Plot through Python tool

CHANGELOG.md

@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Use typescript autogen for backend types in frontend.
 - Try to enforce using metric tools rather than downloading assets.
 - Rule to avoid overvalidating.
+- Plot through python + plotly.
 
 ## Fixed
 - Images not appearing in Literature search (Prompt refactor).

backend/Dockerfile

@@ -6,9 +6,29 @@ RUN apt-get -y update
 RUN apt-get -y install curl \
     build-essential \
     libhdf5-dev \
+    libboost-all-dev \
     ninja-build \
     nodejs \
-    npm
+    npm \
+    wget \
+    && rm -rf /var/lib/apt/lists/* \
+    && TARGETARCH=$(dpkg --print-architecture) \
+    && if [ "$TARGETARCH" = "arm64" ] || [ "$TARGETARCH" = "aarch64" ]; then \
+        wget https://github.com/Kitware/CMake/archive/refs/tags/v4.0.1.tar.gz -O cmake.tar.gz \
+        && tar xzf cmake.tar.gz \
+        && cd CMake-4.0.1 \
+        && ./bootstrap --parallel=$(nproc) \
+        && make -j$(nproc) \
+        && make install \
+        && cd .. \
+        && rm -rf CMake-4.0.1 cmake.tar.gz; \
+    else \
+        apt-get update && apt-get install -y cmake && rm -rf /var/lib/apt/lists/*; \
+    fi
+
+ENV CMAKE=/usr/local/bin/cmake
+ENV CMAKE_POLICY_VERSION_MINIMUM=3.5
+RUN which cmake && cmake --version
 
 RUN npm install -g deno@">=2.5.0"
 RUN pip install --no-cache-dir --upgrade pip
@@ -19,12 +39,14 @@ RUN mv /code/alembic /alembic
 RUN mv /code/alembic.ini /alembic.ini
 RUN mv /code/docker-entrypoint.sh /docker-entrypoint.sh
 
-# Create package.json and install pyodide locally
-RUN mv /code/setup_pyodide.mjs /setup_pyodide.mjs
-WORKDIR /
 RUN chmod +x /docker-entrypoint.sh
 RUN rm -rf /code
 
+WORKDIR /
+
+# Download manual wheels
+RUN mkdir cached_wheels && \
+    pip download --only-binary=:all: --no-deps -d ./cached_wheels plotly
 
 EXPOSE 8078
 ENTRYPOINT ["./docker-entrypoint.sh"]

backend/docker-entrypoint.sh

@@ -3,17 +3,4 @@
 set -o errexit
 
 alembic upgrade head
-neuroagent-api --host 0.0.0.0 --port 8078 &
-SERVER_PID=$!
-
-# Wait for server to be ready
-while ! curl -f http://localhost:8078/healthz 2>/dev/null; do
-  echo "Waiting for server to start..."
-  sleep 2
-done
-
-echo "Server is ready, running setup_pyodide.mjs"
-node setup_pyodide.mjs
-
-# Keep server running
-wait $SERVER_PID
+neuroagent-api --host 0.0.0.0 --port 8078

backend/eval/input/plotting/expected_output.md

@@ -0,0 +1,11 @@
+## Plot of y = x^2
+I generated the plot of y = x^2 for x in [-10, 10]. You should see an interactive Plotly figure above showing the parabola.
+
+Equation: y = x^2
+Range used: x from -10 to 10 (400 points)
+If you'd like:
+
+Different x-range or point density
+The plot exported as a PNG or PDF
+A version with markers, gridlines, or annotations
+tell me which option you prefer and I’ll regenerate it.",

backend/eval/input/plotting/expected_tool_calls.json

@@ -0,0 +1,8 @@
+[
+  {
+  "name": "run-python",
+  "arguments": {
+    "python_script": "import numpy as np\nimport plotly.graph_objects as go\nx = np.linspace(-10,10,400)\ny = x**2\nfig = go.Figure()\nfig.add_trace(go.Scatter(x=x,y=y,mode='lines',name='y=x^2'))\nfig.update_layout(title='Plot of y = x^2',xaxis_title='x',yaxis_title='y')\nfig.show()\n# return something so tool returns\n'plot_generated'"
+    }
+  }
+      ]

backend/eval/input/plotting/user.md

@@ -0,0 +1 @@
+Can you please generate a plot of y=x^2?

