Merge branch 'main' into __init__

.github/workflows/pre-commit.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   pre-commit:
     # pull requests are a duplicate of a branch push if within the same repo.
-    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
+    if: ${{ github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository }}
 
     runs-on: ubuntu-latest
     steps:

src/diffpy/pdfmorph/__init__.py

@@ -16,7 +16,7 @@
 """Tools for manipulating and comparing PDFs.
 """
 # top-level import
-from diffpy.pdfmorph.pdfmorph_api import morph_default_config, pdfmorph, plot_morph
+from diffpy.pdfmorph.pdfmorph_api import morph_default_config, pdfmorph, plot_morph  # noqa: F401
 
 top_level = [
     pdfmorph,

src/diffpy/pdfmorph/morph_helpers/transformpdftordf.py

@@ -18,7 +18,7 @@
 """
 
 
-from diffpy.pdfmorph.morphs.morph import *
+from diffpy.pdfmorph.morphs.morph import LABEL_GR, LABEL_RA, LABEL_RR, Morph
 
 
 class TransformXtalPDFtoRDF(Morph):

src/diffpy/pdfmorph/morph_helpers/transformrdftopdf.py

@@ -20,7 +20,7 @@
 
 import numpy
 
-from diffpy.pdfmorph.morphs.morph import *
+from diffpy.pdfmorph.morphs.morph import LABEL_GR, LABEL_RA, LABEL_RR, Morph
 
 
 class TransformXtalRDFtoPDF(Morph):

src/diffpy/pdfmorph/morphs/__init__.py

@@ -17,8 +17,8 @@
 """
 
 
-from diffpy.pdfmorph.morphs.morph import Morph
-from diffpy.pdfmorph.morphs.morphchain import MorphChain
+from diffpy.pdfmorph.morphs.morph import Morph  # noqa: F401
+from diffpy.pdfmorph.morphs.morphchain import MorphChain  # noqa: F401
 from diffpy.pdfmorph.morphs.morphishape import MorphISphere, MorphISpheroid
 from diffpy.pdfmorph.morphs.morphresolution import MorphResolutionDamping
 from diffpy.pdfmorph.morphs.morphrgrid import MorphRGrid

src/diffpy/pdfmorph/morphs/morphishape.py

@@ -21,7 +21,7 @@ class MorphISpheroid -- apply inverse spheroidal shape function
 
 import numpy
 
-from diffpy.pdfmorph.morphs.morph import *
+from diffpy.pdfmorph.morphs.morph import LABEL_GR, LABEL_RA, Morph
 from diffpy.pdfmorph.morphs.morphshape import _sphericalCF, _spheroidalCF
 
 

src/diffpy/pdfmorph/morphs/morphresolution.py

@@ -20,7 +20,7 @@
 
 import numpy
 
-from diffpy.pdfmorph.morphs.morph import *
+from diffpy.pdfmorph.morphs.morph import LABEL_RA, LABEL_RR, Morph
 
 
 class MorphResolutionDamping(Morph):

src/diffpy/pdfmorph/morphs/morphrgrid.py

@@ -20,7 +20,7 @@
 
 import numpy
 
-from diffpy.pdfmorph.morphs.morph import *
+from diffpy.pdfmorph.morphs.morph import LABEL_GR, LABEL_RA, Morph
 
 # roundoff tolerance for selecting bounds on arrays.
 epsilon = 1e-8

src/diffpy/pdfmorph/morphs/morphscale.py

@@ -18,7 +18,7 @@
 """
 
 
-from diffpy.pdfmorph.morphs.morph import *
+from diffpy.pdfmorph.morphs.morph import LABEL_GR, LABEL_RA, Morph
 
 
 class MorphScale(Morph):

src/diffpy/pdfmorph/morphs/morphshape.py

@@ -24,7 +24,7 @@ class MorphSpheroid -- apply a spheroidal shape function to the morph
 from numpy import arctanh as atanh
 from numpy import sqrt
 
-from diffpy.pdfmorph.morphs.morph import *
+from diffpy.pdfmorph.morphs.morph import LABEL_GR, LABEL_RA, Morph
 
 
 class MorphSphere(Morph):

src/diffpy/pdfmorph/morphs/morphshift.py

@@ -20,7 +20,7 @@
 
 import numpy
 
-from diffpy.pdfmorph.morphs.morph import *
+from diffpy.pdfmorph.morphs.morph import LABEL_GR, LABEL_RA, Morph
 
 
 class MorphShift(Morph):

src/diffpy/pdfmorph/morphs/morphsmear.py

@@ -20,7 +20,7 @@
 
 import numpy
 
-from diffpy.pdfmorph.morphs.morph import *
+from diffpy.pdfmorph.morphs.morph import LABEL_RA, LABEL_RR, Morph
 
 
 class MorphSmear(Morph):

src/diffpy/pdfmorph/morphs/morphstretch.py

@@ -20,7 +20,7 @@
 
 import numpy
 
-from diffpy.pdfmorph.morphs.morph import *
+from diffpy.pdfmorph.morphs.morph import LABEL_GR, LABEL_RA, Morph
 
 
 class MorphStretch(Morph):

src/diffpy/pdfmorph/pdfmorph_api.py

@@ -168,7 +168,6 @@ def pdfmorph(
     print(morph_rv_dict['pcc'])
     print(morph_rv_dict['rw'])
     """
-    operation_dict = {}
     refpars = []
     # input config
     rv_cfg = dict(kwargs)

src/diffpy/pdfmorph/pdfmorphapp.py

@@ -310,19 +310,19 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
     chain.append(morphs.MorphRGrid())
     refpars = []
 
