Reorganise namespaces

docs/source/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 #
 # ChemCoord documentation build configuration file, created by
 # sphinx-quickstart on Tue Jan 12 23:12:55 2016.
@@ -59,7 +58,6 @@
     "pymatgen": ("http://pymatgen.org/", None),
     "python": ("https://docs.python.org/3", None),
 }
-#    'sympy': ('http://www.sympy.org/', None)}
 
 
 # 'numpydoc'
@@ -244,7 +242,7 @@
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_elements = {
+latex_elements: dict = {
     # The paper size ('letterpaper' or 'a4paper').
     # 'papersize': 'letterpaper',
     # The font size ('10pt', '11pt' or '12pt').

mypy.ini

@@ -6,7 +6,7 @@
 
 # explicitly blacklist files, this means we can easily add in stricter type checks
 # by removing them from the blacklist
-[mypy-chemcoord.cartesian_coordinates.asymmetric_unit_cartesian_class,chemcoord.cartesian_coordinates._cartesian_class_core,chemcoord.cartesian_coordinates._cartesian_class_get_zmat,chemcoord.cartesian_coordinates._cartesian_class_io,chemcoord.cartesian_coordinates.cartesian_class_main,chemcoord.cartesian_coordinates._cartesian_class_pandas_wrapper,chemcoord.cartesian_coordinates._cartesian_class_symmetry,chemcoord.cartesian_coordinates._cart_transformation,chemcoord.cartesian_coordinates._indexers,chemcoord.cartesian_coordinates.point_group,chemcoord.cartesian_coordinates.xyz_functions,chemcoord.configuration,chemcoord.constants,chemcoord.exceptions,chemcoord._generic_classes.generic_core,chemcoord._generic_classes.generic_IO,chemcoord.internal_coordinates._indexers,chemcoord.internal_coordinates._zmat_class_core,chemcoord.internal_coordinates._zmat_class_io,chemcoord.internal_coordinates.zmat_class_main,chemcoord.internal_coordinates._zmat_class_pandas_wrapper,chemcoord.internal_coordinates.zmat_functions,chemcoord.internal_coordinates._zmat_transformation,chemcoord.utilities._decorators,chemcoord.utilities._print_versions,chemcoord.utilities._temporary_deprecation_workarounds,chemcoord]
+[mypy-chemcoord._cartesian_coordinates.asymmetric_unit_cartesian_class,chemcoord._cartesian_coordinates._cartesian_class_core,chemcoord._cartesian_coordinates._cartesian_class_get_zmat,chemcoord._cartesian_coordinates._cartesian_class_io,chemcoord._cartesian_coordinates.cartesian_class_main,chemcoord._cartesian_coordinates._cartesian_class_pandas_wrapper,chemcoord._cartesian_coordinates._cartesian_class_symmetry,chemcoord._cartesian_coordinates._cart_transformation,chemcoord._cartesian_coordinates._indexers,chemcoord._cartesian_coordinates.point_group,chemcoord._cartesian_coordinates.xyz_functions,chemcoord.configuration,chemcoord.constants,chemcoord.exceptions,chemcoord._generic_classes.generic_core,chemcoord._generic_classes.generic_IO,chemcoord._internal_coordinates._indexers,chemcoord._internal_coordinates._zmat_class_core,chemcoord._internal_coordinates._zmat_class_io,chemcoord._internal_coordinates.zmat_class_main,chemcoord._internal_coordinates._zmat_class_pandas_wrapper,chemcoord._internal_coordinates.zmat_functions,chemcoord._internal_coordinates._zmat_transformation,chemcoord._utilities._decorators,chemcoord._utilities._print_versions,chemcoord._utilities._temporary_deprecation_workarounds,chemcoord]
     disallow_untyped_defs = False
     check_untyped_defs = False
 

setup.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
 """Setup file for the chemcoord package."""
 
