Download models code (#3)

* Download models and startup and allow modification of README

* bump version and bux fixes

* Changelog

* minor comment

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.0
+current_version = 1.0.1
 commit = False
 message = service version: {current_version} → {new_version}
 tag = False

.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: 1.0.0
+version: 1.0.1
 description: AxonDeepSeg in JupyterLab
 contact: [email protected]
 thumbnail: https://raw.githubusercontent.com/axondeepseg/doc-figures/main/index/fig2.png

CHANGELOG.md

@@ -1,4 +1,6 @@
 # Changelog
+## [1.0.1] - 2024-02
+- Copy source code and models to workspace if not there yest
 
 ## [1.0.0] - 2024-02
 - First version

Makefile

@@ -9,7 +9,7 @@ export VCS_STATUS := $(if $(shell git status -s 2> /dev/null || echo unversioned
 export BUILD_DATE := $(shell date -u +"%Y-%m-%dT%H:%M:%SZ")
 
 export DOCKER_IMAGE_NAME ?= axondeepseg-in-jupyterlab
-export DOCKER_IMAGE_TAG ?= 1.0.0
+export DOCKER_IMAGE_TAG ?= 1.0.1
 
 OSPARC_DIR:=$(CURDIR)/.osparc
 

boot_scripts/boot_notebook.bash

@@ -12,6 +12,13 @@ echo "$INFO" "  Workdir :$(pwd)"
 echo "$INFO" "trust all notebooks in path..."
 find "${NOTEBOOK_BASE_DIR}" -name '*.ipynb' -type f | xargs -I % /bin/bash -c 'jupyter trust "%" || true' || true
 
+# Copy source code and models if not there yet
+if [ ! -d "/home/${NB_USER}/work/workspace/axondeepseg/AxonDeepSeg/models" ] 
+then
+    echo "No AxonDeepSeg models in workspace, copying them and source code to workspace..."
+    cp -r /tmp/axondeepseg/ /home/${NB_USER}/work/workspace/
+fi
+
 # Configure
 # Prevents notebook to open in separate tab
 mkdir --parents "$HOME/.jupyter/custom"

boot_scripts/entrypoint.bash

@@ -58,16 +58,22 @@ else
     echo "adding $NB_USER to group $CONTAINER_GROUPNAME..."
     usermod --append --groups "$CONTAINER_GROUPNAME" "$NB_USER" 
 
-    echo "Chainging owner ship of state directory /home/${NB_USER}/work/workspace"
+    echo "Changing ownership of state directory /home/${NB_USER}/work/workspace"
     chown --recursive "$NB_USER" "/home/${NB_USER}/work/workspace"
-    echo "Chainging owner ship of state directory ${DY_SIDECAR_PATH_INPUTS}"
+    echo "Changing ownership of state directory ${DY_SIDECAR_PATH_INPUTS}"
     chown --recursive "$NB_USER" "${DY_SIDECAR_PATH_INPUTS}"
-    echo "Chainging owner ship of state directory ${DY_SIDECAR_PATH_OUTPUTS}"
+    echo "Changing ownership of state directory ${DY_SIDECAR_PATH_OUTPUTS}"
     chown --recursive "$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" "${NOTEBOOK_BASE_DIR}/workspace/README.ipynb" || true
+fi 
+
+
 echo "Removing write permissions from users in placed where they are not allowed to write:"
 echo "- /home/${NB_USER}/work"
 chmod gu-w "/home/${NB_USER}/work"

docker-compose-local.yml

@@ -1,7 +1,7 @@
 version: '3.7'
 services:
   jupyter-axondeepseg:
-    image: simcore/services/dynamic/jupyter-axondeepseg:1.0.0
+    image: simcore/services/dynamic/jupyter-axondeepseg:1.0.1
     ports:
       - "8888:8888"
     environment: