Fix healtcheck

Add editable dodal to image and helmcharts
Allow the appversion to be specified at deployment
Allow existing helmcharts to be upgraded

Dockerfile

@@ -1,9 +1,15 @@
 FROM python:3.11 AS build
-ADD . /project/
-WORKDIR "/project"
+ADD . /app/hyperion
+WORKDIR "/app/hyperion"
 RUN pip install -e .[dev]
-RUN python -m build
 
-ENTRYPOINT /project/utility_scripts/docker/entrypoint.sh
+# Check out and install dodal locally with no dependencies as this may be a different version to what
+# is referred to in the setup.cfg, but we don't care as it will be overridden by bind mounts in the
+# running container
+RUN mkdir ../dodal && \
+git clone https://github.com/DiamondLightSource/dodal.git ../dodal && \
+pip install --no-deps -e ../dodal
+
+ENTRYPOINT /app/hyperion/utility_scripts/docker/entrypoint.sh
 
 EXPOSE 5005

docs/deploying.md

@@ -62,26 +62,28 @@ Once the docker image is built, the image can be deployed to kubernetes using th
 * From a development hyperion workspace
 ```commandline
 python utility_scripts/deploy/deploy_hyperion.py --kubernetes <beamline>
+cd <path to deployed hyperion folder in /dls_sw>
+./utility_scripts/deploy/deploy_to_k8s.sh --beamline=<beamline> hyperion
 ```
 
-* cd to the new folder and run
-```commandline
-git checkout vX.Y.Z
-./utility_scripts/deploy/deploy_to_k8s.sh hyperion
-```
-
-This will create a helm release "hyperion".
+This will create a helm release "hyperion". The source folders will be mounted as 
+bind mounts to allow the pod to pick up changes in production. For production these are expected to be in the normal 
+place defined in `values.yaml`.
 
 ### development deployment
 
-From your development workspace, either with a release image or using a development image built with :
+
+From a development `hyperion` workspace, either with a release image or using a development image built with the script 
+above, you install a dev deployment to the cluster you are currently logged into with `kubectl`:
 
 ```commandline
 ./utility_scripts/deploy/deploy_to_k8s.sh --dev --beamline=<beamline> --repository=<your image repo> hyperion-test
 ```
 
-Please note, the deployment is intended to be run from a checked-out matching version of the git repository. For 
-production this is expected to be in the normal place defined in `values.yaml`. The source folders will be mounted as 
-bind mounts to allow the pod to pick up changes in production.
+The dev deployment bind-mounts the current `hyperion` workspace and `../dodal` into the container so that you can 
+run against your own development code. **Clusters do not allow bind mounts from arbitrary directories so 
+your workspace will have to be in a permitted directory such as your home directory.**
+
+Please note, the deployment script is intended to be run from a checked-out matching version of the git repository.
 
 `helm list` should then show details of the installed release 

helmchart/templates/deployment.yaml

@@ -43,6 +43,10 @@ spec:
           hostPath:
             path: "{{ .Values.hyperion.projectDir }}/utility_scripts"
             type: Directory
+        - name: dodal
+          hostPath:
+            path: "{{ .Values.dodal.projectDir | clean }}"
+            type: Directory
         {{- if .Values.hyperion.dev }}
         - name: devlogs
           hostPath:
@@ -78,7 +82,7 @@ spec:
           {{- end }}
         readinessProbe:
           exec:
-            command: [ "/project/docker/healthcheck.sh" ]
+            command: [ "/app/hyperion/utility_scripts/docker/healthcheck.sh" ]
           periodSeconds: 5
         volumeMounts:
           - mountPath: "/dls_sw/{{ .Values.hyperion.beamline }}"
@@ -93,13 +97,15 @@ spec:
             name: dls-sw-dasc
             readOnly: true
             mountPropagation: HostToContainer
-          - mountPath: "/project/src"
+          - mountPath: "/app/hyperion/src"
             name: src
-          - mountPath: "/project/tests"
+          - mountPath: "/app/hyperion/tests"
             name: tests
-          - mountPath: "/project/utility_scripts"
+          - mountPath: "/app/hyperion/utility_scripts"
             name: utility-scripts
+          - mountPath: "/app/dodal"
+            name: dodal
           {{- if .Values.hyperion.dev }}
-          - mountPath: "/project/tmp"
+          - mountPath: "/app/hyperion/tmp"
             name: devlogs
           {{ end }}

helmchart/values.yaml

@@ -6,8 +6,10 @@ hyperion:
   beamline: i03
   dev: false
   logDir: "/dls_sw/i03/logs/bluesky"
-  projectDir: "/dls_sw/i03/software/bluesky/hyperion"
-  # This should be overridden at install time
+  # These should be overridden at install time
+  projectDir: SET_ON_INSTALL
   appVersion: SET_ON_INSTALL
+dodal:
+  projectDir: SET_ON_INSTALL
 service:
   type: NodePort

utility_scripts/build_docker_image.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -e
 # builds the docker image
 BUILD=1
 PUSH=1

