diff --git a/.github/actions/setup-poetry-env/action.yml b/.github/actions/setup-poetry-env/action.yml
new file mode 100644
index 0000000..550aa12
--- /dev/null
+++ b/.github/actions/setup-poetry-env/action.yml
@@ -0,0 +1,42 @@
+name: "setup-poetry-env"
+description: "Composite action to setup the Python and poetry environment."
+
+inputs:
+  python-version:
+    required: false
+    description: "The python version to use"
+    default: "3.11"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Set up python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install Poetry
+      env:
+        POETRY_VERSION: "1.7.1"
+      run: curl -sSL https://install.python-poetry.org | python - -y
+      shell: bash
+
+    - name: Add Poetry to Path
+      run: echo "$HOME/.local/bin" >> $GITHUB_PATH
+      shell: bash
+
+#    - name: Configure Poetry virtual environment in project
+#      run: poetry config virtualenvs.in-project true
+#      shell: bash
+
+    - name: Load cached venv
+      id: cached-poetry-dependencies
+      uses: actions/cache@v4
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ inputs.python-version }}-${{ hashFiles('poetry.lock') }}
+
+    - name: Install dependencies
+      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      run: poetry install --no-interaction
+      shell: bash
\ No newline at end of file
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a5651f7..182d4a2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,13 +1,14 @@
 name: Continuous integration
 
 on:
-  - push
+  push:
+  pull_request:
 
 jobs:
   getVersionNumber:
     name: Get version number
-    if: startsWith(github.ref, 'refs/tags/') && github.actor != 'biosimulators-daemon' && !contains(github.event.head_commit.message, '[skip ci]')
-    runs-on: ubuntu-20.04
+    if: "startsWith(github.ref, 'refs/tags/') && github.actor != 'allcontributors' && !contains(github.event.head_commit.message, '[skip ci]')"
+    runs-on: ubuntu-22.04
     outputs:
       version: ${{ steps.get-version-number.outputs.version }}
     steps:
@@ -18,15 +19,21 @@ jobs:
         run: |
           version="${TAG/refs\/tags\//}"
           echo "version=$version" >> $GITHUB_OUTPUT
-          echo "version=$version"
 
   build:
     name: Lint, test, and compile documentation
-    if: github.actor != 'biosimulators-daemon' && !contains(github.event.head_commit.message, '[skip ci]')
-    runs-on: ubuntu-20.04
+    if: "!contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'"
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        python-version: [ "3.10" ]
+      fail-fast: false
+    defaults:
+      run:
+        shell: bash
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
 
@@ -39,17 +46,9 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v2
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
-      - name: Setup pip cache
-        uses: actions/cache@v2
-        with:
-          path: /opt/hostedtoolcache/Python
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Install pip
+      - name: Install pip and setuptools
         run: |
           python -m pip install pip==23.0.0
           python -m pip install pip==23.0.0
@@ -68,23 +67,23 @@ jobs:
 
       - name: Install XPP
         run: |
-          sudo apt-get install -y --no-install-recommends xppaut
+          sudo apt-get install -y --no-install-recommends wget make gcc libx11-dev libc6-dev xppaut
 
       - name: Install Singularity # to validate that the Docker image can be converted into a Singularity image
         uses: eWaterCycle/setup-singularity@v6
 
       # install package
-      - name: Install the package
-        run: |
-          python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy
-          python -m pip install .[all]
+      - name: Set up the environment
+        uses: ./.github/actions/setup-poetry-env
+        with:
+          python-version: ${{ matrix.python-version }}
 
       # zip COMBINE/OMEX archives
       - name: Zip COMBINE/OMEX archives
         run: |
           sudo apt-get update -y
           sudo apt-get install -y --no-install-recommends zipcmp
-          python scripts/zip_examples.py
+          poetry run python scripts/zip_examples.py
 
       - id: commit-archives
         name: Commit zipped COMBINE/OMEX archives
@@ -116,25 +115,18 @@ jobs:
           branch: ${{ steps.commit-archives.outputs.branch }}
 
       # lint
-      - name: Install flake8
-        run: python -m pip install flake8
-
       - name: Lint the package
-        run: python -m flake8
-
-      # test and upload coverage report to Codecov
-      - name: Install pytest
-        run: python -m pip install pytest pytest-cov
-
-      - name: Install the requirements for the tests
-        run: python -m pip install .[tests]
+        run: poetry run python -m flake8 $GITHUB_WORKSPACE/biosimulators_test_suite
 
       - name: Run the tests
-        # env:
-        #   BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/ # uncomment to run tests using the dev deployment
         uses: GabrielBB/xvfb-action@v1
+        env:
+          MPLBACKEND: PDF
+          # BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/  # uncomment to execute tests with the dev deployment
         with:
-          run: python -m pytest tests/ --cov=./biosimulators_test_suite --cov-report=xml
+          run: |
+            poetry run python -m pip install --upgrade setuptools
+            poetry run python -m pytest tests/ --cov=./biosimulators_test_suite --cov-report=xml
 
       - name: Upload the coverage report to Codecov
         uses: codecov/codecov-action@v2
@@ -145,26 +137,31 @@ jobs:
 
       # compile documentation
       - name: Install the requirements for compiling the documentation
-        run: python -m pip install -r docs-src/requirements.txt
+        run: poetry install --with docs
 
       - name: Compile the documentation
         run: |
-          sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
+          poetry run sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
           mkdir -p docs-src/_static
-          sphinx-build docs-src docs
+          poetry run sphinx-build docs-src docs
+
+      - name: Setup tmate session 3 (if failed)
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ failure() }}
+        timeout-minutes: 40
 
   release:
     name: Release a new version
     needs: [getVersionNumber, build]
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     outputs:
       docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
-          branch: deploy
+          ref: dev
 
       - name: Configure Git
         run: |
@@ -172,65 +169,43 @@ jobs:
           git config --local user.name "biosimulatorsdaemon"
           git config pull.rebase false
 
-      - name: Install Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.9'
-
-      - name: Setup pip cache
-        uses: actions/cache@v2
+      - name: Set up the environment
+        uses: ./.github/actions/setup-poetry-env
         with:
-          path: /opt/hostedtoolcache/Python
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Install pip and setuptools
-        run: |
-          #python -m pip install --upgrade pip
-          python -m pip install --upgrade setuptools
-
-      # install package
-      - name: Install the package
-        run: |
-          python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy
-          python -m pip install .[all]
+          python-version: ${{ matrix.python-version }}
 
       # compile and push documentation
       - name: Install the requirements for compiling the documentation
-        run: python -m pip install -r docs-src/requirements.txt
+        run: poetry install --with docs
 
       - name: Compile the documentation
         run: |
-          sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
+          poetry run sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
           mkdir -p docs-src/_static
-          sphinx-build docs-src docs
+          poetry run sphinx-build docs-src docs
 
       - id: commit-docs
         name: Commit the compiled documentation
         run: |
-          git stash || true
+          git stash
           git pull
           set +e
-          git stash pop || true
+          git stash pop
           git add docs
-          git add docs-src
-          git commit -m "chore: Updating compiled documentation [skip ci]"
-          git checkout .
-          git clean -f -d
+          git commit -m "chore: Updated compiled documentation [skip ci]"
           if [[ $? = 0 ]]; then
-            docsChanged=1
+            changed=1
           else
-            docsChanged=0
+            changed=0
           fi
-          echo "docsChanged=$docsChanged" >> $GITHUB_OUTPUT
+          echo "changed=$changed" >> $GITHUB_OUTPUT
 
       - name: Push the compiled documentation
-        if: steps.commit-docs.outputs.docsChanged == '1'
+        if: steps.commit-identifiers-namespaces.outputs.changed == '1' || steps.commit-docs.outputs.changed == '1'
         uses: ad-m/github-push-action@master
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          branch: deploy
+          branch: dev
 
       # Create GitHub release
       - name: Create GitHub release
@@ -242,26 +217,12 @@ jobs:
           release_name: Release ${{ needs.getVersionNumber.outputs.version }}
 
       # Create PyPI release
-      - name: Install pandoc
-        run: |
-          sudo apt-get update -y
-          sudo apt-get install -y pandoc
-
-      - name: Convert README to .rst format
-        run: pandoc --from=gfm --output=README.rst --to=rst README.md
-
-      - name: Install twine
-        run: |
-          python -m pip install wheel twine
-
       - name: Create packages to upload to PyPI
         run: |
-          python setup.py sdist
-          python setup.py bdist_wheel
+          poetry build
 
