Recover commented out code in tests and mark with pytest.mark.skip …

…instead (#4027)

* recover some commented out test unit

* replace legacy random generator

* recover more commented out test

* avoid code-like comment in case we want to enable ERA someday

tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py

@@ -1,10 +1,17 @@
 from __future__ import annotations
 
+import json
+import os
+
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
 from pytest import approx
 
+from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
+ SimpleAbundanceChemenvStrategy,
+ SimplestChemenvStrategy,
+)
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
  AbstractGeometry,
@@ -27,7 +34,7 @@ def setUp(self):
  structure_refinement=self.lgf.STRUCTURE_REFINEMENT_NONE,
  )
 
- #  self.strategies = [SimplestChemenvStrategy(), SimpleAbundanceChemenvStrategy()]
+ # self.strategies = [SimplestChemenvStrategy(), SimpleAbundanceChemenvStrategy()]
 
  def test_abstract_geometry(self):
  cg_ts3 = self.lgf.allcg["TS:3"]
@@ -117,45 +124,47 @@ def test_abstract_geometry(self):
  for perm_csm_dict in permutations_symmetry_measures:
  assert perm_csm_dict["symmetry_measure"] == approx(0.140355832317)
 
- # def _strategy_test(self, strategy):
- # files = []
- # for _dirpath, _dirnames, filenames in os.walk(json_dir):
- # files.extend(filenames)
- # break
-
- # for _ifile, json_file in enumerate(files):
- # with self.subTest(json_file=json_file):
- # with open(f"{json_dir}/{json_file}") as file:
- # dct = json.load(file)
-
- # atom_indices = dct["atom_indices"]
- # expected_geoms = dct["expected_geoms"]
-
- # struct = Structure.from_dict(dct["structure"])
-
- # struct = self.lgf.setup_structure(struct)
- # se = self.lgf.compute_structure_environments_detailed_voronoi(
- # only_indices=atom_indices, maximum_distance_factor=1.5
- # )
-
- # # All strategies should get the correct environment with their default parameters
- # strategy.set_structure_environments(se)
- # for ienv, isite in enumerate(atom_indices):
- # ce = strategy.get_site_coordination_environment(struct[isite])
- # try:
- # coord_env = ce[0]
- # except TypeError:
- # coord_env = ce
- # # Check that the environment found is the expected one
- # assert coord_env == expected_geoms[ienv]
-
- # def test_simplest_chemenv_strategy(self):
- # strategy = SimplestChemenvStrategy()
- # self._strategy_test(strategy)
-
- # def test_simple_abundance_chemenv_strategy(self):
- # strategy = SimpleAbundanceChemenvStrategy()
- # self._strategy_test(strategy)
+ def _strategy_test(self, strategy):
+ files = []
+ for _dirpath, _dirnames, filenames in os.walk(json_dir):
+ files.extend(filenames)
+ break
+
+ for _ifile, json_file in enumerate(files):
+ with self.subTest(json_file=json_file):
+ with open(f"{json_dir}/{json_file}") as file:
+ dct = json.load(file)
+
+ atom_indices = dct["atom_indices"]
+ expected_geoms = dct["expected_geoms"]
+
+ struct = Structure.from_dict(dct["structure"])
+
+ struct = self.lgf.setup_structure(struct)
+ se = self.lgf.compute_structure_environments_detailed_voronoi(
+ only_indices=atom_indices, maximum_distance_factor=1.5
+ )
+
+ # All strategies should get the correct environment with their default parameters
+ strategy.set_structure_environments(se)
+ for ienv, isite in enumerate(atom_indices):
+ ce = strategy.get_site_coordination_environment(struct[isite])
+ try:
+ coord_env = ce[0]
+ except TypeError:
+ coord_env = ce
+ # Check that the environment found is the expected one
+ assert coord_env == expected_geoms[ienv]
+
+ @pytest.mark.skip("TODO: need someone to fix this")
+ def test_simplest_chemenv_strategy(self):
+ strategy = SimplestChemenvStrategy()
+ self._strategy_test(strategy)
+
+ @pytest.mark.skip("TODO: need someone to fix this")
+ def test_simple_abundance_chemenv_strategy(self):
+ strategy = SimpleAbundanceChemenvStrategy()
+ self._strategy_test(strategy)
 
  def test_perfect_environments(self):
  allcg = AllCoordinationGeometries()

tests/analysis/test_molecule_structure_comparator.py

@@ -2,8 +2,11 @@
 
 from unittest import TestCase
 
+import pytest
+
 from pymatgen.analysis.molecule_structure_comparator import MoleculeStructureComparator
 from pymatgen.core.structure import Molecule
+from pymatgen.io.qchem.outputs import QCOutput
 from pymatgen.util.testing import TEST_FILES_DIR
 
