Merge pull request #108 from nlesc-nano/get_formula

MAINT: Fix a documentation failure and deprecate usage of `Molecule.get_formula`

CHANGELOG.rst

@@ -5,6 +5,13 @@ Change Log
 All notable changes to this project will be documented in this file.
 This project adheres to `Semantic Versioning <http://semver.org/>`_.
 
+
+0.7.1
+*****
+* Deprecate usage of ``Molecule.get_formula`` in favor of a PLAMS <=1.5.1-based backport.
+* Fix a failure in the documentation generation
+
+
 0.7.0
 *****
 * Added a new fast-bulkiness workflow.

README.rst

@@ -2,6 +2,8 @@
    :target: https://github.com/nlesc-nano/nano-CAT/actions?query=workflow%3A%22Build+with+Conda%22
 .. image:: https://readthedocs.org/projects/cat/badge/?version=latest
    :target: https://cat.readthedocs.io/en/latest/
+.. image:: https://badge.fury.io/py/nano-CAT.svg
+   :target: https://badge.fury.io/py/nano-CAT
 
 |
 
@@ -14,7 +16,7 @@
 
 
 ##############
-Nano-CAT 0.7.0
+Nano-CAT 0.7.1
 ##############
 
 **Nano-CAT** is a collection of tools for the analysis of nanocrystals,

nanoCAT/__version__.py

@@ -1 +1 @@
-__version__ = '0.7.0'
+__version__ = '0.7.1'

nanoCAT/recipes/__init__.py

@@ -11,7 +11,7 @@
     >>> from nanoCAT.recipes import bulk_workflow
     >>> from nanoCAT.recipes import get_lig_charge
     >>> from nanoCAT.recipes import replace_surface
-    >>> from nanoCAT.recipes import coordination_number
+    >>> from nanoCAT.recipes import get_coordination_number, coordination_outer
     >>> from nanoCAT.recipes import dissociate_surface, row_accumulator, dissociate_bulk
     >>> from nanoCAT.recipes import get_mol_length, filter_mol, filter_data
     >>> from nanoCAT.recipes import run_jobs, get_global_descriptors, cdft
@@ -25,7 +25,7 @@
 from .charges import get_lig_charge
 from .mark_surface import replace_surface
 from .dissociation import dissociate_surface, row_accumulator, dissociate_bulk
-from .coordination_number import coordination_number
+from .coordination_number import get_coordination_number, coordination_outer
 from .multi_lig_job import multi_ligand_job
 from .mol_filter import get_mol_length, filter_mol, filter_data
 from .cdft_utils import run_jobs, get_global_descriptors, cdft
@@ -35,7 +35,8 @@
 __all__ = [
     'bulk_workflow', 'fast_bulk_workflow',
     'replace_surface', 'dissociate_surface', 'dissociate_bulk',
-    'row_accumulator', 'get_lig_charge', 'coordination_number',
+    'row_accumulator', 'get_lig_charge',
+    'get_coordination_number', 'coordination_outer',
     'multi_ligand_job',
     'get_mol_length', 'filter_mol', 'filter_data',
     'run_jobs', 'get_global_descriptors', 'cdft',

nanoCAT/recipes/coordination_number.py

@@ -8,11 +8,13 @@
 -----
 .. currentmodule:: nanoCAT.recipes
 .. autosummary::
-    coordination_number
+    get_coordination_number
+    coordination_outer
 
 API
 ---
-.. autofunction:: coordination_number
+.. autofunction:: get_coordination_number
+.. autofunction:: coordination_outer
 
 """
 
@@ -26,7 +28,7 @@
 from nanoutils import group_by_values
 from nanoCAT.bde.guess_core_dist import guess_core_core_dist
 
-__all__: List[str] = ['coordination_number', 'coordination_outer']
+__all__ = ['get_coordination_number', 'coordination_outer']
 
 #: A nested dictonary
 NestedDict = Dict[str, Dict[int, List[int]]]
@@ -116,8 +118,8 @@ def map_coordination(coord: np.ndarray, idx_dict: Dict[str, np.ndarray]) -> Nest
     return cn_dict
 
 
-def coordination_number(mol: Molecule, shell: str = 'inner',
-                        d_outer: Optional[float] = None) -> NestedDict:
+def get_coordination_number(mol: Molecule, shell: str = 'inner',
+                            d_outer: Optional[float] = None) -> NestedDict:
     """Take a molecule and identify the coordination number of each atom.
 
     The function first compute the pair distance between all reference atoms in **mol**.
@@ -192,3 +194,6 @@ def coordination_number(mol: Molecule, shell: str = 'inner',
 
     # Return the final dictionary
     return map_coordination(coord, idx_dict)
+
+
+coordination_number = get_coordination_number

setup.py

@@ -79,6 +79,11 @@
         'flake8',
     ],
     extras_require={
-        'test': ['pytest', 'pytest-cov', 'pytest-mock'],
+        'test': [
+            'pytest',
+            'pytest-cov',
+            'pytest-mock',
+            'nlesc-CAT>=0.10.1',
+        ],
     }
 )

tests/test_bulk.py

@@ -14,6 +14,7 @@
 from scm.plams import Molecule
 from scipy.spatial.distance import cdist
 from nanoCAT.recipes import bulk_workflow, fast_bulk_workflow
+from CAT.utils import get_formula
 
 if TYPE_CHECKING:
     import _pytest
@@ -45,7 +46,7 @@ def test_bulk_workflow() -> None:
     iterator = enumerate(zip(mol_list, formula_list), start=2)
     for i, (mol, formula) in iterator:
         assertion.eq(mol[i].coords, (0.0, 0.0, 0.0))
-        assertion.eq(mol.get_formula(), formula)
+        assertion.eq(get_formula(mol), formula)
 
     ref = [17.07131616, 64.15117841, 74.79488029]
     np.testing.assert_allclose(bulk_ar, ref)

tests/test_coordination_number.py

@@ -7,18 +7,18 @@
 from scm.plams import Molecule
 from assertionlib import assertion
 
-from nanoCAT.recipes import coordination_number
+from nanoCAT.recipes import get_coordination_number
 
 PATH = Path('tests') / 'test_files'
 MOL = Molecule(PATH / 'Cd68Se55.xyz')
 
 
 def test_coordination_number() -> None:
-    """Tests for :func:`nanoCAT.recipes.coordination_number`."""
+    """Tests for :func:`nanoCAT.recipes.get_coordination_number`."""
 
-    out_inner = coordination_number(MOL, shell='inner')
+    out_inner = get_coordination_number(MOL, shell='inner')
 
-    out_outer = coordination_number(MOL, shell='outer', d_outer=5.2)
+    out_outer = get_coordination_number(MOL, shell='outer', d_outer=5.2)
 
     ref_inner = {'Cd': {3: [30, 31, 34, 35, 36, 46, 47, 52, 53, 54, 57, 58, 59, 60, 63, 64, 65, 67,
                             69, 70, 71, 75, 78, 79],
@@ -50,5 +50,6 @@ def test_coordination_number() -> None:
     np.testing.assert_equal(out_inner, ref_inner)
     np.testing.assert_equal(out_outer, ref_outer)
 
-    assertion.assert_(coordination_number, MOL, shell='bob', exception=ValueError)
-    assertion.assert_(coordination_number, MOL, shell='outer', d_outer=None, exception=TypeError)
+    assertion.assert_(get_coordination_number, MOL, shell='bob', exception=ValueError)
+    assertion.assert_(get_coordination_number, MOL, shell='outer', d_outer=None,
+                      exception=TypeError)