fix(jupyerlab): remove extensions that require downgrading jupyter ve…

…rsion (#39)
SwanseaUniversityMedical · Sep 11, 2023 · 56830dc · 56830dc
1 parent 5e3a99e
commit 56830dc
Show file tree

Hide file tree

Showing 3 changed files with 36 additions and 21 deletions.
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -30,7 +30,7 @@ jobs:
       filters: |
         jupyter-container:
           - './.github/workflows/release.yaml'
-          - 'containers/jupyterlab/**'
+          - 'containers/**'
           - 'plugins/**'
         chart:
           - './.github/workflows/release.yaml'

diff --git a/containers/files/requirements/labextensions.txt b/containers/files/requirements/labextensions.txt
@@ -1,7 +1,6 @@
 jupyterlab==4.0.3
 jupyterlab-theme-solarized-dark
 jupyterlab-midnightsea-theme
-jupyterlab-vim
 runplify
 jupyterlab-theme-onedark
 jupyterlab-ariakedark-theme

diff --git a/containers/files/scripts/session_startup.sh b/containers/files/scripts/session_startup.sh
@@ -69,25 +69,41 @@ BASE_CONDARC_FILE=/opt/conda/.condarc
 
 echo "replace the base config in $BASE_CONDARC_FILE"
 
-conda config --system --set env_prompt '({name}) '
-conda config --system --set auto_update_conda false
-conda config --system --set notify_outdated_conda false
-conda config --system --prepend envs_dirs ~/my-conda-envs/
-
-conda config --system --set channel_alias ${NEXUS_ADDR}/repository/
-
-while IFS= read -r line
-do
-    conda config --system --prepend default_channels ${NEXUS_ADDR}/repository/${line}
-    conda config --system --prepend channels ${line}
-done < "$INPUT"
-
-if [ `conda config --system --get auto_activate_base | wc -l` == 0 ]; then
-    conda config --system --set auto_activate_base true
-fi
-
-conda config --system --prepend create_default_packages ipykernel
-conda config --system --prepend create_default_packages trino-python-client
+cat << EOF > $BASE_CONDARC_FILE
+# Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
+
+auto_update_conda: false
+show_channel_urls: true
+channels:
+  - plotly
+  - bioconda
+  - pytorch
+  - esri
+  - nvidia
+  - rapidsai
+  - r
+  - conda-forge
+  - anaconda
+env_prompt: '({name}) '
+notify_outdated_conda: false
+envs_dirs:
+  - /home/jovyan/my-conda-envs/
+channel_alias: ${NEXUS_ADDR}/repository/
+default_channels:
+  - ${NEXUS_ADDR}/repository/plotly
+  - ${NEXUS_ADDR}/repository/bioconda
+  - ${NEXUS_ADDR}/repository/pytorch
+  - ${NEXUS_ADDR}/repository/esri
+  - ${NEXUS_ADDR}/repository/nvidia
+  - ${NEXUS_ADDR}/repository/rapidsai
+  - ${NEXUS_ADDR}/repository/r
+  - ${NEXUS_ADDR}/repository/conda-forge
+  - ${NEXUS_ADDR}/repository/anaconda
+auto_activate_base: true
+create_default_packages:
+  - ipykernel
+  - trino-python-client
+EOF
 
 
 ## setup default config for R: