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@mpecchi
mpecchi committed May 20, 2024
1 parent a61e3f9 commit 6d6d40a
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13 changes: 10 additions & 3 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,16 @@


@pytest.fixture
def gcms() -> Project:
proj = Project(folder_path=minimal_case_dir, auto_save_to_excel=False)
return proj
def proj() -> Project:
project = Project(
folder_path=minimal_case_dir,
auto_save_to_excel=False,
compounds_to_rename_in_files={
"almost oleic acid": "oleic acid",
"dichlorobenzene": "p-dichlorobenzene",
},
)
return project


@pytest.fixture
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166 changes: 89 additions & 77 deletions tests/test_minimal_case.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,47 +2,36 @@
from pandas.testing import assert_frame_equal


def test_load_files_info(gcms, checked_files_info):
to_check = gcms.load_files_info()

assert_frame_equal(
to_check, checked_files_info, check_exact=False, atol=1e-5, rtol=1e-5
)


def test_create_files_info(gcms, checked_created_files_info):
to_check = gcms.create_files_info()
def test_files_info(proj):
files_info_created = proj.create_files_info(update_saved_files_info=False)
files_info_loaded = proj.load_files_info(update_saved_files_info=False)
assert_frame_equal(
to_check, checked_created_files_info, check_exact=False, atol=1e-5, rtol=1e-5
files_info_created[["samplename", "replicatenumber"]],
files_info_loaded[["samplename", "replicatenumber"]],
check_exact=False,
atol=1e-5,
rtol=1e-5,
)
assert files_info_created["dilution_factor"].tolist() == [1, 1, 1, 1, 1]
assert files_info_loaded["dilution_factor"].tolist() == [2, 2, 1, 1, 1]


def test_load_all_files(gcms, checked_files, checked_is_files_deriv):
def test_load_all_files(proj, checked_files, checked_is_files_deriv):

files_to_check, is_deriv_files_to_check = gcms.load_all_files()
for filename_to_check, checked_filename in zip(files_to_check, checked_files):
assert filename_to_check == checked_filename
files = proj.load_all_files()
assert list(files.keys()) == ["S_1", "S_2", "T_1", "T_2", "T_3"]

for file_to_check, checked_file in zip(
files_to_check.values(), checked_files.values()
):
assert_frame_equal(
file_to_check, checked_file, check_exact=False, atol=1e-5, rtol=1e-5
)

assert is_deriv_files_to_check == checked_is_files_deriv


def test_load_all_files_wrong_names(gcms):
wrong_files_info = gcms.create_files_info()
def test_load_all_files_wrong_names(proj):
wrong_files_info = proj.create_files_info()
wrong_files_info.index = ["Wrong_filename"] + wrong_files_info.index.tolist()[1:]
gcms.files_info = wrong_files_info
proj.files_info = wrong_files_info
with pytest.raises(FileNotFoundError):
gcms.load_all_files()
proj.load_all_files()


def test_load_class_code_fractions(gcms, checked_load_class_code_fractions):
to_check = gcms.load_class_code_frac()
def test_load_class_code_fractions(proj, checked_load_class_code_fractions):
to_check = proj.load_class_code_frac()
assert_frame_equal(
to_check,
checked_load_class_code_fractions,
Expand All @@ -53,37 +42,60 @@ def test_load_class_code_fractions(gcms, checked_load_class_code_fractions):


def test_load_calibrations(
gcms,
proj,
checked_load_calibrations,
):
files_info = gcms.create_files_info()
calib_to_check, is_calib_deriv_to_check = gcms.load_calibrations()
for to_check, checked in zip(calib_to_check, checked_load_calibrations):
assert to_check == checked

for to_check, checked in zip(
calib_to_check.values(), checked_load_calibrations.values()
):
assert_frame_equal(
to_check, checked, check_exact=False, atol=1e-5, rtol=1e-5
)

