diff --git a/.github/workflows/lint_and_test.yml b/.github/workflows/lint_and_test.yml
index 7f5f8c58..88941ee6 100644
--- a/.github/workflows/lint_and_test.yml
+++ b/.github/workflows/lint_and_test.yml
@@ -90,13 +90,13 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - name: Checkout workflow-inference-compiler
+      - name: Checkout sophios
         if: always()
         uses: actions/checkout@v3
         with:
-          repository: ${{ inputs.wic_owner }}/workflow-inference-compiler
+          repository: ${{ inputs.wic_owner }}/sophios
           ref: ${{ inputs.wic_ref }}
-          path: workflow-inference-compiler
+          path: sophios
 
       - name: Checkout biobb_adapters
         if: always()
@@ -127,11 +127,11 @@ jobs:
       # NOTE: pypy actually decreases performance for lint_and_test.yml (by a factor of ~2)
       # - name: Append pypy to conda environment files
       #   if: runner.os != 'Windows'
-      #   run: cd workflow-inference-compiler/install/ && echo "  - pypy" >> system_deps.yml
+      #   run: cd sophios/install/ && echo "  - pypy" >> system_deps.yml
 
       # - name: Append pypy to conda environment files
       #   if: runner.os == 'Windows'
-      #   run: cd workflow-inference-compiler/install/ && echo "  - pypy" >> system_deps_windows.yml
+      #   run: cd sophios/install/ && echo "  - pypy" >> system_deps_windows.yml
 
       - name: Setup miniforge (linux, macos)
         if: runner.os != 'Windows'
@@ -139,7 +139,7 @@ jobs:
         with:
           miniforge-variant: Miniforge-pypy3
           miniforge-version: 24.7.1-0
-          environment-file: workflow-inference-compiler/install/system_deps.yml
+          environment-file: sophios/install/system_deps.yml
           activate-environment: wic
           channels: conda-forge
           python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11
@@ -150,7 +150,7 @@ jobs:
         with:
           miniforge-variant: Miniforge-pypy3
           miniforge-version: 24.7.1-0
-          environment-file: workflow-inference-compiler/install/system_deps_windows.yml
+          environment-file: sophios/install/system_deps_windows.yml
           activate-environment: wic
           channels: conda-forge
           python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11
@@ -158,11 +158,11 @@ jobs:
       - name: ShellCheck Script Quality
         if: always()
         # "SC1017 (error): Literal carriage return. Run script through tr -d '\r' ."
-        run: shellcheck -e SC1017 $(find workflow-inference-compiler/ -name "*.sh" -and -not -path "./3/*")
+        run: shellcheck -e SC1017 $(find sophios/ -name "*.sh" -and -not -path "./3/*")
 
       - name: Install Workflow Inference Compiler
         if: always()
-        run: cd workflow-inference-compiler/ && pip install ".[all_except_runner_src]"
+        run: cd sophios/ && pip install ".[all_except_runner_src]"
 
       - name: Install Molecular Modeling Workflows
         if: always()
@@ -175,39 +175,39 @@ jobs:
 
       - name: Generate Sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+        run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
       - name: Generate Sophios Validation Jsonschema
         if: always()
-        run: cd workflow-inference-compiler/ && sophios --generate_schemas
+        run: cd sophios/ && sophios --generate_schemas
 
         # Please read docs/validation.md#Property-Based-Testing
         # This is essentially an integration test for all of the
         # Sophios Python API workflows as well as the Sophios Python API itself.
       - name: Validate sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+        run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
       - name: Build Documentation
         if: always()
-        run: cd workflow-inference-compiler/docs && make html
+        run: cd sophios/docs && make html
 
       - name: MyPy Check Type Annotations
         if: always()
-        run: cd workflow-inference-compiler/ && mypy src/ examples/ tests/
+        run: cd sophios/ && mypy src/ examples/ tests/
         # NOTE: Do not use `mypy .` because then mypy will check both src/ and build/ causing:
-        # src/workflow-inference-compiler/__init__.py: error: Duplicate module named "wic"
-        # (also at "./build/lib/workflow-inference-compiler/__init__.py")
+        # src/sophios/__init__.py: error: Duplicate module named "wic"
+        # (also at "./build/lib/sophios/__init__.py")
 
       - name: PyLint Check Code Quality
         if: always()
-        run: cd workflow-inference-compiler/ && pylint src/ examples/**/*.py tests/
+        run: cd sophios/ && pylint src/ examples/**/*.py tests/
         # NOTE: See fail-under threshold in .pylintrc
 
       - name: PEP8 Code Formatting
         if: always()
         id: autopep8
-        run: cd workflow-inference-compiler/ && autopep8 --exit-code --recursive --diff --max-line-length 120 examples/ src/ tests/
+        run: cd sophios/ && autopep8 --exit-code --recursive --diff --max-line-length 120 examples/ src/ tests/
       - name: Fail if autopep8 made changes
         if: steps.autopep8.outputs.exit-code == 2
         run: exit 1
@@ -216,13 +216,13 @@ jobs:
 