       - name: Upload packages to PyPI
         env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+          POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
         run: |
-          twine upload dist/*
+          poetry publish --no-interaction --username __token__ --password $POETRY_PYPI_TOKEN_PYPI
diff --git a/.gitignore b/.gitignore
index 037e82f..ae2df6d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,3 +21,7 @@ docs/.buildinfo
 docs/.doctrees/
 docs/_raw_sources/
 docs/_sources/
+
+# Development IDEs
+.idea
+.idea/*
\ No newline at end of file
diff --git a/Pipfile b/Pipfile
new file mode 100644
index 0000000..3dcc6f4
--- /dev/null
+++ b/Pipfile
@@ -0,0 +1,20 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+biosimulators-utils = {version = ">=0.1.175", extras = ["bngl", "cellml", "containers", "lems", "neuroml", "sbml", "smoldyn"]}
+cement = "<=3.0.6"
+docker = "<=5.0.3"
+natsort = "<=8.1.0"
+pypdf2 = "<=2.8.1"
+python-dateutil = "<=2.8.2"
+pyyaml = "<=5.3.1"
+simplejson = "<=3.16.0"
+termcolor = "<=1.1.0"
+
+[dev-packages]
+
+[requires]
+python_version = "3.9"
diff --git a/Pipfile.lock b/Pipfile.lock
new file mode 100644
index 0000000..60a34e5
--- /dev/null
+++ b/Pipfile.lock
@@ -0,0 +1,2551 @@
+{
+    "_meta": {
+        "hash": {
+            "sha256": "3cb1f6518b77800369d535958a5c5ae74dc5900debb64d8d1356e4c407914093"
+        },
+        "pipfile-spec": 6,
+        "requires": {
+            "python_version": "3.9"
+        },
+        "sources": [
+            {
+                "name": "pypi",
+                "url": "https://pypi.org/simple",
+                "verify_ssl": true
+            }
+        ]
+    },
+    "default": {
+        "airspeed": {
+            "hashes": [
+                "sha256:f9d8e1042aaebca9c304b7d14662fbd30a83d7a00cd9a7b7ca5c45c280adf058"
+            ],
+            "version": "==0.5.20"
+        },
+        "anyio": {
+            "hashes": [
+                "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421",
+                "sha256:fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3"
+            ],
+            "markers": "python_full_version >= '3.6.2'",
+            "version": "==3.6.2"
+        },
+        "appdirs": {
+            "hashes": [
+                "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41",
+                "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"
+            ],
+            "version": "==1.4.4"
+        },
+        "argon2-cffi": {
+            "hashes": [
+                "sha256:8c976986f2c5c0e5000919e6de187906cfd81fb1c72bf9d88c01177e77da7f80",
+                "sha256:d384164d944190a7dd7ef22c6aa3ff197da12962bd04b17f64d4e93d934dba5b"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==21.3.0"
+        },
+        "argon2-cffi-bindings": {
+            "hashes": [
+                "sha256:20ef543a89dee4db46a1a6e206cd015360e5a75822f76df533845c3cbaf72670",
+                "sha256:2c3e3cc67fdb7d82c4718f19b4e7a87123caf8a93fde7e23cf66ac0337d3cb3f",
+                "sha256:3b9ef65804859d335dc6b31582cad2c5166f0c3e7975f324d9ffaa34ee7e6583",
+                "sha256:3e385d1c39c520c08b53d63300c3ecc28622f076f4c2b0e6d7e796e9f6502194",
+                "sha256:58ed19212051f49a523abb1dbe954337dc82d947fb6e5a0da60f7c8471a8476c",
+                "sha256:5e00316dabdaea0b2dd82d141cc66889ced0cdcbfa599e8b471cf22c620c329a",
+                "sha256:603ca0aba86b1349b147cab91ae970c63118a0f30444d4bc80355937c950c082",
+                "sha256:6a22ad9800121b71099d0fb0a65323810a15f2e292f2ba450810a7316e128ee5",
+                "sha256:8cd69c07dd875537a824deec19f978e0f2078fdda07fd5c42ac29668dda5f40f",
+                "sha256:93f9bf70084f97245ba10ee36575f0c3f1e7d7724d67d8e5b08e61787c320ed7",
+                "sha256:9524464572e12979364b7d600abf96181d3541da11e23ddf565a32e70bd4dc0d",
+                "sha256:b2ef1c30440dbbcba7a5dc3e319408b59676e2e039e2ae11a8775ecf482b192f",
+                "sha256:b746dba803a79238e925d9046a63aa26bf86ab2a2fe74ce6b009a1c3f5c8f2ae",
+                "sha256:bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3",
+                "sha256:bd46088725ef7f58b5a1ef7ca06647ebaf0eb4baff7d1d0d177c6cc8744abd86",
+                "sha256:ccb949252cb2ab3a08c02024acb77cfb179492d5701c7cbdbfd776124d4d2367",
+                "sha256:d4966ef5848d820776f5f562a7d45fdd70c2f330c961d0d745b784034bd9f48d",
+                "sha256:e415e3f62c8d124ee16018e491a009937f8cf7ebf5eb430ffc5de21b900dad93",
+                "sha256:ed2937d286e2ad0cc79a7087d3c272832865f779430e0cc2b4f3718d3159b0cb",
+                "sha256:f1152ac548bd5b8bcecfb0b0371f082037e47128653df2e8ba6e914d384f3c3e",
+                "sha256:f9f8b450ed0547e3d473fdc8612083fd08dd2120d6ac8f73828df9b7d45bb351"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==21.2.0"
+        },
+        "argparse": {
+            "hashes": [
+                "sha256:62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4",
+                "sha256:c31647edb69fd3d465a847ea3157d37bed1f95f19760b11a47aa91c04b666314"
+            ],
+            "version": "==1.4.0"
+        },
+        "arrow": {
+            "hashes": [
+                "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1",
+                "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==1.2.3"
+        },
+        "asttokens": {
+            "hashes": [
+                "sha256:4622110b2a6f30b77e1473affaa97e711bc2f07d3f10848420ff1898edbe94f3",
+                "sha256:6b0ac9e93fb0335014d382b8fa9b3afa7df546984258005da0b9e7095b3deb1c"
+            ],
+            "version": "==2.2.1"
+        },
+        "attrs": {
+            "hashes": [
+                "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04",
+                "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==23.1.0"
+        },
+        "backcall": {
+            "hashes": [
+                "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e",
+                "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"
+            ],
+            "version": "==0.2.0"
+        },
+        "beautifulsoup4": {
+            "hashes": [
+                "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da",
+                "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"
+            ],
+            "markers": "python_full_version >= '3.6.0'",
+            "version": "==4.12.2"
+        },
+        "bionetgen": {
+            "hashes": [
+                "sha256:239aff646e3b575c251fdb30f7a8d803277588c2cecc0beb1b377d31d62c59d9",
+                "sha256:a1e6feba8d8b58dfa24b009cac2466e496019869cbc76ad2a8e611a3ab55e953"
+            ],
+            "version": "==0.8.0"
+        },
+        "biopython": {
+            "hashes": [
+                "sha256:11d673698b3d0d6589292ea951fb62cb24ea27d273eca0d08dbbd956690f97f5",
+                "sha256:2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0",
+                "sha256:2f9cfaf16d55ab80d514e7aebe5710dabe4e4ff47ede851031202e33b3249da3",
+                "sha256:35506e39822c52d11cf09a3951e82375ca1bb9303960b4286acf02c9a6f6c4cc",
+                "sha256:3b36ba1bf6395c09a365c53530c9d71f3617763fa2c1d452b3d8948368c0f1de",
+                "sha256:655df416936662c0c8a06a549cb25e1560e1fea5067d850f34fb714b8a3fae6c",
+                "sha256:65b93b513ce9dd7b2ce058720eadf42cd03f312db3409356efeb93123d1320aa",
+                "sha256:6ebfbce0d91796c7aef422ee9dffe8827e07e5abaa94545e006f1f20e965c80b",
+                "sha256:762c6c43a8486b5fcd07f136a3217b87d24755618b9ea9da1f17124ff44c2ad6",
+                "sha256:793c42a376cd63f62f8a088ce39b7dc6b5c55e4e9031d887c434de1595bfa4b8",
+                "sha256:7a168709694e10b338718c18d967edd5b56c237dc88642c22275796007a70000",
+                "sha256:7c5c07123ff5f44c9e6b5369df854a38afd3c0c50ef58498a0ae8f7eb799f3e8",
+                "sha256:811796f8d222aa3869a50e31e54ce62b69106b47cd8bb06934867c0d843297b5",
+                "sha256:8bb0c690c7368f255ed45236bf0f5464b476b8c083c8f634533921af78278261",
+                "sha256:919a2c583cabf9c96d2ae4e1245a6b0376932fb342aca302a0fc198b71ab3275",
+                "sha256:97cbdbed01b2512471f36c74b91658d1dfbdcbf39bc038f6ce5a41c3e60a8fc6",
+                "sha256:9ba33244f0eff830beaa7240065bdb5095d96fded6599b76bbb9ddab45cd2bbd",
+                "sha256:a51d9c1d1b4b634447535da74a644fae59bc234fbbf9001e2dc6b6fbabb98019",
+                "sha256:b09efcb4733c8770f25eab5fe555a96a08f5ab9e1bc36939e08ebf2ffbf3e0f1",
+                "sha256:b37c0d24191e5c96ca02415a5188551980c83a0d518bbc4ffe3c9a5d1fe0ee81",
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+                "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"
+            ],
+            "version": "==0.5.1"
+        },
+        "websocket-client": {
+            "hashes": [
+                "sha256:3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40",
+                "sha256:cdf5877568b7e83aa7cf2244ab56a3213de587bbe0ce9d8b9600fc77b455d89e"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==1.5.1"
+        },
+        "xmltodict": {
+            "hashes": [
+                "sha256:341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56",
+                "sha256:aa89e8fd76320154a40d19a0df04a4695fb9dc5ba977cbb68ab3e4eb225e7852"
+            ],
+            "markers": "python_version >= '3.4'",
+            "version": "==0.13.0"
+        },
+        "yamldown": {
+            "hashes": [
+                "sha256:6e9723d479739efa9423834fad005b31220b097ad42606dd0c8159e10677f27a",
+                "sha256:936ad7bdbde725d0bd3adb77236aae4eb75388619f31232595f7dd45f7006598",
+                "sha256:ec1056e5ec3c47a7c14f69d343b73256ad12751361f1a833805a8ee722cf883c"
+            ],
+            "version": "==0.1.8"
+        },
+        "zipp": {
+            "hashes": [
+                "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b",
+                "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"
+            ],
+            "markers": "python_version < '3.10'",
+            "version": "==3.15.0"
+        }
+    },
+    "develop": {}
+}
diff --git a/biosimulators_test_suite/_version.py b/biosimulators_test_suite/_version.py
index 81cb954..b650ceb 100644
--- a/biosimulators_test_suite/_version.py
+++ b/biosimulators_test_suite/_version.py
@@ -1 +1 @@
-__version__ = '0.1.88'
+__version__ = '0.2'
diff --git a/biosimulators_test_suite/config.py b/biosimulators_test_suite/config.py
index 0d51e08..35c6e20 100644
--- a/biosimulators_test_suite/config.py
+++ b/biosimulators_test_suite/config.py
@@ -7,6 +7,7 @@
 """
 
 import os
+from typing import Union
 
 
 class Config(object):
@@ -36,30 +37,27 @@ class Config(object):
         runbiosimulations_api_endpoint (:obj:`str`): Base URL for the runBioSimulations API
         test_case_timeout (:obj:`int`): time out for test cases in seconds
         user_to_exec_in_simulator_containers (:obj:`str` or :obj:`None`): user id or name to execute calls inside simulator containers
-
             * Use ``_CURRENT_USER_`` to indicate that the Docker container should execute commands as the current user (``os.getuid()``)
             * Use the format ``<name|uid>[:<group|gid>]`` to indicate any other user/group that the Docker container should use to
               execute commands
-
         singularity_image_dirname (:obj:`str`): directory to save Singularity images
     """
 
     def __init__(self,
-                 pull_docker_image=None, docker_hub_username=None, docker_hub_token=None,
-                 biosimulators_auth_endpoint=None, biosimulators_audience=None,
-                 biosimulators_api_client_id=None, biosimulators_api_client_secret=None,
-                 biosimulators_prod_api_endpoint=None,
-                 biosimulators_dev_api_endpoint=None,
-                 biosimulators_curator_gh_ids=None, biosimulators_default_specifications_version=None,
-                 biosimulators_default_image_version=None, biosimulators_docker_registry_url=None,
-                 biosimulators_docker_registry_username=None, biosimulators_docker_registry_token=None,
-                 biosimulators_docker_image_url_pattern=None,
-                 runbiosimulations_auth_endpoint=None, runbiosimulations_audience=None,
-                 runbiosimulations_api_client_id=None, runbiosimulations_api_client_secret=None,
-                 runbiosimulations_api_endpoint=None,
-                 test_case_timeout=None,
-                 user_to_exec_in_simulator_containers=None,
-                 singularity_image_dirname=None):
+                 pull_docker_image: bool = None, docker_hub_username: str = None, docker_hub_token: str = None,
+                 biosimulators_auth_endpoint: str = None, biosimulators_audience: str = None,
+                 biosimulators_api_client_id: str = None, biosimulators_api_client_secret: str = None,
+                 biosimulators_prod_api_endpoint: str = None, biosimulators_dev_api_endpoint: str = None,
+                 biosimulators_curator_gh_ids: "list[str]" = None, biosimulators_default_specifications_version: str = None,
+                 biosimulators_default_image_version: str = None, biosimulators_docker_registry_url: str = None,
+                 biosimulators_docker_registry_username: str = None, biosimulators_docker_registry_token: str = None,
+                 biosimulators_docker_image_url_pattern: str = None,
+                 runbiosimulations_auth_endpoint: str = None, runbiosimulations_audience: str = None,
+                 runbiosimulations_api_client_id: str = None, runbiosimulations_api_client_secret: str = None,
+                 runbiosimulations_api_endpoint: str = None,
+                 test_case_timeout: int = None,
+                 user_to_exec_in_simulator_containers: "Union[str, None]" = None,
+                 singularity_image_dirname: str = None):
         """
         Args:
             pull_docker_image (:obj:`bool`, optional): whether to pull the Docker image for the simulator (default: :obj:`True`)
@@ -94,134 +92,135 @@ def __init__(self,
         """
         # Docker registry
         if pull_docker_image is None:
-            self.pull_docker_image = os.getenv('PULL_DOCKER_IMAGE', '1').lower() in ['1', 'true']
+            self.pull_docker_image: bool = os.getenv('PULL_DOCKER_IMAGE', '1').lower() in ['1', 'true']
         else:
-            self.pull_docker_image = pull_docker_image
+            self.pull_docker_image: bool = pull_docker_image
 
         # Docker Hub
         if docker_hub_username is None:
-            self.docker_hub_username = os.getenv('DOCKER_HUB_USERNAME')
+            self.docker_hub_username: str = os.getenv('DOCKER_HUB_USERNAME')
         else:
-            self.docker_hub_username = docker_hub_username
+            self.docker_hub_username: str = docker_hub_username
 
         if docker_hub_token is None:
-            self.docker_hub_token = os.getenv('DOCKER_HUB_TOKEN')
+            self.docker_hub_token: str = os.getenv('DOCKER_HUB_TOKEN')
         else:
-            self.docker_hub_token = docker_hub_token
+            self.docker_hub_token: str = docker_hub_token
 
         # BioSimulators
         if biosimulators_auth_endpoint is None:
-            self.biosimulators_auth_endpoint = os.getenv('BIOSIMULATORS_AUTH_ENDPOINT', 'https://auth.biosimulations.org/oauth/token')
+            self.biosimulators_auth_endpoint: str = os.getenv('BIOSIMULATORS_AUTH_ENDPOINT', 'https://auth.biosimulations.org/oauth/token')
         else:
-            self.biosimulators_auth_endpoint = biosimulators_auth_endpoint
+            self.biosimulators_auth_endpoint: str = biosimulators_auth_endpoint
 
         if biosimulators_audience is None:
-            self.biosimulators_audience = os.getenv('BIOSIMULATORS_AUDIENCE', 'api.biosimulators.org')
+            self.biosimulators_audience: str = os.getenv('BIOSIMULATORS_AUDIENCE', 'api.biosimulators.org')
         else:
-            self.biosimulators_audience = biosimulators_audience
+            self.biosimulators_audience: str = biosimulators_audience
 
         if biosimulators_api_client_id is None:
-            self.biosimulators_api_client_id = os.getenv('BIOSIMULATORS_API_CLIENT_ID')
+            self.biosimulators_api_client_id: str = os.getenv('BIOSIMULATORS_API_CLIENT_ID')
         else:
-            self.biosimulators_api_client_id = biosimulators_api_client_id
+            self.biosimulators_api_client_id: str = biosimulators_api_client_id
 
         if biosimulators_api_client_secret is None:
-            self.biosimulators_api_client_secret = os.getenv('BIOSIMULATORS_API_CLIENT_SECRET')
+            self.biosimulators_api_client_secret: str = os.getenv('BIOSIMULATORS_API_CLIENT_SECRET')
         else:
-            self.biosimulators_api_client_secret = biosimulators_api_client_secret
+            self.biosimulators_api_client_secret: str = biosimulators_api_client_secret
 
         if biosimulators_prod_api_endpoint is None:
-            self.biosimulators_prod_api_endpoint = os.getenv('BIOSIMULATORS_PROD_API_ENDPOINT', 'https://api.biosimulators.org/')
+            self.biosimulators_prod_api_endpoint: str = os.getenv('BIOSIMULATORS_PROD_API_ENDPOINT', 'https://api.biosimulators.org/')
         else:
-            self.biosimulators_prod_api_endpoint = biosimulators_prod_api_endpoint
+            self.biosimulators_prod_api_endpoint: str = biosimulators_prod_api_endpoint
 
         if biosimulators_dev_api_endpoint is None:
-            self.biosimulators_dev_api_endpoint = os.getenv('BIOSIMULATORS_DEV_API_ENDPOINT', 'https://api.biosimulators.dev/')
+            self.biosimulators_dev_api_endpoint: str = os.getenv('BIOSIMULATORS_DEV_API_ENDPOINT', 'https://api.biosimulators.dev/')
         else:
-            self.biosimulators_dev_api_endpoint = biosimulators_dev_api_endpoint
+            self.biosimulators_dev_api_endpoint: str = biosimulators_dev_api_endpoint
 
         if biosimulators_curator_gh_ids is None:
             ids = os.getenv('BIOSIMULATORS_CURATOR_GH_IDS', 'jonrkarr').strip()
             if ids:
-                self.biosimulators_curator_gh_ids = [id.strip() for id in ids.split(',')]
+                self.biosimulators_curator_gh_ids: "list[str]" = [id.strip() for id in ids.split(',')]
             else:
-                self.biosimulators_curator_gh_ids = []
+                self.biosimulators_curator_gh_ids: "list[str]" = []
         else:
-            self.biosimulators_curator_gh_ids = biosimulators_curator_gh_ids
+            self.biosimulators_curator_gh_ids: "list[str]" = biosimulators_curator_gh_ids
 
         if biosimulators_default_specifications_version is None:
-            self.biosimulators_default_specifications_version = os.getenv('BIOSIMULATORS_DEFAULT_SPECIFICATIONS_VERSION', '1.0.0')
+            self.biosimulators_default_specifications_version: str = os.getenv('BIOSIMULATORS_DEFAULT_SPECIFICATIONS_VERSION', '1.0.0')
         else:
-            self.biosimulators_default_specifications_version = biosimulators_default_specifications_version
+            self.biosimulators_default_specifications_version: str = biosimulators_default_specifications_version
 
         if biosimulators_default_image_version is None:
-            self.biosimulators_default_image_version = os.getenv('BIOSIMULATORS_DEFAULT_IMAGE_VERSION', '1.0.0')
+            self.biosimulators_default_image_version: str = os.getenv('BIOSIMULATORS_DEFAULT_IMAGE_VERSION', '1.0.0')
         else:
-            self.biosimulators_default_image_version = biosimulators_default_image_version
+            self.biosimulators_default_image_version: str = biosimulators_default_image_version
 
         if biosimulators_docker_registry_url is None:
-            self.biosimulators_docker_registry_url = os.getenv(
+            self.biosimulators_docker_registry_url: str = os.getenv(
                 'BIOSIMULATORS_DOCKER_REGISTRY_URL', os.getenv('DOCKER_REGISTRY_URL', 'ghcr.io'))
         else:
-            self.biosimulators_docker_registry_url = biosimulators_docker_registry_url
+            self.biosimulators_docker_registry_url: str = biosimulators_docker_registry_url
 
         if biosimulators_docker_registry_username is None:
-            self.biosimulators_docker_registry_username = os.getenv(
+            self.biosimulators_docker_registry_username: str = os.getenv(
                 'BIOSIMULATORS_DOCKER_REGISTRY_USERNAME', os.getenv('DOCKER_REGISTRY_USERNAME'))
         else:
-            self.biosimulators_docker_registry_username = biosimulators_docker_registry_username
+            self.biosimulators_docker_registry_username: str = biosimulators_docker_registry_username
 
         if biosimulators_docker_registry_token is None:
-            self.biosimulators_docker_registry_token = os.getenv(
+            self.biosimulators_docker_registry_token: str = os.getenv(
                 'BIOSIMULATORS_DOCKER_REGISTRY_TOKEN', os.getenv('DOCKER_REGISTRY_TOKEN'))
         else:
-            self.biosimulators_docker_registry_token = biosimulators_docker_registry_token
+            self.biosimulators_docker_registry_token: str = biosimulators_docker_registry_token
 
         if biosimulators_docker_image_url_pattern is None:
-            self.biosimulators_docker_image_url_pattern = os.getenv(
+            self.biosimulators_docker_image_url_pattern: str = os.getenv(
                 'BIOSIMULATORS_DOCKER_REGISTRY_IMAGE_URL_PATTERN', 'ghcr.io/biosimulators/{}:{}')
         else:
-            self.biosimulators_docker_image_url_pattern = biosimulators_docker_image_url_pattern
+            self.biosimulators_docker_image_url_pattern: str = biosimulators_docker_image_url_pattern
 
         # runBioSimulations
         if runbiosimulations_auth_endpoint is None:
-            self.runbiosimulations_auth_endpoint = os.getenv(
+            self.runbiosimulations_auth_endpoint: str = os.getenv(
                 'RUNBIOSIMULATIONS_AUTH_ENDPOINT', 'https://auth.biosimulations.org/oauth/token')
         else:
-            self.runbiosimulations_auth_endpoint = runbiosimulations_auth_endpoint
+            self.runbiosimulations_auth_endpoint: str = runbiosimulations_auth_endpoint
 
         if runbiosimulations_audience is None:
-            self.runbiosimulations_audience = os.getenv('RUNBIOSIMULATIONS_AUDIENCE', 'api.biosimulations.org')
+            self.runbiosimulations_audience: str = os.getenv('RUNBIOSIMULATIONS_AUDIENCE', 'api.biosimulations.org')
         else:
-            self.runbiosimulations_audience = runbiosimulations_audience
+            self.runbiosimulations_audience: str = runbiosimulations_audience
 
         if runbiosimulations_api_client_id is None:
-            self.runbiosimulations_api_client_id = os.getenv('RUNBIOSIMULATIONS_API_CLIENT_ID')
+            self.runbiosimulations_api_client_id: str = os.getenv('RUNBIOSIMULATIONS_API_CLIENT_ID')
         else:
-            self.runbiosimulations_api_client_id = runbiosimulations_api_client_id
+            self.runbiosimulations_api_client_id: str = runbiosimulations_api_client_id
 
         if runbiosimulations_api_client_secret is None:
-            self.runbiosimulations_api_client_secret = os.getenv('RUNBIOSIMULATIONS_API_CLIENT_SECRET')
+            self.runbiosimulations_api_client_secret: str = os.getenv('RUNBIOSIMULATIONS_API_CLIENT_SECRET')
         else:
-            self.runbiosimulations_api_client_secret = runbiosimulations_api_client_secret
+            self.runbiosimulations_api_client_secret: str = runbiosimulations_api_client_secret
 
         if runbiosimulations_api_endpoint is None:
-            self.runbiosimulations_api_endpoint = os.getenv('RUNBIOSIMULATIONS_API_ENDPOINT', 'https://api.biosimulations.org/')
+            self.runbiosimulations_api_endpoint: str = os.getenv('RUNBIOSIMULATIONS_API_ENDPOINT', 'https://api.biosimulations.org/')
         else:
-            self.runbiosimulations_api_endpoint = runbiosimulations_api_endpoint
+            self.runbiosimulations_api_endpoint: str = runbiosimulations_api_endpoint
 
         if test_case_timeout is None:
-            self.test_case_timeout = int(os.getenv('TEST_CASE_TIMEOUT', '600'))  # seconds
+            self.test_case_timeout: int = int(os.getenv('TEST_CASE_TIMEOUT', '600'))  # seconds
         else:
-            self.test_case_timeout = test_case_timeout
+            self.test_case_timeout: int = test_case_timeout
 
         if user_to_exec_in_simulator_containers is None:
-            self.user_to_exec_in_simulator_containers = os.getenv('USER_TO_EXEC_IN_SIMULATOR_CONTAINERS', '_CURRENT_USER_') or None
+            self.user_to_exec_in_simulator_containers: "Union[str, None]" = os.getenv(
+                'USER_TO_EXEC_IN_SIMULATOR_CONTAINERS', '_CURRENT_USER_') or None
         else:
-            self.user_to_exec_in_simulator_containers = user_to_exec_in_simulator_containers
+            self.user_to_exec_in_simulator_containers: "Union[str, None]" = user_to_exec_in_simulator_containers
 
         if singularity_image_dirname is None:
-            self.singularity_image_dirname = os.getenv('SINGULARITY_IMAGE_DIRNAME',
-                                                       os.path.join(os.path.expanduser('~'), '.biosimulators-test-suite', 'singularity'))
+            self.singularity_image_dirname: str = os.getenv('SINGULARITY_IMAGE_DIRNAME', os.path.join(os.path.expanduser('~'),
+                                                            '.biosimulators-test-suite', 'singularity'))
         else:
-            self.singularity_image_dirname = singularity_image_dirname
+            self.singularity_image_dirname: str = singularity_image_dirname
diff --git a/biosimulators_test_suite/data_model.py b/biosimulators_test_suite/data_model.py
index 6df983f..6cdcdb4 100644
--- a/biosimulators_test_suite/data_model.py
+++ b/biosimulators_test_suite/data_model.py
@@ -6,8 +6,7 @@
 :License: MIT
 """
 
-from .config import Config
-from .exceptions import SkippedTestCaseException  # noqa: F401
+from biosimulators_test_suite.config import Config
 from biosimulators_utils.image import get_docker_image
 import abc
 import docker
diff --git a/biosimulators_test_suite/exec_cli.py b/biosimulators_test_suite/exec_cli.py
index 1e5365e..ecdb7f8 100644
--- a/biosimulators_test_suite/exec_cli.py
+++ b/biosimulators_test_suite/exec_cli.py
@@ -6,9 +6,10 @@
 :License: MIT
 """
 
-from .data_model import OutputMedium
-from .results.data_model import TestCaseResultType
-from .results.io import write_test_results
+from biosimulators_test_suite.data_model import OutputMedium
+from biosimulators_test_suite.results.data_model import TestCaseResultType
+from biosimulators_test_suite.results.io import write_test_results
+
 from biosimulators_utils.config import Colors
 import biosimulators_test_suite
 import biosimulators_test_suite.exec_core
diff --git a/biosimulators_test_suite/exec_core.py b/biosimulators_test_suite/exec_core.py
index cddaab5..58e2b17 100644
--- a/biosimulators_test_suite/exec_core.py
+++ b/biosimulators_test_suite/exec_core.py
@@ -6,18 +6,21 @@
 :License: MIT
 """
 
-from .config import Config
-from .data_model import TestCase, OutputMedium
-from .exceptions import SkippedTestCaseException, TimeoutException
-from .results.data_model import TestCaseResult, TestCaseResultType
-from .test_case import cli
-from .test_case import combine_archive
-from .test_case import docker_image
-from .test_case import log
-from .test_case import published_project
-from .test_case import results_report
-from .test_case import sedml
-from .warnings import TestCaseWarning, IgnoredTestCaseWarning
+from biosimulators_test_suite.config import Config
+from biosimulators_test_suite.data_model import TestCase, OutputMedium
+from biosimulators_test_suite.exceptions import SkippedTestCaseException, TimeoutException
+from biosimulators_test_suite.results.data_model import TestCaseResult, TestCaseResultType
+from biosimulators_test_suite.test_case import cli
+from biosimulators_test_suite.test_case import combine_archive
+from biosimulators_test_suite.test_case import docker_image
+from biosimulators_test_suite.test_case import log
+from biosimulators_test_suite.test_case import published_project
+from biosimulators_test_suite.test_case import results_report
+from biosimulators_test_suite.test_case import sedml
+from biosimulators_test_suite.test_warnings import TestCaseWarning, IgnoredTestCaseWarning
+from typing import Union
+from types import ModuleType
+from biosimulators_utils.globals import JSONType
 from biosimulators_utils.config import Colors
 from biosimulators_utils.log.utils import StandardOutputErrorCapturer
 import biosimulators_utils.simulator.io
@@ -54,12 +57,13 @@ class SimulatorValidator(object):
             archives rather than a Docker image
     """
 
-    def __init__(self, specifications, case_ids=None, verbose=False, synthetic_archives_dir=None, output_medium=OutputMedium.console,
-                 log_std_out_err=True, working_dirname=None, dry_run=False, cli=None, validate_specs=True):
+    def __init__(self, specifications: Union[str, JSONType], case_ids: "list[str]" = None, verbose: bool = False, synthetic_archives_dir: str = None,
+                 output_medium: OutputMedium = OutputMedium.console, log_std_out_err: bool = True, working_dirname: str = None,
+                 dry_run: bool = False, cli: str = None, validate_specs: bool = True):
         """
         Args:
             specifications (:obj:`str` or :obj:`dict`): path or URL to the specifications of the simulator, or the specifications of the simulator
-            case_ids (:obj:`list` of :obj:`str`, optional): List of ids of test cases to verify. If :obj:`ids`
+            case_ids (:obj:`list` of :obj:`str`, optional): List of ids of test cases to verify. If :obj:`case_ids`
                 is none, all test cases are verified.
             verbose (:obj:`bool`, optional): if :obj:`True`, display stdout/stderr from executing cases in real time
             synthetic_archives_dir (:obj:`str`, optional): Directory to save the synthetic COMBINE/OMEX archives generated by the test cases
@@ -72,10 +76,8 @@ def __init__(self, specifications, case_ids=None, verbose=False, synthetic_archi
             validate_specs (:obj:`bool`, optional): whether to validate specifications
         """
         # if necessary, get and validate specifications of simulator
-        if isinstance(specifications, str):
-            specifications = biosimulators_utils.simulator.io.read_simulator_specs(specifications, validate=validate_specs)
-
-        self.specifications = specifications
+        self.specifications: JSONType = biosimulators_utils.simulator.io.read_simulator_specs(
+            specifications, validate=validate_specs) if isinstance(specifications, str) else specifications
         self.verbose = verbose
         if synthetic_archives_dir and not os.path.isdir(synthetic_archives_dir):
             os.makedirs(synthetic_archives_dir)
@@ -90,7 +92,7 @@ def __init__(self, specifications, case_ids=None, verbose=False, synthetic_archi
 
         self.test_case_timeout = Config().test_case_timeout
 
-    def find_cases(self, ids=None):
+    def find_cases(self, ids: "list[str]" = None) -> "collections.OrderedDict[ModuleType, TestCase]":
         """ Find test cases
 
         Args:
@@ -98,9 +100,9 @@ def find_cases(self, ids=None):
                 is none, all test cases are verified.
 
         Returns:
-            :obj:`collections.OrderedDict` of :obj:`types.ModuleType` to :obj:`TestCase`: groups of test cases
+            :obj:`collections.OrderedDict` of :obj:`types.ModuleType` mapped to :obj:`list` of :obj:`TestCase`: groups of test cases
         """
-        cases = collections.OrderedDict()
+        cases: collections.OrderedDict[ModuleType, list[TestCase]] = collections.OrderedDict()
 
         # get cases involving curated published COMBINE/OMEX archives
         all_published_projects_test_cases, compatible_published_projects_test_cases = published_project.find_cases(
@@ -156,15 +158,16 @@ def find_cases(self, ids=None):
         # return discovered cases
         return cases
 
-    def find_cases_in_module(self, module, published_projects_test_cases, ids=None):
+    def find_cases_in_module(self, module: ModuleType, published_projects_test_cases: "list[published_project.SimulatorCanExecutePublishedProject]",
+                             ids: "list[str]" = None):
         """ Discover test cases in a module
 
         Args:
             module (:obj:`types.ModuleType`): module
-            ids (:obj:`list` of :obj:`str`, optional): List of ids of test cases to verify. If :obj:`ids`
-                is none, all test cases are verified.
             published_projects_test_cases (:obj:`list` of :obj:`published_project.SimulatorCanExecutePublishedProject`): test cases involving
                 executing curated COMBINE/OMEX archives
+            ids (:obj:`list` of :obj:`str`, optional): List of ids of test cases to verify. If :obj:`ids`
+                is none, all test cases are verified.
 
         Returns:
             :obj:`list` of :obj:`TestCase`: test cases
@@ -235,7 +238,7 @@ def run(self):
         start = datetime.datetime.now()
 
         # execute test cases and collect results
-        results = []
+        results: list[TestCaseResult] = []
         working_dirname = self.working_dirname or tempfile.mkdtemp()
         for suite_name, suite_cases in self.cases.items():
             print('\nExecuting {} {} tests ... {}'.format(len(suite_cases), suite_name, 'done' if not suite_cases else ''))
@@ -243,6 +246,7 @@ def run(self):
                 print('  {}: {} ... '.format(i_case + 1, case.id), end='')
                 sys.stdout.flush()
 
+                # Process one test case.
                 result = self.eval_case(case, os.path.join(working_dirname, suite_name, case.id))
                 results.append(result)
 
@@ -265,7 +269,7 @@ def run(self):
         # return results
         return results
 
-    def eval_case(self, case, working_dirname):
+    def eval_case(self, case: TestCase, working_dirname: str):
         """ Evaluate a test case for a simulator
 
         Args:
@@ -281,7 +285,6 @@ def eval_case(self, case, working_dirname):
             with warnings.catch_warnings(record=True) as caught_warnings:
                 warnings.simplefilter("ignore")
                 warnings.simplefilter("always", TestCaseWarning)
-
                 try:
 
                     with time_limit(seconds=self.test_case_timeout):
diff --git a/biosimulators_test_suite/exec_gh_action.py b/biosimulators_test_suite/exec_gh_action.py
index a2deb6d..97998e4 100644
--- a/biosimulators_test_suite/exec_gh_action.py
+++ b/biosimulators_test_suite/exec_gh_action.py
@@ -7,12 +7,13 @@
 :License: MIT
 """
 
-from .config import Config
-from .data_model import OutputMedium
-from .exec_core import SimulatorValidator
-from .results.data_model import TestCaseResult, TestCaseResultType, TestResultsReport  # noqa: F401
-from .results.io import write_test_results
-from .utils import get_singularity_image_filename
+from biosimulators_test_suite.config import Config
+from biosimulators_test_suite.data_model import OutputMedium
+from biosimulators_test_suite.exec_core import SimulatorValidator
+from biosimulators_test_suite.results.data_model import TestCaseResult, TestCaseResultType, TestResultsReport
+from biosimulators_test_suite.results.io import write_test_results
+from biosimulators_test_suite.utils import get_singularity_image_filename
+from biosimulators_utils.globals import JSONType
 from biosimulators_utils.biosimulations.utils import validate_biosimulations_api_response
 from biosimulators_utils.config import Colors, Config as BioSimulatorsUtilsConfig
 from biosimulators_utils.gh_action.data_model import Comment, GitHubActionCaughtError  # noqa: F401
@@ -22,19 +23,20 @@
 from biosimulators_utils.simulator_registry.process_submission import get_simulator_submission_from_gh_issue_body
 from biosimulators_utils.simulator_registry.query import get_simulator_version_specs
 from natsort import natsort_keygen
+from docker.client import DockerClient
+from typing import Tuple
 import biosimulators_utils.image
 import biosimulators_utils.simulator.io
 import requests
 import requests.exceptions
 import termcolor
 
-
 __all__ = [
     'ValidateCommitSimulatorGitHubAction',
 ]
 
 
-def get_uncaught_exception_msg(exception):
+def get_uncaught_exception_msg(exception: Exception) -> "list[Comment]":
     """ Create an error message to display to users for all exceptions not caught during the
     exception of the :obj:`run` method (exceptions of all types except :obj:`GitHubActionCaughtError`)
 
@@ -42,9 +44,9 @@ def get_uncaught_exception_msg(exception):
         exception (:obj:`Exception`): a failure encountered during the exception of the :obj:`run` method
 
     Returns:
-        :obj:`str`: error message to display to users
+        :obj:`list`: of :obj:`str`: error messages to display to users
     """
-    gh_action_run_url = GitHubAction.get_gh_action_run_url()
+    gh_action_run_url: str = GitHubAction.get_gh_action_run_url()
     return [
         Comment(text='The validation/submission of your simulator failed.'),
         Comment(text=str(exception), error=True),
@@ -64,13 +66,14 @@ class ValidateCommitSimulatorGitHubAction(GitHubAction):
     """ Action to validate a containerized simulator
 
     Attributes:
+        config (:obj:`Config`): configuration of the app
         issue_number (:obj:`str`): number of GitHub issue which triggered the action
     """
 
     def __init__(self):
         super(ValidateCommitSimulatorGitHubAction, self).__init__()
-        self.config = Config()
-        self.issue_number = self.get_issue_number()
+        self.config: Config = Config()
+        self.issue_number: str = self.get_issue_number()
 
     @GitHubActionErrorHandling.catch_errors(uncaught_exception_msg_func=get_uncaught_exception_msg,
                                             caught_error_labels=[IssueLabel.invalid],
@@ -79,11 +82,11 @@ def run(self):
         """ Validate and commit a simulator."""
 
