Trigger CI on master and fix broken build system

.bumpversion.cfg

@@ -0,0 +1,21 @@
+[bumpversion]
+current_version = 2.0.1
+commit = False
+message = service version: {current_version} → {new_version}
+tag = False
+
+[bumpversion:file:.osparc/metadata.yml]
+search = {current_version}
+replace = {new_version}
+
+[bumpversion:file:Makefile]
+search = {current_version}
+replace = {new_version}
+
+[bumpversion:file:docker-compose-local.yml]
+search = {current_version}
+replace = {new_version}
+
+[bumpversion:file:VERSION]
+search = {current_version}
+replace = {new_version}

.github/workflows/check-image.yml

@@ -9,14 +9,14 @@ jobs:
       - name: Checkout repo content
         uses: actions/checkout@v2
       - name: ooil version
-        uses: docker://itisfoundation/ci-service-integration-library:v1.0.1-dev-43
+        uses: docker://itisfoundation/ci-service-integration-library:v2.0.5
         with:
           args: ooil --version
-      - name: Assemble docker-compose spec
-        uses: docker://itisfoundation/ci-service-integration-library:v1.0.1-dev-43
+      - name: Assemble docker compose spec
+        uses: docker://itisfoundation/ci-service-integration-library:v2.0.5
         with:
           args: ooil compose
       - name: Build all images if multiple
-        uses: docker://itisfoundation/ci-service-integration-library:v1.0.1-dev-43
+        uses: docker://itisfoundation/ci-service-integration-library:v2.0.5
         with:
-          args: docker-compose build
+          args: docker compose build

.osparc/metadata.yml

@@ -2,7 +2,7 @@ name: Jupyter Chaste
 key: simcore/services/dynamic/jupyter-chaste
 type: dynamic
 integration-version: 1.0.0
-version: 2.0.0
+version: 2.0.1
 description: JupyterLab with C++ Kernels and Chaste (https://github.com/Chaste/chaste-docker) pre-installed. Chaste version is 2021.1.a18592d.
 contact: iavarone@itis.swiss
 thumbnail: http://www.cs.ox.ac.uk/chaste/figs/chaste-240x298.jpg

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [2.0.1] - 2024-09-07
+- install packages from pinned versions
+- docker complies once more
+- previous version was not starting
+- installed chaste from github master branch
+
 ## [2.0.0] - 2023-06-21
 - updated to run via dynamic-sidecar
 - Base image now uses the same as jupyterlab-math

Makefile

@@ -7,7 +7,7 @@ SHELL = /bin/sh
 .DEFAULT_GOAL := help
 
 export DOCKER_IMAGE_NAME ?= jupyter-chaste
-export DOCKER_IMAGE_TAG ?= 2.0.0
+export DOCKER_IMAGE_TAG ?= 2.0.1
 
 
 # PYTHON ENVIRON ---------------------------------------------------------------------------------------
@@ -38,7 +38,7 @@ define _bumpversion
 	# upgrades as $(subst $(1),,$@) version, commits and tags
 	@docker run -it --rm -v $(PWD):/${DOCKER_IMAGE_NAME} \
 		-u $(shell id -u):$(shell id -g) \
-		itisfoundation/ci-service-integration-library:v1.0.1-dev-43 \
+		itisfoundation/ci-service-integration-library:v2.0.5 \
 		sh -c "cd /${DOCKER_IMAGE_NAME} && bump2version --verbose --list --config-file $(1) $(subst $(2),,$@)"
 endef
 
@@ -52,16 +52,16 @@ version-patch version-minor version-major: .bumpversion.cfg ## increases service
 compose-spec: ## runs ooil to assemble the docker-compose.yml file
 	@docker run -it --rm -v $(PWD):/${DOCKER_IMAGE_NAME} \
 		-u $(shell id -u):$(shell id -g) \
-		itisfoundation/ci-service-integration-library:v1.0.1-dev-43 \
+		itisfoundation/ci-service-integration-library:v2.0.5 \
 		sh -c "cd /${DOCKER_IMAGE_NAME} && ooil compose"
 
 build: | compose-spec	## build docker image
-	docker-compose build
+	docker compose build
 
 # To test built service locally -------------------------------------------------------------------------
 .PHONY: run-local
 run-local:	## runs image with local configuration
-	docker-compose --file docker-compose-local.yml up
+	docker compose --file docker-compose-local.yml up
 
 .PHONY: publish-local
 publish-local: ## push to local throw away registry to test integration

