Merge pull request OpenMS#8594 from OpenMS/copilot/fix-env-imports-in-tests

Replace env.py import hacks in pyOpenMS tests with pytest fixtures

Author: jpfeuffer

src/pyOpenMS/CMakeLists.txt

@@ -188,6 +188,7 @@ _copy_assets("${PROJECT_SOURCE_DIR}/pyopenms/" "*.sh" ${CMAKE_BINARY_DIR}/pyOpen
 _copy_assets("${PROJECT_SOURCE_DIR}/pyopenms/" "*.pyi" ${CMAKE_BINARY_DIR}/pyOpenMS/pyopenms/)
 _copy_assets("${PROJECT_SOURCE_DIR}/pyopenms/" "py.typed" ${CMAKE_BINARY_DIR}/pyOpenMS/pyopenms/)
 _copy_assets("${PROJECT_SOURCE_DIR}/pyTOPP/" "*.py" ${CMAKE_BINARY_DIR}/pyOpenMS/pyTOPP/)
+_copy_assets("${PROJECT_SOURCE_DIR}/tests/" "*.py" ${CMAKE_BINARY_DIR}/pyOpenMS/tests)
 _copy_assets("${PROJECT_SOURCE_DIR}/tests/unittests/" "*" ${CMAKE_BINARY_DIR}/pyOpenMS/tests/unittests)
 _copy_assets("${PROJECT_SOURCE_DIR}/tests/" "*.mzXML" ${CMAKE_BINARY_DIR}/pyOpenMS/tests)
 _copy_assets("${PROJECT_SOURCE_DIR}/tests/memoryleaktests/" "*" ${CMAKE_BINARY_DIR}/pyOpenMS/tests/memoryleaktests)

src/pyOpenMS/README.md

@@ -61,6 +61,24 @@ Build instructions
    ```
 
    "-R" to restrict to pyopenms* tests. If running out of the OpenMS build tree, this should not be necessary.
+   
+   **Alternative: Running tests directly with pytest**
+   
+   For development and debugging, you can run tests directly with pytest:
+   
+   ```bash
+   cd <build-dir>/pyOpenMS
+   python -m pytest tests/unittests
+   python -m pytest tests/integration_tests
+   ```
+   
+   Tests automatically locate test data files using the `conftest.py` configuration. If test data
+   is in a non-standard location, set the `OPENMS_TEST_DATA_PATH` environment variable:
+   
+   ```bash
+   export OPENMS_TEST_DATA_PATH=/path/to/OpenMS/src/tests/topp
+   python -m pytest tests/
+   ```
 
