diffpy · Sparks29032 · Jul 2, 2025 · Jul 2, 2025 · Jul 2, 2025 · Jul 2, 2025
diff --git a/doc/Makefile → docs/Makefile b/doc/Makefile → docs/Makefile
diff --git a/doc/make.bat → docs/make.bat b/doc/make.bat → docs/make.bat
diff --git a/doc/manual/Makefile → docs/manual/Makefile b/doc/manual/Makefile → docs/manual/Makefile
diff --git a/doc/manual/README.txt → docs/manual/README.txt b/doc/manual/README.txt → docs/manual/README.txt
diff --git a/doc/manual/acknowledgements.texinfo → docs/manual/acknowledgements.texinfo b/doc/manual/acknowledgements.texinfo → docs/manual/acknowledgements.texinfo
diff --git a/doc/manual/disclaimer.texinfo → docs/manual/disclaimer.texinfo b/doc/manual/disclaimer.texinfo → docs/manual/disclaimer.texinfo
diff --git a/doc/manual/images/aspirin_smear.png → docs/manual/images/aspirin_smear.png b/doc/manual/images/aspirin_smear.png → docs/manual/images/aspirin_smear.png
diff --git a/doc/manual/images/aspirin_stretch.png → docs/manual/images/aspirin_stretch.png b/doc/manual/images/aspirin_stretch.png → docs/manual/images/aspirin_stretch.png
diff --git a/doc/manual/images/ex_tutorial_bar.png → docs/manual/images/ex_tutorial_bar.png b/doc/manual/images/ex_tutorial_bar.png → docs/manual/images/ex_tutorial_bar.png
diff --git a/doc/manual/images/ex_tutorial_download.png → docs/manual/images/ex_tutorial_download.png b/doc/manual/images/ex_tutorial_download.png → docs/manual/images/ex_tutorial_download.png
diff --git a/doc/manual/images/ex_tutorial_params.png → docs/manual/images/ex_tutorial_params.png b/doc/manual/images/ex_tutorial_params.png → docs/manual/images/ex_tutorial_params.png
diff --git a/...ual/images/ex_tutorial_shape_download.png → ...ual/images/ex_tutorial_shape_download.png b/...ual/images/ex_tutorial_shape_download.png → ...ual/images/ex_tutorial_shape_download.png
diff --git a/...mages/ex_tutorial_shape_sphere_zoomed.png → ...mages/ex_tutorial_shape_sphere_zoomed.png b/...mages/ex_tutorial_shape_sphere_zoomed.png → ...mages/ex_tutorial_shape_sphere_zoomed.png
diff --git a/doc/manual/images/ex_tutorial_stretch.png → docs/manual/images/ex_tutorial_stretch.png b/doc/manual/images/ex_tutorial_stretch.png → docs/manual/images/ex_tutorial_stretch.png
diff --git a/doc/manual/images/ex_tutorial_temp.png → docs/manual/images/ex_tutorial_temp.png b/doc/manual/images/ex_tutorial_temp.png → docs/manual/images/ex_tutorial_temp.png
diff --git a/doc/manual/images/morph_ex1.png → docs/manual/images/morph_ex1.png b/doc/manual/images/morph_ex1.png → docs/manual/images/morph_ex1.png
diff --git a/doc/manual/images/morph_ex2.png → docs/manual/images/morph_ex2.png b/doc/manual/images/morph_ex2.png → docs/manual/images/morph_ex2.png
diff --git a/doc/manual/images/nacl_example.agr → docs/manual/images/nacl_example.agr b/doc/manual/images/nacl_example.agr → docs/manual/images/nacl_example.agr
diff --git a/doc/manual/images/nacl_example.png → docs/manual/images/nacl_example.png b/doc/manual/images/nacl_example.png → docs/manual/images/nacl_example.png
diff --git a/doc/manual/images/pdfmorph_example.agr → docs/manual/images/pdfmorph_example.agr b/doc/manual/images/pdfmorph_example.agr → docs/manual/images/pdfmorph_example.agr
diff --git a/doc/manual/images/pdfmorph_example.png → docs/manual/images/pdfmorph_example.png b/doc/manual/images/pdfmorph_example.png → docs/manual/images/pdfmorph_example.png
diff --git a/doc/manual/images/pdfmorph_example.xcf → docs/manual/images/pdfmorph_example.xcf b/doc/manual/images/pdfmorph_example.xcf → docs/manual/images/pdfmorph_example.xcf
diff --git a/doc/manual/images/pdfmorph_smear.png → docs/manual/images/pdfmorph_smear.png b/doc/manual/images/pdfmorph_smear.png → docs/manual/images/pdfmorph_smear.png
diff --git a/doc/manual/images/pdfmorph_smear2.png → docs/manual/images/pdfmorph_smear2.png b/doc/manual/images/pdfmorph_smear2.png → docs/manual/images/pdfmorph_smear2.png
diff --git a/doc/manual/images/pdfmorph_stretch.png → docs/manual/images/pdfmorph_stretch.png b/doc/manual/images/pdfmorph_stretch.png → docs/manual/images/pdfmorph_stretch.png
diff --git a/doc/manual/images/qs_tutorial_download.png → docs/manual/images/qs_tutorial_download.png b/doc/manual/images/qs_tutorial_download.png → docs/manual/images/qs_tutorial_download.png
diff --git a/doc/manual/images/qs_tutorial_morphed.png → docs/manual/images/qs_tutorial_morphed.png b/doc/manual/images/qs_tutorial_morphed.png → docs/manual/images/qs_tutorial_morphed.png
diff --git a/doc/manual/images/qs_tutorial_scaled.png → docs/manual/images/qs_tutorial_scaled.png b/doc/manual/images/qs_tutorial_scaled.png → docs/manual/images/qs_tutorial_scaled.png
diff --git a/doc/manual/images/qs_tutorial_unmorphed.png → docs/manual/images/qs_tutorial_unmorphed.png b/doc/manual/images/qs_tutorial_unmorphed.png → docs/manual/images/qs_tutorial_unmorphed.png
diff --git a/doc/manual/make.bat → docs/manual/make.bat b/doc/manual/make.bat → docs/manual/make.bat
diff --git a/doc/manual/pdfmorph.pdf → docs/manual/pdfmorph.pdf b/doc/manual/pdfmorph.pdf → docs/manual/pdfmorph.pdf
diff --git a/doc/manual/pdfmorph.texinfo → docs/manual/pdfmorph.texinfo b/doc/manual/pdfmorph.texinfo → docs/manual/pdfmorph.texinfo
diff --git a/doc/manual/redistribution.texinfo → docs/manual/redistribution.texinfo b/doc/manual/redistribution.texinfo → docs/manual/redistribution.texinfo
diff --git a/doc/source/_static/.placeholder → docs/source/_static/.placeholder b/doc/source/_static/.placeholder → docs/source/_static/.placeholder
diff --git a/...source/api/diffpy.morph.morph_helpers.rst → ...source/api/diffpy.morph.morph_helpers.rst b/...source/api/diffpy.morph.morph_helpers.rst → ...source/api/diffpy.morph.morph_helpers.rst
@@ -1,6 +1,6 @@
 :tocdepth: -1
 
