merge from main and add tests for unknown materials

Author: yucongalicechen

.pre-commit-config.yaml

@@ -58,3 +58,10 @@ repos:
       - id: prettier
         additional_dependencies:
           - "prettier@^3.2.4"
+  # docformatter - formats docstrings using PEP 257
+  - repo: https://github.com/s-weigand/docformatter
+    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]

doc/source/examples/tools_example.rst

@@ -114,6 +114,10 @@ After receiving the inputs, the function will write the information to
 the `diffpyconfig.json` file in your home directory.
 
 
+``check_and_build_global_config()`` returns ``True`` if the config file exists (whether it created it or not)
+and ``False`` if the config file does not exist in the user's home allowing you to develop your own
+workflow for handling missing config files after running it with ``skip_config_creation=True``.
+
 I entered the wrong information in my config file so it always loads incorrect information, how do I fix that?
 --------------------------------------------------------------------------------------------------------------
 

news/configupdate.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* no news added: covered in the news from the get_user_info work
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/docformatter.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* docforamtter in pre-commit for automatic formatting of docstrings to PEP 257
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/uuid-rename.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* DiffractionObject's "id" property renamed to "uuid"
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/__init__.py

@@ -16,7 +16,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """diffpy - tools for structure analysis by diffraction.
 
 Blank namespace package.

src/diffpy/utils/__init__.py

@@ -12,8 +12,7 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
-"""Shared utilities for diffpy packages"""
+"""Shared utilities for diffpy packages."""
 
 # package version
 from diffpy.utils.version import __version__

src/diffpy/utils/diffraction_objects.py

@@ -46,12 +46,6 @@ class DiffractionObject:
 
     Attributes
     ----------
-    all_arrays : ndarray
-        The array containing the quantity of q, tth, d values.
-    input_xtype : str
-        The type of the independent variable in `xarray`. Must be one of {*XQUANTITIES}
-    id : uuid
-        The unique identifier for the diffraction object.
     scat_quantity : str
         The type of scattering experiment (e.g., "x-ray", "neutron"). Default is an empty string "".
     wavelength : float
@@ -127,7 +121,7 @@ def __init__(
         >>> print(do.metadata)
         """
 
-        self._id = uuid.uuid4()
+        self._uuid = uuid.uuid4()
         self._input_data(xarray, yarray, xtype, wavelength, scat_quantity, name, metadata)
 
     def _input_data(self, xarray, yarray, xtype, wavelength, scat_quantity, name, metadata):
@@ -284,6 +278,23 @@ def __rtruediv__(self, other):
 
     @property
     def all_arrays(self):
+        """The 2D array containing `xarray` and `yarray` values.
+
+        Returns
+        -------
+        ndarray
+            The shape (len(data), 4) 2D array with columns containing the `yarray` (intensity)
+            and the `xarray` values in q, tth, and d.
+
+        Examples
+        --------
+        To access specific arrays individually, use these slices:
+
+        >>> my_do.all_arrays[:, 0]  # yarray
+        >>> my_do.all_arrays[:, 1]  # xarray in q
+        >>> my_do.all_arrays[:, 2]  # xarray in tth
+        >>> my_do.all_arrays[:, 3]  # xarray in d
+        """
         return self._all_arrays
 
     @all_arrays.setter
@@ -292,19 +303,33 @@ def all_arrays(self, _):
 
     @property
     def input_xtype(self):
+        """The type of the independent variable in `xarray`.
+
+        Returns
+        -------
+        str
+            The type of `xarray`, which must be one of {*XQUANTITIES}.
+        """
         return self._input_xtype
 
     @input_xtype.setter
     def input_xtype(self, _):
         raise AttributeError(_setter_wmsg("input_xtype"))
 
     @property
-    def id(self):
-        return self._id
+    def uuid(self):
+        """The unique identifier for the DiffractionObject instance.
+
+        Returns
+        -------
+        uuid
+            The unique identifier of the DiffractionObject instance.
+        """
+        return self._uuid
 
-    @id.setter
-    def id(self, _):
-        raise AttributeError(_setter_wmsg("id"))
+    @uuid.setter
+    def uuid(self, _):
+        raise AttributeError(_setter_wmsg("uuid"))
 
     def get_array_index(self, value, xtype=None):
         """Return the index of the closest value in the array associated with
@@ -319,7 +344,8 @@ def get_array_index(self, value, xtype=None):
 
         Returns
         -------
-        the index of the value in the array
+        list
+            The list containing the index of the closest value in the array.
         """
 
         xtype = self._input_xtype

src/diffpy/utils/parsers/__init__.py

@@ -12,6 +12,4 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-
-"""Various utilities related to data parsing and manipulation.
-"""
+"""Various utilities related to data parsing and manipulation."""

src/diffpy/utils/parsers/serialization.py

@@ -33,8 +33,8 @@ def serialize_data(
     show_path=True,
     serial_file=None,
 ):
-    """Serialize file data into a dictionary. Can also save dictionary into a serial language file. Dictionary is
-    formatted as {filename: data}.
+    """Serialize file data into a dictionary. Can also save dictionary into a
+    serial language file. Dictionary is formatted as {filename: data}.
 
     Requires hdata and data_table (can be generated by loadData).