dependencies = [
+    'core',
+    'pixl_cli',
+    'pytest-pixl',
+    "hasher",
+    "pixl_dcmd",
+    "pixl_export",
+    "pixl_imaging",
+]
+
+
+[tool.uv.sources]
+pixl_cli = { workspace = true }
+core = { workspace = true }
+pytest-pixl = { workspace = true }
+hasher = { workspace = true }
+pixl_dcmd = { workspace = true }
+pixl_export = { workspace = true }
+pixl_imaging = { workspace = true }
+
+[tool.uv.workspace]
+members = [
+    "cli",
+    "pixl_core",
+    "pytest-pixl",
+    "hasher",
+    "pixl_dcmd",
+    "pixl_export",
+    "pixl_imaging",
+]
+
+[tool.hatch.build.targets.wheel]
+dev-mode-dirs = [
+    "cli",
+    "pixl_core",
+    "pytest-pixl",
+    "hasher",
+    "pixl_dcmd",
+    "pixl_export",
+    "pixl_imaging",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+

pytest-pixl/pyproject.toml

@@ -27,8 +27,14 @@ dev = [
 ]
 
 [build-system]
-requires = ["setuptools>=61.0", "setuptools-scm>=8.0"]
-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]
@@ -66,4 +72,4 @@ extend = "../ruff.toml"
 "./tests/**" = ["D100"]
 
 [project.entry-points.pytest11]
-pytest_pixl = "pytest_pixl.plugin"
+pytest_pixl = "pytest_pixl.plugin"