       - name: PyTest CWL Embedding Independence
         if: always()
-        run: cd workflow-inference-compiler/ && pytest -k test_cwl_embedding_independence # --cov --cov-config=.coveragerc_serial
+        run: cd sophios/ && pytest -k test_cwl_embedding_independence # --cov --cov-config=.coveragerc_serial
         # NOTE: This test MUST be run in serial! See is_isomorphic_with_timeout()
         timeout-minutes: 20 # backup timeout for windows
 
       - name: PyTest Inline Subworkflows
         if: always()
-        run: cd workflow-inference-compiler/ && pytest -k test_inline_subworkflows # --cov --cov-config=.coveragerc_serial
+        run: cd sophios/ && pytest -k test_inline_subworkflows # --cov --cov-config=.coveragerc_serial
         # NOTE: This test MUST be run in serial! See is_isomorphic_with_timeout()
         timeout-minutes: 20 # backup timeout for windows
 
@@ -231,7 +231,7 @@ jobs:
         # Avoid Windows and macOS due to 2X and 10X minute multipliers.
         # https://docs.github.com/en/billing/managing-billing-for-github-actions/about-billing-for-github-actions#minute-multipliers
         # Also, cannot run on Windows (natively) yet
-        run: cd workflow-inference-compiler/ && pytest -k test_scattering_scaling
+        run: cd sophios/ && pytest -k test_scattering_scaling
 
       # NOTE: The steps below are for repository_dispatch only. For all other steps, please insert above
       # this comment.
@@ -269,7 +269,7 @@ jobs:
         # https://github.com/actions/runner/issues/834#issuecomment-907096707
         # Use inputs.sender_repo to reply the original sender.
         if: always()
-        uses: ./workflow-inference-compiler/.github/my_actions/reply_sender/ # Must start with ./
+        uses: ./sophios/.github/my_actions/reply_sender/ # Must start with ./
         with:
           github_repository: ${{ github.repository }}
           event_type: ${{ inputs.event_type }}
diff --git a/.github/workflows/run_workflows.yml b/.github/workflows/run_workflows.yml
index f2c51e62..b2011439 100644
--- a/.github/workflows/run_workflows.yml
+++ b/.github/workflows/run_workflows.yml
@@ -68,12 +68,12 @@ jobs:
     runs-on: [self-hosted, linux]
 
     steps:
-    - name: Checkout workflow-inference-compiler
+    - name: Checkout sophios
       uses: actions/checkout@v3
       with:
-        repository: ${{ inputs.wic_owner }}/workflow-inference-compiler
+        repository: ${{ inputs.wic_owner }}/sophios
         ref: ${{ inputs.wic_ref }}
-        path: workflow-inference-compiler
+        path: sophios
 
     - name: Checkout biobb_adapters
       if: always()
@@ -109,7 +109,7 @@ jobs:
     # Using pypy increases performance / decreases cwltool runtime by about a minute.
     - name: Append pypy to conda environment files
       if: runner.os != 'Windows'
-      run: cd workflow-inference-compiler/install/ && echo "  - pypy" >> system_deps.yml
+      run: cd sophios/install/ && echo "  - pypy" >> system_deps.yml
 
     - name: Remove old mamba environment
       if: always()
@@ -128,7 +128,7 @@ jobs:
       with:
         miniforge-variant: Miniforge-pypy3
         miniforge-version: 24.7.1-0
-        environment-file: workflow-inference-compiler/install/system_deps.yml
+        environment-file: sophios/install/system_deps.yml
         activate-environment: wic_github_actions
         channels: conda-forge
         python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11
@@ -140,7 +140,7 @@ jobs:
 
     - name: Install Workflow Inference Compiler
       if: always()
-      run: cd workflow-inference-compiler/ && pip install ".[all_except_runner_src]"
+      run: cd sophios/ && pip install ".[all_except_runner_src]"
 
     - name: Install Molecular Modeling Workflows
       if: always()
@@ -153,48 +153,48 @@ jobs:
 
     - name: Generate Sophios Python API Workflows (*.py -> *.wic)
       if: always()
-      run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+      run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
     - name: Generate Sophios Validation Jsonschema
       if: always()
-      run: cd workflow-inference-compiler/ && sophios --generate_schemas
+      run: cd sophios/ && sophios --generate_schemas
 
       # Please read docs/validation.md#Property-Based-Testing
       # This is essentially an integration test for all of the
       # WIC Python API workflows as well as the WIC Python API itself.
     - name: Validate Sophios Python API Workflows (*.py -> *.wic)
       if: always()
-      run: cd workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+      run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
 
     - name: cwl-docker-extract (i.e. recursively docker pull)
       if: always()
-      run: cd workflow-inference-compiler/ && pytest tests/test_examples.py -k test_cwl_docker_extract
+      run: cd sophios/ && pytest tests/test_examples.py -k test_cwl_docker_extract
       # For self-hosted runners, make sure the docker cache is up-to-date.
 
