Fix trash (#4)

* Disable trash

* Bumped version

* Improve start-up errors

* Not fixing loader.js error

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.1
+current_version = 1.0.2
 commit = False
 message = service version: {current_version} → {new_version}
 tag = False

.github/CODEOWNERS

@@ -9,7 +9,7 @@ Dockerfile          @elisabettai
 Makefile            @elisabettai
 
 # NOTE: '/' denotes the root of the repository
-/.github/            @pcrespov @GitHK
-/.osparc/            @pcrespov @GitHK @elisabettai
+/.github/            @elisabettai
+/.osparc/            @elisabettai
 /kernels/            @elisabettai
-/docker/             @pcrespov @GitHK
+/docker/             @elisabettai @GitHK

.osparc/metadata.yml

@@ -2,7 +2,7 @@ name: AxonDeepSeg in JupyterLab
 key: simcore/services/dynamic/jupyter-axondeepseg
 type: dynamic
 integration-version: 2.0.0
-version: 1.0.1
+version: 1.0.2
 description: AxonDeepSeg in JupyterLab
 contact: [email protected]
 thumbnail: https://raw.githubusercontent.com/axondeepseg/doc-figures/main/index/fig2.png

CHANGELOG.md

@@ -1,4 +1,10 @@
 # Changelog
+
+## [1.0.2] - 2024-05
+### Fixed
+- Do not create `.Trash-1000` folder (caused service to fail after re-opening a study) ([#1296](https://github.com/ITISFoundation/osparc-issues/issues/1296))
+- Remove partially-installed latex extension
+
 ## [1.0.1] - 2024-02
 - Copy source code and models to workspace if not there yest
 

Dockerfile

@@ -162,7 +162,6 @@ WORKDIR /tmp
 RUN mamba install --yes \
     'jupyterlab' \
     'notebook' \
-    'jupyterlab_latex' \
     'voila' \
     'jupyterlab-git' && \
     jupyter server --generate-config && \
@@ -199,8 +198,10 @@ RUN git clone https://github.com/neuropoly/axondeepseg.git && \
 # "Activate" the conda env
 SHELL ["conda", "run", "-n", "ads_venv", "/bin/bash", "-c" ]
 
+#opencv requested by ACA
 RUN  cd axondeepseg && \
      pip install -e . plugins/ && \
+     pip install opencv-python && \ 
      axondeepseg_test
 
 # Create a jupyter kernel for AxonDeepSeg

Makefile

@@ -8,8 +8,8 @@ export VCS_REF    := $(shell git rev-parse --short HEAD 2> /dev/null || echo unv
 export VCS_STATUS := $(if $(shell git status -s 2> /dev/null || echo unversioned repo),'modified/untracked','clean')
 export BUILD_DATE := $(shell date -u +"%Y-%m-%dT%H:%M:%SZ")
 
-export DOCKER_IMAGE_NAME ?= axondeepseg-in-jupyterlab
-export DOCKER_IMAGE_TAG ?= 1.0.1
+export DOCKER_IMAGE_NAME ?= axondeepseg-jupyterlab
+export DOCKER_IMAGE_TAG ?= 1.0.2
 
 OSPARC_DIR:=$(CURDIR)/.osparc
 
@@ -63,12 +63,12 @@ compose-spec: ## runs ooil to assemble the docker-compose.yml file
 		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 oSPARC throw away registry to test integration

boot_scripts/boot_notebook.bash

@@ -29,6 +29,7 @@ define(['base/js/namespace'], function(Jupyter){
 EOF
 
 # SEE https://jupyter-server.readthedocs.io/en/latest/other/full-config.html
+# For LapApp tornado_settings, see https://discourse.jupyter.org/t/jupyter-lab-4-0-6-error-on-startup-about-yarn-configuration-and-worker-threads/21859/2
 cat > .jupyter_config.json <<EOF
 {
     "FileCheckpoints": {
@@ -45,17 +46,20 @@ cat > .jupyter_config.json <<EOF
         "disable_check_xsrf": true,
         "extra_static_paths": ["/static"],
         "ip": "0.0.0.0",
-        "notebook_dir": "${NOTEBOOK_BASE_DIR}",
+        "root_dir": "${NOTEBOOK_BASE_DIR}",
         "open_browser": false,
         "port": 8888,
         "preferred_dir": "${NOTEBOOK_BASE_DIR}/workspace/",
         "quit_button": false,
-        "root_dir": "${NOTEBOOK_BASE_DIR}",
         "token": "${NOTEBOOK_TOKEN}",
         "webbrowser_open_new": 0
     },
     "KernelSpecManager": {
         "allowed_kernelspecs": ["ads_venv"]
+    },
+    "FileContentsManager": {
+        "preferred_dir": "${NOTEBOOK_BASE_DIR}/workspace/",
+        "delete_to_trash": false
     }
 }
 EOF
@@ -90,5 +94,5 @@ if [ "${DY_BOOT_OPTION_BOOT_MODE}" -eq 1 ] && [ -f "${VOILA_NOTEBOOK}" ]; then
 else
     ls -la /usr/local/bin/start-notebook.sh
     # call the notebook with the basic parameters
-    start-notebook.sh --config .jupyter_config.json "$@" --LabApp.default_url='/lab/tree/workspace/README.ipynb' 
+    start-notebook.py --config .jupyter_config.json "$@" --LabApp.default_url='/lab/tree/workspace/README.ipynb' 
 fi

boot_scripts/entrypoint.bash

@@ -66,8 +66,6 @@ else
     chown --recursive "$NB_USER" "${DY_SIDECAR_PATH_OUTPUTS}"
 fi
 
-mv "${NOTEBOOK_BASE_DIR}/README.ipynb" "${NOTEBOOK_BASE_DIR}/workspace/README.ipynb" || true
-
 if [ ! -f "${NOTEBOOK_BASE_DIR}/workspace/README.ipynb" ] # Allow users to modify the README.ipynb, so do not copy if it already exists
 then
     mv "${NOTEBOOK_BASE_DIR}/README.ipynb" "${NOTEBOOK_BASE_DIR}/workspace/README.ipynb" || true

docker-compose-local.yml

@@ -1,7 +1,7 @@
 version: '3.7'
 services:
   jupyter-axondeepseg:
-    image: simcore/services/dynamic/jupyter-axondeepseg:1.0.1
+    image: simcore/services/dynamic/jupyter-axondeepseg:1.0.2
     ports:
       - "8888:8888"
     environment: