Merge pull request #450 from AllenInstitute/dev

Dev

Author: rcpeene

.github/workflows/build.yml

@@ -26,20 +26,23 @@ jobs:
           ref: ${{ github.ref }}
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: '3.10.11'
 
       # - name: Upgrading pip
       #   run: pip install --upgrade pip
 
-      - name: Install deps
-        run: pip install cython numpy==1.26
+      # - name: Install deps
+      #   run: pip install cython numpy==1.26
 
       - name: Installing package
         run: pip install -e .
 
-      - name: Installing packages again (this prevents a weird error in cell matching nb)
+      # Some git-based dependencies (e.g., ophys-nway-matching) in requirements.txt
+      # are not reliably installed via `pip install -e .` due to setuptools limitations.
+      # This second install ensures all such dependencies are properly installed.
+      - name: Installing packages again (to avoid setuptools limitations)
         run: pip install -r requirements.txt
 
       - name: Installing build dependencies
@@ -53,6 +56,16 @@ jobs:
       - name: Printing environment
         run: pip freeze
 
+      - name: Testing Embargoed Notebooks
+        run: |
+          pytest --nbmake --nbmake-timeout=8000 -n=auto "./docs/embargoed"
+          rm ./docs/embargoed/*.nwb
+
+      - name: Testing Higher-Order Notebooks
+        run: |
+          pytest --nbmake --nbmake-timeout=8000 -n=auto "./docs/higher-order" --ignore docs/higher-order/behavioral_state.ipynb
+          rm ./docs/higher-order/*.nwb
+
       - name: Testing Basics Notebooks
         run: |
           pytest --nbmake --nbmake-timeout=100000 -n=auto "./docs/basics"
@@ -68,21 +81,11 @@ jobs:
           pytest --nbmake --nbmake-timeout=8000 -n=auto "./docs/first-order"
           rm ./docs/first-order/*.nwb
         
-      - name: Testing Higher-Order Notebooks
-        run: |
-          pytest --nbmake --nbmake-timeout=8000 -n=auto "./docs/higher-order"
-          rm ./docs/higher-order/*.nwb
-
       - name: Testing Project Notebooks
         run: |
           pytest --nbmake --nbmake-timeout=8000 -n=auto "./docs/projects"
           rm ./docs/projects/*.nwb
         
-      - name: Testing Embargoed Notebooks
-        run: |
-          pytest --nbmake --nbmake-timeout=8000 -n=auto "./docs/embargoed"
-          rm ./docs/embargoed/*.nwb        
-
       - name: Printing log
         run: |
           git config --global --add safe.directory /__w/openscope_databook/openscope_databook

.github/workflows/test.yml

@@ -21,12 +21,14 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9.13'
+
       # - name: Upgrading pip
       #   run: pip install --upgrade pip
 
-      - name: Install cython
-        run: pip install cython numpy==1.26
-
       - name: Installing requirements
         run: pip install -r ./requirements.txt
 

docs/embargoed/cell_matching.ipynb

@@ -44,7 +44,12 @@
    "source": [
     "import numpy as np\n",
     "\n",
-    "from ccfwidget import CCFWidget"
+    "from ccfwidget import CCFWidget\n",
+    "\n",
+    "# required because CCFwidgets is not using latest version of collections.abc\n",
+    "import collections\n",
+    "import collections.abc\n",
+    "collections.Sequence = collections.abc.Sequence"
    ]
   },
   {
@@ -72,13 +77,6 @@
    "execution_count": 4,
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "A newer version (0.62.2) of dandi/dandi-cli is available. You are using 0.61.2\n"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -157,31 +155,48 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "tags": [
+     "skip-execution"
+    ]
+   },
+   "outputs": [
+    {
+     "ename": "",
+     "evalue": "",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31mThe Kernel crashed while executing code in the current cell or a previous cell. \n",
+      "\u001b[1;31mPlease review the code in the cell(s) to identify a possible cause of the failure. \n",
+      "\u001b[1;31mClick <a href='https://aka.ms/vscodeJupyterKernelCrash'>here</a> for more info. \n",
+      "\u001b[1;31mView Jupyter <a href='command:jupyter.viewOutput'>log</a> for further details."
+     ]
+    }
+   ],
    "source": [
     "# the 'markers' parameter will expect an iterable where each point is represented as [x,y,z]\n",
     "ccf = CCFWidget(markers=[points])"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
-   "metadata": {},
+   "execution_count": 1,
+   "metadata": {
+    "tags": [
+     "skip-execution"
+    ]
+   },
    "outputs": [
     {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "683c4a818ea14ff69df65c1d0d563866",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "CCFWidget(children=(VBox(children=(Viewer(background=(0.85, 0.85, 0.85), camera=array([[ 1.3441567e+03, -2.172…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
+     "ename": "NameError",
+     "evalue": "name 'ccf' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[1;32mIn[1], line 1\u001b[0m\n\u001b[1;32m----> 1\u001b[0m \u001b[43mccf\u001b[49m\n",
+      "\u001b[1;31mNameError\u001b[0m: name 'ccf' is not defined"
+     ]
     }
    ],
    "source": [
@@ -191,7 +206,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -205,7 +220,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,

docs/visualization/visualize_neuropixels_probes.ipynb

@@ -1,28 +1,31 @@
 autograd==1.7
 ccfwidget==0.5.3
 cebra
-cython
 dandi==0.67.2
 elephant==1.1.1
 h5py>=3.8
 ipympl==0.9.4
 ipywidgets==7.8.1
 itkwidgets==0.32.6
 jupyter==1.0.0
+markupsafe==2.0.1
 matplotlib==3.6.2
 mpl-interactions==0.22.0
+nbmake==1.5.3
 neo==0.13.0
-numpy==1.26
+numcodecs==0.11.0
+numpy==1.26.0
 nwbwidgets
-ophys-nway-matching @ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458
+ophys-nway-matching @ git+https://github.com/AllenInstitute/ophys_nway_matching.git
 pandas==1.5.2
 Pillow==11
 pynwb==2.6.0
+pytest-xdist==3.5.0
 quantities==0.14.1
 remfile==0.1.10
-scikit-image==0.25
-scipy==1.15
-ssm @ git+https://github.com/lindermanlab/ssm
+scikit-image==0.18.3
+scipy==1.13.1
+# ssm @ git+https://github.com/lindermanlab/ssm
 statsmodels==0.14.0
 suite2p==0.14
 tensortools==0.4