backend/eval/input/sin_plot/expected_output.md

@@ -1 +1,11 @@
-Here is the scatter plot of y = sin(x) with 8 points evenly spaced from 0 to 2π. The points show the sine values at these specific x coordinates. If you want, I can also provide a line plot connecting these points. Would you like that?
+Plot: y = sin(x) (8 evenly spaced points from 0 to 2π)
+Points used (coordinates):
+(x: 0.0000, y: 0.0000)
+(x: 0.8976, y: 0.7820)
+(x: 1.7952, y: 0.9755)
+(x: 2.6928, y: 0.4384)
+(x: 3.5904, y: -0.4423)
+(x: 4.4880, y: -0.9749)
+(x: 5.3856, y: -0.7891)
+(x: 6.2832, y: -0.0000)
+The plotted figure is shown above. If you want different styling (lines only, markers only, more points, or a downloadable image), tell me which option you prefer.

backend/eval/input/sin_plot/expected_tool_calls.json

@@ -1,84 +1,8 @@
 [
   {
-    "name": "execute-python-code",
-    "arguments": {
-      "python_code": "import numpy as np\n\n# Generate 8 evenly spaced points from 0 to 2*pi\nx_values = np.linspace(0, 2 * np.pi, 8)\n# Calculate sin(x) for these points\ny_values = np.sin(x_values)\n\n# Prepare data for plotting\npoints = [{'x': float(x), 'y': float(y)} for x, y in zip(x_values, y_values)]\npoints"
-    }
-  },
-  {
-    "name": "plot-generator",
-    "arguments": {
-      "plot_type": "json-scatterplot",
-      "title": "Plot of y = sin(x) with 8 evenly spaced points from 0 to 2π",
-      "description": "This scatter plot shows the values of y = sin(x) at 8 points evenly spaced between 0 and 2π.",
-      "x_label": "x (radians)",
-      "y_label": "sin(x)",
-      "piechart_values": null,
-      "barplot_values": null,
-      "scatter_values": [
-        {
-          "x": 0,
-          "y": 0,
-          "label": null,
-          "color": null,
-          "size": null
-        },
-        {
-          "x": 0.8975979010256552,
-          "y": 0.7818314824680298,
-          "label": null,
-          "color": null,
-          "size": null
-        },
-        {
-          "x": 1.7951958020513104,
-          "y": 0.9749279121818236,
-          "label": null,
-          "color": null,
-          "size": null
-        },
-        {
-          "x": 2.6927937030769655,
-          "y": 0.43388373911755823,
-          "label": null,
-          "color": null,
-          "size": null
-        },
-        {
-          "x": 3.5903916041026207,
-          "y": -0.433883739117558,
-          "label": null,
-          "color": null,
-          "size": null
-        },
-        {
-          "x": 4.487989505128276,
-          "y": -0.9749279121818236,
-          "label": null,
-          "color": null,
-          "size": null
-        },
-        {
-          "x": 5.385587406153931,
-          "y": -0.7818314824680299,
-          "label": null,
-          "color": null,
-          "size": null
-        },
-        {
-          "x": 6.283185307179586,
-          "y": -2.4492935982947064e-16,
-          "label": null,
-          "color": null,
-          "size": null
-        }
-      ],
-      "histogram_values": null,
-      "histogram_bins": 10,
-      "histogram_color": null,
-      "linechart_values": null,
-      "line_style": "solid",
-      "line_color": null
+  "name": "run-python",
+  "arguments": {
+    "python_script": "import numpy as np\nimport plotly.graph_objects as go\n\n# generate 8 evenly spaced points from 0 to 2pi\nx = np.linspace(0, 2*np.pi, 8)\ny = np.sin(x)\n\nfig = go.Figure()\nfig.add_trace(go.Scatter(x=x, y=y, mode='markers+lines', name='sin(x)'))\nfig.update_layout(title='y = sin(x) (8 evenly spaced points from 0 to 2π)',\n                  xaxis_title='x', yaxis_title='y',\n                  xaxis = dict(tickmode='array', tickvals=x, ticktext=[f'{val:.2f}' for val in x]))\n\nfig.show()\n\n# return numeric lists for reference\n{\"x\": x.tolist(), \"y\": y.tolist()}"
     }
   }
 ]