 __author__ = "xiaohuiqu"
@@ -129,14 +132,15 @@ def test_to_and_from_dict(self):
  d2 = MoleculeStructureComparator.from_dict(d1).as_dict()
  assert d1 == d2
 
- # def test_structural_change_in_geom_opt(self):
- # qcout_path = f"{TEST_DIR}/mol_1_3_bond.qcout"
- # qcout = QcOutput(qcout_path)
- # mol1 = qcout.data[0]["molecules"][0]
- # mol2 = qcout.data[0]["molecules"][-1]
- # priority_bonds = [[0, 1], [0, 2], [1, 3], [1, 4], [1, 7], [2, 5], [2, 6], [2, 8], [4, 6], [4, 10], [6, 9]]
- # msc = MoleculeStructureComparator(priority_bonds=priority_bonds)
- # assert msc.are_equal(mol1, mol2)
+ @pytest.mark.skip("TODO: need someone to fix this")
+ def test_structural_change_in_geom_opt(self):
+ qcout_path = f"{TEST_DIR}/mol_1_3_bond.qcout"
+ qcout = QCOutput(qcout_path)
+ mol1 = qcout.data[0]["molecules"][0]
+ mol2 = qcout.data[0]["molecules"][-1]
+ priority_bonds = [[0, 1], [0, 2], [1, 3], [1, 4], [1, 7], [2, 5], [2, 6], [2, 8], [4, 6], [4, 10], [6, 9]]
+ msc = MoleculeStructureComparator(priority_bonds=priority_bonds)
+ assert msc.are_equal(mol1, mol2)
 
  def test_get_13_bonds(self):
  priority_bonds = [

tests/analysis/test_surface_analysis.py

@@ -2,6 +2,7 @@
 
 import json
 
+import pytest
 from numpy.testing import assert_allclose
 from pytest import approx
 from sympy import Number, Symbol
@@ -248,41 +249,43 @@ def test_entry_dict_from_list(self):
  surf_ene_plotter = SurfaceEnergyPlotter(all_Pt_slab_entries, self.Pt_analyzer.ucell_entry)
  assert surf_ene_plotter.list_of_chempots == self.Pt_analyzer.list_of_chempots
 
