Install all extras for upstream linkml tests (fix pandera tests)

Author: dalito

.github/workflows/test-upstream.yaml

@@ -42,7 +42,7 @@ jobs:
         run: |
           set +e
           set +o pipefail
-          
+
           UPSTREAM_BRANCH=$( \
             echo "$PR_BODY" | \
             head -2 | \
@@ -52,12 +52,12 @@ jobs:
           )
           echo "Got upstream branch:"
           echo $UPSTREAM_BRANCH
-          
+
           if [[ -z "$UPSTREAM_BRANCH" ]]; then
             echo "Using main as default"
             UPSTREAM_BRANCH="main"
           fi
-          
+
           UPSTREAM_REPO=$( \
             echo "$PR_BODY" | \
             head -2 | \
@@ -67,7 +67,7 @@ jobs:
           )
           echo "Got upstream repo:"
           echo $UPSTREAM_REPO
-          
+
           if [[ -z "$UPSTREAM_REPO" ]]; then
             echo "Using linkml/linkml as default"
             UPSTREAM_REPO="linkml/linkml"
@@ -128,11 +128,6 @@ jobs:
           path: linkml/.venv
           key: venv-${{ matrix.python-version }}-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
 
-      # make extra sure we're removing any old version of linkml-runtime that exists
-      - name: uninstall potentially cached linkml-runtime
-        working-directory: linkml
-        run: poetry run pip uninstall -y linkml-runtime
-
       # we are not using linkml-runtime's lockfile, but simulating what will happen
       # when we merge this and update linkml's lockfile
       - name: add linkml-runtime to lockfile
@@ -145,7 +140,7 @@ jobs:
       # the cache will still speedup the rest of the installation
       - name: install linkml
         working-directory: linkml
-        run: poetry install --no-interaction -E tests
+        run: poetry sync --no-interaction --all-extras
 
       - name: print linkml-runtime version
         working-directory: linkml