Fix workflow warnings with updates.

.github/workflows/ci.yml

@@ -37,9 +37,9 @@ jobs:
         run: |
           mainBranch=$(git symbolic-ref refs/remotes/origin/HEAD | cut -d '/' -f 4)
           mainBranchHeadRevision=$(git rev-parse refs/remotes/origin/${mainBranch})
-          echo "::set-output name=mainBranch::$mainBranch"
-          echo "::set-output name=mainBranchRef::refs/heads/$mainBranch"
-          echo "::set-output name=mainBranchHeadRevision::$mainBranchHeadRevision"
+          echo "mainBranch=$mainBranch" >> $GITHUB_OUTPUT
+          echo "mainBranchRef=refs/heads/$mainBranch" >> $GITHUB_OUTPUT
+          echo "mainBranchHeadRevision=$mainBranchHeadRevision" >> $GITHUB_OUTPUT
 
       - name: Checkout ref
         run: |
@@ -70,13 +70,13 @@ jobs:
       #############################################
       ## Install package and its dependencies
       #############################################
-      - name: Install Python
-        uses: actions/setup-python@v2
+      - name: Set up the python environment
+        uses: ./.github/actions/setup-poetry-env
         with:
-          python-version: '3.9'
+          python-version: "3.9"
 
       - name: Setup caching for Python packages
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /opt/hostedtoolcache/Python
           key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
@@ -131,7 +131,8 @@ jobs:
             version=$(python -c "import glob; import importlib.util; version_filename = glob.glob('**/_version.py', recursive=True)[0]; spec = importlib.util.spec_from_file_location('module.name', version_filename); module = importlib.util.module_from_spec(spec); spec.loader.exec_module(module); print(module.__version__)")
           fi
 
-          echo "::set-output name=version::$version"
+          echo "version=$version" >> $GITHUB_OUTPUT
+          echo "version=$version"
 
       - id: get-docker-image-tag
         name: Determine Docker image tag
@@ -145,11 +146,11 @@ jobs:
           IMAGE_BASE_URL=$(jq -r '.image.url' biosimulators.json | cut -d : -f 1)
           DOCKER_REGISTRY=$(echo $IMAGE_BASE_URL | cut -d / -f 1)
 
-          echo "::set-output name=simulatorId::${SIMULATOR_ID}"
-          echo "::set-output name=simulatorVersion::${SIMULATOR_VERSION}"
-          echo "::set-output name=simulatorName::${SIMULATOR_NAME}"
-          echo "::set-output name=dockerImageBaseUrl::${IMAGE_BASE_URL}"
-          echo "::set-output name=dockerRegistry::${DOCKER_REGISTRY}"
+          echo "simulatorId=${SIMULATOR_ID}" >> $GITHUB_OUTPUT
+          echo "simulatorVersion=${SIMULATOR_VERSION}" >> $GITHUB_OUTPUT
+          echo "simulatorName=${SIMULATOR_NAME}" >> $GITHUB_OUTPUT
+          echo "dockerImageBaseUrl=${IMAGE_BASE_URL}" >> $GITHUB_OUTPUT
+          echo "dockerRegistry=${DOCKER_REGISTRY}" >> $GITHUB_OUTPUT
 
       - name: Build Docker image
         run: |
@@ -243,7 +244,8 @@ jobs:
             fi
           fi
 
-          echo "::set-output name=release::$release"
+          echo "release=$release" >> $GITHUB_OUTPUT
+          echo "release=$release"
 
       # If new tag, commit and push documentation
       - id: commit-docs
@@ -267,7 +269,7 @@ jobs:
           else
             docsChanged=0
           fi
-          echo "::set-output name=docsChanged::$docsChanged"
+          echo "docsChanged=$docsChanged" >> $GITHUB_OUTPUT
 
       - name: Push the compiled documentation
         if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1' && steps.commit-docs.outputs.docsChanged == '1'