         # Get properties of submission
-        issue_props = self.get_issue(self.issue_number)
-        submission = get_simulator_submission_from_gh_issue_body(issue_props['body'])
-        submitter = issue_props['user']['login']
+        issue_props: JSONType = self.get_issue(self.issue_number)
+        submission: SimulatorSubmission = get_simulator_submission_from_gh_issue_body(issue_props['body'])
+        submitter: str = issue_props['user']['login']
 
-        # Send message that validation is starting
+        # Send message that validation/submission is starting
         self.add_comment_to_issue(self.issue_number, self.get_initial_message(submission, submitter))
 
         # reset labels except approved
@@ -96,12 +99,12 @@ def run(self):
         self.add_labels_to_issue(self.issue_number, [IssueLabel.validated.value])
 
         # get specifications of other versions of simulator
-        config = BioSimulatorsUtilsConfig()
-        existing_version_specifications = get_simulator_version_specs(specifications['id'], config)
+        config: Config = BioSimulatorsUtilsConfig()
+        existing_version_specifications: JSONType = get_simulator_version_specs(specifications['id'], config)
 
         # determine if simulator is approved: issue is a revision of an existing version of a validated simulator,
         # a new version of a validated simulator, or the issue has been manually approved by the BioSimulators Team
-        approved = self.is_simulator_approved(specifications, existing_version_specifications)
+        approved: bool = self.is_simulator_approved(specifications, existing_version_specifications)
 
         # if approved, label the issue as approved
         if approved and IssueLabel.approved.value not in self.get_labels_for_issue(self.issue_number):
@@ -135,38 +138,35 @@ def run(self):
                     ('A member of the BioSimulators team will review your submission and '
                      'publish your image before final committment to the registry.'))
 
-    def get_initial_message(self, submission, submitter):
+    def get_initial_message(self, submission: SimulatorSubmission, submitter: str) -> str:
         """ Peport message that validation is starting
 
         Args:
             submission (:obj:`SimulatorSubmission`): simulator submission
             submitter (:obj:`str`): GitHub user name of person who executed the submission
         """
-        actions = []
-        not_actions = []
+        actions_list: list[str] = []
+        not_actions_list: list[str] = []
 
-        actions.append('validating the specifications of your simulator')
+        actions_list.append('validating the specifications of your simulator')
         if submission.validate_image:
-            actions.append('validating your Docker image')
-            test_results_msg = (
+            actions_list.append('validating your Docker image')
+            test_results_msg: str = (
                 ' The results of the validation of your tool will also be saved as a JSON file. '
                 'A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.'
             )
         else:
-            not_actions.append('You have chosen not to have the Docker image for your simulator validated.')
-            test_results_msg = ''
+            not_actions_list.append('You have chosen not to have the Docker image for your simulator validated.')
+            test_results_msg: str = ''
         if submission.commit_simulator:
-            job_type = 'submission'
-            actions.append('committing your simulator to the BioSimulators registry')
+            job_type: str = 'submission'
+            actions_list.append('committing your simulator to the BioSimulators registry')
         else:
-            job_type = 'validation'
-            not_actions.append('You have chosen not to submit your simulator to the BioSimulators registry.')
+            job_type: str = 'validation'
+            not_actions_list.append('You have chosen not to submit your simulator to the BioSimulators registry.')
 
-        if len(actions) == 1:
-            actions = actions[0]
-        else:
-            actions = ', '.join(actions[0:-1]) + ', and ' + actions[-1]
-        not_actions = ' '.join(action.strip() for action in not_actions)
+        actions: str = actions_list[0] if len(actions_list) == 1 else str(', '.join(actions_list[0:-1]) + ', and ' + actions_list[-1])
+        not_actions: str = str(' '.join(action.strip() for action in not_actions_list))
 
         return ('Thank you @{} for your submission to the BioSimulators simulator validation/submission system!\n\n'
                 'The BioSimulators validator bot is {}. {}\n\n'
@@ -174,7 +174,7 @@ def get_initial_message(self, submission, submitter):
                 'A complete log of your simulator {} job will be available for 90 days [here]({}).{}\n\n'
                 ).format(submitter, actions, not_actions, job_type, self.get_gh_action_run_url(), test_results_msg)
 
-    def exec_core(self, submission, submitter):
+    def exec_core(self, submission: SimulatorSubmission, submitter: str) -> Tuple[JSONType, "list[TestCaseResult]"]:
         """ Validate simulator
 
         * Validate specifications
@@ -187,11 +187,11 @@ def exec_core(self, submission, submitter):
         Returns:
             :obj:`tuple`:
 
-                * :obj:`dict`: specifications of a simulation tool
-                * :obj:`list` of :obj:`TestCaseResults`: results of test cases
+                * :obj:`dict`: json-parsed specifications of a simulation tool
+                * :obj:`list` of :obj:`TestCaseResult`: results of test cases
         """
         # validate specifications
-        specifications = biosimulators_utils.simulator.io.read_simulator_specs(
+        specifications: JSONType = biosimulators_utils.simulator.io.read_simulator_specs(
             submission.specifications_url, submission.specifications_patch,
             validate=True)
 
@@ -203,7 +203,7 @@ def exec_core(self, submission, submitter):
 
         # validate image
         if submission.validate_image:
-            test_results = self.validate_image(specifications)
+            test_results: list[TestCaseResult] = self.validate_image(specifications)  # Main executable
             self.add_comment_to_issue(self.issue_number, 'The image for your simulator is valid!')
         else:
             test_results = None
@@ -281,20 +281,20 @@ def validate_permissions(self, simulator_id, simulator_name, submitter):
                 ).format(submitter, simulator_name, simulator_id, simulator_name, simulator_name)
                 self.add_error_comment_to_issue(self.issue_number, [Comment(text=msg, error=True)])
 
-    def validate_image(self, specifications):
+    def validate_image(self, specifications: JSONType) -> "list[TestCaseResult]":
         """ Validate a Docker image for simulation tool
 
         Args:
             specifications (:obj:`dict`): specifications of a simulation tool
 
         Returns:
-            :obj:`list` of :obj:`TestCaseResults`: results of test cases
+            :obj:`list` of :obj:`TestCaseResult`: results of test cases
         """
-        docker_client = biosimulators_utils.image.login_to_docker_registry(
+        docker_client: DockerClient = biosimulators_utils.image.login_to_docker_registry(
             'docker.io', self.config.docker_hub_username, self.config.docker_hub_token)
 
         # validate that container (Docker image) exists
-        image_url = specifications['image']['url']
+        image_url: str = specifications['image']['url']
         get_docker_image(docker_client, image_url, pull=True)
 
         # validate that Docker image can be converted to a Singularity image
@@ -303,8 +303,8 @@ def validate_image(self, specifications):
             singularity_filename=get_singularity_image_filename(image_url))
 
         # validate that image is consistent with the BioSimulators standards
-        validator = SimulatorValidator(specifications, output_medium=OutputMedium.gh_issue)
-        case_results = validator.run()
+        validator: SimulatorValidator = SimulatorValidator(specifications, output_medium=OutputMedium.gh_issue)
+        case_results: list[TestCaseResult] = validator.run()
         write_test_results(case_results, '.biosimulators-test-suite-results.json',
                            gh_issue=int(self.issue_number), gh_action_run=int(self.get_gh_action_run_id()))
         summary, failure_details, warning_details, skipped_details = validator.summarize_results(
@@ -584,7 +584,7 @@ def get_auth_headers_for_biosimulations_api(self, endpoint, audience, client_id,
         return {'Authorization': response_data['token_type'] + ' ' + response_data['access_token']}
 
     @classmethod
-    def add_comment_to_issue(cls, issue_number, comment, alternative_comment=None, max_len=65536):
+    def add_comment_to_issue(cls, issue_number: str, comment: str, alternative_comment: str = None, max_len: int = 65536) -> None:
         """ Post a comment to the GitHub issue
 
         Args:
diff --git a/biosimulators_test_suite/results/data_model.py b/biosimulators_test_suite/results/data_model.py
index ef4f328..63d75c4 100644
--- a/biosimulators_test_suite/results/data_model.py
+++ b/biosimulators_test_suite/results/data_model.py
@@ -6,8 +6,7 @@
 :License: MIT
 """
 
-from .._version import __version__
-from ..warnings import TestCaseWarning  # noqa: F401
+from biosimulators_test_suite._version import __version__
 import enum
 import traceback
 
diff --git a/biosimulators_test_suite/results/io.py b/biosimulators_test_suite/results/io.py
index 16f7a87..b11e401 100644
--- a/biosimulators_test_suite/results/io.py
+++ b/biosimulators_test_suite/results/io.py
@@ -6,7 +6,7 @@
 :License: MIT
 """
 
-from .data_model import TestCaseResult, TestResultsReport  # noqa: F401
+from biosimulators_test_suite.results.data_model import TestResultsReport
 import json
 
 __all__ = ['write_test_results']
diff --git a/biosimulators_test_suite/test_case/cli.py b/biosimulators_test_suite/test_case/cli.py
index c11c117..d859c12 100644
--- a/biosimulators_test_suite/test_case/cli.py
+++ b/biosimulators_test_suite/test_case/cli.py
@@ -6,8 +6,8 @@
 :License: MIT
 """
 
-from ..data_model import TestCase
-from ..warnings import TestCaseWarning
+from biosimulators_test_suite.data_model import TestCase
+from biosimulators_test_suite.test_warnings import TestCaseWarning
 from biosimulators_utils.simulator.environ import ENVIRONMENT_VARIABLES
 import re
 import subprocess
diff --git a/biosimulators_test_suite/test_case/combine_archive.py b/biosimulators_test_suite/test_case/combine_archive.py
index 490da19..b748e37 100644
--- a/biosimulators_test_suite/test_case/combine_archive.py
+++ b/biosimulators_test_suite/test_case/combine_archive.py
@@ -6,8 +6,8 @@
 :License: MIT
 """
 
-from ..warnings import InvalidOutputsWarning
-from .published_project import SingleMasterSedDocumentCombineArchiveTestCase
+from biosimulators_test_suite.test_warnings import InvalidOutputsWarning
+from biosimulators_test_suite.test_case.published_project import SingleMasterSedDocumentCombineArchiveTestCase
 from biosimulators_utils.combine.data_model import CombineArchive, CombineArchiveContent, CombineArchiveContentFormat  # noqa: F401
 from biosimulators_utils.report.io import ReportReader
 from biosimulators_utils.sedml.data_model import SedDocument, Report  # noqa: F401
diff --git a/biosimulators_test_suite/test_case/docker_image.py b/biosimulators_test_suite/test_case/docker_image.py
index 02a7ff1..94150b1 100644
--- a/biosimulators_test_suite/test_case/docker_image.py
+++ b/biosimulators_test_suite/test_case/docker_image.py
@@ -6,9 +6,9 @@
 :License: MIT
 """
 
