Merge pull request #3 from CogStack/CU-2rjxfzj

upgrade medcat to 1.3.0

Author: baixiac

.github/workflows/main.yml

@@ -29,8 +29,11 @@ jobs:
       - name: Install dependencies
         run: |
           pip install -U pip
-          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
+      - name: Install IPython kernel
+        run: |
+          python -m ipykernel install --name smoketests
       - name: Smoke test tutorial
         run: |
           pytest --collect-only --nbmake ./notebooks/${{ matrix.part }}
-          pytest --nbmake --nbmake-timeout=1800 ./notebooks/${{ matrix.part }}
+          pytest --nbmake -n=auto --nbmake-kernel=smoketests --nbmake-timeout=1800 ./notebooks/${{ matrix.part }}

README.md

@@ -29,8 +29,14 @@ These tutorials expand upon specific aspects of the topics covered across the in
 
 ## Development/Editing
 
-Make sure [jupyter](https://docs.jupyter.org/en/latest/install.html) and [jq](https://stedolan.github.io/jq/download/) are installed and available on your path. Modifying the companion HTML version directly is discouraged and instead install the following pre-commit hook which will generate them during committing your change on .ipynb files:
+Make sure [jupyter](https://docs.jupyter.org/en/latest/install.html) and [jq](https://stedolan.github.io/jq/download/) are installed and available on your path. Modifying the companion HTML version directly is discouraged and instead install the following pre-commit hook which will generate them during committing your change on `.ipynb` files:
 ```
 git config --local core.hooksPath git-config/hooks
 ```
-To inspect change during code review, visit [Colab](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob) and select the target branch and tutorial. After it is opened, click `File | Revision history` and select   start and end revisions you are interested in.
+
+To inspect change during code review, visit [Colab](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob) and select the target branch and tutorial. After it is opened, click `File | Revision history` and select start and end revisions you are interested in.
+
+
+## Known Issues:
+* For ContextualVersionConflict on Google Colab, you need to restart the runtime and run the cell again.
+* The pre-commit hook requires nbconvert<6 and jinja2<=3.0.

git-config/hooks/pre-commit

@@ -4,22 +4,21 @@ set -eu
 
 if ! command -v jupyter &> /dev/null
 then
-    echo "Warning: Cannot find 'jupyter' on your path so the HTML version won't be created/updated automatically"
-    echo "Warning: Install 'jupyter' from https://docs.jupyter.org/en/latest/install.html to fix this"
+    echo "ERROR: Cannot find 'jupyter' on your path so the HTML version won't be created/updated automatically"
+    echo "ERROR: Install 'jupyter' from https://docs.jupyter.org/en/latest/install.html to fix this"
+    exit 1
 elif ! command -v jq &> /dev/null
 then
-    echo "Warning: Cannot find 'jq' on your path so the HTML version won't be created/updated automatically"
-    echo "Warning: Install 'jq' from https://stedolan.github.io/jq/download/ to fix this"
+    echo "ERROR: Cannot find 'jq' on your path so the HTML version won't be created/updated automatically"
+    echo "ERROR: Install 'jq' from https://stedolan.github.io/jq/download/ to fix this"
+    exit 1
 else
     notebook_paths=`git diff --cached --name-only --diff-filter=d | grep  .ipynb; echo ""`
 
     if [ ! -z "$notebook_paths" ]
     then
         for path in $notebook_paths
         do
-            # Remove widget states which would fail nbconvert
-            cat <<< `jq 'del(.metadata.widgets)' $path` > $path
-
             jupyter nbconvert --to html $path
             jupyter nbconvert --clear-output --inplace $path
             git add ${path/.ipynb/.html}