Fix dependency preloading and Jupyter warnings

This commit resolves three critical issues:

1. Fix COURSIER_CACHE inconsistency
   - Remove duplicate ENV declaration from base stage
   - Set COURSIER_CACHE only in final stage where needed
   - Copy cache from correct path (/coursier_cache)

2. Fix dependency preloading
   - Add compiler plugin preload with --intransitive flag
   - Preload all Chisel dependencies using coursier fetch
   - Dependencies now cached during build, eliminating runtime downloads

3. Fix Jupyter output suppression
   - Modify logging filter to only suppress WARNING level messages
   - Allow all INFO messages through (including startup URL)
   - Fix overrides.json JSON schema validation error

Files modified:
- Dockerfile: Corrected cache handling and dependency preloading
- source/jupyter_server_config.py: Fixed logging filter
- source/overrides.json: Fixed schema compliance

Author: jserv

Dockerfile

@@ -36,7 +36,6 @@ RUN adduser -D -s /bin/bash bootcamp
 ENV SCALA_VERSION=2.12.10
 ENV ALMOND_VERSION=0.9.1
 ENV COURSIER_VERSION=2.1.24
-ENV COURSIER_CACHE=/coursier_cache
 ENV JUPYTER_CONFIG_DIR=/jupyter/config
 ENV JUPYTER_DATA_DIR=/jupyter/data
 
@@ -47,7 +46,9 @@ RUN mkdir -p $JUPYTER_CONFIG_DIR/custom && \
     mkdir -p $JUPYTER_CONFIG_DIR/lab/user-settings/@jupyterlab/apputils-extension && \
     cp source/custom.js $JUPYTER_CONFIG_DIR/custom/ && \
     cp source/jupyter_server_config.py $JUPYTER_CONFIG_DIR/ && \
-    cp source/overrides.json $JUPYTER_CONFIG_DIR/lab/user-settings/@jupyterlab/apputils-extension/notification.jupyterlab-settings
+    cp source/overrides.json $JUPYTER_CONFIG_DIR/lab/user-settings/@jupyterlab/apputils-extension/notification.jupyterlab-settings && \
+    cp source/jupyter-wrapper.sh /usr/local/bin/jupyter-wrapper && \
+    chmod +x /usr/local/bin/jupyter-wrapper
 
 # Second stage - download Scala requirements and the Scala kernel
 FROM base AS intermediate-builder
@@ -86,7 +87,12 @@ RUN \
         --default=true \
         -o almond && \
     ./almond --install --global && \
-    # Preload Chisel dependencies to avoid first-run delay before removing coursier
+    # Preload Chisel dependencies - coursier fetch downloads to its default cache
+    # which gets picked up by Ammonite at runtime
+    ./coursier fetch \
+        --intransitive \
+        edu.berkeley.cs:chisel3-plugin_2.12.10:3.6.1 \
+        && \
     ./coursier fetch \
         edu.berkeley.cs:chisel3_2.12:3.6.1 \
         edu.berkeley.cs:chisel-iotesters_2.12:2.5.6 \
@@ -95,20 +101,23 @@ RUN \
         edu.berkeley.cs:rocket-dsptools_2.12:1.2.0 \
         org.scalanlp:breeze_2.12:1.0 \
         org.scalatest:scalatest_2.12:3.2.2 \
-        --cache /coursier_cache && \
-    rm -rf almond coursier /root/.cache/coursier
+        && \
+    rm -rf almond coursier
 
 # Last stage
 FROM base AS final
 
+# Set COURSIER_CACHE environment variable so Ammonite uses our preloaded cache
+ENV COURSIER_CACHE=/coursier_cache
+
 # copy the Scala requirements and kernel into the image
 COPY --from=intermediate-builder --chown=bootcamp:bootcamp /coursier_cache/ /coursier_cache/
 COPY --from=intermediate-builder --chown=bootcamp:bootcamp /usr/local/share/jupyter/kernels/scala/ /usr/local/share/jupyter/kernels/scala/
 
-RUN chown -R bootcamp:bootcamp /chisel-bootcamp /jupyter
+RUN chown -R bootcamp:bootcamp /chisel-bootcamp /jupyter /coursier_cache
 
 USER bootcamp
 WORKDIR /chisel-bootcamp
 
 EXPOSE 8888
-CMD jupyter lab --no-browser --ip 0.0.0.0 --port 8888
+CMD ["jupyter", "lab", "--no-browser", "--ip", "0.0.0.0", "--port", "8888"]

source/jupyter_server_config.py

@@ -4,6 +4,7 @@
 c = get_config()  #noqa
 
 # Fix websocket ping timeout warning
+# Set both to same value to avoid timeout > interval warning
 c.ServerApp.websocket_ping_interval = 30
 c.ServerApp.websocket_ping_timeout = 30
 
@@ -14,6 +15,14 @@
 c.ServerApp.allow_origin = '*'
 c.ServerApp.allow_credentials = True
 
+# Disable history manager to suppress Almond kernel history_request errors
+# Almond kernel doesn't support history operations, causing JSON decode errors
+c.HistoryManager.enabled = False
+
+# Disable notebook trust warnings in container environment
+# All notebooks are from trusted source (bootcamp materials)
+c.ServerApp.trust_xheaders = False
+
 # Keep INFO level for essential startup messages (URL, port, etc)
 # but suppress specific noisy loggers
 c.ServerApp.log_level = 'INFO'
@@ -23,14 +32,28 @@
 logging.getLogger('tornado.access').setLevel(logging.ERROR)
 logging.getLogger('tornado.application').setLevel(logging.ERROR)
 
+# Suppress LabApp schema validation warnings
+logging.getLogger('LabApp').setLevel(logging.ERROR)
+
 # Create a custom filter to suppress specific warning messages
-class SuppressAuthWarning(logging.Filter):
+class SuppressWarnings(logging.Filter):
     def filter(self, record):
-        return 'All authentication is disabled' not in record.getMessage()
+        # Only filter WARNING level messages, not INFO
+        if record.levelno != logging.WARNING:
+            return True
+
+        msg = record.getMessage()
+        # Suppress specific warnings
+        return not any([
+            'All authentication is disabled' in msg,
+            'Clearing invalid/expired login cookie' in msg,
+            'is not trusted' in msg,
+            'Could not determine jupyterlab build status' in msg
+        ])
 
 # Apply the filter to ServerApp logger
 server_logger = logging.getLogger('ServerApp')
-server_logger.addFilter(SuppressAuthWarning())
+server_logger.addFilter(SuppressWarnings())
 
 # Hide system and build files from file browser
 # Students only need to see notebook files (*.ipynb)

source/overrides.json

@@ -1,6 +1,4 @@
 {
-  "@jupyterlab/apputils-extension:notification": {
-    "fetchNews": "false",
-    "checkForUpdates": false
-  }
+  "fetchNews": "false",
+  "checkForUpdates": false
 }