-    ## Scale
+    # Scale
     if opts.scale is not None:
         scale_in = opts.scale
         chain.append(morphs.MorphScale())
         config["scale"] = opts.scale
         refpars.append("scale")
-    ## Stretch
+    # Stretch
     if opts.stretch is not None:
         stretch_in = opts.stretch
         chain.append(morphs.MorphStretch())
         config["stretch"] = opts.stretch
         refpars.append("stretch")
-    ## Smear
+    # Smear
     if opts.smear is not None:
         smear_in = opts.smear
         chain.append(helpers.TransformXtalPDFtoRDF())
@@ -334,7 +334,7 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
         if opts.baselineslope is None:
             refpars.append("baselineslope")
             config["baselineslope"] = -0.5
-    ## Size
+    # Size
     radii = [opts.radius, opts.pradius]
     nrad = 2 - radii.count(None)
     if nrad == 1:
@@ -362,7 +362,7 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
         refpars.append("ipradius")
         chain.append(morphs.MorphISpheroid())
 
-    ## Resolution
+    # Resolution
     if opts.qdamp is not None:
         chain.append(morphs.MorphResolutionDamping())
         refpars.append("qdamp")
@@ -426,7 +426,7 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
             stdout_flag=stdout_flag,
         )
 
-    except (FileNotFoundError, RuntimeError) as e:
+    except (FileNotFoundError, RuntimeError):
         save_fail_message = "Unable to save to designated location."
         parser.custom_error(save_fail_message)
 
@@ -518,7 +518,7 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
             save_morphs_here = io.create_morphs_directory(save_directory)
 
         # Could not create directory or find names to save morphs as
-        except (FileNotFoundError, RuntimeError) as e:
+        except (FileNotFoundError, RuntimeError):
             save_fail_message = "\nUnable to create directory"
             parser.custom_error(save_fail_message)
 
@@ -565,7 +565,7 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
             verbose=opts.verbose,
             stdout_flag=stdout_flag,
         )
-    except (FileNotFoundError, RuntimeError) as e:
+    except (FileNotFoundError, RuntimeError):
         save_fail_message = "Unable to save summary to directory."
         parser.custom_error(save_fail_message)
 

src/diffpy/pdfmorph/pdfplot.py

@@ -18,8 +18,6 @@
 import numpy
 from bg_mpl_stylesheet.bg_mpl_stylesheet import bg_mpl_style
 
-import diffpy.pdfmorph.tools as tools
-
 plt.style.use(bg_mpl_style)
 
 

src/diffpy/pdfmorph/tests/test_morph_func.py

@@ -16,7 +16,7 @@ def test_morphfunc_verbose():
     x_morph = x_target.copy()
     y_morph = heaviside(x_target, lb * (1 + stretch), ub * (1 + stretch))
     cfg = morph_default_config(stretch=0.1)  # off init
-    morph_rv = pdfmorph(x_morph, y_morph, x_target, y_target, verbose=True, **cfg)
+    pdfmorph(x_morph, y_morph, x_target, y_target, verbose=True, **cfg)
 
 
 def test_fixed_morph_with_morphfunc():
@@ -29,7 +29,7 @@ def test_fixed_morph_with_morphfunc():
     y_morph = heaviside(x_target, lb * (1 + stretch), ub * (1 + stretch))
     cfg = morph_default_config(stretch=0.1)  # off init
     cfg["scale"] = 30
-    morph_rv = pdfmorph(
+    pdfmorph(
         x_morph,
         y_morph,
         x_target,

src/diffpy/pdfmorph/tests/test_morphchain.py

@@ -6,15 +6,15 @@
 import numpy
 import pytest
 
+from diffpy.pdfmorph.morphs.morphchain import MorphChain
+from diffpy.pdfmorph.morphs.morphrgrid import MorphRGrid
+from diffpy.pdfmorph.morphs.morphscale import MorphScale
+
 # useful variables
 thisfile = locals().get("__file__", "file.py")
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 # testdata_dir = os.path.join(tests_dir, 'testdata')
 
-from diffpy.pdfmorph.morphs.morphchain import MorphChain
-from diffpy.pdfmorph.morphs.morphrgrid import MorphRGrid
-from diffpy.pdfmorph.morphs.morphscale import MorphScale
-
 
 class TestMorphChain:
     @pytest.fixture

src/diffpy/pdfmorph/tests/test_morphpdftordf.py

@@ -6,13 +6,13 @@
 import numpy
 import pytest
 
+from diffpy.pdfmorph.morph_helpers.transformpdftordf import TransformXtalPDFtoRDF
+
 # useful variables
 thisfile = locals().get("__file__", "file.py")
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 # testdata_dir = os.path.join(tests_dir, 'testdata')
 