- # def test_monolayer_vs_BE(self):
- # for el in self.Oads_analyzer_dict:
- # # Test WulffShape for adsorbed surfaces
- # analyzer = self.Oads_analyzer_dict[el]
- # plt = analyzer.monolayer_vs_BE()
- #
- # def test_area_frac_vs_chempot_plot(self):
- #
- # for el in self.Oads_analyzer_dict:
- # # Test WulffShape for adsorbed surfaces
- # analyzer = self.Oads_analyzer_dict[el]
- # plt = analyzer.area_frac_vs_chempot_plot(x_is_u_ads=True)
- #
- # def test_chempot_vs_gamma_clean(self):
- #
- # plt = self.Cu_analyzer.chempot_vs_gamma_clean()
- # for el in self.Oads_analyzer_dict:
- # # Test WulffShape for adsorbed surfaces
- # analyzer = self.Oads_analyzer_dict[el]
- # plt = analyzer.chempot_vs_gamma_clean(x_is_u_ads=True)
- #
- # def test_chempot_vs_gamma_facet(self):
- #
- # for el, val in self.metals_O_entry_dict.items():
- # for hkl in val:
- # # Test WulffShape for adsorbed surfaces
- # analyzer = self.Oads_analyzer_dict[el]
- # plt = analyzer.chempot_vs_gamma_facet(hkl)
- # def test_surface_chempot_range_map(self):
- #
- # for el, val in self.metals_O_entry_dict.items():
- # for hkl in val:
- # # Test WulffShape for adsorbed surfaces
- # analyzer = self.Oads_analyzer_dict[el]
- # plt = analyzer.chempot_vs_gamma_facet(hkl)
+ @pytest.mark.skip("TODO: need someone to fix this")
+ def test_monolayer_vs_BE(self):
+ for el in self.Oads_analyzer_dict:
+ # Test WulffShape for adsorbed surfaces
+ analyzer = self.Oads_analyzer_dict[el]
+ analyzer.monolayer_vs_BE()
+
+ @pytest.mark.skip("TODO: need someone to fix this")
+ def test_area_frac_vs_chempot_plot(self):
+ for el in self.Oads_analyzer_dict:
+ # Test WulffShape for adsorbed surfaces
+ analyzer = self.Oads_analyzer_dict[el]
+ analyzer.area_frac_vs_chempot_plot(x_is_u_ads=True)
+
+ @pytest.mark.skip("TODO: need someone to fix this")
+ def test_chempot_vs_gamma_clean(self):
+ self.Cu_analyzer.chempot_vs_gamma_clean()
+ for el in self.Oads_analyzer_dict:
+ # Test WulffShape for adsorbed surfaces
+ analyzer = self.Oads_analyzer_dict[el]
+ analyzer.chempot_vs_gamma_clean(x_is_u_ads=True)
+
+ @pytest.mark.skip("TODO: need someone to fix this")
+ def test_chempot_vs_gamma_facet(self):
+ for el, val in self.metals_O_entry_dict.items():
+ for hkl in val:
+ # Test WulffShape for adsorbed surfaces
+ analyzer = self.Oads_analyzer_dict[el]
+ analyzer.chempot_vs_gamma_facet(hkl)
+
+ @pytest.mark.skip("TODO: need someone to fix this")
+ def test_surface_chempot_range_map(self):
+ for el, val in self.metals_O_entry_dict.items():
+ for hkl in val:
+ # Test WulffShape for adsorbed surfaces
+ analyzer = self.Oads_analyzer_dict[el]
+ analyzer.chempot_vs_gamma_facet(hkl)
 
 
 class TestWorkFunctionAnalyzer(PymatgenTest):

tests/command_line/test_critic2_caller.py

@@ -90,6 +90,22 @@ def setUp(self):
  self.c2o_new_format = Critic2Analysis(structure, reference_stdout_new_format)
 
  def test_to_from_dict(self):
+ """
+ reference dictionary for c2o.critical_points[0].as_dict()
+ {'@class': 'CriticalPoint',
+ '@module': 'pymatgen.command_line.critic2_caller',
+ 'coords': None,
+ 'field': 93848.0413,
+ 'field_gradient': 0.0,
+ 'field_hessian': [[-2593274446000.0, -3.873587547e-19, -1.704530713e-08],
+ [-3.873587547e-19, -2593274446000.0, 1.386877485e-18],
+ [-1.704530713e-08, 1.386877485e-18, -2593274446000.0]],
+ 'frac_coords': [0.333333, 0.666667, 0.213295],
+ 'index': 0,
+ 'multiplicity': 1.0,
+ 'point_group': 'D3h',
+ 'type': < CriticalPointType.nucleus: 'nucleus' >}
+ """
  assert len(self.c2o.critical_points) == 6
  assert len(self.c2o.nodes) == 14
  assert len(self.c2o.edges) == 10
@@ -98,21 +114,6 @@ def test_to_from_dict(self):
  assert len(self.c2o_new_format.nodes) == 14
  assert len(self.c2o_new_format.edges) == 10
 
- # reference dictionary for c2o.critical_points[0].as_dict()
- # {'@class': 'CriticalPoint',
- # '@module': 'pymatgen.command_line.critic2_caller',
- # 'coords': None,
- # 'field': 93848.0413,
- # 'field_gradient': 0.0,
- # 'field_hessian': [[-2593274446000.0, -3.873587547e-19, -1.704530713e-08],
- # [-3.873587547e-19, -2593274446000.0, 1.386877485e-18],
- # [-1.704530713e-08, 1.386877485e-18, -2593274446000.0]],
- # 'frac_coords': [0.333333, 0.666667, 0.213295],
- # 'index': 0,
- # 'multiplicity': 1.0,
- # 'point_group': 'D3h',
- # 'type': < CriticalPointType.nucleus: 'nucleus' >}
-
  assert str(self.c2o.critical_points[0].type) == "CriticalPointType.nucleus"
 
  # test connectivity