ci: use python to download checkpoint

.github/workflows/pytest-multiversion.yml

@@ -31,13 +31,11 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install -r requirements.txt
           python -m pip install -r requirements-dev.txt
-      - name: Test notebooks on Windows
-        if: ${{ matrix.os }} == windows-latest
+      - name: Test notebooks
         run: |
-          $env:PYDEVD_DISABLE_FILE_VALIDATION=1; python -m ipykernel install --user --name instanovo
-          pytest --nbmake "./notebooks"  --nbmake-kernel=instanovo --nbmake-timeout=10000
-      - name: Test notebooks on Linux
-        if: ${{ matrix.os }} != windows-latest
-        run: |
-          PYDEVD_DISABLE_FILE_VALIDATION=1 python -m ipykernel install --user --name instanovo
+          if [ ${{ matrix.os }} == 'windows-latest' ]; then
+            $env:PYDEVD_DISABLE_FILE_VALIDATION=1; python -m ipykernel install --user --name instanovo
+          else
+            PYDEVD_DISABLE_FILE_VALIDATION=1 python -m ipykernel install --user --name instanovo
+          fi
           pytest --nbmake "./notebooks"  --nbmake-kernel=instanovo --nbmake-timeout=10000

.gitignore

@@ -169,4 +169,5 @@ docs_public/
 logs/
 mlruns/
 notebooks/checkpoints
+notebooks/predictions.csv
 secrets/

notebooks/getting_started_with_instanovo.ipynb

@@ -98,7 +98,8 @@
     "import torch\n",
     "import os\n",
     "import numpy as np\n",
-    "import pandas as pd"
+    "import pandas as pd\n",
+    "import urllib.request"
    ]
   },
   {
@@ -127,8 +128,11 @@
    "outputs": [],
    "source": [
     "# Download checkpoint locally\n",
-    "!mkdir checkpoints/\n",
-    "!wget -nc https://github.com/instadeepai/InstaNovo/releases/download/0.1.4/instanovo_yeast.pt -P ./checkpoints/"
+    "os.makedirs('checkpoints', exist_ok=True)\n",
+    "url = \"https://github.com/instadeepai/InstaNovo/releases/download/0.1.4/instanovo_yeast.pt\"\n",
+    "file_path = os.path.join('checkpoints', 'instanovo_yeast.pt')\n",
+    "if not os.path.exists(file_path):\n",
+    "    urllib.request.urlretrieve(url, file_path)"
    ]
   },
   {
@@ -838,9 +842,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "instanovo-py3.8",
+   "display_name": "instanovo",
    "language": "python",
-   "name": "instanovo-py3.8"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -852,7 +856,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.9"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,