assert is_calib_deriv_to_check == False


def test_list_of_all_compounds(gcms, checked_list_of_all_compounds):
to_check = gcms.create_list_of_all_compounds()
assert to_check.sort() == checked_list_of_all_compounds.sort()
calibrations = proj.load_calibrations()
assert calibrations["cal_minimal"].index.tolist() == [
"phenol",
"naphthalene",
"dodecane",
"capric acid",
]
assert calibrations["cal_minimal"].columns.tolist() == [
"MW",
"PPM 1",
"PPM 2",
"PPM 3",
"PPM 4",
"PPM 5",
"PPM 6",
"Area 1",
"Area 2",
"Area 3",
"Area 4",
"Area 5",
"Area 6",
]


def test_list_of_all_compounds(proj):
to_check = proj.create_list_of_all_compounds()
print(to_check.sort())
assert (
to_check.sort()
== [
"capric acid",
"dodecane",
"notvalidcomp",
"p-dichlorobenzene",
# "oleic acid",
# "phenol",
# "naphthalene",
"palmitic acid",
].sort()
)
# assert to_check.sort() == checked_list_of_all_compounds.sort()


# def test_list_of_all_deriv_compounds(gcms, checked_list_of_all_deriv_compounds):
# to_check = gcms.create_list_of_all_deriv_compounds()
# def test_list_of_all_deriv_compounds(proj, checked_list_of_all_deriv_compounds):
# to_check = proj.create_list_of_all_deriv_compounds()
# assert to_check.sort() == checked_list_of_all_deriv_compounds.sort()


@pytest.mark.slow
def test_create_compounds_properties(gcms, checked_compounds_properties):
to_check = gcms.create_compounds_properties()
def test_create_compounds_properties(proj, checked_compounds_properties):
to_check = proj.create_compounds_properties()
assert_frame_equal(
to_check.sort_index(),
checked_compounds_properties.sort_index(),
Expand All @@ -95,8 +107,8 @@ def test_create_compounds_properties(gcms, checked_compounds_properties):


# @pytest.mark.slow
# def test_create_deriv_compounds_properties(gcms, checked_deriv_compounds_properties):
# to_check = gcms.create_deriv_compounds_properties()
# def test_create_deriv_compounds_properties(proj, checked_deriv_compounds_properties):
# to_check = proj.create_deriv_compounds_properties()
# assert_frame_equal(
# to_check.sort_index(),
# checked_deriv_compounds_properties.sort_index(),
Expand All @@ -106,8 +118,8 @@ def test_create_compounds_properties(gcms, checked_compounds_properties):
# )


def test_load_compounds_properties(gcms, checked_compounds_properties):
to_check = gcms.load_compounds_properties()
def test_load_compounds_properties(proj, checked_compounds_properties):
to_check = proj.load_compounds_properties()
assert_frame_equal(
to_check.sort_index(),
checked_compounds_properties.sort_index(),
Expand All @@ -117,8 +129,8 @@ def test_load_compounds_properties(gcms, checked_compounds_properties):
)


# def test_load_deriv_compounds_properties(gcms, checked_deriv_compounds_properties):
# to_check = gcms.load_deriv_compounds_properties()
# def test_load_deriv_compounds_properties(proj, checked_deriv_compounds_properties):
# to_check = proj.load_deriv_compounds_properties()
# assert_frame_equal(
# to_check.sort_index(),
# checked_deriv_compounds_properties.sort_index(),
Expand All @@ -128,8 +140,8 @@ def test_load_compounds_properties(gcms, checked_compounds_properties):
# )


def test_create_samples_info(gcms, checked_samples_info, checked_samples_info_std):
to_check, to_check_std = gcms.create_samples_info()
def test_create_samples_info(proj, checked_samples_info, checked_samples_info_std):
to_check, to_check_std = proj.create_samples_info()
assert_frame_equal(
to_check, checked_samples_info, check_exact=False, atol=1e-5, rtol=1e-5
)
Expand All @@ -150,8 +162,8 @@ def test_create_samples_info(gcms, checked_samples_info, checked_samples_info_st
"fraction_of_feedstock_fr",
],
)
def test_files_param_reports(gcms, checked_files_param_reports, parameter):
to_check = gcms.create_files_param_report(param=parameter)
def test_files_param_reports(proj, checked_files_param_reports, parameter):
to_check = proj.create_files_param_report(param=parameter)
checked_report = checked_files_param_reports[parameter]
assert_frame_equal(
to_check.sort_index(),
Expand All @@ -162,9 +174,9 @@ def test_files_param_reports(gcms, checked_files_param_reports, parameter):
)


