Merge pull request #63 from the-virtual-brain/fix-notebookrun

Fix notebooks run

.github/workflows/build.yml

@@ -15,10 +15,10 @@ jobs:
       matrix:
         python-version: [ "3.8", "3.9" ]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/notebooks.yml

@@ -1,27 +1,35 @@
 name: Test Notebooks
 on:
+  push:
+    branches:
+      - '*'
   pull_request:
     types: [opened, synchronize, reopened]
 
 jobs:
   build:
     name: Run notebooks
-    runs-on: windows-latest
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: 3.8
 
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgl1 xvfb
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install -r requirements.txt
           python -m pip install nbformat nbconvert
 
       - name: Run notebooks
-        run: python ./dev/notebook_runner.py notebooks
+        run: xvfb-run -a python ./dev/notebook_runner.py notebooks

.github/workflows/release.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install dependencies
         run: |

notebooks/TimeSeriesEDF.ipynb

@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "56d5c4b6-7804-46d6-931f-fcc5593977d1",
    "metadata": {},
    "outputs": [],
@@ -36,26 +36,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "28420169-2274-4e0e-a73d-c1ab54e6da9c",
    "metadata": {
     "scrolled": true,
     "tags": []
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "17-04-2024 05:02:37 - DEBUG - tvbwidgets - Package is not fully installed\n",
-      "17-04-2024 05:02:37 - DEBUG - tvbwidgets - Version read from the internal package.json file\n",
-      "17-04-2024 05:02:37 - INFO - tvbwidgets - Version: 2.0.0\n",
-      "Using matplotlib as 2D backend.\n",
-      "   INFO  Cannot import syncrypto library.\n",
-      "17-04-2024 05:02:49 - INFO - tvbwidgets.core.pse.parameters - ImportError: Dask dependency is not included, so this functionality won't be available\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import numpy as np\n",
     "from tvbwidgets.api import plot_timeseries\n",
@@ -72,45 +59,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "94687d23-0222-4e9f-887e-e97169737304",
    "metadata": {
     "tags": []
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Extracting EDF parameters from C:\\Work\\TVB\\tvb-widgets\\tvbwidgets\\tests\\data\\test_file.edf...\n",
-      "EDF file detected\n",
-      "Setting channel info structure...\n",
-      "Creating raw.info structure...\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "edf_file_path = '../tvbwidgets/tests/data/test_file.edf' # replace path with your actual EDF file path\n",
+    "edf_file_path = 'tvbwidgets/tests/data/test_file.edf' # replace path with your actual EDF file path\n",
+    "                                                      # set this path file for notebooks tests\n",
+    "# you can use: '../tvbwidgets/tests/data/test_file.edf'\n",
     "data, freq, index = read_edf_file(edf_file_path)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "12da93b3-f96f-44cf-8555-52eee8aaecfd",
    "metadata": {
     "tags": []
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "(92000, 32)\n",
-      "400.0\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(data.shape)\n",
     "print(freq)"
@@ -126,7 +95,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "cac83fe3-b4fe-486a-8955-70203dda1004",
    "metadata": {},
    "outputs": [],
@@ -136,35 +105,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "20c3eae2-49dd-4d01-af9a-06a0dba15888",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "17-04-2024 05:02:49 - INFO - tvbwidgets.ui.ts.plotly_ts_widget - TimeSeries Widget with Plotly initialized\n",
-      "Creating RawArray with float64 data, n_channels=32, n_times=92000\n",
-      "    Range : 0 ... 91999 =      0.000 ...   229.998 secs\n",
-      "Ready.\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "28d8ffb85be94f28b59e85b521e4aeeb",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "TimeSeriesWidgetPlotly(children=(HBox(children=(Output(),)), VBox(children=(Dropdown(description='Colormap:', …"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "tsw = plot_timeseries(data=data, sample_freq=freq, ch_idx=index, backend=backend)"
    ]
@@ -194,7 +138,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.18"
+   "version": "3.9.19"
   }
  },
  "nbformat": 4,

tvbwidgets/ui/connectivity_ipy/connectivity_widget.py

@@ -20,9 +20,9 @@
 from tvbwidgets.ui.connectivity_ipy.global_context import CONTEXT, ObservableAttrs
 
 DROPDOWN_KEY = 'dropdown'
-
 pyvista.set_jupyter_backend('trame')
 
+
 class CustomOutput(ipywidgets.Output):
     CONFIG = ConnectivityConfig()
 
@@ -118,10 +118,9 @@ def __init__(self, width, height, **kwargs):
         super(Connectivity3DViewer, self).__init__([self.output], *kwargs)
 
         self.__init_view_connectivity()
-        CONTEXT.observe(lambda *args: self.__init_view_connectivity(), ObservableAttrs.CONNECTIVITY)
+        CONTEXT.observe(lambda *args: self.__refresh_connectivity(), ObservableAttrs.CONNECTIVITY)
 
     def __init_view_connectivity(self):
-        self.output.plotter.clear()
         points, edges = self.__add_actors()
         points_toggle, edges_toggle = self.__init_controls()
 
@@ -143,13 +142,16 @@ def on_change_edges(change):
 
         edges_toggle.observe(on_change_edges, 'value')
 
-
         self.children = [
             ipywidgets.HBox(children=(
                 points_toggle, edges_toggle)),
             self.output]
         self.output.display_actor(points)
         self.output.display_actor(edges)
+
+    def __refresh_connectivity(self):
+        self.output.plotter.clear()
+        self.__init_view_connectivity()
         self.output.update_plot()
 
     def __init_controls(self):

tvbwidgets/ui/head_widget.py

@@ -16,7 +16,9 @@
 
 from tvbwidgets.ui.base_widget import TVBWidget
 from tvbwidgets.ui.widget_with_browser import TVBWidgetWithBrowser
+from tvbwidgets.core.logger.builder import get_logger
 
+LOGGER = get_logger(__name__)
 pyvista.set_jupyter_backend('trame')
 
 
@@ -85,6 +87,7 @@ def hide_actor(self, actor):
 
     def update_plot(self):
         with self:
+            LOGGER.info('Update plot.')
             self.clear_output(wait=True)
             self.plotter.show()