 from setuptools import find_packages, setup

src/chemcoord/__init__.py

@@ -1,38 +1,24 @@
-# ruff: noqa: E402
-# ruff: noqa: PLC0414
 # ruff: noqa: F401
 
 from importlib.metadata import version
 
-__version__ = version("chemcoord")
-_git_branch = "master"
-
-
-def export(func):
-    if callable(func) and hasattr(func, "__name__"):
-        globals()[func.__name__] = func
-    try:
-        __all__.append(func.__name__)
-    except NameError:
-        __all__ = [func.__name__]  # noqa: F841
-    return func
-
-
-# have to be imported after export definition
-import sys
-
-import chemcoord.cartesian_coordinates.xyz_functions as xyz_functions
-import chemcoord.configuration as configuration
+import chemcoord.configuration
 import chemcoord.constants
-import chemcoord.internal_coordinates.zmat_functions as zmat_functions
-import chemcoord.utilities
-from chemcoord.cartesian_coordinates.asymmetric_unit_cartesian_class import (
-    AsymmetricUnitCartesian as AsymmetricUnitCartesian,
+import chemcoord.xyz_functions
+import chemcoord.zmat_functions
+from chemcoord._cartesian_coordinates.asymmetric_unit_cartesian_class import (
+    AsymmetricUnitCartesian,
+)
+from chemcoord._cartesian_coordinates.cartesian_class_main import Cartesian
+from chemcoord._cartesian_coordinates.point_group import PointGroupOperations
+from chemcoord._internal_coordinates.zmat_class_main import Zmat
+from chemcoord._utilities._print_versions import show_versions
+from chemcoord.configuration import settings
+from chemcoord.zmat_functions import (
+    DummyManipulation,
+    PureInternalMovement,
+    TestOperators,
 )
-from chemcoord.cartesian_coordinates.cartesian_class_main import Cartesian as Cartesian
-from chemcoord.configuration import settings as settings
-from chemcoord.internal_coordinates.zmat_class_main import Zmat as Zmat
-from chemcoord.utilities._print_versions import show_versions as show_versions
 
-sys.modules["chemcoord.xyz_functions"] = xyz_functions
-sys.modules["chemcoord.zmat_functions"] = zmat_functions
+__version__ = version("chemcoord")
+_git_branch = "master"

src/chemcoord/cartesian_coordinates/_cart_transformation.py → src/chemcoord/_cartesian_coordinates/_cart_transformation.py

@@ -1,13 +1,11 @@
-# -*- coding: utf-8 -*-
-
 import numba as nb
 import numpy as np
 from numba import jit
 from numba.extending import overload
 from numpy import arccos, arctan2, sqrt
 
 import chemcoord.constants as constants
-from chemcoord.cartesian_coordinates.xyz_functions import (
+from chemcoord._cartesian_coordinates.xyz_functions import (
     _jit_cross,
     _jit_isclose,
     _jit_normalize,

src/chemcoord/cartesian_coordinates/_cartesian_class_core.py → src/chemcoord/_cartesian_coordinates/_cartesian_class_core.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import collections
 import copy
 import itertools
@@ -10,12 +9,12 @@
 from numba import jit
 from sortedcontainers import SortedSet
 
-import chemcoord.cartesian_coordinates.xyz_functions as xyz_functions
+import chemcoord._cartesian_coordinates.xyz_functions as xyz_functions
 import chemcoord.constants as constants
-from chemcoord._generic_classes.generic_core import GenericCore
-from chemcoord.cartesian_coordinates._cartesian_class_pandas_wrapper import (
+from chemcoord._cartesian_coordinates._cartesian_class_pandas_wrapper import (
     PandasWrapper,
 )
+from chemcoord._generic_classes.generic_core import GenericCore
 from chemcoord.configuration import settings
 from chemcoord.exceptions import IllegalArgumentCombination, PhysicalMeaning
 
