fixed test function names

Author: stefdoerr

pyproject.toml

@@ -82,7 +82,6 @@ dev = [{ include-group = "test" }, "ipython>=8.18.1"]
 override-dependencies = ["docutils>=0.20"]
 
 [tool.pytest.ini_options]
-python_functions = "_test*"
 testpaths = ["tests"]
 
 

tests/test_atomselect.py

@@ -113,7 +113,7 @@ def _pdbmols():
 
 @pytest.mark.parametrize("pdbid", _PDBIDS)
 @pytest.mark.parametrize("sel", _SELECTIONS)
-def _test_atomselect(pdbid, sel, _pdbmols):
+def test_atomselect(pdbid, sel, _pdbmols):
     from moleculekit.atomselect.analyze import analyze
     from moleculekit.atomselect.atomselect import atomselect
     import pickle
@@ -183,7 +183,7 @@ def _test_atomselect(pdbid, sel, _pdbmols):
             pickle.dump(results, f)
 
 
-def _test_empty_molecule():
+def test_empty_molecule():
     mol = Molecule()
     selections = [
         "all",
@@ -214,7 +214,7 @@ def _test_empty_molecule():
         assert res.dtype == bool, f"Expected bool dtype for '{sel}', got {res.dtype}"
 
 
-def _test_single_atom_molecule():
+def test_single_atom_molecule():
     mol = Molecule()
     mol.empty(1)
     mol.record[:] = "ATOM"
@@ -266,7 +266,7 @@ def _test_single_atom_molecule():
         assert not res[0], f"Expected False for '{sel}'"
 
 
-def _test_numprop_list_equality():
+def test_numprop_list_equality():
     pdb = os.path.join(curr_dir, "test_atomselect", "test.pdb")
     mol = Molecule(pdb)
     selections = ["beta 1 2", "beta 2 3"]
@@ -329,7 +329,7 @@ def _test_numprop_list_equality():
 
 
 @pytest.mark.parametrize("sel", _PARSER_SELECTIONS)
-def _test_parser(sel):
+def test_parser(sel):
     from moleculekit.atomselect._languageparser import parser
 
     # Parse an expression

tests/test_atomtyper.py

@@ -13,7 +13,7 @@
     HAS_OPENBABEL = True
 
 
-def _test_preparation():
+def test_preparation():
     from moleculekit.molecule import Molecule, mol_equal
     from moleculekit.tools.atomtyper import prepareProteinForAtomtyping
     from os import path
@@ -30,7 +30,7 @@ def _test_preparation():
 @pytest.mark.skipif(
     sys.platform.startswith("win"), reason="Windows OBabel fails at atom typing"
 )
-def _test_obabel_atomtyping():
+def test_obabel_atomtyping():
     from moleculekit.molecule import Molecule
     from moleculekit.tools.atomtyper import getPDBQTAtomTypesAndCharges
     from os import path

tests/test_autosegment.py

@@ -5,7 +5,7 @@
 curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 
-def _test_autoSegment2_deprecated_shim():
+def test_autoSegment2_deprecated_shim():
     import warnings
     from moleculekit.molecule import Molecule
     from moleculekit.tools.autosegment import autoSegment, autoSegment2
@@ -26,7 +26,7 @@ def _test_autoSegment2_deprecated_shim():
     assert np.array_equal(shim.chain, ref.chain)
 
 
-def _test_autoSegment_classify():
+def test_autoSegment_classify():
     from moleculekit.molecule import Molecule
     from moleculekit.tools.autosegment import _classify_residues
 
@@ -41,7 +41,7 @@ def _test_autoSegment_classify():
     assert "nucleic" not in cats
 
 
-def _test_autoSegment_linked():
+def test_autoSegment_linked():
     from moleculekit.molecule import Molecule
     from moleculekit.tools.autosegment import _polymer_linked, _classify_residues
 
@@ -66,7 +66,7 @@ def _test_autoSegment_linked():
     assert np.mean(linked) > 0.95
 
 
-def _test_autoSegment_1aud_continuous():
+def test_autoSegment_1aud_continuous():
     from os import path
     from moleculekit.molecule import Molecule
     from moleculekit.tools.autosegment import autoSegment
@@ -78,14 +78,14 @@ def _test_autoSegment_1aud_continuous():
     assert len(rna_segids) == 1, f"expected 1 RNA segment, got {rna_segids}"
 
