Merge branch 'test_audit' into 'master'

Improvement of CoreMS tests

See merge request mass-spectrometry/corems!126

Author: corilo

SettingsCoreMS.json

@@ -0,0 +1,36 @@
+import pytest
+from pathlib import Path
+
+from corems.transient.input.brukerSolarix import ReadBrukerSolarix
+from corems.encapsulation.factory.parameters import MSParameters
+
+@pytest.fixture
+def mass_spectrum_ftms(bruker_transient):
+    """Creates a mass spectrum object to be used in the tests"""
+    # Instantiate the mass spectrum object
+    mass_spectrum = bruker_transient.get_mass_spectrum(
+        plot_result=False, auto_process=False, keep_profile=True
+    )
+    mass_spectrum.parameters = MSParameters(use_defaults=True)
+    # Process the mass spectrum
+    mass_spectrum.process_mass_spec()
+
+    return mass_spectrum
+
+@pytest.fixture
+def ref_file_location():
+    """Returns the location of the reference file for calibration for the tests"""
+    return Path.cwd() / "tests/tests_data/ftms/SRFA.ref"
+
+@pytest.fixture
+def ftms_file_location():
+    """Returns the location of the FTMS file for the tests"""
+    return Path.cwd() / "tests/tests_data/ftms/ESI_NEG_SRFA.d/"
+
+@pytest.fixture
+def bruker_transient(ftms_file_location):
+    """Returns the transient object for the FTMS file"""
+    bruker_reader = ReadBrukerSolarix(ftms_file_location)
+    bruker_transient = bruker_reader.get_transient()
+
+    return bruker_transient

SettingsCoreMS.toml

@@ -1,4 +1,5 @@
 [pytest]
+# To run tests with coverage, uncomment the following line
 addopts = -ra -v --cov=corems --cov-config=pytest.ini --cov-report html --cov-report term -p no:warnings
 norecursedirs = win_only
 testpaths = tests

conftest.py

@@ -1,6 +1,6 @@
 pylint
-pytest~=7.2.1
-pytest-cov
+pytest~=8.3.2
+pytest-cov~=5.0.0
 pyprof2calltree
 memory_profiler
 twine

pytest.ini

@@ -1,3 +1,4 @@
+'''
 import sys
 
 sys.path.append(".")
@@ -46,3 +47,4 @@
     mass_spec = lcms.get_mass_spec_by_scan_number(1)
     mass_spec.plot_mz_domain_profile()
     mass_spec.plot_profile_and_noise_threshold()
+'''