Minor tweaks to local deployment script

.github/workflows/api-tests.yml

@@ -0,0 +1,34 @@
+name: API smoke tests
+
+on:
+  push:
+    branches: [ master, dev*, feature/docker*, feature/repo*, jupyterhub-update ]
+  pull_request:
+    branches: [ master, dev*, feature/docker*, feature/repo*, jupyterhub-update ]
+
+jobs:
+
+  build:
+
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.12" ]
+        runs-on: [ ubuntu-latest ]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        pip install pytest requests==2.31.0
+
+    - name: Run API tests
+      run: |
+        pytest tests/test_apis.py -vs

applications/workspaces/server/workspaces/service/osbrepository/adapters/biomodelsadapter.py

@@ -19,13 +19,13 @@ class BiomodelsAdapter:
     """
     Adapter for Biomodels
 
-    https://www.ebi.ac.uk/biomodels/
+    https://www.biomodels.org/
     """
 
     def __init__(self, osbrepository, uri=None):
         self.osbrepository = osbrepository
         self.uri = uri if uri else osbrepository.uri
-        self.api_url = "https://www.ebi.ac.uk/biomodels"
+        self.api_url = "https://www.biomodels.org"
 
         try:
             self.model_id = re.search(

local-scripts/osbv2-local.sh

@@ -15,7 +15,8 @@ CLOUD_HARNESS_DIR="${CLOUD_HARNESS_DIR_LOCATION}/cloud-harness"
 CLOUD_HARNESS_DEFAULT="develop"
 CLOUD_HARNESS_BRANCH=""
 SKAFFOLD="skaffold"
-SKAFFOLD_MAX_VERSION="2.14.2"
+SKAFFOLD_MAX_VERSION="2.15.0"
+HELM_MAX_VERSION="4.0.0"
 
 # Application to deploy
 DEPLOYMENT_APP=""
@@ -54,7 +55,7 @@ start_minikube () {
         echo "🍏  Assuming Docker is already running on OS: $(uname -s)"
     fi
 
-    echo "-> starting minkube"
+    echo "-> starting minikube"
     if minikube status
     then
         echo "-> Minikube is already running: not restarting it"
@@ -66,10 +67,10 @@ start_minikube () {
         minikube addons enable metrics-server || notify_fail "Failed: ingress add on"
         echo "-> setting up ${OSB_NAMESPACE} namespace"
         kubectl get ns ${OSB_NAMESPACE} || kubectl create ns ${OSB_NAMESPACE} || notify_fail "Failed: ns set up"
-        kubectl config set-context NAME --namespace=${OSB_NAMESPACE} || notify_fail "Failed: ns set up"
+        kubectl config set-context --current --namespace=${OSB_NAMESPACE} || notify_fail "Failed: ns set up"
         echo "-> setting up minikube docker env"
 
-    eval $(minikube docker-env) || notify_fail "Failed: env setup"
+    eval "$(minikube docker-env)" || notify_fail "Failed: env setup"
     fi
 }
 
@@ -86,7 +87,7 @@ deploy_live () {
 
     LIVE="YES"
 
-    pushd $OSB_DIR
+    pushd $OSB_DIR || exit 1
         echo "-> deploying live configuration"
 
         start_minikube
@@ -97,9 +98,9 @@ deploy_live () {
         echo
         echo "-> Deploying with helm: helm install -n ${OSB_NAMESPACE} osb deployment/helm"
 
-        helm install -n ${OSB_NAMESPACE} osb deployment/helm
+        helm install --debug -n ${OSB_NAMESPACE} osb deployment/helm
 
-    popd
+    popd || exit 1
 }
 
 show_deployment_status () {
@@ -137,29 +138,43 @@ deploy () {
 
     skaffold_version="$($SKAFFOLD version)"
 
-    if [ $(get_version ${skaffold_version:1}) -gt $(get_version $SKAFFOLD_MAX_VERSION) ]
+    if [ "$(get_version ${skaffold_version:1})" -gt "$(get_version $SKAFFOLD_MAX_VERSION)" ]
     then
         echo "-> Found Skaffold version: ${skaffold_version:1}"
-        echo "-> Skaffold version <= ${SKAFFOLD_MAX_VERSION} is currently required"
+        echo "-> Skaffold version < ${SKAFFOLD_MAX_VERSION} is currently required"
         echo "-> Please install it from: https://github.com/GoogleContainerTools/skaffold/releases/tag/v${SKAFFOLD_MAX_VERSION}"
         echo "-> See: https://github.com/GoogleContainerTools/skaffold/issues/9788"
         exit 1
+    else
+        echo "Got skaffold version: ${skaffold_version}"
     fi
 
-    pushd $OSB_DIR
+
+    helm_version="$(helm version |  grep -o 'Version:"v[^"]*"' | cut -d'"' -f2 )"
+
+    if [ "$(get_version ${helm_version:1})" -gt "$(get_version $HELM_MAX_VERSION)" ]
+    then
+        echo "-> Found helm version: ${skaffold_version:1}"
+        echo "-> helm version < ${HELM_MAX_VERSION} is currently required"
+        echo "-> Please install it from: https://github.com/helm/helm/releases#release-v${HELM_MAX_VERSION}"
+        exit 1
+    else
+        echo "Got helm version: ${helm_version}"
+    fi
+    pushd $OSB_DIR || exit 1
         echo "-> deploying"
         start_minikube
 
