Merge Template

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

@@ -311,6 +311,10 @@ jobs:
           Copy-Item "openms-bin/${file}.exe" -Destination "streamlit_exe/${file}.exe"
         }
 
+    - name: Remove server address for local Windows deployment
+      run: |
+        (Get-Content streamlit_exe/.streamlit/config.toml) -notmatch '^address' | Set-Content streamlit_exe/.streamlit/config.toml
+
     - name: Generate Readme.txt
       shell: bash
       run: |

.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

.github/workflows/test-win-exe-w-embed-py.yaml

@@ -61,6 +61,10 @@ jobs:
           cp settings.json streamlit_exe
           cp default-parameters.json streamlit_exe
           cp ${{ env.APP_NAME }}.bat streamlit_exe
+
+      - name: Remove server address for local Windows deployment
+        run: |
+          (Get-Content streamlit_exe/.streamlit/config.toml) -notmatch '^address' | Set-Content streamlit_exe/.streamlit/config.toml
 
       - name: Generate Readme.txt
         shell: bash

.streamlit/config.toml

@@ -7,9 +7,6 @@ developmentMode = false
 [server]
 maxUploadSize = 1000 #MB
 port = 8501 # should be same as configured in deployment repo
-address = "0.0.0.0"
-enableCORS = false
-enableXsrfProtection = false
 
 
 [theme]

gdpr_consent/src/main.ts

@@ -114,6 +114,16 @@ function onRender(event: Event): void {
             }
         )
     }
+    if (data.args['matomo']) {
+        klaroConfig.services.push(
+            {
+                name: 'matomo',
+                purposes: ['analytics'],
+                onAccept: callback,
+                onDecline: callback,
+            }
+        )
+    }
 
     // Create a new script element
     var script = document.createElement('script')

hooks/hook-analytics.py

@@ -56,6 +56,21 @@ def piwik_pro_body(piwik_tag):
     """
 
 
+def matomo_head(matomo_url, matomo_tag):
+    return f"""
+    <!-- Matomo Tag Manager -->
+    <script>
+    var _mtm = window._mtm = window._mtm || [];
+    _mtm.push({{'mtm.startTime': (new Date().getTime()), 'event': 'mtm.Start'}});
+    (function() {{
+        var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
+        g.async=true; g.src='{matomo_url}/container_{matomo_tag}.js'; s.parentNode.insertBefore(g,s);
+    }})();
+    </script>
+    <!-- End Matomo Tag Manager -->
+    """
+
+
 if __name__ == '__main__':
 
     # Load configuration
@@ -79,6 +94,12 @@ def piwik_pro_body(piwik_tag):
         piwik_tag = settings['analytics']['piwik-pro']['tag']
         index = patch_body(index, piwik_pro_body(piwik_tag))
 
+    # Configure matomo tag manager
+    if settings['analytics']['matomo']['enabled']:
+        matomo_url = settings['analytics']['matomo']['url']
+        matomo_tag = settings['analytics']['matomo']['tag']
+        index = patch_head(index, matomo_head(matomo_url, matomo_tag))
+
     # Save index.html
     with open(index_path, 'w') as f:
         f.write(index)

settings.json

@@ -9,8 +9,13 @@
             "tag": ""
         },
         "piwik-pro": {
+            "enabled": false,
+            "tag": ""
+        },
+        "matomo": {
             "enabled": true,
-            "tag": "57690c44-d635-43b0-ab43-f8bd3064ca06"
+            "url": "https://cdn.matomo.cloud/openms.matomo.cloud",
+            "tag": "yDGK8bfY"
         }
     },
     "online_deployment": false,

src/common/captcha_.py

@@ -208,12 +208,13 @@ def captcha_control():
         # Check if consent for tracking was given
         ga = st.session_state.settings['analytics']['google-analytics']['enabled']
         pp = st.session_state.settings['analytics']['piwik-pro']['enabled']
-        if (ga or pp) and (st.session_state.tracking_consent is None):
+        mt = st.session_state.settings['analytics']['matomo']['enabled']
+        if (ga or pp or mt) and (st.session_state.tracking_consent is None):
             consent_component = st_components.declare_component("gdpr_consent", path=Path("gdpr_consent"))
             with st.spinner():
                 # Ask for consent
                 st.session_state.tracking_consent = consent_component(
-                    google_analytics=ga, piwik_pro=pp
+                    google_analytics=ga, piwik_pro=pp, matomo=mt
                 )
                 if st.session_state.tracking_consent is None:
                     # No response by user yet

src/common/common.py

@@ -405,6 +405,23 @@ def page_setup(page: str = "") -> dict[str, Any]:
                 width=1,
                 height=1,
             )
+        if (st.session_state.settings["analytics"]["matomo"]["enabled"]) and (
+            st.session_state.tracking_consent["matomo"] == True
+        ):
+            html(
+                """
+                <!DOCTYPE html>
+                <html lang="en">
+                    <head></head>
+                    <body><script>
+                    window.parent._mtm = window.parent._mtm || [];
+                    window.parent._mtm.push(['MTMSetConsentGiven']);
+                    </script></body>
+                </html>
+                """,
+                width=1,
+                height=1,
+            )
 
     # Determine the workspace for the current session
     if ("workspace" not in st.session_state) or (

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