Merge branch 'hot-fixes' into Knowledge_Extraction_Fix

NeuromatchAcademy · Jul 9, 2024 · 3f18cb9 · 3f18cb9
2 parents 21e353e + 942e35c
commit 3f18cb9
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diff --git a/.github/workflows/notebook-pr.yaml b/.github/workflows/notebook-pr.yaml
@@ -15,7 +15,22 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-
+      - name: Free up disk space
+        uses: jlumbroso/free-disk-space@main
+        with:
+          # this might remove tools that are actually needed,
+          # if set to "true" but frees about 6 GB
+          tool-cache: false
+
+          # all of these default to true, but feel free to set to
+          # "false" if necessary for your workflow
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          docker-images: true
+          swap-storage: true
+
       - name: Checkout
         uses: actions/checkout@v3
         with:
@@ -48,6 +63,7 @@ jobs:
       - name: Install dependencies
         if: "!contains(env.COMMIT_MESSAGE, 'skip ci') && contains(env.COMMIT_MESSAGE, 'ci:execute')"
         run: |
+          sudo apt-get update && sudo apt install xvfb -y
           python -m pip install --upgrade pip wheel
           pip install -r requirements.txt
           pip install jupyter_client==7.3.5  # downgrade jupyter-client to fix hangs

diff --git a/projects/NaturalLanguageProcessing/sentiment_analysis.ipynb b/projects/NaturalLanguageProcessing/sentiment_analysis.ipynb
diff --git a/projects/Neuroscience/blurry_vision.ipynb b/projects/Neuroscience/blurry_vision.ipynb
@@ -60,7 +60,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "  Building wheel for torch-intermediate-layer-getter (setup.py) ... \u001b[?25l\u001b[?25hdone\n"
+      "  Building wheel for torch-intermediate-layer-getter (setup.py) ... \u001B[?25l\u001B[?25hdone\n"
      ]
     }
    ],
@@ -1877,7 +1877,7 @@
     "# # Download the Data\n",
     "# if \"cats-and-dogs.zip\" not in os.listdir():\n",
     "#   !wget --no-check-certificate \\\n",
-    "#     \"https://download.microsoft.com/download/3/E/1/3E1C3F21-ECDB-4869-8368-6DEBA77B919F/kagglecatsanddogs_3367a.zip\" \\\n",
+    "#     \"https://download.microsoft.com/download/3/E/1/3E1C3F21-ECDB-4869-8368-6DEBA77B919F/kagglecatsanddogs_5340.zip\" \\\n",
     "#     -O \"cats-and-dogs.zip\"\n",
     "\n",
     "# local_zip = 'cats-and-dogs.zip'\n",

diff --git a/projects/Neuroscience/cellular_segmentation.ipynb b/projects/Neuroscience/cellular_segmentation.ipynb
@@ -304,14 +304,14 @@
     "labels_train = np.zeros((len(masks_train), 2,\n",
     "                         masks_train.shape[-2],\n",
     "                         masks_train.shape[-1]),\n",
-    "                        np.long)\n",
+    "                        np.longlong)\n",
     "labels_train[:, 0] = masks_train == 0\n",
     "labels_train[:, 1] = masks_train > 0\n",
     "\n",
     "labels_test = np.zeros((len(masks_test), 2,\n",
     "                        masks_test.shape[-2],\n",
     "                        masks_test.shape[-1]),\n",
-    "                       np.long)\n",
+    "                       np.longlong)\n",
     "labels_test[:, 0] = masks_test == 0\n",
     "labels_test[:, 1] = masks_test > 0"
    ]
@@ -831,12 +831,15 @@
     "    for ibatch in np.arange(0, n_train, batch_size):\n",
     "      # augment the data\n",
     "      inds = np.arange(ibatch, min(n_train, ibatch+batch_size))\n",
+    "      train_data = train_data.astype(np.float32)\n",
+    "      train_labels = train_labels.astype(np.float32)\n",
     "      imgs, lbls, _ = random_rotate_and_resize(train_data[inds],\n",
     "                                               train_labels[inds])\n",
     "\n",
     "      # transfer to torch + GPU\n",
     "      imgs = torch.from_numpy(imgs).to(device=device)\n",
     "      lbls = torch.from_numpy(lbls).to(device=device)\n",
+    "      lbls = lbls.long()\n",
     "\n",
     "      # compute the loss\n",
     "      y = net(imgs)\n",
@@ -1379,7 +1382,7 @@
     "from tifffile import imread\n",
     "\n",
     "fname = \"gt1.tif\"\n",
-    "url = \"https://www.suite2p.org/test_data/gt1.tif\"\n",
+    "url = \"https://www.suite2p.org/test_data/gt1.tif\" # This URL does not exist.\n",
     "\n",
     "if not os.path.isfile(fname):\n",
     "  try:\n",

diff --git a/projects/ReinforcementLearning/human_rl.ipynb b/projects/ReinforcementLearning/human_rl.ipynb
@@ -64,24 +64,24 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\u001b[31mERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.\n",
-      "numba 0.56.4 requires numpy<1.24,>=1.18, but you have numpy 1.25.1 which is incompatible.\u001b[0m\u001b[31m\n",
-      "\u001b[0m\u001b[31mERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.\n",
-      "chex 0.1.81 requires numpy>=1.25.0, but you have numpy 1.23.3 which is incompatible.\u001b[0m\u001b[31m\n",
-      "\u001b[0m"
+      "\u001B[31mERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.\n",
+      "numba 0.56.4 requires numpy<1.24,>=1.18, but you have numpy 1.25.1 which is incompatible.\u001B[0m\u001B[31m\n",
+      "\u001B[0m\u001B[31mERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.\n",
+      "chex 0.1.81 requires numpy>=1.25.0, but you have numpy 1.23.3 which is incompatible.\u001B[0m\u001B[31m\n",
+      "\u001B[0m"
      ]
     }
    ],
    "source": [
     "# @title Install dependencies\n",
-    "!pip install jedi --quiet\n",
-    "!pip install --upgrade pip setuptools wheel --quiet\n",
-    "!pip install dm-acme[jax] --quiet\n",
-    "!pip install dm-sonnet --quiet\n",
-    "!pip install trfl --quiet\n",
-    "!pip install numpy==1.23.3 --quiet --ignore-installed\n",
-    "!pip uninstall seaborn -y --quiet\n",
-    "!pip install seaborn --quiet"
+    "!pip install jedi --quiet --root-user-action=ignore\n",
+    "!pip install --upgrade pip setuptools wheel --quiet --root-user-action=ignore\n",
+    "!pip install dm-acme[jax] --quiet --root-user-action=ignore\n",
+    "!pip install dm-sonnet --quiet --root-user-action=ignore\n",
+    "!pip install trfl --quiet --root-user-action=ignore\n",
+    "!pip install numpy==1.23.3 --quiet --ignore-installed --root-user-action=ignore\n",
+    "!pip uninstall seaborn -y --quiet --root-user-action=ignore\n",
+    "!pip install seaborn --quiet --root-user-action=ignore"
    ]
   },
   {

diff --git a/requirements.txt b/requirements.txt
@@ -10,3 +10,6 @@ torchvision
 pathlib
 xkcd
 decorator==5.0.9
+pyvirtualdisplay
+tensorboard
+moviepy