More docstring formatting

SMTG-Bham · Jan 30, 2025 · e80f69b · e80f69b
1 parent 169e55e
commit e80f69b
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Showing 2 changed files with 12 additions and 12 deletions.
diff --git a/shakenbreak/analysis.py b/shakenbreak/analysis.py
@@ -271,7 +271,7 @@ def analyse_defect_site(
     site_num: Optional[int] = None,
     vac_site: Optional[list] = None,
 ) -> tuple:
-    """
+    r"""
     Analyse coordination environment and bond distances to nearest
     neighbours of defect site.
 
@@ -290,7 +290,7 @@ def analyse_defect_site(
 
     Returns:
         :obj:`tuple`:
-            Tuple of coordination analysis and bond length DataFrames,
+            Tuple of coordination analysis and bond length ``DataFrame``\s,
             respectively.
     """
     # get defect site
@@ -338,7 +338,7 @@ def analyse_structure(
     structure: Structure,
     output_path: str = ".",
 ) -> tuple:
-    """
+    r"""
     Analyse the local distortion of the input defect structure. Requires
     access to the ``distortion_metadata.json`` file generated with
     ShakeNBreak to read info about defect site. If lacking this,
@@ -355,7 +355,7 @@ def analyse_structure(
 
     Returns:
         :obj:`tuple`:
-            Tuple of coordination analysis and bond length DataFrames,
+            Tuple of coordination analysis and bond length ``DataFrame``\s,
             respectively.
     """
     defect_name_without_charge = defect_species.rsplit("_", 1)[0]

diff --git a/shakenbreak/input.py b/shakenbreak/input.py
@@ -1,7 +1,7 @@
 """
 Module containing functions to generate rattled and bond-distorted structures,
 as well as input files to run Gamma point relaxations with ``VASP``, ``CP2K``,
-`Quantum-Espresso``, ``FHI-aims`` and ``CASTEP``.
+``Quantum-Espresso``, ``FHI-aims`` and ``CASTEP``.
 """
 
 import contextlib
@@ -287,7 +287,7 @@ def _create_vasp_input(
     output_path: str = ".",
     **kwargs,
 ) -> str:
-    """
+    r"""
     Creates folders for storing VASP ShakeNBreak files.
 
     Args:
@@ -304,7 +304,7 @@ def _create_vasp_input(
         user_potcar_settings (:obj:`dict`):
             Dictionary of user VASP POTCAR settings, to overwrite/update
             the ``doped`` defaults (e.g. {'Fe': 'Fe_pv', 'O': 'O'}}). Highly
-            recommended to look at output ``POTCAR`s, or
+            recommended to look at output ``POTCAR``\s, or
             ``shakenbreak/SnB_input_files/default_POTCARs.yaml``, to see what
             the default ``POTCAR`` settings are. (Default: None)
         output_path (:obj:`str`):
@@ -1660,7 +1660,7 @@ def __init__(
         distorted_atoms: Optional[list] = None,
         **mc_rattle_kwargs,
     ):
-        """
+        r"""
         Args:
             defect_entries (Union[DefectsGenerator, list, dict, DefectEntry]):
                 Either a ``DefectsGenerator`` object from ``doped``, or a list/dictionary
@@ -1671,7 +1671,7 @@ def __init__(
                 set equal to ``defect_species`` (with charge states included). If
                 a list or single ``DefectEntry`` object is provided, the defect
                 folder names will be set equal to ``DefectEntry.name`` if the ``name``
-                attribute is set for all input ``DefectEntry`s, otherwise generated
+                attribute is set for all input ``DefectEntry``\s, otherwise generated
                 according to the ``doped`` convention
                 (see: https://doped.readthedocs.io/en/latest/generation_tutorial.html).
 
@@ -2464,15 +2464,15 @@ def write_vasp_files(
         verbose: Optional[bool] = None,
         **kwargs,
     ) -> tuple[dict, dict]:
-        """
+        r"""
         Generates the input files for ``vasp_gam`` relaxations of all output
         structures.
 
         Args:
             user_incar_settings (:obj:`dict`):
                 Dictionary of user VASP INCAR settings (e.g.
                 {"ENCUT": 300, ...}), to overwrite the ``ShakenBreak`` defaults
-                for those tags. Highly recommended to look at output ``INCAR`s,
+                for those tags. Highly recommended to look at output ``INCAR``\s,
                 or ``shakenbreak/SnB_input_files/incar.yaml`` to see what the default
                 ``INCAR`` settings are. Note that any flags that aren't numbers or
                 True/False need to be input as strings with quotation marks
@@ -2483,7 +2483,7 @@ def write_vasp_files(
             user_potcar_settings (:obj:`dict`):
                 Dictionary of user VASP POTCAR settings, to overwrite/update
                 the ``doped`` defaults (e.g. {'Fe': 'Fe_pv', 'O': 'O'}}). Highly
-                recommended to look at output ``POTCAR`s, or
+                recommended to look at output ``POTCAR``\s, or
                 ``shakenbreak/SnB_input_files/default_POTCARs.yaml``, to see what
                 the default ``POTCAR`` settings are. (Default: None)
             write_files (:obj:`bool`):