@@ -69,8 +68,7 @@ def __init__(
             raise ValueError("Need a pd.DataFrame as input")
         if not self._required_cols <= set(frame.columns):
             raise PhysicalMeaning(
-                "There are columns missing for a "
-                "meaningful description of a molecule"
+                "There are columns missing for a meaningful description of a molecule"
             )
         self._frame = frame.copy()
         if metadata is None:
@@ -596,9 +594,9 @@ def _preserve_bonds(self, sliced_cartesian, use_lookup=None):
             use_lookup = settings["defaults"]["use_lookup"]
 
         included_atoms_set = set(sliced_cartesian.index)
-        assert included_atoms_set.issubset(
-            set(self.index)
-        ), "The sliced Cartesian has to be a subset of the bigger frame"
+        assert included_atoms_set.issubset(set(self.index)), (
+            "The sliced Cartesian has to be a subset of the bigger frame"
+        )
         bond_dic = self.get_bonds(use_lookup=use_lookup)
         new_atoms = set([])
         for atom in included_atoms_set:

src/chemcoord/cartesian_coordinates/_cartesian_class_get_zmat.py → src/chemcoord/_cartesian_coordinates/_cartesian_class_get_zmat.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import warnings
 from collections import OrderedDict
 from functools import partial
@@ -8,10 +7,12 @@
 import pandas as pd
 from numba.core.errors import NumbaPerformanceWarning
 
-import chemcoord.cartesian_coordinates._cart_transformation as transformation
-import chemcoord.cartesian_coordinates.xyz_functions as xyz_functions
+import chemcoord._cartesian_coordinates._cart_transformation as transformation
+import chemcoord._cartesian_coordinates.xyz_functions as xyz_functions
 import chemcoord.constants as constants
-from chemcoord.cartesian_coordinates._cartesian_class_core import CartesianCore
+from chemcoord._cartesian_coordinates._cartesian_class_core import CartesianCore
+from chemcoord._internal_coordinates.zmat_class_main import Zmat
+from chemcoord._utilities._temporary_deprecation_workarounds import replace_without_warn
 from chemcoord.configuration import settings
 from chemcoord.exceptions import (
     ERR_CODE_OK,
@@ -20,8 +21,6 @@
     InvalidReference,
     UndefinedCoordinateSystem,
 )
-from chemcoord.internal_coordinates.zmat_class_main import Zmat
-from chemcoord.utilities._temporary_deprecation_workarounds import replace_without_warn
 
 
 class CartesianGetZmat(CartesianCore):
@@ -82,7 +81,7 @@ def _get_frag_constr_table(
 
         if start_atom is not None and predefined_table is not None:
             raise IllegalArgumentCombination(
-                "Either start_atom or " "predefined_table has to be None"
+                "Either start_atom or predefined_table has to be None"
             )
         if bond_dict is None:
             bond_dict = self._give_val_sorted_bond_dict(use_lookup=use_lookup)

src/chemcoord/cartesian_coordinates/_cartesian_class_io.py → src/chemcoord/_cartesian_coordinates/_cartesian_class_io.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import json
 import os
 import re
@@ -13,8 +12,8 @@
 import pandas as pd
 
 from chemcoord import constants
+from chemcoord._cartesian_coordinates._cartesian_class_core import CartesianCore
 from chemcoord._generic_classes.generic_IO import GenericIO
-from chemcoord.cartesian_coordinates._cartesian_class_core import CartesianCore
 from chemcoord.configuration import settings
 
 

src/chemcoord/cartesian_coordinates/_cartesian_class_pandas_wrapper.py → src/chemcoord/_cartesian_coordinates/_cartesian_class_pandas_wrapper.py

@@ -1,7 +1,6 @@
-# -*- coding: utf-8 -*-
 import copy
 
-import chemcoord.cartesian_coordinates._indexers as indexers
+import chemcoord._cartesian_coordinates._indexers as indexers
 from chemcoord.exceptions import PhysicalMeaning
 
 
@@ -156,8 +155,7 @@ def columns(self):
     def columns(self, value):
         if not self._required_cols <= set(value):
             raise PhysicalMeaning(
-                "There are columns missing for a "
-                "meaningful description of a molecule"
+                "There are columns missing for a meaningful description of a molecule"
             )
         self._frame.columns = value
 

src/chemcoord/cartesian_coordinates/_cartesian_class_symmetry.py → src/chemcoord/_cartesian_coordinates/_cartesian_class_symmetry.py