         harness_deployment
 
         echo "-> running skaffold"
-        $SKAFFOLD dev --cleanup=false || { notify_fail "Failed: skaffold" ; minikube stop; }
-        #$SKAFFOLD dev || notify_fail "Failed: skaffold"
-    popd
+        #$SKAFFOLD dev --cleanup=false || { notify_fail "Failed: skaffold" ; minikube stop; }
+        $SKAFFOLD dev || notify_fail "Failed: skaffold"
+    popd || exit 1
 }
 
 list_versions () {
-    if !  command -v harness-deployment  2>&1 >/dev/null ; then
+    if !  command -v harness-deployment >/dev/null 2>&1 ; then
         echo "cloud-harness is required but were not found."
         echo "To install cloud-harness, please see the -u/-U options"
         exit 1
@@ -189,7 +204,7 @@ harness_deployment() {
     # use -e dev for that, but that will send e-mails to Metacell folks
     # suggested: create a new file in deploy/values-something.yaml where you use
     # your e-mail address, and then use `-e something` to use these values.
-    pushd $OSB_DIR
+    pushd $OSB_DIR || exit 1
         if [ "YES" == "$LIVE" ]
         then
             echo "-> harnessing live configuration deployment, and deploying"
@@ -198,7 +213,7 @@ harness_deployment() {
             echo "-> harnessing development deployment"
             harness-deployment ../cloud-harness . -l  -n ${OSB_NAMESPACE} -d osb.local -dtls -e "local" ${DEPLOYMENT_APP:+-i $DEPLOYMENT_APP} || notify_fail "Failed: harness-deployment (dev)"
         fi
-    popd
+    popd || exit 1
 }
 
 notify_fail () {
@@ -213,20 +228,35 @@ notify_fail () {
 
 update_cloud_harness() {
     echo "Updating cloud harness"
-    CLOUD_HARNESS_PACKAGES=$(pip list | grep cloud | tr -s " " | cut -d " " -f1 | tr '\n' ' ')
-    pip uninstall ${CLOUD_HARNESS_PACKAGES} -y || echo "No cloud harness packages installed"
+    if command -v uv >/dev/null
+    then
+        CLOUD_HARNESS_PACKAGES=$(uv pip list | grep cloud | tr -s " " | cut -d " " -f1 | tr '\n' ' ')
+        uv pip uninstall ${CLOUD_HARNESS_PACKAGES} || echo "No cloud harness packages installed"
+    else
+        CLOUD_HARNESS_PACKAGES=$(pip list | grep cloud | tr -s " " | cut -d " " -f1 | tr '\n' ' ')
+        pip uninstall "${CLOUD_HARNESS_PACKAGES}" -y || echo "No cloud harness packages installed"
+    fi
     if ! [ -d "${CLOUD_HARNESS_DIR}" ]
     then
         echo "Cloud harness folder does not exist. Cloning"
-        pushd "${CLOUD_HARNESS_DIR_LOCATION}" && git clone "${CLOUD_HARNESS_URL}" && popd
+        pushd "${CLOUD_HARNESS_DIR_LOCATION}" && git clone "${CLOUD_HARNESS_URL}" && popd || exit 1
+    fi
+    if command -v uv >/dev/null
+    then
+        pushd "$CLOUD_HARNESS_DIR" && git clean -dfx && git fetch && git checkout "${CLOUD_HARNESS_BRANCH}" && git pull && uv pip install -r requirements.txt && popd || exit 1
+    else
+        pushd "$CLOUD_HARNESS_DIR" && git clean -dfx && git fetch && git checkout "${CLOUD_HARNESS_BRANCH}" && git pull && pip install -r requirements.txt && popd || exit 1
     fi
-    pushd "$CLOUD_HARNESS_DIR" && git clean -dfx && git fetch && git checkout ${CLOUD_HARNESS_BRANCH} && git pull && pip install -r requirements.txt && popd
 }
 
 activate_venv() {
     if [ -f "${VENV_DIR}/bin/activate" ]
     then
         source "${VENV_DIR}/bin/activate"
+    elif command -v uv >/dev/null
+    then
+        echo "No virtual environment found at ${VENV_DIR}. Creating (uv)"
+        uv venv --python "${PY_VERSION}" "${VENV_DIR}" && source "${VENV_DIR}/bin/activate"
     else
         echo "No virtual environment found at ${VENV_DIR}. Creating"
         ${PY_VERSION} -m venv "${VENV_DIR}" && source "${VENV_DIR}/bin/activate"
@@ -245,7 +275,7 @@ print_versions() {
     echo -e "\n** minikube **"
     minikube version
     echo -e "\n** cloud harness **"
-    pushd "${CLOUD_HARNESS_DIR}" && git log --oneline | head -1 && popd
+    pushd "${CLOUD_HARNESS_DIR}" && git log --oneline | head -1 && popd || exit 1
     echo -e "\n** helm **"
     helm version
     echo -e "\n** skaffold **"
@@ -257,7 +287,7 @@ print_versions() {
 }
 
 clean () {
-    pushd $OSB_DIR
+    pushd $OSB_DIR || exit 1
         echo "-> Cleaning up all images."
         #docker image prune --all
         docker builder prune --all
@@ -266,7 +296,7 @@ clean () {
         minikube delete
         #docker image prune --all
         docker builder prune --all
-    popd
+    popd || exit 1
 }
 
 usage () {
@@ -355,7 +385,6 @@ do
             exit 0
             ;;
         l)
-            CLOUD_HARNESS_BRANCH="${OPTARG}"
             activate_venv
             deploy_live
             exit 0

pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+markers =
+    network: marks tests as requiring network access (deselect with '-m "not network"')