Fix integration test failures caused by sys.modules pollution and shutil.SameFileError

[Copilot]

Two test files were replacing sys.modules['streamlit'] and sys.modules['pyopenms'] with MagicMocks at module level, causing pytest to poison the global module registry during collection — before any tests ran. This broke all test_gui.py AppTest runs with ModuleNotFoundError: No module named 'streamlit.emojis'; 'streamlit' is not a package. A separate shutil.SameFileError caused test failures when symlinks created by test_file_upload_load_example were re-copied in subsequent tests.

Changes

• tests/test_parameter_presets.py — Removed the unnecessary pyopenms mock. The streamlit mock is still needed because ParameterManager imports streamlit at the top level and the tests need st.session_state to be a controllable plain dict for unit testing preset logic without a running Streamlit app context. The mock is now saved and restored immediately after importing ParameterManager, and cached src.workflow.* entries are evicted so AppTest re-imports them with the real package:

  _original_streamlit = sys.modules.get('streamlit')
  sys.modules['streamlit'] = mock_streamlit
  from src.workflow.ParameterManager import ParameterManager
  # Restore so test_gui.py AppTests get the real streamlit
  sys.modules['streamlit'] = _original_streamlit  # (or pop if was absent)
  for _key in list(sys.modules.keys()):
      if _key.startswith('src.workflow'):
          sys.modules.pop(_key, None)

• tests/test_topp_workflow_parameter.py — Removed all module-level mocks entirely. The tests use pure MagicMock objects and don't import any src.* modules, so the pyopenms mock served no purpose. Also removed the test_mock_pyopenms test that only verified the mock was working.

• test_gui.py — Catch shutil.SameFileError when copying example mzML files into the workspace. On Linux, load_example_mzML_files() creates symlinks pointing back to the same source files, so a subsequent shutil.copy raises SameFileError:

  for f in Path("example-data", "mzML").glob("*.mzML"):
      try:
          shutil.copy(f, mzML_dir)
      except shutil.SameFileError:
          pass  # already exists as a symlink to the same source

• .github/workflows/ci.yml — Replace conda-incubator/setup-miniconda + conda install openms with actions/setup-python@v4. pyopenms is already a standalone PyPI package in requirements.txt; the conda layer was redundant and conflicted with the pip-installed streamlit.

• .github/workflows/build-windows-executable-app.yaml — Fix the "Clean up unnecessary Python files" step which used a hardcoded wrong path py/Lib/site-packages instead of python-${{ env.PYTHON_VERSION }}/Lib/site-packages, matching the path used by the "Install Required Packages" step.

Original prompt

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This section details on the original issue you should resolve

<issue_title>Integration Tests are failing.</issue_title>
<issue_description>continuous-integration / test (ubuntu-latest, 3.11) (push)
continuous-integration / test (ubuntu-latest, 3.11) (push)Failing after 2m
Test workflow functions / build (pull_request)
Test workflow functions / build (pull_request)Failing after 1m</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Integration Tests are failing. #348

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[t0mdavid-m]

@copilot Why do we need mocks here?

[Copilot]

@copilot Why do we need mocks here?

The pyopenms mock in test_topp_workflow_parameter.py wasn't needed — the tests use pure MagicMock objects and don't import any src.* modules. Removed it entirely in c3715d1.

In test_parameter_presets.py, the streamlit mock is still needed: ParameterManager does import streamlit as st at the top level, and the tests need st.session_state to be a controllable plain dict (for testing apply_preset, clear_parameter_session_state, etc.) without requiring a running Streamlit app context. Removed the unnecessary pyopenms mock from there too.

[t0mdavid-m]

@copilot fix the error in the windows build

[Copilot]

@copilot fix the error in the windows build

The "Clean up unnecessary Python files" step in build-windows-executable-app.yaml used a hardcoded path py/Lib/site-packages that doesn't exist — the embeddable Python is installed at python-3.11.0/Lib/site-packages. Fixed the path to use python-${{ env.PYTHON_VERSION }}/Lib/site-packages to match the install step on line 246. This was a pre-existing bug, not introduced by my changes. Fixed in 6af0435.