diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 45e0d066d..2ecdb6144 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -20,15 +20,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: ~/.cache
         key: ${{ runner.os }}-${{ matrix.python-version }}-ci-base
@@ -41,7 +41,7 @@ jobs:
       run: tox -e base
 
     - name: Coverage
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -54,15 +54,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: ~/.cache
         key: ${{ runner.os }}-${{ matrix.python-version }}-ci-petab
@@ -75,7 +75,7 @@ jobs:
       run: tox -e petab
 
     - name: Coverage
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -88,10 +88,10 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -129,15 +129,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: ~/.cache
         key: ${{ runner.os }}-${{ matrix.python-version }}-ci-optimize
@@ -150,7 +150,7 @@ jobs:
       run: tox -e optimize
 
     - name: Coverage
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -163,15 +163,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: ~/.cache
         key: ${{ runner.os }}-${{ matrix.python-version }}-ci-select
@@ -184,7 +184,7 @@ jobs:
       run: tox -e select
 
     - name: Coverage
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -197,15 +197,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: ~/.cache
         key: ${{ runner.os }}-${{ matrix.python-version }}-ci-quality
@@ -231,15 +231,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: ~/.cache
         key: ${{ runner.os }}-${{ matrix.python-version }}-ci-docs
@@ -262,15 +262,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: ~/.cache
         key: ${{ runner.os }}-${{ matrix.python-version }}-ci-notebooks1
@@ -290,15 +290,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: ~/.cache
         key: ${{ runner.os }}-${{ matrix.python-version }}-ci-notebooks2
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index b065a114e..1b2f31cbc 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -13,10 +13,10 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
diff --git a/test/petab/doc/example/tmp/benchmark-models b/test/petab/doc/example/tmp/benchmark-models
deleted file mode 160000
index d12485361..000000000
--- a/test/petab/doc/example/tmp/benchmark-models
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit d124853617dcda0b65bc23435afb7a19a94e526e