Fix integration test failures caused by sys.modules pollution and shutil.SameFileError (#349)

* Initial plan

* Fix integration test failures: restore sys.modules mocks, handle SameFileError, update CI workflow

Co-authored-by: t0mdavid-m <57191390+t0mdavid-m@users.noreply.github.com>

* Remove unnecessary pyopenms mock from test_topp_workflow_parameter.py, simplify test_parameter_presets.py

Co-authored-by: t0mdavid-m <57191390+t0mdavid-m@users.noreply.github.com>

* Fix Windows build: correct site-packages path in cleanup step

Co-authored-by: t0mdavid-m <57191390+t0mdavid-m@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: t0mdavid-m <57191390+t0mdavid-m@users.noreply.github.com>

Author: Copilot

.github/workflows/build-windows-executable-app.yaml

@@ -248,7 +248,7 @@ jobs:
     - name: Clean up unnecessary Python files
       shell: pwsh
       run: |
-        $sitePkgs = "py/Lib/site-packages"
+        $sitePkgs = "python-${{ env.PYTHON_VERSION }}/Lib/site-packages"
 
         # Remove __pycache__ directories
         Get-ChildItem -Path $sitePkgs -Recurse -Directory -Filter "__pycache__" | Remove-Item -Recurse -Force

.github/workflows/ci.yml

@@ -8,19 +8,14 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        # Requirements file generated with python=3.11 
+        # Requirements file generated with python=3.12; tested with python=3.11
         python-version: ["3.11"]
     steps:
     - uses: actions/checkout@v4
-    - uses: conda-incubator/setup-miniconda@v3
+    - uses: actions/setup-python@v4
       with:
-        activate-environment: openms
         python-version: ${{ matrix.python-version }}
-        channels: defaults,bioconda,conda-forge
 
-    - name: Install OpenMS
-      run: |
-        conda install openms -y
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

test_gui.py

@@ -93,7 +93,10 @@ def test_view_raw_ms_data(launch, example):
 
     # Copy files from example-data/mzML to workspace mzML directory, add to selected files
     for f in Path("example-data", "mzML").glob("*.mzML"):
-        shutil.copy(f, mzML_dir)
+        try:
+            shutil.copy(f, mzML_dir)
+        except shutil.SameFileError:
+            pass  # File already exists as a symlink to the same source (on Linux)
     launch.run()
 
     ## TODO: Figure out a way to select a spectrum to be displayed
@@ -119,7 +122,10 @@ def test_run_workflow(launch, example):
 
     # Copy files from example-data/mzML to workspace mzML directory, add to selected files
     for f in Path("example-data", "mzML").glob("*.mzML"):
-        shutil.copy(f, mzML_dir)
+        try:
+            shutil.copy(f, mzML_dir)
+        except shutil.SameFileError:
+            pass  # File already exists as a symlink to the same source (on Linux)
     launch.run()
 
     ## Select experiments to process

tests/test_parameter_presets.py

@@ -16,19 +16,33 @@
 PROJECT_ROOT = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 sys.path.append(PROJECT_ROOT)
 
-# Create mock for streamlit before importing ParameterManager
+# Mock streamlit before importing ParameterManager so that the imported module
+# uses a controllable `st.session_state` (a plain dict) instead of the real one,
+# which requires a running Streamlit app context. This allows unit-testing
+# ParameterManager's preset logic (apply_preset, clear_parameter_session_state)
+# in isolation.
 mock_streamlit = MagicMock()
 mock_streamlit.session_state = {}
-sys.modules['streamlit'] = mock_streamlit
 
-# Create mock for pyopenms
-mock_pyopenms = MagicMock()
-mock_pyopenms.__version__ = "2.9.1"
-sys.modules['pyopenms'] = mock_pyopenms
+# Temporarily replace streamlit in sys.modules so that ParameterManager's
+# `import streamlit as st` picks up the mock. Restore immediately after import
+# so other test files (e.g., test_gui.py AppTest) get the real streamlit.
+_original_streamlit = sys.modules.get('streamlit')
+sys.modules['streamlit'] = mock_streamlit
 
-# Now import after mocks are set up
 from src.workflow.ParameterManager import ParameterManager
 
+if _original_streamlit is not None:
+    sys.modules['streamlit'] = _original_streamlit
+else:
+    sys.modules.pop('streamlit', None)
+
+# Remove cached src.workflow modules that were imported with mocked streamlit so
+# that AppTest (in test_gui.py) re-imports them fresh with the real package.
+for _key in list(sys.modules.keys()):
+    if _key.startswith('src.workflow'):
+        sys.modules.pop(_key, None)
+
 
 @pytest.fixture
 def temp_workflow_dir():

tests/test_topp_workflow_parameter.py

@@ -14,11 +14,6 @@
 PROJECT_ROOT = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 sys.path.append(PROJECT_ROOT)
 
-# Create mock for pyopenms to avoid dependency on actual OpenMS installation
-mock_pyopenms = MagicMock()
-mock_pyopenms.__version__ = "2.9.1"  # Mock version for testing
-sys.modules['pyopenms'] = mock_pyopenms
-
 @pytest.fixture
 def mock_streamlit():
     """Mock essential Streamlit components for testing parameter display."""
@@ -47,12 +42,6 @@ def mock_streamlit():
         }
 
 
-def test_mock_pyopenms():
-    """Verify that pyopenms mock is working correctly."""
-    import pyopenms
-    assert hasattr(pyopenms, '__version__')
-
-
 def test_topp_parameter_correctness():
     """Test that TOPP parameters are displayed with correct values."""
     # Define expected parameters with values