README.md

@@ -63,5 +63,3 @@ build_project.sh lung
 ```
 ### Test the JupyterLab C++ kernels
 Open a new notebook with any of the existing C++ kernels and run one of the existing notebooks in the `xeus-cling` repository, for example [xcpp.ipynb](https://github.com/jupyter-xeus/xeus-cling/blob/main/notebooks/xcpp.ipynb).
-
-

VERSION

@@ -1 +1 @@
-2.0.0
+2.0.1

docker-compose-local.yml

@@ -1,7 +1,7 @@
 version: '3.7'
 services:
   jupyter-chaste:
-    image: simcore/services/dynamic/jupyter-chaste:2.0.0
+    image: simcore/services/dynamic/jupyter-chaste:2.0.1
     ports:
       - "8888:8888"
     environment:

docker/boot_notebook.bash

@@ -6,24 +6,11 @@ IFS=$'\n\t'
 INFO="INFO: [$(basename "$0")] "
 WARNING="WARNING: [$(basename "$0")] "
 
-# create output folder
-echo
-echo "$INFO" "creating inputs/outputs folder"
-mkdir --parents "${INPUTS_FOLDER}"
-mkdir --parents "${OUTPUTS_FOLDER}"
 
-# Restore previous state pulling it from S3
-if [ -n "${SIMCORE_NODE_BASEPATH}" ]; then
-  echo "$INFO" "Restoring previous state..."
-  python /docker/state_puller.py "${SIMCORE_NODE_APP_STATE_PATH}"
-else
-  echo "$WARNING" "SIMCORE_NODE_APP_STATE_PATH was not set. Saving states feature is disabled."
-fi
 
 # Trust all notebooks in the notebooks folder
 echo "$INFO" "trust all notebooks in path..."
-find "${SIMCORE_NODE_APP_STATE_PATH}" -name '*.ipynb' -type f -exec jupyter trust {} +
-
+find "${NOTEBOOK_BASE_DIR}" -name '*.ipynb' -type f -exec jupyter trust {} +
 
 
 # Configure
@@ -42,9 +29,9 @@ cat > .jupyter_config.json <<EOF
     "NotebookApp": {
         "ip": "0.0.0.0",
         "port": 8888,
-        "base_url": "${SIMCORE_NODE_BASEPATH}",
-        "extra_static_paths": ["${SIMCORE_NODE_BASEPATH}/static"],
-        "notebook_dir": "${SIMCORE_NODE_APP_STATE_PATH}",
+        "base_url": "",
+        "extra_static_paths": ["/static"],
+        "notebook_dir": "${NOTEBOOK_BASE_DIR}",
         "token": "",
         "quit_button": false,
         "open_browser": false,

docker/custom/Dockerfile

@@ -43,7 +43,7 @@ RUN apt-get update && \
 
 # Install the Chaste repo list and key
 # https://chaste.cs.ox.ac.uk/trac/wiki/InstallGuides/UbuntuPackage
-RUN echo "deb http://www.cs.ox.ac.uk/chaste/ubuntu focal/" >> /etc/apt/sources.list.d/chaste.list && \
+RUN echo "deb https://chaste.github.io/ubuntu focal/" >> /etc/apt/sources.list.d/chaste.list && \
   apt-key adv --recv-keys --keyserver hkp://keyserver.ubuntu.com:80 422C4D99
 
 RUN pip --no-cache --quiet install --upgrade \
@@ -84,10 +84,6 @@ RUN apt-get update && \
 # Fix CMake warnings: https://github.com/autowarefoundation/autoware/issues/795
 RUN update-alternatives --install /usr/bin/vtk vtk /usr/bin/vtk7 7
 
-# Install TextTest for regression testing (this requires pygtk)
-RUN pip install texttest
-ENV TEXTTEST_HOME /usr/local/bin/texttest
-
 
 # Allow CHASTE_DIR to be set at build time if desired
 ARG CHASTE_DIR="/home/jovyan/chaste"
@@ -136,6 +132,7 @@ WORKDIR ${HOME}
 
 RUN python3 -m venv .venv &&\
   .venv/bin/pip --no-cache --quiet install --upgrade pip~=21.3 wheel setuptools &&\
+  .venv/bin/pip --no-cache --quiet install  texttest==4.3.0 &&\
   .venv/bin/pip --no-cache --quiet install ipykernel &&\
   .venv/bin/python -m ipykernel install \
   --user \
@@ -146,7 +143,7 @@ RUN python3 -m venv .venv &&\
   .venv/bin/python -m jupyter kernelspec list
 
 RUN conda install --quiet --yes \
-  'texinfo' \
+  'texinfo=7.0' \
   'xeus-cling=0.13.0' \
   'xtensor=0.23.10' \
   'xtensor-blas=0.19.2' \

kernels/chaste/scripts/build_chaste.sh

@@ -22,7 +22,7 @@ fi
 if [ $VERSION != '.' ]; then
     if [ $VERSION = 'master' ] || [ $VERSION = 'develop' ]; then
         # Override GIT_REMOTE to build from the upstream server
-        GIT_REMOTE=https://chaste.cs.ox.ac.uk/git/chaste.git
+        GIT_REMOTE=https://github.com/Chaste/Chaste.git
     fi
     echo "Cloning Chaste from remote: ${GIT_REMOTE}#${VERSION} into ${CHASTE_SOURCE_DIR}..."
     mkdir -p $CHASTE_SOURCE_DIR