 6. Install locally (and in-place for live edits [option -e]) into current Python with
 
@@ -156,3 +174,42 @@ After modifying addon `.pyx` files, force regeneration:
 rm OpenMS-build/pyOpenMS/.cpp_extension_generated
 cmake --build OpenMS-build --target pyopenms -j4
 ```
+
+### Writing Tests
+
+Tests are located in `src/pyOpenMS/tests/`:
+- `unittests/` - Unit tests for individual components
+- `integration_tests/` - Integration tests requiring test data files
+- `memoryleaktests/` - Memory leak detection tests
+
+**Accessing test data files:**
+
+Tests automatically find test data through the `openms_test_data_dir` pytest fixture defined in `conftest.py`:
+
+```python
+import pytest
+import os
+
+class TestMyFeature(unittest.TestCase):
+    
+    @pytest.fixture(autouse=True)
+    def setup_test_data(self, openms_test_data_dir):
+        """Setup test with test data directory."""
+        self.test_file = os.path.join(openms_test_data_dir, "my_test_file.mzML")
+    
+    def test_something(self):
+        # Use self.test_file here
+        pass
+```
+
+The fixture automatically locates test data using multiple strategies:
+1. `OPENMS_TEST_DATA_PATH` environment variable (for custom locations)
+2. Relative path from source tree (works in development)
+3. CMake-configured env.py (backwards compatibility)
+
+To override test data location:
+```bash
+export OPENMS_TEST_DATA_PATH=/path/to/OpenMS/src/tests/topp
+python -m pytest tests/
+```
+

src/pyOpenMS/tests/conftest.py

@@ -0,0 +1,80 @@
+"""
+Pytest configuration file for pyOpenMS tests.
+
+This file provides fixtures and configuration for test data paths,
+replacing the old env.py import pattern.
+"""
+
+import os
+
+# Import pytest only if available (needed for fixtures)
+try:
+    import pytest
+    _HAS_PYTEST = True
+except ImportError:
+    _HAS_PYTEST = False
+
+
+def _get_test_data_dir():
+    """
+    Get the path to the OpenMS test data directory.
+    
+    This function tries multiple strategies to find the test data:
+    1. Check the OPENMS_TEST_DATA_PATH environment variable (for custom locations)
+    2. Use relative path from this file (works for regular source clones)
+    3. Try to import env.py if available (for CMake builds, backwards compatibility)
+    
+    Returns:
+        str: Path to the test data directory (src/tests/topp)
+    """
+    # Strategy 1: Check environment variable for override
+    env_path = os.environ.get('OPENMS_TEST_DATA_PATH')
+    if env_path and os.path.isdir(env_path):
+        return env_path
+    
+    # Strategy 2: Use relative path from this conftest.py file
+    # This works for regular clones where the structure is:
+    # src/pyOpenMS/tests/conftest.py  (this file)
+    # src/tests/topp/                 (test data)
+    tests_dir = os.path.dirname(os.path.abspath(__file__))
+    relative_path = os.path.join(tests_dir, '..', '..', '..', 'src', 'tests', 'topp')
+    relative_path = os.path.normpath(relative_path)
+    if os.path.isdir(relative_path):
+        return relative_path
+    
+    # Strategy 3: Try to import env.py (backwards compatibility for CMake builds)
+    try:
+        import env
+        if hasattr(env, 'PYOPENMS_SRC_DIR'):
+            env_based_path = os.path.join(env.PYOPENMS_SRC_DIR, "..", "..", "src", "tests", "topp")
+            env_based_path = os.path.normpath(env_based_path)
+            if os.path.isdir(env_based_path):
+                return env_based_path
+    except ImportError:
+        pass
+    
+    # If all strategies fail, raise an error
+    raise RuntimeError(
+        "Could not locate OpenMS test data directory. "
+        "Please set the OPENMS_TEST_DATA_PATH environment variable to point to "
+        "the 'src/tests/topp' directory, or ensure you're running tests from a "
+        "complete OpenMS source tree."
+    )
+
+
+# Only define pytest fixtures if pytest is available
+if _HAS_PYTEST:
+    @pytest.fixture(scope='session')
+    def openms_test_data_dir():
+        """
+        Pytest fixture providing the path to the OpenMS test data directory.
+        
+        Usage in tests:
+            def test_something(openms_test_data_dir):
+                data_file = os.path.join(openms_test_data_dir, "test_file.mzML")
+        
+        Returns:
+            str: Path to the test data directory
+        """
+        return _get_test_data_dir()
+

src/pyOpenMS/tests/integration_tests/test_MRMRTNormalizer.py

@@ -1,7 +1,7 @@
-import unittest,os
+import unittest
+import os
+import pytest
 
-## UGLY HACK!! This imports the *FILE* env.py that is configured by CMake. Even uglier since there is a module called env!!
-import env
 import pyopenms
 from collections import defaultdict
 
@@ -28,9 +28,10 @@ def simple_find_best_feature(output, pairs, targeted):
 class TestMRMRTNormalizer(unittest.TestCase):
     """Emulates the behavior of OpenSwathMRMRTNormalizer"""
 
-    def setUp(self):
-        # TODO make the tests self-consistent to only use files under the pyOpenMS directory
-        self.testdirname = os.path.join(env.PYOPENMS_SRC_DIR, "..", "..", "src/tests/topp")
+    @pytest.fixture(autouse=True)
+    def setup_test_data(self, openms_test_data_dir):
+        """Setup test with test data directory from pytest fixture."""
+        self.testdirname = openms_test_data_dir
         # set up files
         self.chromatograms = os.path.join(self.testdirname, "OpenSwathRTNormalizer_1_input.mzML").encode()
         self.tramlfile = os.path.join(self.testdirname, "OpenSwathRTNormalizer_1_input.TraML").encode()

src/pyOpenMS/tests/unittests/test_MRMFeatureFinderScoring.py

@@ -1,19 +1,18 @@
 import unittest
 import os
+import pytest
 
 import pyopenms
 
-## UGLY HACK!! This imports the *FILE* env.py that is configured by CMake. Even uglier since there is a module called env!!
-import env
-
 eps = 2
 
 class TestMRMFeatureFinderScoring(unittest.TestCase):
 
-    def setUp(self):
+    @pytest.fixture(autouse=True)
+    def setup_test_data(self, openms_test_data_dir):
+        """Setup test with test data directory from pytest fixture."""
         self.dirname = os.path.dirname(os.path.abspath(__file__))
-        # TODO make the tests self-consistent to only use files under the pyOpenMS directory
-        self.testdirname = os.path.join(env.PYOPENMS_SRC_DIR, "..", "..", "src/tests/topp")
+        self.testdirname = openms_test_data_dir
         # set up files
         self.chromatograms = os.path.join(self.testdirname, "OpenSwathAnalyzer_1_input_chrom.mzML").encode()
         self.tramlfile = os.path.join(self.testdirname, "OpenSwathAnalyzer_1_input.TraML").encode()