From e95e2317f23e8b7881757ef365b55358b6fcc3c5 Mon Sep 17 00:00:00 2001
From: Elisabetta Iavarone <18575092+elisabettai@users.noreply.github.com>
Date: Fri, 3 May 2024 15:40:20 +0200
Subject: [PATCH 1/4] Disable trash

---
 .github/CODEOWNERS              | 6 +++---
 Dockerfile                      | 2 ++
 boot_scripts/boot_notebook.bash | 3 ++-
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index ca4e0da..a43ef3a 100644
--- a/.github/CODEOWNERS
+++ b/.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
diff --git a/Dockerfile b/Dockerfile
index 93738c3..f8c91fb 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -199,8 +199,10 @@ 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
diff --git a/boot_scripts/boot_notebook.bash b/boot_scripts/boot_notebook.bash
index 127eafa..5ecd0df 100755
--- a/boot_scripts/boot_notebook.bash
+++ b/boot_scripts/boot_notebook.bash
@@ -55,7 +55,8 @@ cat > .jupyter_config.json <<EOF
         "webbrowser_open_new": 0
     },
     "KernelSpecManager": {
-        "allowed_kernelspecs": ["ads_venv"]
+        "allowed_kernelspecs": ["ads_venv"],
+         "delete_to_trash": false
     }
 }
 EOF

From 9f774ff63b1bb66d0c24991868c852d12ffb5f51 Mon Sep 17 00:00:00 2001
From: Elisabetta Iavarone <18575092+elisabettai@users.noreply.github.com>
Date: Fri, 3 May 2024 16:15:06 +0200
Subject: [PATCH 2/4] Bumped version

---
 .bumpversion.cfg         | 2 +-
 .osparc/metadata.yml     | 2 +-
 CHANGELOG.md             | 5 +++++
 Makefile                 | 8 ++++----
 docker-compose-local.yml | 2 +-
 5 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index b7e84ca..3abcb05 100644
--- a/.bumpversion.cfg
+++ b/.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
diff --git a/.osparc/metadata.yml b/.osparc/metadata.yml
index 579052e..710d19f 100644
--- a/.osparc/metadata.yml
+++ b/.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: iavarone@itis.swiss
 thumbnail: https://raw.githubusercontent.com/axondeepseg/doc-figures/main/index/fig2.png
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ed311d9..9b564b8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,9 @@
 # Changelog
+
+## [1.0.2] - 2024-05
+### Fixed
+Do not create `.Trash-1000` folder (caused service to fail after re-opening a study)
+
 ## [1.0.1] - 2024-02
 - Copy source code and models to workspace if not there yest
 
diff --git a/Makefile b/Makefile
index c82ab72..4a4934e 100644
--- a/Makefile
+++ b/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
diff --git a/docker-compose-local.yml b/docker-compose-local.yml
index d02f8e2..3433190 100644
--- a/docker-compose-local.yml
+++ b/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:

From 0ecc030572306dc113c4a3f55bd2240171ab757b Mon Sep 17 00:00:00 2001
From: Elisabetta Iavarone <18575092+elisabettai@users.noreply.github.com>
Date: Mon, 6 May 2024 12:41:41 +0200
Subject: [PATCH 3/4] Improve start-up errors

---
 CHANGELOG.md                    |  3 ++-
 Dockerfile                      |  2 +-
 boot_scripts/boot_notebook.bash | 18 ++++++++++++++----
 boot_scripts/entrypoint.bash    |  2 --
 4 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9b564b8..0d51660 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,7 +2,8 @@
 
 ## [1.0.2] - 2024-05
 ### Fixed
-Do not create `.Trash-1000` folder (caused service to fail after re-opening a study)
+- 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
diff --git a/Dockerfile b/Dockerfile
index f8c91fb..2ef130e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -162,7 +162,7 @@ WORKDIR /tmp
 RUN mamba install --yes \
     'jupyterlab' \
     'notebook' \
-    'jupyterlab_latex' \
+    #'jupyterlab_latex' \
     'voila' \
     'jupyterlab-git' && \
     jupyter server --generate-config && \
diff --git a/boot_scripts/boot_notebook.bash b/boot_scripts/boot_notebook.bash
index 5ecd0df..0a69ca4 100755
--- a/boot_scripts/boot_notebook.bash
+++ b/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": {
@@ -45,7 +46,7 @@ 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": "${NOTEBOOK_BASE_DIR}/workspace/",
@@ -54,9 +55,18 @@ cat > .jupyter_config.json <<EOF
         "token": "${NOTEBOOK_TOKEN}",
         "webbrowser_open_new": 0
     },
+    "LabApp": {
+        "tornado_settings": {
+            "page_config_data": {
+                "buildCheck": false,
+                "buildAvailable": false,
+            },
     "KernelSpecManager": {
-        "allowed_kernelspecs": ["ads_venv"],
-         "delete_to_trash": false
+        "allowed_kernelspecs": ["ads_venv"]
+    },
+    "FileContentsManager": {
+        "preferred_dir": "${NOTEBOOK_BASE_DIR}/workspace/",
+        "delete_to_trash": false
     }
 }
 EOF
@@ -91,5 +101,5 @@ if [ "${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 "$@" --LabApp.default_url='/lab/tree/workspace/README.ipynb' 
 fi
diff --git a/boot_scripts/entrypoint.bash b/boot_scripts/entrypoint.bash
index 247288e..88d3b24 100755
--- a/boot_scripts/entrypoint.bash
+++ b/boot_scripts/entrypoint.bash
@@ -66,8 +66,6 @@ else
     chown --recursive "$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

From 3cbb2b37df5016f23c4c08edeb6dd0053fe677a6 Mon Sep 17 00:00:00 2001
From: Elisabetta Iavarone <18575092+elisabettai@users.noreply.github.com>
Date: Mon, 6 May 2024 13:30:19 +0200
Subject: [PATCH 4/4] Not fixing loader.js error

---
 Dockerfile                      | 1 -
 boot_scripts/boot_notebook.bash | 7 -------
 2 files changed, 8 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 2ef130e..68e8ba2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -162,7 +162,6 @@ WORKDIR /tmp
 RUN mamba install --yes \
     'jupyterlab' \
     'notebook' \
-    #'jupyterlab_latex' \
     'voila' \
     'jupyterlab-git' && \
     jupyter server --generate-config && \
diff --git a/boot_scripts/boot_notebook.bash b/boot_scripts/boot_notebook.bash
index 0a69ca4..8fe2b44 100755
--- a/boot_scripts/boot_notebook.bash
+++ b/boot_scripts/boot_notebook.bash
@@ -51,16 +51,9 @@ cat > .jupyter_config.json <<EOF
         "port": 8888,
         "preferred_dir": "${NOTEBOOK_BASE_DIR}/workspace/",
         "quit_button": false,
-        "root_dir": "${NOTEBOOK_BASE_DIR}",
         "token": "${NOTEBOOK_TOKEN}",
         "webbrowser_open_new": 0
     },
-    "LabApp": {
-        "tornado_settings": {
-            "page_config_data": {
-                "buildCheck": false,
-                "buildAvailable": false,
-            },
     "KernelSpecManager": {
         "allowed_kernelspecs": ["ads_venv"]
     },