 
-def _test_autoSegment_3ptb_buckets():
+def test_autoSegment_3ptb_buckets():
     from moleculekit.molecule import Molecule
     from moleculekit.tools.autosegment import autoSegment
 
     mol = Molecule("3ptb")
     out = autoSegment(mol, fields=("chain", "segid"))
 
-    # Same index ranges as the existing _test_autosegment_detailed
+    # Same index ranges as the existing test_autosegment_detailed
     prot_idx = np.arange(1629)
     ca_idx = np.array([1629])
     ben_idx = np.arange(1630, 1639)
@@ -109,7 +109,7 @@ def _test_autoSegment_3ptb_buckets():
     assert len(set(groups)) == 4
 
 
-def _test_autoSegment_system_matrix():
+def test_autoSegment_system_matrix():
     from os import path
     from moleculekit.molecule import Molecule
     from moleculekit.tools.autosegment import autoSegment
@@ -132,7 +132,7 @@ def _test_autoSegment_system_matrix():
         assert got == n, f"{pid}: expected {n} segments, got {got}"
 
 
-def _test_autoSegment_chain_change_splits():
+def test_autoSegment_chain_change_splits():
     from moleculekit.molecule import Molecule
     from moleculekit.tools.autosegment import autoSegment
 
@@ -148,7 +148,7 @@ def _test_autoSegment_chain_change_splits():
     assert len(set(out.segid[prot_idx])) >= 2
 
 
-def _test_autoSegment_single_other_segment():
+def test_autoSegment_single_other_segment():
     from os import path
     from moleculekit.molecule import Molecule
     from moleculekit.tools.autosegment import autoSegment, _classify_residues
@@ -172,7 +172,7 @@ def _test_autoSegment_single_other_segment():
     assert merged.segid[other_atoms][0] not in set(merged.segid[non_other])
 
 
-def _test_autoSegment_gfp_chromophore():
+def test_autoSegment_gfp_chromophore():
     # 1gfl: the GFP chromophore residue 65 (SER) is missing its backbone O, so
     # the standard "backbone" selection drops it. autoSegment classifies it by
     # N/CA/C presence and keeps each chain continuous through it.
@@ -191,7 +191,7 @@ def _test_autoSegment_gfp_chromophore():
         assert before[0] == after[0], f"chromophore split chain {ch}"
 
 
-def _test_autoSegment_missing_carbonyl_continuity():
+def test_autoSegment_missing_carbonyl_continuity():
     # 1hgu: residues 148/151 are missing their carbonyl O (AS2 over-splits there),
     # while 37-39 are a genuine missing loop. autoSegment stays continuous through
     # the missing-O residues but splits at the real gap.
@@ -213,7 +213,7 @@ def seg(rid):
     assert seg(36) != seg(40)
 
 
-def _test_autoSegment_heavy_water_dod():
+def test_autoSegment_heavy_water_dod():
     # 2mb5 is a neutron structure with 89 DOD (D2O) residues. With DOD recognized
     # as water they collapse into a single water segment instead of 89 'other' ones.
     from os import path
@@ -227,7 +227,7 @@ def _test_autoSegment_heavy_water_dod():
     assert len(set(out.segid[dod])) == 1
 
 
-def _test_autoSegment_glycan_tree():
+def test_autoSegment_glycan_tree():
     # 3gbn: an N-linked glycan tree (NAG-NAG-BMA-MAN) must stay together as one
     # connected-component 'other' segment, separate from isolated small molecules.
     from os import path
@@ -249,7 +249,7 @@ def _test_autoSegment_glycan_tree():
     assert len(multi[0]) >= 3
 
 
-def _test_autoSegment_5mat_internal_gaps():
+def test_autoSegment_5mat_internal_gaps():
     # 5MAT (renin) has two protein chains (A, C), each with a real missing-loop
     # gap, so autoSegment yields 4 polymer segments. The gaps are detected by
     # backbone distance (C-N 4.4 A in chain A, 10.4 A in chain C), not resids.

tests/test_bondguesser.py

@@ -25,7 +25,7 @@
         "5vav",
     ],
 )
-def _test_bond_guessing(pdbid):
+def test_bond_guessing(pdbid):
     from moleculekit.molecule import Molecule, calculateUniqueBonds
     from moleculekit.bondguesser import guess_bonds
     import os
@@ -44,7 +44,7 @@ def _test_bond_guessing(pdbid):
     assert np.array_equal(bonds, bondsref)
 
