Docker updates 2025 summer

dockerfiles/r-stat-201/Dockerfile

@@ -55,6 +55,9 @@ COPY config/shortcuts.jupyterlab-settings /home/${NB_USER}/.jupyter/lab/user-set
 # Copy jupyter_server_config.py which allows students to see and delete hidden files
 COPY config/jupyter_server_config.py /home/${NB_USER}/.jupyter
 
+# Copy jupyter_notebook_config.py with automatic backup script
+COPY config/jupyter_notebook_config.py /home/${NB_USER}/.jupyter
+
 # Copy gitconfig that sets global default pull strategy to rebase
 COPY config/.gitconfig /home/${NB_USER}/
 

dockerfiles/r-stat-201/conda-linux-64.lock

@@ -224,7 +224,6 @@ https://conda.anaconda.org/conda-forge/noarch/nbformat-5.10.4-pyhd8ed1ab_0.conda
 https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-he2d9a6e_10.conda#f29b857679e49c026984531249e542fd
 https://conda.anaconda.org/conda-forge/noarch/requests-2.32.3-pyhd8ed1ab_0.conda#5ede4753180c7a550a443c430dc8ab52
 https://conda.anaconda.org/conda-forge/noarch/jupyter_events-0.10.0-pyhd8ed1ab_0.conda#ed45423c41b3da15ea1df39b1f80c2ca
-https://conda.anaconda.org/conda-forge/noarch/jupytext-1.16.4-pyh80e38bb_0.conda#1df7fd1594a7f2f6496ff23834a099bf
 https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.0-pyhd8ed1ab_0.conda#15b51397e0fe8ea7d7da60d83eb76ebc
 https://conda.anaconda.org/conda-forge/noarch/r-abind-1.4_5-r43hc72bb7e_1006.conda#75d26096ffa98e1cde7b27b9530899a1
 https://conda.anaconda.org/conda-forge/noarch/r-assertthat-0.2.1-r43hc72bb7e_5.conda#830d74ef2014697ec7f95922cd6edcef

dockerfiles/r-stat-201/config/jupyter_notebook_config.py

@@ -0,0 +1,47 @@
+# Configuration file for notebook.
+
+c = get_config()  #noqa
+
+# When a notebook is saved, save a timestamped copy in directory .history. Clear outputs.
+import os
+import shutil
+import time
+import glob
+import subprocess
+from datetime import datetime
+from zoneinfo import ZoneInfo
+
+def post_save(model, os_path, contents_manager):
+    """post-save hook for saving backups of jupyter files."""
+
+    if model['type'] != 'notebook':
+        return # only do this for notebooks
+
+    directory, filename = os.path.split(os_path)
+    history_directory = os.path.join(directory, '.history')
+
+    if not os.path.isdir(history_directory):
+        os.mkdir(history_directory)
+
+    files = list(filter(os.path.isfile, glob.glob(os.path.join(history_directory, '*'))))
+    files.sort(key=lambda x: os.path.getctime(x))
+
+    # If the last backup was taken less than time_since seconds ago, return and do not save copy
+    if len(files) > 0:
+        time_since = 15*60
+        if time.time() - os.stat(files[-1]).st_ctime < time_since:
+            return
+
+    now = datetime.now(ZoneInfo('America/Vancouver'))
+    backup_path=os.path.join(history_directory,now.strftime("%d_%m_%Y_%H_%M_%S")+"_"+filename)
+    shutil.copy2(os_path, backup_path)
+
+    # Clear all backup notebook outputs
+    subprocess.call(["jupyter", "nbconvert", "--clear-output", "--inplace", backup_path])
+
+    # Keep num_saved latest saved notebooks
+    num_saved = 5 # No less than 1
+    if len(files) + 1 > num_saved:
+        os.remove(files[0])
+
+c.FileContentsManager.post_save_hook = post_save

dockerfiles/r-stat-201/config/shortcuts.jupyterlab-settings

@@ -1,12 +1,139 @@
 {
     "shortcuts": [
+        {
+            "args": {},
+            "command": "notebook:change-cell-to-code",
+            "keys": [
+                "Y"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:change-cell-to-heading-1",
+            "keys": [
+                "1"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:change-cell-to-heading-2",
+            "keys": [
+                "2"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:change-cell-to-heading-3",
+            "keys": [
+                "3"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:change-cell-to-heading-4",
+            "keys": [
+                "4"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:change-cell-to-heading-5",
+            "keys": [
+                "5"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:change-cell-to-heading-6",
+            "keys": [
+                "6"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:change-cell-to-markdown",
+            "keys": [
+                "M"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:change-cell-to-raw",
+            "keys": [
+                "R"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:collapse-all-headings",
+            "keys": [
+                "Ctrl Shift ArrowLeft"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:copy-cell",
+            "keys": [
+                "C"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:cut-cell",
+            "keys": [
+                "X"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:delete-cell",
+            "keys": [
+                "D",
+                "D"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:enter-command-mode",
+            "keys": [
+                "Ctrl M"
+            ],
+            "selector": ".jp-Notebook.jp-mod-editMode",
+            "disabled": true
+        },
         {
             "args": {},
             "command": "notebook:merge-cell-above",
             "keys": [
                 "Ctrl Backspace"
             ],
-            "selector": ".jp-Notebook:focus",
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
             "disabled": true
         },
         {
@@ -15,7 +142,7 @@
             "keys": [
                 "Ctrl Shift M"
             ],
-            "selector": ".jp-Notebook:focus",
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
             "disabled": true
         },
         {
@@ -24,7 +151,25 @@
             "keys": [
                 "Shift M"
             ],
-            "selector": ".jp-Notebook:focus",
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:paste-cell-below",
+            "keys": [
+                "V"
+            ],
+            "selector": ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus",
+            "disabled": true
+        },
+        {
+            "args": {},
+            "command": "notebook:split-cell-at-cursor",
+            "keys": [
+                "Ctrl Shift -"
+            ],
+            "selector": ".jp-Notebook.jp-mod-editMode",
             "disabled": true
         }
     ]

dockerfiles/r-stat-201/environment.yml

@@ -8,7 +8,6 @@ dependencies:
   - jupyterlab
   - jupyterlab-git
   - jupyter-resource-usage
-  - jupytext
   - nbgitpuller
   - python=3.11
   - r-aer