-from diffpy.pdfmorph.morph_helpers.transformpdftordf import TransformXtalPDFtoRDF
-
 
 class TestTransformXtalPDFtoRDF:
     @pytest.fixture

src/diffpy/pdfmorph/tests/test_morphrdftopdf.py

@@ -6,13 +6,13 @@
 import numpy
 import pytest
 
+from diffpy.pdfmorph.morph_helpers.transformrdftopdf import TransformXtalRDFtoPDF
+
 # useful variables
 thisfile = locals().get("__file__", "file.py")
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 # testdata_dir = os.path.join(tests_dir, 'testdata')
 
-from diffpy.pdfmorph.morph_helpers.transformrdftopdf import TransformXtalRDFtoPDF
-
 
 class TestTransformXtalRDFtoPDF:
     @pytest.fixture

src/diffpy/pdfmorph/tests/test_morphresolution.py

@@ -6,13 +6,13 @@
 import numpy
 import pytest
 
+from diffpy.pdfmorph.morphs.morphresolution import MorphResolutionDamping
+
 # useful variables
 thisfile = locals().get("__file__", "file.py")
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 testdata_dir = os.path.join(tests_dir, "testdata")
 
-from diffpy.pdfmorph.morphs.morphresolution import MorphResolutionDamping
-
 
 class TestMorphScale:
     @pytest.fixture

src/diffpy/pdfmorph/tests/test_morphrgrid.py

@@ -6,13 +6,13 @@
 import numpy
 import pytest
 
+from diffpy.pdfmorph.morphs.morphrgrid import MorphRGrid
+
 # useful variables
 thisfile = locals().get("__file__", "file.py")
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 # testdata_dir = os.path.join(tests_dir, 'testdata')
 
-from diffpy.pdfmorph.morphs.morphrgrid import MorphRGrid
-
 
 ##############################################################################
 class TestMorphRGrid:

src/diffpy/pdfmorph/tests/test_morphscale.py

@@ -6,13 +6,13 @@
 import numpy
 import pytest
 
+from diffpy.pdfmorph.morphs.morphscale import MorphScale
+
 # useful variables
 thisfile = locals().get("__file__", "file.py")
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 # testdata_dir = os.path.join(tests_dir, 'testdata')
 
-from diffpy.pdfmorph.morphs.morphscale import MorphScale
-
 
 class TestMorphScale:
     @pytest.fixture

src/diffpy/pdfmorph/tests/test_morphshape.py

@@ -6,14 +6,16 @@
 import numpy
 import pytest
 
+from diffpy.pdfmorph.morphs.morphishape import MorphISpheroid
+from diffpy.pdfmorph.morphs.morphshape import MorphSphere, MorphSpheroid
+
+# FIXME: add MorphISphere test
+
 # useful variables
 thisfile = locals().get("__file__", "file.py")
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 testdata_dir = os.path.join(tests_dir, "testdata")
 
-from diffpy.pdfmorph.morphs.morphishape import MorphISphere, MorphISpheroid
-from diffpy.pdfmorph.morphs.morphshape import MorphSphere, MorphSpheroid
-
 
 class TestMorphSphere:
     @pytest.fixture

src/diffpy/pdfmorph/tests/test_morphsmear.py

@@ -6,13 +6,13 @@
 import numpy
 import pytest
 
+from diffpy.pdfmorph.morphs.morphsmear import MorphSmear
+
 # useful variables
 thisfile = locals().get("__file__", "file.py")
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 # testdata_dir = os.path.join(tests_dir, 'testdata')
 
-from diffpy.pdfmorph.morphs.morphsmear import MorphSmear
-
 
 class TestMorphSmear:
     @pytest.fixture

src/diffpy/pdfmorph/tests/test_morphstretch.py

@@ -6,13 +6,13 @@
 import numpy
 import pytest
 
+from diffpy.pdfmorph.morphs.morphstretch import MorphStretch
+
 # useful variables
 thisfile = locals().get("__file__", "file.py")
 tests_dir = os.path.dirname(os.path.abspath(thisfile))
 # testdata_dir = os.path.join(tests_dir, 'testdata')
 
-from diffpy.pdfmorph.morphs.morphstretch import MorphStretch
-
 
 class TestMorphStretch:
     @pytest.fixture

src/diffpy/pdfmorph/tests/test_pdfmorphio.py

@@ -4,14 +4,14 @@
 
 import pytest
 
+from diffpy.pdfmorph.pdfmorphapp import create_option_parser, multiple_morphs, single_morph
+
 # Support Python 2
 try:
     from future_builtins import filter, zip
 except ImportError:
     pass
 
-from diffpy.pdfmorph.pdfmorphapp import create_option_parser, multiple_morphs, single_morph
-
 thisfile = locals().get("__file__", "file.py")
 tests_dir = Path(thisfile).parent.resolve()
 testdata_dir = tests_dir.joinpath("testdata")