Merge pull request #83 from diffpy/cookie

Cookie

Author: sbillinge

Diff for: CHANGELOG.rst

@@ -4,23 +4,6 @@ Release Notes
 
 .. current developments
 
-Version 3.2.0 - 2024-7-2
---------------------------
-**Added:**
-
-**Changed:**
-
-**Deprecated:**
-
-**Removed:**
-
-**Fixed:**
-
-- Repo structure modified to the new diffpy standard
-
-**Security:**
-
-
 Version 3.1.0 - 2022-12-04
 --------------------------
 

Diff for: README.rst

@@ -66,7 +66,7 @@ by citing the following paper in your publication:
 Requirements
 ------------------------------------------------------------------------
 
-The diffpy.structure package requires Python 3.7 or later or 2.7 and
+The diffpy.structure package requires Python 3.7 or later and
 the following software:
 
 * ``setuptools`` - software distribution tools for Python

Diff for: doc/source/api/diffpy.structure.applications.rst

@@ -16,7 +16,6 @@ Subpackages
 
     diffpy.structure.parsers
     diffpy.structure.expansion
-    diffpy.structure.applications
     diffpy.structure.apps
 
 Submodules

Diff for: doc/source/api/diffpy.structure.rst

@@ -48,6 +48,8 @@
     "m2r",
 ]
 
+autodoc_member_order = "groupwise"
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -118,6 +120,12 @@
 # Display all warnings for missing links.
 nitpicky = True
 
+nitpick_ignore = [
+    ("py:class", "array_like"),
+    ("py:class", "Parser"),
+    ("py:class", "CifFile"),
+]
+
 # -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -289,3 +297,7 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 # intersphinx_mapping = {'http://docs.python.org/': None}
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+}

Diff for: doc/source/conf.py

@@ -0,0 +1,25 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* All docstrings style updated to numpydoc.
+
+**Deprecated:**
+
+* Deprecated the `diffpy.structure.applications` module. Use
+  `diffpy.structure.apps` instead.
+
+**Removed:**
+
+* Removed all `six` compatibility code. The package is now going to 
+  Python > 3.10.
+
+**Fixed:**
+
+* Repo structure modified to the new diffpy standard.
+
+**Security:**
+
+* <news item>

Diff for: news/changlog.rst

@@ -1,3 +1,2 @@
 numpy < 2.0.0  # Need to fix deprecations before 2.0.0 compat
 pycifrw
-six

Diff for: requirements/run.txt

@@ -13,12 +13,13 @@
 #
 ##############################################################################
 
-"""
-Support import of old camel-case module names with DeprecationWarning.
+"""Support import of old camel-case module names with `DeprecationWarning`.
 
 The imported camel-case modules are aliases for the current module
-instances.  Their `__name__` attributes are thus all in lower-case.
+instances. Their `__name__` attributes are thus all in lower-case.
 
+Warning
+-------
 This module is deprecated and will be removed in the future.
 """
 

Diff for: src/diffpy/Structure.py

@@ -13,16 +13,26 @@
 #
 ##############################################################################
 
-"""classes related to structure of materials
-Classes:
-    Atom
-    Lattice
-    Structure
-    PDFFitStructure
+"""
+Crystal structure container and parsers for structure formats.
+
+Classes related to the structure of materials:
+    * Atom
+    * Lattice
+    * Structure
+    * PDFFitStructure
+
+Other classes:
+    * SpaceGroup
+    * SymOp
+    * ExpandAsymmetricUnit
+    * GeneratorSite
+    * SymmetryConstraints
+
 Exceptions:
-    StructureFormatError
-    LatticeError
-    SymmetryError
+    * StructureFormatError
+    * LatticeError
+    * SymmetryError
 """
 
 # Interface definitions ------------------------------------------------------
@@ -37,27 +47,24 @@
 # package version
 from diffpy.structure.version import __version__
 
-"""Crystal structure container and parsers for structure formats."""
-
 # top level routines
 
 
 def loadStructure(filename, fmt="auto", **kw):
-    """
-    Load new structure object from the specified file.
+    """Load new structure object from the specified file.
 
     Parameters
     ----------
 
     filename : str
         Path to the file to be loaded.
-    fmt : str, optional
-        Format of the structure file such as 'cif' or 'xyz'.  Must be
+    fmt : str, Optional
+        Format of the structure file such as 'cif' or 'xyz'. Must be
         one of the formats listed by the `parsers.inputFormats` function.
         When 'auto', all supported formats are tried in a sequence.
-    kw : misc, optional
+    kw : Optional
         Extra keyword arguments that are passed to `parsers.getParser`
-        function.  These configure the dedicated Parser object that
+        function. These configure the dedicated Parser object that
         is used to read content in filename.
 
     Returns

Diff for: src/diffpy/structure/__init__.py

@@ -17,33 +17,23 @@
 Support import of old camel-case module names with DeprecationWarning.
 
 The imported camel-case modules are aliases for the current module
-instances.  Their `__name__` attributes are thus all in lower-case.
+instances. Their `__name__` attributes are thus all in lower-case.
 
-This module is deprecated and will be removed in the future.
+Note
+----
+this module must be only imported from `diffpy.Structure`.
 
-NOTE: this module must be only imported from `diffpy.Structure`.
+Warning
+-------
+This module is deprecated and will be removed in the future.
 """
 
 
+import importlib.abc
 import sys
 from warnings import warn
 
-import six
-
-if six.PY2:
-    import importlib
-
-    class mock_importlib_abc(object):
-        MetaPathFinder = object
-        Loader = object
-
-    importlib.abc = mock_importlib_abc
-    sys.modules.setdefault("importlib.abc", mock_importlib_abc)
-    del mock_importlib_abc
-
-import importlib.abc
-
-WMSG = "Module {!r} is deprecated.  Use {!r} instead."
+WMSG = "Module {!r} is deprecated. Use {!r} instead."
 
 # ----------------------------------------------------------------------------
 
@@ -63,25 +53,14 @@ def find_spec(self, fullname, path=None, target=None):
             spec.loader = MapRenamedStructureModule()
         return spec
 
-    if six.PY2:
-
-        def find_module(self, fullname, path):
-            # only handle submodules of diffpy.Structure
-            loader = None
-            if fullname.startswith(self.prefix):
-                loader = MapRenamedStructureModule()
-            return loader
-
 
 # end of class FindRenamedStructureModule
 
 # ----------------------------------------------------------------------------
 
 
 class MapRenamedStructureModule(importlib.abc.Loader):
-    """
-    Loader for old camel-case module names.
-
+    """Loader for old camel-case module names.
     Import the current module and alias it under the old name.
     """
 
@@ -95,15 +74,6 @@ def create_module(self, spec):
     def exec_module(self, module):
         return
 
-    if six.PY2:
-        from collections import namedtuple
-
-        ModuleSpec = namedtuple("ModuleSpec", "name")
-
-        def load_module(self, fullname):
-            spec = self.ModuleSpec(fullname)
-            return self.create_module(spec)
-
 
 # end of class MapRenamedStructureModule
 

Diff for: src/diffpy/structure/_legacy_importer.py

@@ -13,5 +13,5 @@
 #
 ##############################################################################
 
-"""Script applications that use the diffpy.structure package.
+"""Script applications that use the `diffpy.structure` package.
 """