Update Jupyter notebook base image to jupyter/scipy-notebook:2024-12-09 and reorganize package installations in Dockerfile

Author: flaviomartins

notebook/Dockerfile

@@ -1,6 +1,6 @@
 # Copyright (c) SIPist Development Team
 # Distributed under the terms of the Modified BSD License.
-FROM quay.io/jupyter/scipy-notebook:2024-11-11
+FROM quay.io/jupyter/scipy-notebook:2024-12-09
 
 LABEL maintainer="Flavio Martins <[email protected]>"
 
@@ -29,32 +29,34 @@ RUN apt-get update --yes && \
 
 USER ${NB_UID}
 
-# Install PostgreSQL Python drivers
-RUN mamba install --yes \
-    'psycopg' \
-    'psycopg-c' \
-    'psycopg-pool' && \
-    mamba clean --all -f -y && \
-    fix-permissions "${CONDA_DIR}" && \
-    fix-permissions "/home/${NB_USER}"
-
-# Install PostgreSQL extras
-RUN mamba install --yes \
-    'pgcli' && \
-    mamba clean --all -f -y && \
-    fix-permissions "${CONDA_DIR}" && \
-    fix-permissions "/home/${NB_USER}"
-
-# Install sqlite
+# Install utils
 RUN mamba install --yes \
-    'sqlite' && \
+    'bat' \
+    'fd-find' \
+    'file' \
+    'git-delta' \
+    'git-lfs' \
+    'htop' \
+    'jc' \
+    'jq' \
+    'ncdu' \
+    'ripgrep' \
+    'rclone' \
+    'rsync' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Install sqlite-utils
+# Install special extras
 RUN mamba install --yes \
-    'sqlite-utils' && \
+    'cchardet' \
+    'dateparser' \
+    'ftfy' \
+    'html5lib' \
+    'langcodes' \
+    'lxml' \
+    'tld' \
+    'yarl' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
@@ -68,80 +70,56 @@ RUN echo 'redis-server=7.2.*' >> "${CONDA_DIR}/conda-meta/pinned" && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Install DuckDB
+# Install DuckDB and SQLalchemy driver
 RUN mamba install --yes \
     'duckdb-cli' \
+    'duckdb-engine' \
     'python-duckdb' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Install DuckDB SQLAlchemy driver
-RUN mamba install --yes \
-    'duckdb-engine' && \
-    mamba clean --all -f -y && \
-    fix-permissions "${CONDA_DIR}" && \
-    fix-permissions "/home/${NB_USER}"
-
-# Install JupySQL
+# Install sqlite
 RUN mamba install --yes \
-    'jupysql' && \
+    'sqlite' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Install measurement extras
+# Install PostgreSQL Python drivers
 RUN mamba install --yes \
-    'jupyterlab_execute_time' && \
+    'psycopg' \
+    'psycopg-c' \
+    'psycopg-pool' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Install utility extras
+# Install PostgreSQL extras
 RUN mamba install --yes \
-    'jupyter-archive' \
-    'jupyterlab-spellchecker' && \
+    'pgcli' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Install Python language server
+# Install JupySQL
 RUN mamba install --yes \
-    'jupyterlab-lsp' \
-    'python-lsp-server' \
-    'python-lsp-ruff' && \
+    'jupysql' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Install utils
+# Install utility extras
 RUN mamba install --yes \
-    'bat' \
-    'fd-find' \
-    'file' \
-    'git-delta' \
-    'git-lfs' \
-    'htop' \
-    'jc' \
-    'jq' \
-    'ncdu' \
-    'ripgrep' \
-    'rclone' \
-    'rsync' && \
+    'jupyterlab_execute_time' \
+    'jupyterlab-spellchecker' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Install special extras
+# Install collaboration extras
 RUN mamba install --yes \
-    'cchardet' \
-    'dateparser' \
-    'ftfy' \
-    'html5lib' \
-    'langcodes' \
-    'lxml' \
-    'tld' \
-    'yarl' && \
+    'jupyter-archive' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
@@ -154,7 +132,6 @@ RUN mamba install --yes \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-
 USER ${NB_UID}
 
 COPY --chown=${NB_UID}:${NB_GID} ./.psqlrc ${HOME}/.psqlrc