-from ..data_model import TestCase
-from ..warnings import TestCaseWarning
-from .sedml import SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
+from biosimulators_test_suite.data_model import TestCase
+from biosimulators_test_suite.test_warnings import TestCaseWarning
+from biosimulators_test_suite.test_case.sedml import SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
 from biosimulators_utils.simulator.environ import ENVIRONMENT_VARIABLES
 import warnings
 
diff --git a/biosimulators_test_suite/test_case/log.py b/biosimulators_test_suite/test_case/log.py
index ceb45d3..99180ca 100644
--- a/biosimulators_test_suite/test_case/log.py
+++ b/biosimulators_test_suite/test_case/log.py
@@ -6,8 +6,8 @@
 :License: MIT
 """
 
-from ..config import Config
-from ..exceptions import InvalidOutputsException, SkippedTestCaseException
+from biosimulators_test_suite.config import Config
+from biosimulators_test_suite.exceptions import InvalidOutputsException, SkippedTestCaseException
 from .published_project import SingleMasterSedDocumentCombineArchiveTestCase
 from biosimulators_utils.combine.data_model import CombineArchive  # noqa: F401
 from biosimulators_utils.config import get_config
diff --git a/biosimulators_test_suite/test_case/published_project.py b/biosimulators_test_suite/test_case/published_project.py
index 35718b6..5a13bb1 100644
--- a/biosimulators_test_suite/test_case/published_project.py
+++ b/biosimulators_test_suite/test_case/published_project.py
@@ -6,14 +6,17 @@
 :License: MIT
 """
 
-from ..config import Config
-from ..data_model import (TestCase, SedTaskRequirements, ExpectedSedReport, ExpectedSedDataSet, ExpectedSedPlot,
-                          AlertType, OutputMedium)
-from ..exceptions import InvalidOutputsException, SkippedTestCaseException, TimeoutException, TestCaseException
-from ..utils import get_singularity_image_filename, simulation_results_isnan
-from ..warnings import IgnoredTestCaseWarning, SimulatorRuntimeErrorWarning, InvalidOutputsWarning
-from .utils import are_array_shapes_equivalent
+from biosimulators_test_suite.config import Config
+from biosimulators_test_suite.data_model import TestCase, SedTaskRequirements, ExpectedSedReport, ExpectedSedDataSet, \
+    ExpectedSedPlot, AlertType, OutputMedium
+from biosimulators_test_suite.exceptions import InvalidOutputsException, SkippedTestCaseException, TimeoutException, \
+    TestCaseException
+from biosimulators_test_suite.utils import get_singularity_image_filename, simulation_results_isnan
+from biosimulators_test_suite.test_warnings import IgnoredTestCaseWarning, SimulatorRuntimeErrorWarning, \
+    InvalidOutputsWarning
+from biosimulators_test_suite.test_case.utils import are_array_shapes_equivalent
 from biosimulators_utils.combine.data_model import CombineArchive, CombineArchiveContentFormatPattern  # noqa: F401
+from biosimulators_utils.globals import JSONType
 from biosimulators_utils.combine.io import CombineArchiveReader, CombineArchiveWriter
 from biosimulators_utils.config import get_config
 from biosimulators_utils.image import convert_docker_image_to_singularity
@@ -272,11 +275,17 @@ def compatible_with_specifications(self, specifications):
         for task_reqs in self.task_requirements:
             reqs_satisfied = False
             for alg_specs in specifications['algorithms']:
+                # TEMPORARY RBA REMOVAL
+                if alg_specs['kisaoId']["id"] == "KISAO_0000669":
+                    raise RuntimeError("Error with Algorithm Specification (KISAO_0000669):\n\tDue to incompatible, "
+                                       "outdated releases of RBApy, BioSimulators can no longer "
+                                       "support RBA processing."
+                                       f"{(alg_specs['id']) if 'id' in alg_specs else alg_specs['kisaoId']}")
                 format_reqs_satisfied = False
-                for format in alg_specs['modelFormats']:
+                for format_in_specs in alg_specs['modelFormats']:
                     if (
-                        task_reqs.model_format == format['id']
-                        and task_reqs.model_format_features == set(format.get('supportedFeatures', []) or [])
+                        task_reqs.model_format == format_in_specs['id']
+                        and task_reqs.model_format_features == set(format_in_specs.get('supportedFeatures', []) or [])
                     ):
                         format_reqs_satisfied = True
                         break
@@ -673,6 +682,7 @@ def _eval_synthetic_archive(self, specifications, expected_results_of_synthetic_
                 cmd = [
                     'singularity', 'run',
                     '-B', outputs_dir + ':/root',
+                    "--containall",
                     singularity_filename,
                     '-i', '/root/' + os.path.basename(synthetic_archive_filename),
                     '-o', '/root',
@@ -680,8 +690,10 @@ def _eval_synthetic_archive(self, specifications, expected_results_of_synthetic_
                 result = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=False)
                 os.remove(temp_filename)
                 if result.returncode != 0:
-                    msg = 'The Docker image could not be successfully executed as a Singularity image:\n  {}'.format(
-                        result.stderr.decode().replace('\n', '\n  '))
+                    returned_statement = result.stdout.decode().replace('\n', '\n  ') if result.stdout.strip() \
+                        else result.stdout.decode().replace('\n', '\n  ')
+                    msg = (f'The Docker image could not be successfully executed as a'
+                           f' Singularity image (error code {result.returncode}:\n  {returned_statement}')
                     raise TestCaseException(msg)
 
             else:
@@ -899,7 +911,7 @@ def __init__(self, archive, sed_documents, is_success_expected=True, environment
         self.environment = environment or {}
 
 
-def find_cases(specifications, dir_name=None, output_medium=OutputMedium.console):
+def find_cases(specifications: JSONType, dir_name: str = None, output_medium: OutputMedium = OutputMedium.console):
     """ Collect test cases
 
     Args:
@@ -908,15 +920,17 @@ def find_cases(specifications, dir_name=None, output_medium=OutputMedium.console
         output_medium (:obj:`OutputMedium`, optional): medium the description should be formatted for
 
     Returns:
-        :obj:`list` of :obj:`SimulatorCanExecutePublishedProject`: test cases
+        :obj:`tuple`:
+                * :obj:`list` of :obj:`SimulatorCanExecutePublishedProject`: all test cases
+                * :obj:`list` of :obj:`SimulatorCanExecutePublishedProject`: compatible test cases
     """
     if dir_name is None:
         dir_name = EXAMPLES_DIR
     if not os.path.isdir(dir_name):
         warnings.warn('Directory of example COMBINE/OMEX archives is not available', IgnoredTestCaseWarning)
 
-    all_cases = []
-    compatible_cases = []
+    all_cases: list[SimulatorCanExecutePublishedProject] = []
+    compatible_cases: list[SimulatorCanExecutePublishedProject] = []
     for example_filename in glob.glob(os.path.join(dir_name, '**/*.omex'), recursive=True):
         md_filename = os.path.join(example_filename[0:-5], 'expected-results.json')
         rel_filename = os.path.relpath(md_filename, dir_name)
diff --git a/biosimulators_test_suite/test_case/results_report.py b/biosimulators_test_suite/test_case/results_report.py
index 1ea310d..1b8a2d5 100644
--- a/biosimulators_test_suite/test_case/results_report.py
+++ b/biosimulators_test_suite/test_case/results_report.py
@@ -6,9 +6,9 @@
 :License: MIT
 """
 
-from ..utils import simulation_results_isnan
-from ..warnings import TestCaseWarning
-from .published_project import SingleMasterSedDocumentCombineArchiveTestCase
+from biosimulators_test_suite.utils import simulation_results_isnan
+from biosimulators_test_suite.test_warnings import TestCaseWarning
+from biosimulators_test_suite.test_case.published_project import SingleMasterSedDocumentCombineArchiveTestCase
 from biosimulators_utils.combine.data_model import CombineArchive  # noqa: F401
 from biosimulators_utils.report.data_model import ReportFormat
 from biosimulators_utils.report.io import ReportReader
@@ -73,17 +73,17 @@ def eval_outputs(self, specifications, synthetic_archive, synthetic_sed_docs, ou
 
                     with h5py.File(os.path.join(outputs_dir, 'reports.h5'), 'r') as file:
 
-                        temp = file[uri].attrs.get('uri', None)
+                        temp = ReportReader.parse_dataset_str_value(file[uri].attrs.get('uri', None))
                         if temp != uri:
                             raise ValueError('`uri` of HDF5 data set `{}` must be `{}`, not `{}`.'.format(uri, uri, temp))
 
                         for i_group in range(len(uri_parts) - 1):
                             group_uri = '/'.join(uri_parts[0:i_group + 1])
-                            temp = file[group_uri].attrs.get('uri', None)
+                            temp = ReportReader.parse_dataset_str_value(file[group_uri].attrs.get('uri', None))
                             if temp != group_uri:
                                 raise ValueError('`uri` of HDF5 group `{}` must be `{}`, not `{}`.'.format(group_uri, group_uri, temp))
 
-                            temp = file[group_uri].attrs.get('combineArchiveLocation', None)
+                            temp = ReportReader.parse_dataset_str_value(file[group_uri].attrs.get('combineArchiveLocation', None))
                             if temp != group_uri:
                                 raise ValueError('`combineArchiveLocation` of HDF5 group `{}` must be `{}`, not `{}`.'.format(
                                     group_uri, group_uri, temp))
diff --git a/biosimulators_test_suite/test_case/sedml.py b/biosimulators_test_suite/test_case/sedml.py
index 0ec0c91..e52d18a 100644
--- a/biosimulators_test_suite/test_case/sedml.py
+++ b/biosimulators_test_suite/test_case/sedml.py
@@ -5,10 +5,11 @@
 :Copyright: 2020, Center for Reproducible Biomedical Modeling
 :License: MIT
 """
-from ..exceptions import InvalidOutputsException, SkippedTestCaseException
-from ..utils import simulation_results_isnan
-from ..warnings import InvalidOutputsWarning
-from .published_project import SingleMasterSedDocumentCombineArchiveTestCase, UniformTimeCourseTestCase, ExpectedResultOfSyntheticArchive
+from biosimulators_test_suite.exceptions import InvalidOutputsException, SkippedTestCaseException
+from biosimulators_test_suite.utils import simulation_results_isnan
+from biosimulators_test_suite.test_warnings import InvalidOutputsWarning
+from biosimulators_test_suite.test_case.published_project import SingleMasterSedDocumentCombineArchiveTestCase, \
+    UniformTimeCourseTestCase, ExpectedResultOfSyntheticArchive
 from biosimulators_utils.combine.data_model import CombineArchive  # noqa: F401
 from biosimulators_utils.archive.io import ArchiveReader
 from biosimulators_utils.config import get_config
diff --git a/biosimulators_test_suite/warnings.py b/biosimulators_test_suite/test_warnings.py
similarity index 100%
rename from biosimulators_test_suite/warnings.py
rename to biosimulators_test_suite/test_warnings.py
diff --git a/biosimulators_test_suite/utils.py b/biosimulators_test_suite/utils.py
index 554530d..1577bd2 100644
--- a/biosimulators_test_suite/utils.py
+++ b/biosimulators_test_suite/utils.py
@@ -6,14 +6,14 @@
 :License: MIT
 """
 
-from .config import Config
+from biosimulators_test_suite.config import Config
 import numpy
 import os
 
 __all__ = ['get_singularity_image_filename', 'simulation_results_isnan']
 
 
-def get_singularity_image_filename(docker_image):
+def get_singularity_image_filename(docker_image: str) -> str:
     """ Get the location where a Singularity version of a Docker image should be saved
 
