Moved resample out of parsers to its own sub-package

news/resample-relocation.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Moved resampler out of parsers, new path is diffpy.utils.resampler
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* Relative imports in parser's __init__.py
+
+**Fixed:**
+
+* File and function names are now all in PEP8 format
+
+**Security:**
+
+* <news item>

src/diffpy/utils/parsers/__init__.py

@@ -16,12 +16,4 @@
 """Various utilities related to data parsing and manipulation.
 """
 
-from .loaddata import loadData
-from .resample import resample
-from .serialization import deserialize_data, serialize_data
-
-# silence the pyflakes syntax checker
-assert loadData or resample or True
-assert serialize_data or deserialize_data or True
-
 # End of file

src/diffpy/utils/parsers/loaddata.py → src/diffpy/utils/parsers/data_loader.py

@@ -16,7 +16,7 @@
 import numpy
 
 
-def loadData(filename, minrows=10, headers=False, hdel="=", hignore=None, **kwargs):
+def load_data(filename, minrows=10, headers=False, hdel="=", hignore=None, **kwargs):
     """Find and load data from a text file.
 
     The data block is identified as the first matrix block of at least minrows rows and constant number of columns.

src/diffpy/utils/scattering_objects/diffraction_objects.py

@@ -17,7 +17,7 @@
 )
 
 
-class Diffraction_object:
+class DiffractionObject:
     def __init__(self, name="", wavelength=None):
         self.name = name
         self.wavelength = wavelength
@@ -29,7 +29,7 @@ def __init__(self, name="", wavelength=None):
         self.metadata = {}
 
     def __eq__(self, other):
-        if not isinstance(other, Diffraction_object):
+        if not isinstance(other, DiffractionObject):
             return NotImplemented
         self_attributes = [key for key in self.__dict__ if not key.startswith("_")]
         other_attributes = [key for key in other.__dict__ if not key.startswith("_")]
@@ -59,8 +59,8 @@ def __add__(self, other):
         if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
             summed.on_tth[1] = self.on_tth[1] + other
             summed.on_q[1] = self.on_q[1] + other
-        elif not isinstance(other, Diffraction_object):
-            raise TypeError("I only know how to sum two Diffraction_object objects")
+        elif not isinstance(other, DiffractionObject):
+            raise TypeError("I only know how to sum two DiffractionObject objects")
         elif self.on_tth[0].all() != other.on_tth[0].all():
             raise RuntimeError(x_grid_emsg)
         else:
@@ -73,7 +73,7 @@ def __radd__(self, other):
         if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
             summed.on_tth[1] = self.on_tth[1] + other
             summed.on_q[1] = self.on_q[1] + other
-        elif not isinstance(other, Diffraction_object):
+        elif not isinstance(other, DiffractionObject):
             raise TypeError("I only know how to sum two Scattering_object objects")
         elif self.on_tth[0].all() != other.on_tth[0].all():
             raise RuntimeError(x_grid_emsg)
@@ -87,7 +87,7 @@ def __sub__(self, other):
         if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
             subtracted.on_tth[1] = self.on_tth[1] - other
             subtracted.on_q[1] = self.on_q[1] - other
-        elif not isinstance(other, Diffraction_object):
+        elif not isinstance(other, DiffractionObject):
             raise TypeError("I only know how to subtract two Scattering_object objects")
         elif self.on_tth[0].all() != other.on_tth[0].all():
             raise RuntimeError(x_grid_emsg)
@@ -101,7 +101,7 @@ def __rsub__(self, other):
         if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
             subtracted.on_tth[1] = other - self.on_tth[1]
             subtracted.on_q[1] = other - self.on_q[1]
-        elif not isinstance(other, Diffraction_object):
+        elif not isinstance(other, DiffractionObject):
             raise TypeError("I only know how to subtract two Scattering_object objects")
         elif self.on_tth[0].all() != other.on_tth[0].all():
             raise RuntimeError(x_grid_emsg)
@@ -115,7 +115,7 @@ def __mul__(self, other):
         if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
             multiplied.on_tth[1] = other * self.on_tth[1]
             multiplied.on_q[1] = other * self.on_q[1]
-        elif not isinstance(other, Diffraction_object):
+        elif not isinstance(other, DiffractionObject):
             raise TypeError("I only know how to multiply two Scattering_object objects")
         elif self.on_tth[0].all() != other.on_tth[0].all():
             raise RuntimeError(x_grid_emsg)
@@ -141,7 +141,7 @@ def __truediv__(self, other):
         if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
             divided.on_tth[1] = other / self.on_tth[1]
             divided.on_q[1] = other / self.on_q[1]
-        elif not isinstance(other, Diffraction_object):
+        elif not isinstance(other, DiffractionObject):
             raise TypeError("I only know how to multiply two Scattering_object objects")
         elif self.on_tth[0].all() != other.on_tth[0].all():
             raise RuntimeError(x_grid_emsg)
@@ -389,7 +389,7 @@ def scale_to(self, target_diff_object, xtype=None, xvalue=None):
 