utility_scripts/deploy/deploy_to_k8s.sh

@@ -14,6 +14,10 @@ for option in "$@"; do
             REPOSITORY="${option#*=}"
             shift
             ;;
+        --appVersion=*)
+            APP_VERSION="${option#*=}"
+            shift
+            ;;
         --help|--info|--h)
             CMD=`basename $0`
             echo "$CMD [options] <release>"
@@ -22,6 +26,8 @@ for option in "$@"; do
             echo "  --dev                   Install to a development kubernetes cluster (assumes project checked out under /home)"
             echo "  -b, --beamline=BEAMLINE Overrides the BEAMLINE environment variable with the given beamline"
             echo "  --repository=REPOSITORY Override the repository to fetch the image from"
+            echo "  --appVersion=version    Version of the image to fetch from the repository otherwise it is deduced
+             from the setuptools_scm"
             exit 0
             ;;
         -*|--*)
@@ -46,10 +52,34 @@ fi
 HELM_OPTIONS=""
 PROJECTDIR=$(readlink -e $(dirname $0)/../..)
 
+ensure_version_py() {
+  # We require the _version.py to be created, this needs a minimal virtual environment
+  if [[ ! -d $PROJECTDIR/.venv ]]; then
+    echo "Creating _version.py"
+    echo "Virtual environment not found - creating"
+    module load python/3.11
+    python -m venv $PROJECTDIR/.venv
+    . $PROJECTDIR/.venv/bin/activate
+    pip install setuptools_scm
+  fi  
+}
+
+app_version() {
+  ensure_version_py
+
+  . $PROJECTDIR/.venv/bin/activate
+  python -m setuptools_scm --force-write-version-files
+}
+
 if [[ -n $REPOSITORY ]]; then
   HELM_OPTIONS+="--set hyperion.imageRepository=$REPOSITORY "
 fi
 
+ensure_version_py
+if [[ -z $APP_VERSION ]]; then
+  APP_VERSION=$(app_version)
+fi
+
 if [[ -n $DEV ]]; then
   GID=`id -g`
   SUPPLEMENTAL_GIDS=37904
@@ -58,25 +88,17 @@ hyperion.dev=true,\
 hyperion.runAsUser=$EUID,\
 hyperion.runAsGroup=$GID,\
 hyperion.supplementalGroups=[$SUPPLEMENTAL_GIDS],\
-hyperion.logDir=/project/tmp,\
-hyperion.projectDir=$PROJECTDIR \
---replace "
+hyperion.logDir=/app/hyperion/tmp "
   mkdir -p $PROJECTDIR/tmp
-elif [[ ! -e $PROJECTDIR/src/hyperion/_version.py ]]; then
-  # Production install requires the _version.py to be created, this needs a minimal virtual environment
-  echo "Creating _version.py"
-  if [[ -d $PROJECTDIR/.venv/bin/activate ]]; then
-    echo "Virtual environment not found - creating"
-    module load python/3.11
-    python -m venv $PROJECTDIR/.venv
-    . $PROJECTDIR/.venv/bin/activate
-    pip install setuptools_scm
-  else
-    . $PROJECTDIR/.venv/bin/activate
-  fi
-  python -m setuptools_scm --force-write-version-files
+  DEPLOYMENT_DIR=$PROJECTDIR
+else
+  DEPLOYMENT_DIR=/dls_sw/i03/software/bluesky/hyperion_v${APP_VERSION}/hyperion
 fi
-APP_VERSION=`python -m setuptools_scm | sed -e 's/[^a-zA-Z0-9._-]/_/g'`
-HELM_OPTIONS+="--set hyperion.appVersion=$APP_VERSION "
+
+HELM_OPTIONS+="--set hyperion.appVersion=$APP_VERSION,\
+hyperion.projectDir=$DEPLOYMENT_DIR,\
+dodal.projectDir=$DEPLOYMENT_DIR/../dodal " 
+
 helm package $PROJECTDIR/helmchart --app-version $APP_VERSION
-helm install $HELM_OPTIONS $RELEASE hyperion-0.0.1.tgz
+# Helm package generates a file suffixed with the chart version
+helm upgrade --install $HELM_OPTIONS $RELEASE hyperion-0.0.1.tgz

utility_scripts/docker/entrypoint.sh

@@ -1,4 +1,4 @@
-#!/bin/bash -x
+#!/bin/bash
 # Entry point for the production docker image that launches the external callbacks
 # as well as the main server
 
@@ -29,6 +29,13 @@ for option in "$@"; do
     esac
 done
 
+kill_active_apps () {
+    echo "Killing active instances of hyperion and hyperion-callbacks..."
+    pkill -e -f "python.*hyperion"
+    pkill -e -f "SCREEN.*hyperion"
+    echo "done."
+}
+
 RELATIVE_SCRIPT_DIR=$( dirname -- "$0"; )
 cd ${RELATIVE_SCRIPT_DIR}
 
@@ -64,6 +71,8 @@ do
     fi;
 done
 
+trap kill_active_apps TERM 
+
 if [ "$EXTERNAL_CALLBACK_SERVICE" = true ]; then
     hyperion-callbacks `echo $cb_commands;`>$callback_start_log_path 2>&1 &
 fi