     Args:
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..6f79d0c
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,5138 @@
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+
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+version = "0.0.5"
+description = "A collection of accessible pygments styles"
+optional = false
+python-versions = ">=3.9"
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+    {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"},
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+
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+pygments = ">=1.5"
+
+[package.extras]
+dev = ["pillow", "pkginfo (>=1.10)", "playwright", "pre-commit", "setuptools", "twine (>=5.0)"]
+tests = ["hypothesis", "pytest"]
+
+[[package]]
+name = "airspeed"
+version = "0.6.0"
+description = "Airspeed is a powerful and easy-to-use templating engine for Python that aims for a high level of compatibility with the popular Velocity library for Java."
+optional = false
+python-versions = "*"
+files = [
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+]
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+[package.dependencies]
+cachetools = "*"
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+
+[[package]]
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+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
+optional = false
+python-versions = ">=3.9"
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+]
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+[[package]]
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+description = "High level compatibility layer for multiple asynchronous event loop implementations"
+optional = false
+python-versions = ">=3.8"
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+    {file = "anyio-4.5.0.tar.gz", hash = "sha256:c5a275fe5ca0afd788001f58fca1e69e29ce706d746e317d660e21f70c530ef9"},
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+trio = ["trio (>=0.26.1)"]
+
+[[package]]
+name = "appdirs"
+version = "1.4.4"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+optional = false
+python-versions = "*"
+files = [
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+    {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
+]
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+[[package]]
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+version = "0.1.4"
+description = "Disable App Nap on macOS >= 10.9"
+optional = false
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+
+[[package]]
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+version = "23.1.0"
+description = "Argon2 for Python"
+optional = false
+python-versions = ">=3.7"
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+[package.dependencies]
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+
+[package.extras]
+dev = ["argon2-cffi[tests,typing]", "tox (>4)"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-copybutton", "sphinx-notfound-page"]
+tests = ["hypothesis", "pytest"]
+typing = ["mypy"]
+
+[[package]]
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+version = "21.2.0"
+description = "Low-level CFFI bindings for Argon2"
+optional = false
+python-versions = ">=3.6"
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+description = "Better dates & times for Python"
+optional = false
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+brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
+secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
+socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+
+[[package]]
+name = "vtk"
+version = "9.3.1"
+description = "VTK is an open-source toolkit for 3D computer graphics, image processing, and visualization"
+optional = false
+python-versions = "*"
+files = [
+    {file = "vtk-9.3.1-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:c41ed344b9cc90ee9dcfc5967815de272985647d0c8e0a57f0e8b4229bc1b0b9"},
+    {file = "vtk-9.3.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:84c04327becc4c4dfe1fb04248baa4b5c480f188a9d52f4b912b163d33622442"},
+    {file = "vtk-9.3.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:890aee533fc0caca70bd1c8a4026b0d7f877518f237cc976ed4fb509d5f1dd83"},
+    {file = "vtk-9.3.1-cp310-cp310-win_amd64.whl", hash = "sha256:b8feed5029486703f4f8f81d8544a30d1788de87dc3396e16a281c343e1ac1cc"},
+    {file = "vtk-9.3.1-cp311-cp311-macosx_10_10_x86_64.whl", hash = "sha256:55e2df9e6993b959b482b79a6d68b8d46397b479d69738d41b1501396fcad50c"},
+    {file = "vtk-9.3.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:c977486b0e4d87cddb3f2c7c0710d1c86243cdd01286cbd036231143d8eb4f6e"},
+    {file = "vtk-9.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f8edc04e0f8b6719cfc769e575a777267d667f447d1948c62fa97fb756cd75bb"},
+    {file = "vtk-9.3.1-cp311-cp311-win_amd64.whl", hash = "sha256:59cc043f611e3eca2870cc50f27e67852a182857de322415e942bdc133594acd"},
+    {file = "vtk-9.3.1-cp312-cp312-macosx_10_10_x86_64.whl", hash = "sha256:05a4b6e387a906e8c8d6844441f9200116e937069fcf81f43e2600f26eb046de"},
+    {file = "vtk-9.3.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:bdbefb1aef9599a0a0b8222c9582f26946732a93534e6ec37d4b8e2c524c627e"},
+    {file = "vtk-9.3.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f728bb61f43fce850d622ced3b3d51b3116f767685ca4e4e0076f624e2d2307d"},
+    {file = "vtk-9.3.1-cp312-cp312-win_amd64.whl", hash = "sha256:685988e09070e06c8605886591698fd42d8225489509b6537a5046cd034cc93e"},
+    {file = "vtk-9.3.1-cp36-cp36m-macosx_10_10_x86_64.whl", hash = "sha256:7b8b8b77b903d5515f2fe551807a6b2ee3e7e3cd112174b184a921ab57352f1e"},
+    {file = "vtk-9.3.1-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:42684f38d8718b918fe1e4fee4e698d564b6daa16215c21811540c383e47dda2"},
+    {file = "vtk-9.3.1-cp36-cp36m-win_amd64.whl", hash = "sha256:4a5de9f424647bc3c02e2d2882401eac8ecd33f1a5f18261dcc69e7a05915c14"},
+    {file = "vtk-9.3.1-cp37-cp37m-macosx_10_10_x86_64.whl", hash = "sha256:279da9aee0fda31ee975e97b7b23480b54ea3b12d24ad8260760a3ededc32fad"},
+    {file = "vtk-9.3.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:102ac70e8dad0b111347f00ccef39aea1771f4f0381a4b0ff3f1ea6539e500c8"},
+    {file = "vtk-9.3.1-cp37-cp37m-win_amd64.whl", hash = "sha256:ee95c741a1ec3dc223c8233b1b59c5735c8249d4a15ee0b6370e7b010188397e"},
+    {file = "vtk-9.3.1-cp38-cp38-macosx_10_10_x86_64.whl", hash = "sha256:6adf4b812528a4658667602de8f023400c4381b8166f11b0ea8e0ab83c066539"},
+    {file = "vtk-9.3.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eaf90d0a797b5b7ada3fd0100c072dd146e674a2ccd25411036a4aca676f9101"},
+    {file = "vtk-9.3.1-cp38-cp38-win_amd64.whl", hash = "sha256:872e964c38dc1d969aaa29d10a5e56fd0324d61392e21dc044c679797fbdf0ef"},
+    {file = "vtk-9.3.1-cp39-cp39-macosx_10_10_x86_64.whl", hash = "sha256:3ae62397364be3a40f89025fa844cbf38b422633c0dff1065d90eec74ca6facb"},
+    {file = "vtk-9.3.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:ab96d6923fa37a202874cb8b8b4202d537bd4702bb151638d384e1966d877e3a"},
+    {file = "vtk-9.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:592b303f96b4cf907df7914bbf8c1f374df382c70c1d0b4fa4bd32ac1f4365ce"},
+    {file = "vtk-9.3.1-cp39-cp39-win_amd64.whl", hash = "sha256:6dee68abcd15603ad8ef6cef21fb13e2996d520a16880780abc41eb409dbec0c"},
+]
+
+[package.dependencies]
+matplotlib = ">=2.0.0"
+
+[package.extras]
+numpy = ["numpy (>=1.9)"]
+web = ["wslink (>=1.0.4)"]
+
+[[package]]
+name = "wcwidth"
+version = "0.2.13"
+description = "Measures the displayed width of unicode strings in a terminal"
+optional = false
+python-versions = "*"
+files = [
+    {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"},
+    {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
+]
+
+[[package]]
+name = "webcolors"
+version = "24.8.0"
+description = "A library for working with the color formats defined by HTML and CSS."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "webcolors-24.8.0-py3-none-any.whl", hash = "sha256:fc4c3b59358ada164552084a8ebee637c221e4059267d0f8325b3b560f6c7f0a"},
+    {file = "webcolors-24.8.0.tar.gz", hash = "sha256:08b07af286a01bcd30d583a7acadf629583d1f79bfef27dd2c2c5c263817277d"},
+]
+
+[package.extras]
+docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"]
+tests = ["coverage[toml]"]
+
+[[package]]
+name = "webencodings"
+version = "0.5.1"
+description = "Character encoding aliases for legacy web content"
+optional = false
+python-versions = "*"
+files = [
+    {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"},
+    {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"},
+]
+
+[[package]]
+name = "websocket-client"
+version = "1.8.0"
+description = "WebSocket client for Python with low level API options"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"},
+    {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"},
+]
+
+[package.extras]
+docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"]
+optional = ["python-socks", "wsaccel"]
+test = ["websockets"]
+
+[[package]]
+name = "xmltodict"
+version = "0.13.0"
+description = "Makes working with XML feel like you are working with JSON"
+optional = false
+python-versions = ">=3.4"
+files = [
+    {file = "xmltodict-0.13.0-py2.py3-none-any.whl", hash = "sha256:aa89e8fd76320154a40d19a0df04a4695fb9dc5ba977cbb68ab3e4eb225e7852"},
+    {file = "xmltodict-0.13.0.tar.gz", hash = "sha256:341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56"},
+]
+
+[[package]]
+name = "yamldown"
+version = "0.1.8"
+description = "Python library for loading and dumping \"yamldown\" (markdown with embedded yaml) files."
+optional = false
+python-versions = "*"
+files = [
+    {file = "yamldown-0.1.8-py3-none-any.whl", hash = "sha256:936ad7bdbde725d0bd3adb77236aae4eb75388619f31232595f7dd45f7006598"},
+    {file = "yamldown-0.1.8.tar.gz", hash = "sha256:ec1056e5ec3c47a7c14f69d343b73256ad12751361f1a833805a8ee722cf883c"},
+]
+
+[package.dependencies]
+pyYaml = "*"
+
+[metadata]
+lock-version = "2.0"
+python-versions = "~3.10"
+content-hash = "be65f99ae1bcc90efcf9a30c70596a771515400da486a50b29636c1877a48070"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..9839afb
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,61 @@
+[tool.poetry]
+name = "biosimulators-test-suite"
+version = "0.2"
+description = "Tools for validating that biosimulation tools are consistent with the BioSimulators standards"
+authors = ["Center for Reproducible Modeling <info@biosimulators.org>"]
+license = "MIT License (MIT)"
+readme = "README.md"
+homepage = "https://github.com/biosimulators/Biosimulators_test_suite"
+repository = "https://github.com/biosimulators/Biosimulators_test_suite"
+classifiers = [
+        'Development Status :: 3 - Alpha',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: MIT License',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+]
+keywords = ['systems', 'biology', 'modeling', 'simulation', 'BioSimulators']
+
+[tool.poetry.dependencies]
+python = "~3.10"
+
+cement = "<=3.0.6"
+docker = "^7.1.0"
+natsort = "<=8.1.0"
+pypdf2 = "<=2.8.1"
+requests = "<=2.28.1"
+python-dateutil = "<2.9"
+pyyaml = "<5.4"
+simplejson = "<3.17.0"
+termcolor = "<1.2"
+#biosimulators-utils = {git = "https://github.com/biosimulators/Biosimulators_utils.git", rev = "dev", extras = ["bngl", "cellml", "lems", "neuroml", "sbml", "simularium", "escher", "containers", "logging", "rba", "smoldyn"]}
+biosimulators-utils = {version = ">=0.2", extras = ["bngl", "cellml", "lems", "neuroml", "sbml", "simularium", "escher", "containers", "logging", "smoldyn"]} # add back "rba" after it is fixed
+
+[tool.poetry.group.dev.dependencies]
+capturer = "^3.0"
+docker = "^7.1.0"
+bezier = "*"
+flake8 = "^7.1.1"
+pytest = "^8.3.2"
+pytest-cov = "^5.0.0"
+flaky = "^3.8.1"
+jsonschema = "^4.23.0"
+
+[tool.poetry.group.docs.dependencies]
+pydata-sphinx-theme = "*"  # for building documentation
+sphinx = ">=1.8"
+sphinxprettysearchresults = { git = "https://github.com/biosimulators/sphinx-pretty-searchresults.git" }
+
+[tool.poetry.group.test.dependencies]
+setuptools = "^75.1.0"
+pytest = "^8.3.2"
+pytest-cov = "^5.0.0"
+flake8 = "^7.1.1"
+parameterized = "*"
+biosimulators_simularium = "*"
+
+[tool.poetry.scripts]
+biosimulators-test-suite = "biosimulators_test_suite.exec_cli:main"
+
+[build-system]
+requires = ["poetry-core", "flake8", "pytest"]
+build-backend = "poetry.core.masonry.api"
diff --git a/requirements.optional.txt b/requirements.optional.txt
deleted file mode 100644
index 5c51984..0000000
--- a/requirements.optional.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-[logging]
-biosimulators_utils[logging]
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 50766ff..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-numpy < 1.23.0
-biosimulators_utils[containers,bngl,cellml,lems,neuroml,sbml,smoldyn] >= 0.1.172
-cement
-docker
-natsort
-PyPDF2
-python_dateutil
-pyyaml
-simplejson
-termcolor
diff --git a/tests/results/test_results_io.py b/tests/results/test_results_io.py
index 1575970..8b39e8b 100644
--- a/tests/results/test_results_io.py
+++ b/tests/results/test_results_io.py
@@ -2,7 +2,7 @@
 from biosimulators_test_suite.data_model import TestCase
 from biosimulators_test_suite.results.data_model import TestCaseResult, TestCaseResultType
 from biosimulators_test_suite.results.io import write_test_results
-from biosimulators_test_suite.warnings import TestCaseWarning
+from biosimulators_test_suite.test_warnings import TestCaseWarning
 import json
 import os
 import shutil
diff --git a/tests/test_case/test_cli.py b/tests/test_case/test_cli.py
index d577325..2ca6f7f 100644
--- a/tests/test_case/test_cli.py
+++ b/tests/test_case/test_cli.py
@@ -1,5 +1,5 @@
 from biosimulators_test_suite.test_case import cli
-from biosimulators_test_suite.warnings import TestCaseWarning
+from biosimulators_test_suite.test_warnings import TestCaseWarning
 import shutil
 import tempfile
 import unittest
diff --git a/tests/test_case/test_combine_archive.py b/tests/test_case/test_combine_archive.py
index aa2de60..de44aa3 100644
--- a/tests/test_case/test_combine_archive.py
+++ b/tests/test_case/test_combine_archive.py
@@ -1,6 +1,6 @@
 from biosimulators_test_suite.test_case import combine_archive
 from biosimulators_test_suite.test_case.published_project import SimulatorCanExecutePublishedProject
-from biosimulators_test_suite.warnings import InvalidOutputsWarning
+from biosimulators_test_suite.test_warnings import InvalidOutputsWarning
 from biosimulators_utils.combine.data_model import CombineArchive, CombineArchiveContent, CombineArchiveContentFormat
 from biosimulators_utils.report.data_model import DataSetResults
 from biosimulators_utils.report.io import ReportWriter
diff --git a/tests/test_case/test_docker_image.py b/tests/test_case/test_docker_image.py
index c402dc0..9fcfd51 100644
--- a/tests/test_case/test_docker_image.py
+++ b/tests/test_case/test_docker_image.py
@@ -1,7 +1,7 @@
 from biosimulators_test_suite.test_case import docker_image
 from biosimulators_test_suite.test_case.published_project import SimulatorCanExecutePublishedProject
 from biosimulators_test_suite.exceptions import TestCaseException
-from biosimulators_test_suite.warnings import TestCaseWarning
+from biosimulators_test_suite.test_warnings import TestCaseWarning
 import os
 import shutil
 import tempfile
diff --git a/tests/test_case/test_published_project.py b/tests/test_case/test_published_project.py
index f13caf1..cd1eadf 100644
--- a/tests/test_case/test_published_project.py
+++ b/tests/test_case/test_published_project.py
@@ -1,10 +1,12 @@
+import pytest
+
 from biosimulators_test_suite import data_model
 from biosimulators_test_suite.exceptions import InvalidOutputsException, SkippedTestCaseException
 from biosimulators_test_suite.results.data_model import TestCaseResult, TestCaseResultType
 from biosimulators_test_suite.test_case.published_project import (
     SimulatorCanExecutePublishedProject, find_cases, SyntheticCombineArchiveTestCase,
     ExpectedResultOfSyntheticArchive, UniformTimeCourseTestCase)
-from biosimulators_test_suite.warnings import IgnoredTestCaseWarning, SimulatorRuntimeErrorWarning, InvalidOutputsWarning
+from biosimulators_test_suite.test_warnings import IgnoredTestCaseWarning, SimulatorRuntimeErrorWarning, InvalidOutputsWarning
 from biosimulators_utils.archive.data_model import Archive, ArchiveFile
 from biosimulators_utils.archive.io import ArchiveWriter
 from biosimulators_utils.combine.data_model import CombineArchive
@@ -58,6 +60,19 @@ def test_find_cases(self):
         self.assertEqual(len(all_cases), 0)
         self.assertEqual(len(compatible_cases), 0)
 
