diff --git a/prolint2/tests/test_api.py b/prolint2/tests/test_api.py deleted file mode 100644 index d96ac5c..0000000 --- a/prolint2/tests/test_api.py +++ /dev/null @@ -1,103 +0,0 @@ -import warnings -import pandas as pd -import pytest - -import MDAnalysis as mda -from typing import Literal, get_args - -from prolint2 import Universe -from prolint2.core.groups import ExtendedAtomGroup -from prolint2.sampledata import GIRKDataSample, COX1DataSample, SMODataSample - -GIRK = GIRKDataSample() -COX1 = COX1DataSample() -SMO = SMODataSample() - -warnings.filterwarnings("ignore") - -TimeUnitLiteral = Literal["fs", "ps", "ns", "us", "ms", "s"] - -# Build VALID_UNITS from TimeUnitLiteral -VALID_UNITS = get_args(TimeUnitLiteral) - - -@pytest.fixture(scope="module") -def universes(): - return [ - Universe(GIRK.coordinates, GIRK.trajectory), - Universe(COX1.coordinates, COX1.trajectory), - Universe(SMO.coordinates, SMO.trajectory), - ] - - -class TestUniverse: - def test_init_with_universe(self, universes): - for u in universes: - assert isinstance(u, Universe) - assert isinstance(u, mda.Universe) - - def test_query_property(self, universes): - for u in universes: - assert u.query is not None - assert isinstance(u.query, ExtendedAtomGroup) - - def test_database_property(self, universes): - for u in universes: - assert u.database is not None - assert isinstance(u.database, ExtendedAtomGroup) - - # def test_compute_contacts(self, universes): - # dict_of_contacts = {0: GIRK, 1: COX1, 2: SMO} - # for i, u in enumerate(universes): - # contacts = u.compute_contacts(cutoff=7) - # calc_df = contacts.create_dataframe(u.trajectory.n_frames) - # ref_df = pd.read_csv(dict_of_contacts[i].contacts, index_col=[0, 1]) - # ref_df.columns = ref_df.columns.astype(int) - # ref_df = ref_df.astype("int8") - # pd.testing.assert_frame_equal(calc_df, ref_df) - - # def test_load_contacts_from_file(self, universes): - # dict_of_contacts = {0: GIRK, 1: COX1, 2: SMO} - # for i, u in enumerate(universes): - # contacts = u.load_contacts_from_file(dict_of_contacts[i].contacts) - # calc_df = contacts.create_dataframe(u.trajectory.n_frames) - # ref_df = pd.read_csv(dict_of_contacts[i].contacts, index_col=[0, 1]) - # ref_df.columns = ref_df.columns.astype(int) - # ref_df = ref_df.astype("int8") - # pd.testing.assert_frame_equal(calc_df, ref_df) - - # def test_units_property(self, universes): - # for u in universes: - # assert u.units in VALID_UNITS - - # def test_units_property_setter(self, universes): - # for u in universes: - # new_units = "ns" - # u.units = new_units - # assert u.units == new_units - # assert u.units in VALID_UNITS - - # def test_normalize_by_property(self, universes): - # for u in universes: - # assert u.normalize_by in ["counts", "actual_time", "time_fraction"] - - # def test_normalize_by_property_setter(self, universes): - # for u in universes: - # new_normalize_by = "counts" - # u.normalize_by = new_normalize_by - # assert u.normalize_by == new_normalize_by - # assert u.normalize_by in ["counts", "actual_time", "time_fraction"] - - # def test_query_property_setter(self, universes): - # for u in universes: - # new_query = u.select_atoms("protein and (name CA or name BB)") - # u.query = new_query - # assert u.query is not None - # assert isinstance(u.query, ExtendedAtomGroup) - - # def test_database_property_setter(self, universes): - # for u in universes: - # new_database = u.select_atoms("resname CHOL or resname CHL1") - # u.database = new_database - # assert u.database is not None - # assert isinstance(u.database, ExtendedAtomGroup)