@@ -1,6 +1,5 @@
-# -*- coding: utf-8 -*-
-from chemcoord.cartesian_coordinates._cartesian_class_core import CartesianCore
-from chemcoord.cartesian_coordinates.point_group import PointGroupOperations
+from chemcoord._cartesian_coordinates._cartesian_class_core import CartesianCore
+from chemcoord._cartesian_coordinates.point_group import PointGroupOperations
 
 
 class CartesianSymmetry(CartesianCore):
@@ -115,7 +114,7 @@ def symmetrize(self, max_n=10, tolerance=0.3, epsilon=1e-3):
     def get_asymmetric_unit(self, eq=None):
         eq = self.get_equivalent_atoms() if (eq is None) else eq
         new_frame = self.loc[eq["eq_sets"].keys(), :]._frame
-        from chemcoord.cartesian_coordinates.asymmetric_unit_cartesian_class import (  # noqa: PLC0415
+        from chemcoord._cartesian_coordinates.asymmetric_unit_cartesian_class import (  # noqa: PLC0415
             AsymmetricUnitCartesian,
         )
 

src/chemcoord/cartesian_coordinates/_indexers.py → src/chemcoord/_cartesian_coordinates/_indexers.py

@@ -1,8 +1,6 @@
-# -*- coding: utf-8 -*-
-
 import warnings
 
-from chemcoord.utilities._temporary_deprecation_workarounds import is_iterable
+from chemcoord._utilities._temporary_deprecation_workarounds import is_iterable
 
 
 class _generic_Indexer(object):

src/chemcoord/cartesian_coordinates/asymmetric_unit_cartesian_class.py → src/chemcoord/_cartesian_coordinates/asymmetric_unit_cartesian_class.py

@@ -1,8 +1,7 @@
-# -*- coding: utf-8 -*-
 import numpy as np
 import pandas as pd
 
-from chemcoord.cartesian_coordinates.cartesian_class_main import Cartesian
+from chemcoord._cartesian_coordinates.cartesian_class_main import Cartesian
 
 
 class AsymmetricUnitCartesian(Cartesian):

src/chemcoord/cartesian_coordinates/cartesian_class_main.py → src/chemcoord/_cartesian_coordinates/cartesian_class_main.py

@@ -1,7 +1,6 @@
-# -*- coding: utf-8 -*-
-from chemcoord.cartesian_coordinates._cartesian_class_get_zmat import CartesianGetZmat
-from chemcoord.cartesian_coordinates._cartesian_class_io import CartesianIO
-from chemcoord.cartesian_coordinates._cartesian_class_symmetry import CartesianSymmetry
+from chemcoord._cartesian_coordinates._cartesian_class_get_zmat import CartesianGetZmat
+from chemcoord._cartesian_coordinates._cartesian_class_io import CartesianIO
+from chemcoord._cartesian_coordinates._cartesian_class_symmetry import CartesianSymmetry
 
 
 class Cartesian(CartesianIO, CartesianGetZmat, CartesianSymmetry):

src/chemcoord/cartesian_coordinates/point_group.py → src/chemcoord/_cartesian_coordinates/point_group.py

@@ -1,8 +1,3 @@
-# -*- coding: utf-8 -*-
-from chemcoord import export
-
-
-@export
 class PointGroupOperations(list):
     """Defines a point group as sequence of symmetry operations.
 

src/chemcoord/cartesian_coordinates/xyz_functions.py → src/chemcoord/_cartesian_coordinates/xyz_functions.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import math as m
 import os
 import subprocess
@@ -155,7 +154,7 @@ def read_molden(inputfile, start_index=0, get_bonds=True):
     Returns:
         list: A list containing :class:`~chemcoord.Cartesian` is returned.
     """
-    from chemcoord.cartesian_coordinates.cartesian_class_main import (  # noqa: PLC0415
+    from chemcoord._cartesian_coordinates.cartesian_class_main import (  # noqa: PLC0415
         Cartesian,
     )
 
