Update, review, tidy and fix across s/scripts and Docker setup

Dockerfile

@@ -25,17 +25,13 @@ COPY requirements.txt ./
 # Copy the full source (needed for editable install)
 COPY rcpchgrowth rcpchgrowth
 
-# Upgrade pip/setuptools/wheel first
-RUN pip install --upgrade pip setuptools wheel
-
-# Install runtime + notebook deps first (ensures wheels pulled before editable wiring)
-RUN pip install python-dateutil scipy pandas matplotlib jupyterlab ipykernel
-
-# Install dev/test tools
-RUN pip install -r requirements.txt
-
-# Finally perform editable install (should be fast now; minimal build isolation work)
-RUN pip install -e . || (echo '--- Editable install failed; running pip debug ---' && python -m pip debug && exit 1)
+# Upgrade build tooling, install the package (with notebook extras) editable,
+# and install dev/test deps. Notebook extras (jupyterlab, ipykernel, pandas,
+# matplotlib) and runtime deps (python-dateutil, scipy) come from pyproject.toml.
+RUN pip install --upgrade pip setuptools wheel \
+ && pip install -e .[notebook] \
+ && pip install -r requirements.txt \
+ && python -m ipykernel install --name rcpchgrowth --display-name 'rcpchgrowth' --sys-prefix
 
 # Bring in notebooks only after package install so they are never considered for package discovery
 COPY notebooks notebooks

docker-compose.yml

@@ -13,22 +13,11 @@ services:
       - PYTHONPATH=/app
     ports:
       - "8888:8888"
-    command:
-      - bash
-      - -lc
-      - |
-        set -e
-        mkdir -p /app/notebooks
-        echo '[DEV] Editable install'
-        pip install -e /app[notebook]
-        echo '[DEV] Installing test dependencies'
-        pip install pytest
-        echo '[DEV] Sanity import'
-        echo '[DEV] Register kernel'
-        python -m ipykernel install --name rcpchgrowth --display-name 'rcpchgrowth' --sys-prefix
-        echo '[DEV] Launching JupyterLab in background'
-        jupyter lab --ip=0.0.0.0 --no-browser --allow-root \
-          --NotebookApp.token='' --NotebookApp.password='' \
-          --notebook-dir=/app/notebooks &
-        echo '[DEV] Container ready for testing'
-        wait
+    # Re-wire the editable install against the bind-mounted source (creates
+    # rcpchgrowth.egg-info on the host on first run), then exec JupyterLab.
+    # All deps and the Jupyter kernel are baked into the image at build time.
+    command: >
+      bash -lc "pip install -e . -q &&
+      exec jupyter lab --ip=0.0.0.0 --no-browser --allow-root
+      --NotebookApp.token='' --NotebookApp.password=''
+      --notebook-dir=/app/notebooks"

notebooks/AdditionalFunctions.ipynb

@@ -201,7 +201,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,

s/build

@@ -1,10 +1,5 @@
 #!/bin/bash
-
-set -v  # Enable verbose mode
-set -e  # Exit on error
-
-# scripts may need to be made executable on some platforms before they can be run
-# chmod +x <filename> is the command to do this on unixy systems
+set -e
 
 # Build the development container image
-docker compose build
+docker compose build "$@"

s/down

@@ -1,10 +1,5 @@
 #!/bin/bash
+set -e
 
-set -v  # Enable verbose mode
-set -e  # Exit on error
-
-# scripts may need to be made executable on some platforms before they can be run
-# chmod +x <filename> is the command to do this on unixy systems
-
-# shuts down the Docker Compose setup but does not destroy containers or images
+# Stop the Compose setup (containers and images are preserved).
 docker compose down

s/notebook

@@ -2,32 +2,33 @@
 
 set -e  # Exit on error
 
-# Check if container is running
-CONTAINER_NAME="rcpchgrowth-python"
-CONTAINER_STATUS=$(docker inspect -f '{{.State.Running}}' $CONTAINER_NAME 2>/dev/null || echo "false")
+JUPYTER_URL="http://localhost:8888/lab"
 
-if [ "$CONTAINER_STATUS" = "false" ]; then
-    echo "Container not running. Starting container..."
-    docker compose up -d
-    echo "Waiting for JupyterLab to start..."
-    sleep 15
-fi
+# Always run docker compose up -d; it's idempotent (no-op if already running)
+echo "Ensuring container is running..."
+docker compose up -d
 
-# Get the JupyterLab URL
-JUPYTER_URL="http://localhost:8888/lab"
+# Wait for JupyterLab to respond rather than a blind sleep
+echo "Waiting for JupyterLab to be ready..."
+for i in $(seq 1 30); do
+    if curl -s -o /dev/null -w '' "$JUPYTER_URL" 2>/dev/null; then
+        break
+    fi
+    sleep 2
+done
 
 echo ""
 echo "🎓 JupyterLab is running!"
 echo "Opening: $JUPYTER_URL"
 echo ""
 
-# Try to open in browser (works on macOS, Linux with xdg-open, etc.)
+# Try to open in browser (suppress stderr to avoid Chromium noise)
 if command -v open &> /dev/null; then
     # macOS
     open "$JUPYTER_URL"
 elif command -v xdg-open &> /dev/null; then
     # Linux
-    xdg-open "$JUPYTER_URL"
+    xdg-open "$JUPYTER_URL" 2>/dev/null &
 elif command -v wslview &> /dev/null; then
     # WSL
     wslview "$JUPYTER_URL"

s/rebuild

@@ -1,12 +1,9 @@
 #!/bin/bash
+set -e
 
-set -v  # Enable verbose mode
-set -e  # Exit on error
+# Rebuild the container from scratch.
+DIR="$(cd "$(dirname "$0")" && pwd)"
+"$DIR/remove-containers-and-images"
+"$DIR/build"
+"$DIR/up"
 
-# scripts may need to be made executable on some platforms before they can be run
-# chmod +x <filename> is the command to do this on unixy systems
-
-# Rebuild the container from scratch
-s/remove-containers-and-images
-s/build
-s/up

s/remove-containers-and-images

@@ -1,10 +1,7 @@
 #!/bin/bash
+set -e
 
-set -v  # Enable verbose mode
-set -e  # Exit on error
+# Stop the Compose setup AND remove containers and locally-built images
+# (named/anonymous volumes are preserved).
+docker compose down --rmi local
 
-# scripts may need to be made executable on some platforms before they can be run
-# chmod +x <filename> is the command to do this on unixy systems
-
-# shuts down the Docker Compose setup AND deletes containers and images (but not volumes)
-docker compose down --rmi local # removes the container and local images

s/up

@@ -1,18 +1,6 @@
 #!/bin/bash
+set -e
 
-set -v  # Enable verbose mode
-set -e  # Exit on error
+# Build (if needed) and start the development container in detached mode.
+docker compose up -d "$@"
 
-# scripts may need to be made executable on some platforms before they can be run
-# chmod +x <filename> is the command to do this on unixy systems
-
-# Build and start the development container in detached mode
-docker compose up -d
-
-echo ""
-echo "Container started! Use these commands:"
-echo "  s/shell  - Enter the container for interactive work"
-echo "  s/test   - Run pytest inside the container"
-echo "  s/python - Run Python REPL inside the container"
-echo "  s/down   - Stop the container"
-echo ""