Merge pull request #957 from SoanKim/conflict_solved

Solved some issues
NeuromatchAcademy · Jul 8, 2024 · 8a38eb8 · 8a38eb8
2 parents 41faa2a + d159bb5
commit 8a38eb8
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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/projects/ReinforcementLearning/lunar_lander.ipynb b/projects/ReinforcementLearning/lunar_lander.ipynb
@@ -87,12 +87,11 @@
     "!pip install rarfile --quiet\n",
     "!pip install stable-baselines3[extra] --quiet\n",
     "!pip install ale-py --quiet\n",
+    "!pip install -q swig --quiet\n",
     "!pip install gym[box2d] --quiet\n",
     "!pip install pyvirtualdisplay --quiet\n",
     "!pip install pyglet --quiet\n",
     "!pip install pygame --quiet\n",
-    "!pip install minigrid --quiet\n",
-    "!pip install -q swig --quiet\n",
     "!pip install -q gymnasium[box2d] --quiet\n",
     "!pip install 'minigrid<=2.1.1' --quiet\n",
     "!pip3 install box2d-py --quiet"
@@ -383,7 +382,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/usr/local/lib/python3.10/dist-packages/gym/wrappers/monitoring/video_recorder.py:101: DeprecationWarning: \u001b[33mWARN: <class 'gym.wrappers.monitoring.video_recorder.VideoRecorder'> is marked as deprecated and will be removed in the future.\u001b[0m\n",
+      "/usr/local/lib/python3.10/dist-packages/gym/wrappers/monitoring/video_recorder.py:101: DeprecationWarning: \u001B[33mWARN: <class 'gym.wrappers.monitoring.video_recorder.VideoRecorder'> is marked as deprecated and will be removed in the future.\u001B[0m\n",
       "  logger.deprecation(\n"
      ]
     },
@@ -543,7 +542,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/usr/local/lib/python3.10/dist-packages/gym/wrappers/monitoring/video_recorder.py:101: DeprecationWarning: \u001b[33mWARN: <class 'gym.wrappers.monitoring.video_recorder.VideoRecorder'> is marked as deprecated and will be removed in the future.\u001b[0m\n",
+      "/usr/local/lib/python3.10/dist-packages/gym/wrappers/monitoring/video_recorder.py:101: DeprecationWarning: \u001B[33mWARN: <class 'gym.wrappers.monitoring.video_recorder.VideoRecorder'> is marked as deprecated and will be removed in the future.\u001B[0m\n",
       "  logger.deprecation(\n"
      ]
     },