@@ -460,7 +459,7 @@ def apply_grad_zmat_tensor(grad_C, construction_table, cart_dist):
     if (construction_table.index != cart_dist.index).any():
         message = "construction_table and cart_dist must use the same index"
         raise ValueError(message)
-    from chemcoord.internal_coordinates.zmat_class_main import Zmat  # noqa: PLC0415
+    from chemcoord._internal_coordinates.zmat_class_main import Zmat  # noqa: PLC0415
 
     dtypes = [
         ("atom", str),

src/chemcoord/_generic_classes/generic_IO.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import numpy as np
 import sympy
 

src/chemcoord/_generic_classes/generic_core.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import pandas as pd
 
 import chemcoord.constants as constants

src/chemcoord/internal_coordinates/_indexers.py → src/chemcoord/_internal_coordinates/_indexers.py

@@ -1,9 +1,7 @@
-# -*- coding: utf-8 -*-
-
 import warnings
 
+from chemcoord._utilities._temporary_deprecation_workarounds import is_iterable
 from chemcoord.exceptions import InvalidReference
-from chemcoord.utilities._temporary_deprecation_workarounds import is_iterable
 
 
 class _generic_Indexer(object):

src/chemcoord/internal_coordinates/_zmat_class_core.py → src/chemcoord/_internal_coordinates/_zmat_class_core.py

@@ -1,24 +1,23 @@
-# -*- coding: utf-8 -*-
 import copy
 import warnings
 from functools import partial
 
 import numpy as np
 import pandas as pd
 
+import chemcoord._internal_coordinates._indexers as indexers
+import chemcoord._internal_coordinates._zmat_transformation as transformation
 import chemcoord.constants as constants
-import chemcoord.internal_coordinates._indexers as indexers
-import chemcoord.internal_coordinates._zmat_transformation as transformation
 from chemcoord._generic_classes.generic_core import GenericCore
+from chemcoord._internal_coordinates._zmat_class_pandas_wrapper import PandasWrapper
+from chemcoord._utilities import _decorators
+from chemcoord._utilities._temporary_deprecation_workarounds import replace_without_warn
 from chemcoord.exceptions import (
     ERR_CODE_OK,
     ERR_CODE_InvalidReference,
     InvalidReference,
     PhysicalMeaning,
 )
-from chemcoord.internal_coordinates._zmat_class_pandas_wrapper import PandasWrapper
-from chemcoord.utilities import _decorators
-from chemcoord.utilities._temporary_deprecation_workarounds import replace_without_warn
 
 append_indexer_docstring = _decorators.Appender(
     """In the case of obtaining elements, the indexing behaves like
@@ -58,8 +57,7 @@ def __init__(self, frame, metadata=None, _metadata=None):
         """
         if not self._required_cols <= set(frame.columns):
             raise PhysicalMeaning(
-                "There are columns missing for a "
-                "meaningful description of a molecule"
+                "There are columns missing for a meaningful description of a molecule"
             )
         self._frame = frame.copy()
         if metadata is None:
@@ -508,7 +506,7 @@ def change_numbering(self, new_index=None):
             c_table = c_table.astype("i8")
         except ValueError:
             raise ValueError(
-                "Due to a bug in pandas it is necessary to have " "integer columns"
+                "Due to a bug in pandas it is necessary to have integer columns"
             )
         c_table = c_table.replace(self.index, new_index)
         c_table = c_table.replace({v: k for k, v in constants.int_label.items()})
@@ -667,7 +665,7 @@ def create_cartesian(positions, row):
             )
             xyz_frame["atom"] = self.loc[xyz_frame.index, "atom"]
             xyz_frame.loc[:, ["x", "y", "z"]] = positions[:row]
-            from chemcoord.cartesian_coordinates.cartesian_class_main import (  # noqa: PLC0415
+            from chemcoord._cartesian_coordinates.cartesian_class_main import (  # noqa: PLC0415
                 Cartesian,
             )
 
@@ -829,7 +827,7 @@ def drop_dummies(grad_X, zmolecule):
             grad_X = drop_dummies(grad_X, self)
 
         if as_function:
-            from chemcoord.internal_coordinates.zmat_functions import (  # noqa: PLC0415
+            from chemcoord._internal_coordinates.zmat_functions import (  # noqa: PLC0415
                 apply_grad_cartesian_tensor,
             )