Merge pull request #193 from AllenInstitute/dev

Dev
AllenInstitute · Apr 20, 2023 · 753789b · 753789b
2 parents 8ff3811 + cbe1711
commit 753789b
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Showing 23 changed files with 1,994 additions and 1,653 deletions.
diff --git a/.binder/postBuild b/.binder/postBuild
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -33,10 +33,9 @@ jobs:
           pip install jupyter
           pip install -U jupyter-book
           pip install nbmake
-          pip install pytest-xdist
 
       - name: Testing notebooks
-        run: pytest --nbmake --nbmake-timeout=5000 -n=auto "./docs"
+        run: pytest --nbmake --nbmake-timeout=5000 "./docs"
 
       - name: Build Jupyter book
         run: |

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -32,7 +32,6 @@ jobs:
           pip install jupyter
           pip install -U jupyter-book
           pip install nbmake
-          pip install pytest-xdist
       
       - name: Getting changed files
         id: changed_files
@@ -41,5 +40,6 @@ jobs:
           filter: "*.ipynb"
 
       - name: Testing notebooks
-        run: pytest --nbmake --nbmake-timeout=5000 -n=auto ${{ steps.changed_files.outputs.added_modified }}
+        if: ${{ steps.changed_files.outputs.added_modified }} != ""
+        run: pytest --nbmake --nbmake-timeout=5000 ${{ steps.changed_files.outputs.added_modified }}
 
diff --git a/.binder/apt.txt → apt.txt b/.binder/apt.txt → apt.txt
diff --git a/docs/basics/download_nwb.ipynb b/docs/basics/download_nwb.ipynb
@@ -20,6 +20,20 @@
   {
    "cell_type": "code",
    "execution_count": 1,
+   "id": "014235db",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "### if running on Google Colab, run this cell once, then restart the runtime and run the rest of the notebook\n",
+    "import os\n",
+    "if \"COLAB_GPU\" in os.environ:\n",
+    "    !wget https://raw.githubusercontent.com/AllenInstitute/openscope_databook/main/requirements.txt\n",
+    "    %pip install -r requirements.txt --user"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
    "id": "8f34eecf",
    "metadata": {},
    "outputs": [],
@@ -38,7 +52,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "id": "67536d37",
    "metadata": {},
    "outputs": [],
@@ -51,17 +65,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "id": "a309c067",
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "A newer version (0.46.6) of dandi/dandi-cli is available. You are using 0.46.3\n"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -91,7 +98,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "id": "fe9aa40c",
    "metadata": {},
    "outputs": [],
@@ -101,7 +108,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "id": "c176c129",
    "metadata": {},
    "outputs": [],
@@ -112,7 +119,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 7,
    "id": "a110beeb",
    "metadata": {},
    "outputs": [
@@ -143,10 +150,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "id": "1c42049e",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Downloaded directory to ./000021\n"
+     ]
+    }
+   ],
    "source": [
     "# patience isn't just a virtue, it's a requirement\n",
     "my_dandiset.download_directory(\"./\", f\"{download_loc}/{dandiset_id}\")\n",