         Parameters
         ----------
-        target_diff_object: Diffraction_object
+        target_diff_object: DiffractionObject
           the diffractoin object you want to scale the current one on to
         xtype: string, optional.  Default is Q
           the xtype, from {XQUANTITIES}, that you will specify a point from to scale to
@@ -400,7 +400,7 @@ def scale_to(self, target_diff_object, xtype=None, xvalue=None):
 
         Returns
         -------
-        the rescaled Diffraction_object as a new object
+        the rescaled DiffractionObject as a new object
 
         """
         scaled = deepcopy(self)
@@ -454,7 +454,7 @@ def dump(self, filepath, xtype=None):
 
         with open(filepath, "w") as f:
             f.write(
-                f"[Diffraction_object]\nname = {self.name}\nwavelength = {self.wavelength}\n"
+                f"[DiffractionObject]\nname = {self.name}\nwavelength = {self.wavelength}\n"
                 f"scat_quantity = {self.scat_quantity}\n"
             )
             for key, value in self.metadata.items():

tests/test_diffraction_objects.py

@@ -4,7 +4,7 @@
 import pytest
 from freezegun import freeze_time
 
-from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
+from diffpy.utils.scattering_objects.diffraction_objects import DiffractionObject
 
 params = [
     (  # Default
@@ -222,8 +222,8 @@
 
 @pytest.mark.parametrize("inputs1, inputs2, expected", params)
 def test_diffraction_objects_equality(inputs1, inputs2, expected):
-    diffraction_object1 = Diffraction_object()
-    diffraction_object2 = Diffraction_object()
+    diffraction_object1 = DiffractionObject()
+    diffraction_object2 = DiffractionObject()
     diffraction_object1_attributes = [key for key in diffraction_object1.__dict__ if not key.startswith("_")]
     for i, attribute in enumerate(diffraction_object1_attributes):
         setattr(diffraction_object1, attribute, inputs1[i])
@@ -235,7 +235,7 @@ def test_dump(tmp_path, mocker):
     x, y = np.linspace(0, 5, 6), np.linspace(0, 5, 6)
     directory = Path(tmp_path)
     file = directory / "testfile"
-    test = Diffraction_object()
+    test = DiffractionObject()
     test.wavelength = 1.54
     test.name = "test"
     test.scat_quantity = "x-ray"
@@ -251,7 +251,7 @@ def test_dump(tmp_path, mocker):
     with open(file, "r") as f:
         actual = f.read()
     expected = (
-        "[Diffraction_object]\nname = test\nwavelength = 1.54\nscat_quantity = x-ray\nthing1 = 1\n"
+        "[DiffractionObject]\nname = test\nwavelength = 1.54\nscat_quantity = x-ray\nthing1 = 1\n"
         "thing2 = thing2\npackage_info = {'package2': '3.4.5', 'diffpy.utils': '3.3.0'}\n"
         "creation_time = 2012-01-14 00:00:00\n\n"
         "#### start data\n0.000000000000000000e+00 0.000000000000000000e+00\n"

tests/test_loaddata.py

@@ -8,7 +8,7 @@
 import numpy
 import pytest
 
-from diffpy.utils.parsers import loadData
+from diffpy.utils.parsers.data_loader import load_data
 
 
 ##############################################################################
@@ -21,29 +21,29 @@ def test_loadData_default(self):
         """check loadData() with default options"""
         loaddata01 = self.datafile("loaddata01.txt")
         d2c = numpy.array([[3, 31], [4, 32], [5, 33]])
-        self.assertRaises(IOError, loadData, "doesnotexist")
+        self.assertRaises(IOError, load_data, "doesnotexist")
         # the default minrows=10 makes it read from the third line
-        d = loadData(loaddata01)
+        d = load_data(loaddata01)
         self.assertTrue(numpy.array_equal(d2c, d))
         # the usecols=(0, 1) would make it read from the third line
-        d = loadData(loaddata01, minrows=1, usecols=(0, 1))
+        d = load_data(loaddata01, minrows=1, usecols=(0, 1))
         self.assertTrue(numpy.array_equal(d2c, d))
         # check the effect of usecols effect
-        d = loadData(loaddata01, usecols=(0,))
+        d = load_data(loaddata01, usecols=(0,))
         self.assertTrue(numpy.array_equal(d2c[:, 0], d))
-        d = loadData(loaddata01, usecols=(1,))
+        d = load_data(loaddata01, usecols=(1,))
         self.assertTrue(numpy.array_equal(d2c[:, 1], d))
         return
 