     - name: PyTest Run Workflows
       if: always()
       # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
-      run: cd workflow-inference-compiler/ && pytest tests/test_examples.py -k test_run_workflows_on_push --workers 8 --cwl_runner cwltool # --cov
+      run: cd sophios/ && pytest tests/test_examples.py -k test_run_workflows_on_push --workers 8 --cwl_runner cwltool # --cov
 
     - name: PyTest Run REST Core Tests
       if: always()
       # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
-      run: cd workflow-inference-compiler/ && pytest tests/test_rest_core.py -k test_rest_core --cwl_runner cwltool
+      run: cd sophios/ && pytest tests/test_rest_core.py -k test_rest_core --cwl_runner cwltool
 
     - name: PyTest Run REST WFB Tests
       if: always()
       # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
-      run: cd workflow-inference-compiler/ && pytest tests/test_rest_wfb.py -k test_rest_wfb --cwl_runner cwltool
+      run: cd sophios/ && pytest tests/test_rest_wfb.py -k test_rest_wfb --cwl_runner cwltool
 
     - name: PyTest Run ICT to CLT conversion Tests
       if: always()
       # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
-      run: cd workflow-inference-compiler/ && pytest tests/test_ict_to_clt_conversion.py -k test_ict_to_clt
+      run: cd sophios/ && pytest tests/test_ict_to_clt_conversion.py -k test_ict_to_clt
 
     - name: PyTest Run update wfb payload Tests
       if: always()
       # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
-      run: cd workflow-inference-compiler/ && pytest tests/test_fix_payload.py -k test_fix
+      run: cd sophios/ && pytest tests/test_fix_payload.py -k test_fix
 
     # NOTE: The steps below are for repository_dispatch only. For all other steps, please insert above
     # this comment.
@@ -232,7 +232,7 @@ jobs:
       # https://github.com/actions/runner/issues/834#issuecomment-907096707
       # Use inputs.sender_repo to reply the original sender.
       if: always()
-      uses: ./workflow-inference-compiler/.github/my_actions/reply_sender/ # Must start with ./
+      uses: ./sophios/.github/my_actions/reply_sender/ # Must start with ./
       with:
         github_repository: ${{ github.repository }}
         event_type: ${{ inputs.event_type }}
diff --git a/src/sophios/input_output.py b/src/sophios/input_output.py
index a29581f5..9a1ea36a 100644
--- a/src/sophios/input_output.py
+++ b/src/sophios/input_output.py
@@ -141,6 +141,21 @@ def write_config_to_disk(config: Json, config_file: Path) -> None:
         json.dump(config, f, indent=4, sort_keys=True)
 
 
+def check_sister_directories(parent_dir: Path, target_names: list[str]) -> bool:
+    """Checks if sister directories with given names exist."""
+
+    parent_path = Path(parent_dir)
+    if not parent_path.is_dir():
+        return False
+
+    for target_name in target_names:
+        sister_path = parent_path.parent / target_name
+        if not sister_path.is_dir():
+            return False
+
+    return True
+
+
 def get_config(config_file: Path, default_config_file: Path) -> Json:
     """Returns the config json object from config_file with absolute paths
 
@@ -152,10 +167,10 @@ def get_config(config_file: Path, default_config_file: Path) -> Json:
         Json: The config json object with absolute filepaths
     """
     global_config: Json = {}
-    proj_root_dir = 'workflow-inference-compiler'
+    ci_sister_dirs = ['mm-workflows', 'image-workflows']
     if not config_file.exists():
-        # check if sophios is run from  'project root' dir
-        if str(Path.cwd()).endswith(proj_root_dir):
+        # check if sophios is run from  'ci environment' dir
+        if check_sister_directories(Path.cwd(), ci_sister_dirs):
             if config_file == default_config_file:
                 global_config = get_default_config()
                 # write the default config object to the 'global_config.json' file in user's ~/wic directory
diff --git a/tests/test_rest_core.py b/tests/test_rest_core.py
index 1802d039..cc9cf46a 100644
--- a/tests/test_rest_core.py
+++ b/tests/test_rest_core.py
@@ -132,6 +132,7 @@ async def receive() -> Json:
     res: Json = asyncio.run(restapi.compile_wf(req))  # call to rest api
     return res
 
+
 @pytest.mark.skip_pypi_ci
 @pytest.mark.fast
 def test_rest_core_single_node() -> None:
@@ -148,6 +149,7 @@ def test_rest_core_single_node() -> None:
     retval = run_cwl_local(workflow_name, 'cwltool', 'docker', False)
     assert retval == 0
 
+
 @pytest.mark.skip_pypi_ci
 def test_rest_core_single_node_bbbc() -> None:
     """A simple single node sophios/restapi test"""
@@ -163,6 +165,7 @@ def test_rest_core_single_node_bbbc() -> None:
     retval = run_cwl_local(workflow_name, 'cwltool', 'docker', False)
     assert retval == 0
 
+
 @pytest.mark.skip_pypi_ci
 def test_rest_core_bbbc_download_wfb() -> None:
     """A simple multi node (inline cwl) sophios/restapi test"""