Install module requirements before module in docker (#285)

* Install module requirements before module in docker

* Update python to 3.11 in Dockerfiles

* Remove unused dockerfile

.github/workflows/main.yml

@@ -246,6 +246,15 @@ jobs:
           python-version: 3.10.6
           cache: "pip"
 
+      - name: Build test services
+        working-directory: test
+        run: |
+          docker compose build
+
+      - name: Build services
+        run: |
+          docker compose build
+
       - name: Run tests
         working-directory: test
         run: |

docker/ehr-api/Dockerfile

@@ -11,7 +11,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-FROM python:3.10.6-slim-bullseye
+FROM python:3.11.7-slim-bullseye
 SHELL ["/bin/bash", "-o", "pipefail", "-e", "-u", "-x", "-c"]
 
 ARG TEST="false"
@@ -25,6 +25,13 @@ RUN  apt-get autoremove && apt-get clean && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /app
 
+# Install requirements before copying modules
+COPY ./pixl_core/pyproject.toml ./pixl_core/pyproject.toml
+COPY ./pixl_ehr/pyproject.toml ./pixl_ehr/pyproject.toml
+RUN --mount=type=cache,target=/root/.cache \
+    pip3 install pixl_core/ \
+    && pip3 install pixl_ehr/
+
 COPY ./pixl_core/ core/
 COPY ./pixl_ehr/ .
 RUN --mount=type=cache,target=/root/.cache \

docker/hasher-api/Dockerfile

@@ -11,7 +11,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-FROM python:3.10.7-slim-bullseye
+FROM python:3.11.7-slim-bullseye
 SHELL ["/bin/bash", "-o", "pipefail", "-e", "-u", "-x", "-c"]
 
 # OS setup
@@ -25,6 +25,11 @@ 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/*
 
 WORKDIR /app
+# Install requirements before copying modules
+COPY ./hasher/pyproject.toml .
+RUN --mount=type=cache,target=/root/.cache \
+    pip install /app/
+
 COPY ./hasher/ .
 RUN --mount=type=cache,target=/root/.cache \
     pip install .

docker/imaging-api/Dockerfile

@@ -11,7 +11,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-FROM python:3.10.6-slim-bullseye
+FROM python:3.11.7-slim-bullseye
 SHELL ["/bin/bash", "-o", "pipefail", "-e", "-u", "-x", "-c"]
 
 ARG TEST="false"
@@ -25,6 +25,13 @@ RUN  apt-get autoremove && apt-get clean && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /app
 
+# Install requirements before copying modules
+COPY ./pixl_core/pyproject.toml ./pixl_core/pyproject.toml
+COPY ./pixl_imaging/pyproject.toml ./pixl_imaging/pyproject.toml
+RUN --mount=type=cache,target=/root/.cache \
+    pip3 install pixl_core/ \
+    && pip3 install pixl_imaging/
+
 COPY ./pixl_core/ core/
 COPY ./pixl_imaging/ .
 RUN --mount=type=cache,target=/root/.cache \

docker/orthanc-anon/Dockerfile

@@ -14,11 +14,20 @@
 FROM osimis/orthanc:22.9.0-full-stable
 SHELL ["/bin/bash", "-o", "pipefail", "-e", "-u", "-x", "-c"]
 
+# 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 \
+    pip3 install pixl_core/ \
+    && pip3 install pixl_dcmd/
+
 COPY ./orthanc/orthanc-anon/plugin/pixl.py /etc/orthanc/pixl.py
 COPY ./orthanc/orthanc-anon/plugin/tag-operations.yaml /etc/orthanc/tag-operations.yaml
 
 COPY ./pixl_core/ ./pixl_core
-RUN pip3 install --no-cache-dir ./pixl_core
+RUN --mount=type=cache,target=/root/.cache \
+    pip3 install ./pixl_core
 
 COPY ./pixl_dcmd/ ./pixl_dcmd
-RUN pip3 install --no-cache-dir ./pixl_dcmd
+RUN --mount=type=cache,target=/root/.cache \
+    pip3 install ./pixl_dcmd

docker/postgres/Dockerfile

@@ -27,8 +27,16 @@ COPY --chmod=0777 ./postgres/pixl-db_init.sh /docker-entrypoint-initdb.d/pixl-db
 
 COPY --chmod=0777 ./postgres/create_pixl_tbls.py /pixl/create_pixl_tbls.py
 
+# Install requirements before copying modules
+COPY ./pixl_core/pyproject.toml /pixl/pixl_core/pyproject.toml
+RUN --mount=type=cache,target=/root/.cache \
+    python3 -m venv /pixl/venv \
+        && cd /pixl/venv/bin \
+        && ./pip install /pixl/pixl_core/
+
+WORKDIR /pixl/venv/bin
+
 COPY ./pixl_core/ /pixl/pixl_core
 
-RUN python3 -m venv /pixl/venv \
-    && cd /pixl/venv/bin \
-    && ./pip install /pixl/pixl_core/
+RUN --mount=type=cache,target=/root/.cache \
+    ./pip install /pixl/pixl_core/

test/Dockerfile.fake_emap_star

@@ -42,10 +42,11 @@ RUN if [ "$TAG" != "" ] ; then \
       rm -rf /Satellite && \
       git clone --depth 1 --branch ${TAG} https://github.com/UCLH-DIF/Satellite.git ;\
     fi && \
-    pip install --no-cache-dir --upgrade pip==22.3.1
+    pip install --upgrade pip==22.3.1
 
 WORKDIR /Satellite
-RUN pip install --no-cache-dir . && \
+RUN --mount=type=cache,target=/root/.cache \
+    pip install . && \
     satellite print-db-create-command > /docker-entrypoint-initdb.d/create.sql && \
     satellite print-create-command >> /docker-entrypoint-initdb.d/create.sql
 

test/dummy-services/cogstack/Dockerfile

@@ -11,7 +11,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-FROM python:3.10.6-slim-bullseye
+FROM python:3.11.7-slim-bullseye
 
 RUN export DEBIAN_FRONTEND=noninteractive && \
     apt-get update && \
@@ -23,6 +23,7 @@ WORKDIR /app
 COPY cogstack.py .
 COPY pyproject.toml .
 
-RUN pip install -e .
+RUN --mount=type=cache,target=/root/.cache \
+    pip install -e .
 
 ENTRYPOINT ["uvicorn", "cogstack:app", "--host", "0.0.0.0", "--port", "8000"]