Merge pull request #70 from SMTG-Bham/develop

Develop

.gitattributes

@@ -1 +1 @@
-tutorials/* linguist-documentation
+docs/* linguist-documentation

docs/ShakeNBreak_Example_Workflow.ipynb

@@ -46,16 +46,16 @@
    ]
   },
   {
-   "cell_type": "code",
-   "outputs": [],
+   "cell_type": "markdown",
    "source": [
-    "# Install ShakeNBreak (if not already installed)\n",
-    "!pip install shakenbreak"
+    "```{tip}\n",
+    "You can run this notebook interactively through Google Colab or Binder using the launch buttons at the top of the docs tutorial page (click the Rocket ?? icon). If running on Colab, then you'll need to run `!pip install shakenbreak` in a cell to install the package, and `!git clone https://github.com/SMTG-Bham/shakenbreak` to download the example data (and update paths in the code cells accordingly).\n",
+    "```"
    ],
    "metadata": {
     "collapsed": false
    },
-   "id": "b766bdc7fe8ff74e"
+   "id": "91fbd4d745464ba"
   },
   {
    "cell_type": "code",

shakenbreak/distortions.py

@@ -329,6 +329,7 @@ def rattle(
             (Default: 1)
         active_atoms (:obj:`list`, optional):
             List of which atomic indices should undergo Monte Carlo rattling.
+            If not set, rattles all atoms in the structure.
             (Default: None)
         nbr_cutoff (:obj:`float`):
             The radial cutoff distance (in Angstroms) used to construct the

tests/test_cli.py

@@ -261,7 +261,8 @@ def test_snb_generate(self):
                 catch_exceptions=False,
             )
         print([str(warning.message) for warning in w])  # for debugging
-        assert not w
+        non_potcar_warnings = [warning for warning in w if "POTCAR" not in str(warning.message)]
+        assert not non_potcar_warnings  # no warnings other than POTCAR warnings
         self.assertEqual(result.exit_code, 0)
         self.assertIn(
             f"Auto site-matching identified {self.VASP_CDTE_DATA_DIR}/CdTe_V_Cd_POSCAR "
@@ -439,8 +440,9 @@ def test_snb_generate(self):
                 catch_exceptions=False,
             )
         print([str(warning.message) for warning in w])  # for debugging
-        assert len(w) == 1  # only overwriting structures warning
-        assert "has the same Unperturbed defect structure" in str(w[0].message)
+        non_potcar_warnings = [warning for warning in w if "POTCAR" not in str(warning.message)]
+        assert len(non_potcar_warnings) == 1  # only overwriting structures warning
+        assert "has the same Unperturbed defect structure" in str(non_potcar_warnings[0].message)
         self.assertEqual(result.exit_code, 0)
         self.assertIn(f"Defect: {defect_name}", result.output)
         self.assertIn("Number of missing electrons in neutral state: 2", result.output)
@@ -489,8 +491,9 @@ def test_snb_generate(self):
                 catch_exceptions=False,
             )
         print([str(warning.message) for warning in w])  # for debugging
-        assert len(w) == 1  # only overwriting structures warning
-        assert "has the same Unperturbed defect structure" in str(w[0].message)
+        non_potcar_warnings = [warning for warning in w if "POTCAR" not in str(warning.message)]
+        assert len(non_potcar_warnings) == 1  # only overwriting structures warning
+        assert "has the same Unperturbed defect structure" in str(non_potcar_warnings[0].message)
         self.assertEqual(result.exit_code, 0)
         self.assertIn(f"Defect: {defect_name}", result.output)
         self.assertIn("Number of missing electrons in neutral state: 2", result.output)
@@ -548,8 +551,9 @@ def test_snb_generate(self):
                 catch_exceptions=False,
             )
         print([str(warning.message) for warning in w])  # for debugging
-        assert len(w) == 1  # only overwriting structures warning
-        assert "has the same Unperturbed defect structure" in str(w[0].message)
+        non_potcar_warnings = [warning for warning in w if "POTCAR" not in str(warning.message)]
+        assert len(non_potcar_warnings) == 1  # only overwriting structures warning
+        assert "has the same Unperturbed defect structure" in str(non_potcar_warnings[0].message)
         self.assertEqual(result.exit_code, 0)
         self.assertIn(f"Defect: {defect_name}", result.output)
         self.assertIn("Number of missing electrons in neutral state: 2", result.output)
@@ -603,8 +607,9 @@ def test_snb_generate(self):
                 catch_exceptions=False,
             )
         print([str(warning.message) for warning in w])  # for debugging
-        assert len(w) == 1  # only overwriting structures warning
-        assert "has the same Unperturbed defect structure" in str(w[0].message)
+        non_potcar_warnings = [warning for warning in w if "POTCAR" not in str(warning.message)]
+        assert len(non_potcar_warnings) == 1  # only overwriting structures warning
+        assert "has the same Unperturbed defect structure" in str(non_potcar_warnings[0].message)
         self.assertEqual(result.exit_code, 0)
         self.assertIn(f"Defect: {defect_name}", result.output)
         self.assertIn("Number of missing electrons in neutral state: 2", result.output)