def test_files_param_reports_exception(gcms):
def test_files_param_reports_exception(proj):
with pytest.raises(ValueError):
gcms.create_files_param_report(param="wrong_parameter")
proj.create_files_param_report(param="wrong_parameter")


@pytest.mark.parametrize(
Expand All @@ -179,8 +191,8 @@ def test_files_param_reports_exception(gcms):
"fraction_of_feedstock_fr",
],
)
def test_files_param_aggrreps(gcms, checked_files_param_aggrreps, parameter):
to_check = gcms.create_files_param_aggrrep(param=parameter)
def test_files_param_aggrreps(proj, checked_files_param_aggrreps, parameter):
to_check = proj.create_files_param_aggrrep(param=parameter)
checked_report = checked_files_param_aggrreps[parameter]
assert_frame_equal(
to_check.sort_index(),
Expand All @@ -191,9 +203,9 @@ def test_files_param_aggrreps(gcms, checked_files_param_aggrreps, parameter):
)


def test_files_param_aggreps_exception(gcms):
def test_files_param_aggreps_exception(proj):
with pytest.raises(ValueError):
gcms.create_files_param_aggrrep(param="wrong_parameter")
proj.create_files_param_aggrrep(param="wrong_parameter")


@pytest.mark.parametrize(
Expand All @@ -209,9 +221,9 @@ def test_files_param_aggreps_exception(gcms):
],
)
def test_samples_param_reports(
gcms, checked_samples_param_reports, checked_samples_param_reports_std, parameter
proj, checked_samples_param_reports, checked_samples_param_reports_std, parameter
):
to_check, to_check_std = gcms.create_samples_param_report(param=parameter)
to_check, to_check_std = proj.create_samples_param_report(param=parameter)
checked_report = checked_samples_param_reports[parameter]
checked_report_std = checked_samples_param_reports_std[parameter]
assert_frame_equal(
Expand All @@ -230,9 +242,9 @@ def test_samples_param_reports(
)


def test_samples_param_reports_exception(gcms):
def test_samples_param_reports_exception(proj):
with pytest.raises(ValueError):
gcms.create_samples_param_report(param="wrong_parameter")
proj.create_samples_param_report(param="wrong_parameter")


@pytest.mark.parametrize(
Expand All @@ -248,9 +260,9 @@ def test_samples_param_reports_exception(gcms):
],
)
def test_samples_param_aggrreps(
gcms, checked_samples_param_aggrreps, checked_samples_param_aggrreps_std, parameter
proj, checked_samples_param_aggrreps, checked_samples_param_aggrreps_std, parameter
):
to_check, to_check_std = gcms.create_samples_param_aggrrep(param=parameter)
to_check, to_check_std = proj.create_samples_param_aggrrep(param=parameter)
checked_report = checked_samples_param_aggrreps[parameter]
checked_report_std = checked_samples_param_aggrreps_std[parameter]
assert_frame_equal(
Expand All @@ -269,6 +281,6 @@ def test_samples_param_aggrreps(
)


def test_samples_param_aggrreps_exception(gcms):
def test_samples_param_aggrreps_exception(proj):
with pytest.raises(ValueError):
gcms.create_samples_param_aggrrep(param="wrong_parameter")
proj.create_samples_param_aggrrep(param="wrong_parameter")
2 changes: 2 additions & 0 deletions tests/test_project_class.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,11 @@
"dichlorobenzene": "p-dichlorobenzene",
},
)

# %%
files_info_created = proj.create_files_info(update_saved_files_info=False)
print(files_info_created.T)

files_info_loaded = proj.load_files_info(update_saved_files_info=False)
print(files_info_loaded.T)
# %%
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