+        ### TEMPORARY RBA REMOVAL, REMOVE THIS NEXT SECTION IF RESTORED
+        with pytest.raises(RuntimeError):
+            all_cases, _ = find_cases({
+                'algorithms': [
+                    {
+                        'id': "rba",
+                        'kisaoId': {'id': 'KISAO_0000669'},
+                        'modelFormats': [{'id': 'format_2585', 'supportedFeatures': []}],
+                    }
+                ]
+            })
+
+
     def test_SimulatorCanExecutePublishedProject_description(self):
         case = SimulatorCanExecutePublishedProject(task_requirements=[
             data_model.SedTaskRequirements(model_format='format_2585', simulation_algorithm='KISAO_0000027'),
diff --git a/tests/test_case/test_results_report.py b/tests/test_case/test_results_report.py
index 2f697c8..533d3f6 100644
--- a/tests/test_case/test_results_report.py
+++ b/tests/test_case/test_results_report.py
@@ -1,6 +1,6 @@
 from biosimulators_test_suite.test_case import results_report
 from biosimulators_test_suite.test_case.published_project import SimulatorCanExecutePublishedProject
-from biosimulators_test_suite.warnings import TestCaseWarning
+from biosimulators_test_suite.test_warnings import TestCaseWarning
 from biosimulators_utils.report.data_model import DataSetResults
 from biosimulators_utils.report.io import ReportWriter
 from biosimulators_utils.sedml.data_model import SedDocument, Report, DataSet
diff --git a/tests/test_case/test_sedml.py b/tests/test_case/test_sedml.py
index 2822c0d..c31879f 100644
--- a/tests/test_case/test_sedml.py
+++ b/tests/test_case/test_sedml.py
@@ -1,7 +1,7 @@
 from biosimulators_test_suite.exceptions import InvalidOutputsException, SkippedTestCaseException
 from biosimulators_test_suite.test_case import sedml
 from biosimulators_test_suite.test_case.published_project import SimulatorCanExecutePublishedProject, SyntheticCombineArchiveTestCase
-from biosimulators_test_suite.warnings import InvalidOutputsWarning
+from biosimulators_test_suite.test_warnings import InvalidOutputsWarning
 from biosimulators_utils.archive.data_model import Archive, ArchiveFile
 from biosimulators_utils.archive.io import ArchiveWriter
 from biosimulators_utils.config import get_config
diff --git a/tests/test_examples.py b/tests/test_examples.py
index aedd390..9686ae0 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -1,3 +1,4 @@
+import pytest
 from biosimulators_utils.combine.io import CombineArchiveReader
 from biosimulators_utils.combine.data_model import CombineArchiveContentFormat
 from biosimulators_utils.combine.utils import get_sedml_contents
@@ -36,8 +37,22 @@ def setUp(self):
     def tearDown(self):
         shutil.rmtree(self.dirname)
 
+    # @parameterized.parameterized.expand(EXAMPLES)
+    # def test_example_should_fail(self, name, example_filename):
+    #     ### TEMPORARY RBA REMOVAL, REMOVE THIS TEST WHEN FIXED
+    #     if "rba" not in example_filename:
+    #         return
+    #     with pytest.raises(RuntimeError):
+    #         self.run_test_example(name, example_filename)
+
     @parameterized.parameterized.expand(EXAMPLES)
-    def test_example(self, name, example_filename):
+    def test_example_should_pass(self, name, example_filename):
+        ### TEMPORARY RBA REMOVAL
+        if "rba" in example_filename:
+            return
+        self.run_test_example(name, example_filename)
+
+    def run_test_example(self, name, example_filename):
         example_specs_filename = os.path.join(example_filename[0:-5], 'expected-results.json')
 
         example_base_dir = os.path.join(os.path.dirname(example_filename))
diff --git a/tests/test_exec_cli.py b/tests/test_exec_cli.py
index 7b652af..f4de971 100644
--- a/tests/test_exec_cli.py
+++ b/tests/test_exec_cli.py
@@ -4,7 +4,7 @@
 import biosimulators_test_suite.exec_core
 import biosimulators_test_suite.results.data_model
 import biosimulators_test_suite.test_case.published_project
-import biosimulators_test_suite.warnings
+import biosimulators_test_suite.test_warnings
 import json
 import os
 import shutil
@@ -96,8 +96,8 @@ def test_warnings(self):
                 type=biosimulators_test_suite.results.data_model.TestCaseResultType.passed,
                 duration=1.,
                 warnings=[
-                    mock.Mock(message=biosimulators_test_suite.warnings.TestCaseWarning('Warning-1')),
-                    mock.Mock(message=biosimulators_test_suite.warnings.TestCaseWarning('Warning-2')),
+                    mock.Mock(message=biosimulators_test_suite.test_warnings.TestCaseWarning('Warning-1')),
+                    mock.Mock(message=biosimulators_test_suite.test_warnings.TestCaseWarning('Warning-2')),
                 ],
             ),
         ]
diff --git a/tests/test_exec_core.py b/tests/test_exec_core.py
index 2afd567..84611f2 100644
--- a/tests/test_exec_core.py
+++ b/tests/test_exec_core.py
@@ -4,7 +4,7 @@
 from biosimulators_test_suite.results.data_model import TestCaseResult, TestCaseResultType
 from biosimulators_test_suite.test_case import published_project
 from biosimulators_test_suite.test_case.docker_image import HasBioContainersLabels
-from biosimulators_test_suite.warnings import TestCaseWarning, IgnoredTestCaseWarning
+from biosimulators_test_suite.test_warnings import TestCaseWarning, IgnoredTestCaseWarning
 from unittest import mock
 import sys
 import shutil
diff --git a/tests/test_exec_gh_action.py b/tests/test_exec_gh_action.py
index beab037..d6d4fab 100644
--- a/tests/test_exec_gh_action.py
+++ b/tests/test_exec_gh_action.py
@@ -3,7 +3,7 @@
 from biosimulators_test_suite.config import Config
 from biosimulators_test_suite.results.data_model import TestCaseResult, TestCaseResultType
 from biosimulators_test_suite.test_case.published_project import SimulatorCanExecutePublishedProject
-from biosimulators_test_suite.warnings import TestCaseWarning
+from biosimulators_test_suite.test_warnings import TestCaseWarning
 from biosimulators_utils.gh_action.data_model import GitHubActionCaughtError
 from biosimulators_utils.simulator_registry.data_model import SimulatorSubmission, IssueLabel
 from unittest import mock