 
-def _test_zero_atoms():
+def test_zero_atoms():
     from moleculekit.molecule import Molecule
     from moleculekit.bondguesser import guess_bonds
 
@@ -54,7 +54,7 @@ def _test_zero_atoms():
     assert bonds.dtype == np.uint32
 
 
-def _test_single_atom():
+def test_single_atom():
     from moleculekit.molecule import Molecule
     from moleculekit.bondguesser import guess_bonds
 
@@ -69,7 +69,7 @@ def _test_single_atom():
     assert bonds.dtype == np.uint32
 
 
-def _test_solvated_bond_guessing():
+def test_solvated_bond_guessing():
     from moleculekit.molecule import Molecule, calculateUniqueBonds
     from moleculekit.bondguesser import guess_bonds
     import os
@@ -85,7 +85,7 @@ def _test_solvated_bond_guessing():
 
 
 @pytest.mark.parametrize("span", [1e4, 1e5, 1e6, 1e7])
-def _test_unwrapped_coordinates(span):
+def test_unwrapped_coordinates(span):
     # Two bonded atoms plus distant ones spanning a large unwrapped range must not
     # crash bond_grid_search (regression: uint32 overflow on xyz_boxes products).
     from moleculekit.bondguesser import bond_grid_search
@@ -108,7 +108,7 @@ def _test_unwrapped_coordinates(span):
     assert sorted(bonds[0].tolist()) == [0, 1]
 
 
-def _test_high_atom_indices_preserved(monkeypatch):
+def test_high_atom_indices_preserved(monkeypatch):
     # Atom indices above 2**24 must survive the result-assembly path
     # (regression: float32 round-trip rounds odd indices and corrupts bonds).
     from moleculekit import bondguesser
@@ -139,7 +139,7 @@ def fake_grid_bonds(
     assert int(bonds[0, 1]) == HIGH_B
 
 
-def _test_nan_coords_raises():
+def test_nan_coords_raises():
     from moleculekit.bondguesser import bond_grid_search
 
     coords = np.array(
@@ -152,7 +152,7 @@ def _test_nan_coords_raises():
         bond_grid_search(coords, 2.04, is_h, radii)
 
 
-def _test_zero_grid_cutoff_raises():
+def test_zero_grid_cutoff_raises():
     from moleculekit.bondguesser import bond_grid_search
 
     coords = np.array([[0.0, 0.0, 0.0], [1.5, 0.0, 0.0]], dtype=np.float32)

tests/test_crystalpacking.py

@@ -4,7 +4,7 @@
 curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 
-def _test_crystalpacking_asymmetric_unit():
+def test_crystalpacking_asymmetric_unit():
     from os.path import join
     from moleculekit.molecule import Molecule, mol_equal
     from moleculekit.tools.crystalpacking import generateCrystalPacking
@@ -14,7 +14,7 @@ def _test_crystalpacking_asymmetric_unit():
     assert mol_equal(mol, refmol, fieldPrecision={"coords": 1e-3})
 
 
-def _test_crystalpacking_biological_unit():
+def test_crystalpacking_biological_unit():
     from os.path import join
     from moleculekit.molecule import Molecule, mol_equal
     from moleculekit.tools.crystalpacking import generateCrystalPacking

tests/test_detect.py

@@ -11,7 +11,7 @@ def _compare(arr1, arr2):
     ), f"Different results:\n{arr1}\n{arr2}"
 
 
-def _test_atom_detection():
+def test_atom_detection():
     import os
     from moleculekit.molecule import Molecule
     from moleculekit.tools.detect import detectEquivalentAtoms
@@ -29,7 +29,7 @@ def _test_atom_detection():
     _compare(eqgroupbyatom, eqgroupbyatom_ref)
 
 
-def _test_charged_detection():
+def test_charged_detection():
     import os
     from moleculekit.molecule import Molecule
     from moleculekit.tools.detect import detectEquivalentAtoms
@@ -59,7 +59,7 @@ def _test_charged_detection():
     _compare(eqgroupbyatom, eqgroupbyatom_ref)
 
 
-def _test_detect_dihedrals():
+def test_detect_dihedrals():
     import os
     from moleculekit.molecule import Molecule
     from moleculekit.tools.detect import detectParameterizableDihedrals