tests/test_energy_lowering_distortions.py

@@ -7,7 +7,7 @@
 import ase
 import numpy as np
 from monty.serialization import dumpfn, loadfn
-from pymatgen.core.structure import Element, Structure
+from pymatgen.core.structure import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
 
 from shakenbreak import analysis, distortions, energy_lowering_distortions, io

tests/test_input.py

@@ -1091,6 +1091,7 @@ def test_create_vasp_input(self):
                 for el_symbol in V_Cd_POSCAR.structure.symbol_set
             }
         else:  # test POTCAR warning
+            print([str(warning.message) for warning in w])
             assert (
                 len(w) == 2
             )  # general POTCAR warning and NELECT/NUPDOWN INCAR warning
@@ -3300,9 +3301,9 @@ def test_apply_distortions(self):
         self.assertTrue("Bond_Distortion_-75.0%" in V_Cd_distortions_dict)
 
         # test short interatomic distance distortions not omitted when Hydrogen knocking about
-        fake_hydrogen_V_Cd_dict = copy.copy(self.V_Cd_dict)
+        fake_hydrogen_V_Cd_dict = copy.deepcopy(self.V_Cd_dict)  # deepcopy to avoid overwriting
         fake_hydrogen_V_Cd_dict["charges"] = [0]
-        fake_hydrogen_bulk = copy.copy(self.cdte_doped_defect_dict["bulk"])
+        fake_hydrogen_bulk = copy.deepcopy(self.cdte_doped_defect_dict["bulk"])
         fake_hydrogen_bulk["supercell"]["structure"][4].species = "H"
         fake_hydrogen_bulk["supercell"]["structure"].add_oxidation_state_by_element(
             {"Cd": +2, "Te": -2, "H": +1}

tests/test_plotting.py

@@ -5,15 +5,18 @@
 import warnings
 from collections import OrderedDict
 from copy import deepcopy
-from unittest.mock import patch
+from unittest.mock import Mock, patch
 
 import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 import pytest
-from monty.serialization import dumpfn, loadfn
+from monty.serialization import loadfn
 
 from shakenbreak import analysis, plotting
+from test_energy_lowering_distortions import assert_not_called_with
+
+Mock.assert_not_called_with = assert_not_called_with
 
 
 def if_present_rm(path):

tests/test_shakenbreak.py

@@ -3,14 +3,17 @@
 import shutil
 import unittest
 import warnings
-from unittest.mock import call, patch
+from unittest.mock import Mock, patch
 
 import pytest
 from monty.serialization import dumpfn, loadfn
 from pymatgen.core.structure import Structure
 from pymatgen.io.vasp.inputs import UnknownPotcarWarning
 
-from shakenbreak import cli, energy_lowering_distortions, input, io, plotting
+from shakenbreak import energy_lowering_distortions, input, io, plotting
+from test_energy_lowering_distortions import assert_not_called_with
+
+Mock.assert_not_called_with = assert_not_called_with
 
 file_path = os.path.dirname(__file__)