     def test_loadData_1column(self):
         """check loading of one-column data."""
         loaddata01 = self.datafile("loaddata01.txt")
         d1c = numpy.arange(1, 6)
-        d = loadData(loaddata01, usecols=[0], minrows=1)
+        d = load_data(loaddata01, usecols=[0], minrows=1)
         self.assertTrue(numpy.array_equal(d1c, d))
-        d = loadData(loaddata01, usecols=[0], minrows=2)
+        d = load_data(loaddata01, usecols=[0], minrows=2)
         self.assertTrue(numpy.array_equal(d1c, d))
-        d = loadData(loaddata01, usecols=[0], minrows=3)
+        d = load_data(loaddata01, usecols=[0], minrows=3)
         self.assertFalse(numpy.array_equal(d1c, d))
         return
 
@@ -52,7 +52,7 @@ def test_loadData_headers(self):
         loaddatawithheaders = self.datafile("loaddatawithheaders.txt")
         hignore = ["# ", "// ", "["]  # ignore lines beginning with these strings
         delimiter = ": "  # what our data should be separated by
-        hdata = loadData(loaddatawithheaders, headers=True, hdel=delimiter, hignore=hignore)
+        hdata = load_data(loaddatawithheaders, headers=True, hdel=delimiter, hignore=hignore)
         # only fourteen lines of data are formatted properly
         assert len(hdata) == 14
         # check the following are floats

tests/test_resample.py

@@ -1,7 +1,7 @@
 import numpy as np
 import pytest
 
-from diffpy.utils.parsers.resample import wsinterp
+from diffpy.utils.resampler import wsinterp
 
 
 def test_wsinterp():

tests/test_serialization.py

@@ -3,8 +3,9 @@
 import numpy
 import pytest
 
-from diffpy.utils.parsers import deserialize_data, loadData, serialize_data
 from diffpy.utils.parsers.custom_exceptions import ImproperSizeError, UnsupportedTypeError
+from diffpy.utils.parsers.data_loader import load_data
+from diffpy.utils.parsers.serializer import deserialize_data, serialize_data
 
 tests_dir = os.path.dirname(os.path.abspath(locals().get("__file__", "file.py")))
 
@@ -20,8 +21,8 @@ def test_load_multiple(tmp_path, datafile):
     for hfname in tlm_list:
         # gather data using loadData
         headerfile = os.path.normpath(os.path.join(tests_dir, "testdata", "dbload", hfname))
-        hdata = loadData(headerfile, headers=True)
-        data_table = loadData(headerfile)
+        hdata = load_data(headerfile, headers=True)
+        data_table = load_data(headerfile)
 
         # check path extraction
         generated_data = serialize_data(headerfile, hdata, data_table, dt_colnames=["r", "gr"], show_path=True)
@@ -50,8 +51,8 @@ def test_exceptions(datafile):
     loadfile = datafile("loadfile.txt")
     warningfile = datafile("generatewarnings.txt")
     nodt = datafile("loaddatawithheaders.txt")
-    hdata = loadData(loadfile, headers=True)
-    data_table = loadData(loadfile)
+    hdata = load_data(loadfile, headers=True)
+    data_table = load_data(loadfile)
 
     # improper file types
     with pytest.raises(UnsupportedTypeError):
@@ -87,15 +88,15 @@ def test_exceptions(datafile):
     assert numpy.allclose(r_extract[data_name]["r"], r_list)
     assert numpy.allclose(gr_extract[data_name]["gr"], gr_list)
     # no datatable
-    nodt_hdata = loadData(nodt, headers=True)
-    nodt_dt = loadData(nodt)
+    nodt_hdata = load_data(nodt, headers=True)
+    nodt_dt = load_data(nodt)
     no_dt = serialize_data(nodt, nodt_hdata, nodt_dt, show_path=False)
     nodt_data_name = list(no_dt.keys())[0]
     assert numpy.allclose(no_dt[nodt_data_name]["data table"], nodt_dt)
 
     # ensure user is warned when columns are overwritten
-    hdata = loadData(warningfile, headers=True)
-    data_table = loadData(warningfile)
+    hdata = load_data(warningfile, headers=True)
+    data_table = load_data(warningfile)
     with pytest.warns(RuntimeWarning) as record:
         serialize_data(
             warningfile,