-diffpy.morph.morph_helpers package
+diffpy.morph.morp_helpers package
 ==================================
 
 .. automodule:: diffpy.morph.morph_helpers
@@ -11,18 +11,18 @@ diffpy.morph.morph_helpers package
 Submodules
 ----------
 
-diffpy.morph.morph_helpers.transformpdftordf module
+diffpy.morph.morph_helpers.transformrdftopdf module
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.morph_helpers.transformpdftordf
+.. automodule:: diffpy.morph.morph_helpers.transformrdftopdf
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.morph_helpers.transformrdftopdf module
+diffpy.morph.morph_helpers.transformpdftordf module
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.morph_helpers.transformrdftopdf
+.. automodule:: diffpy.morph.morph_helpers.transformpdftordf
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/doc/source/api/diffpy.morph.morphs.rst → docs/source/api/diffpy.morph.morphs.rst b/doc/source/api/diffpy.morph.morphs.rst → docs/source/api/diffpy.morph.morphs.rst
@@ -11,42 +11,58 @@ diffpy.morph.morphs package
 Submodules
 ----------
 
-diffpy.morph.morphs.morphishape module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+diffpy.morph.morphs.morphscale module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.morphs.morphishape
+.. automodule:: diffpy.morph.morphs.morphscale
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.morphs.morphchain module
+diffpy.morph.morphs.morphshape module
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.morphs.morphchain
+.. automodule:: diffpy.morph.morphs.morphshape
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.morphs.morphresolution module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+diffpy.morph.morphs.morphshift module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.morphs.morphresolution
+.. automodule:: diffpy.morph.morphs.morphshift
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.morphs.morphshape module
+diffpy.morph.morphs.morphfuncy module
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.morphs.morphshape
+.. automodule:: diffpy.morph.morphs.morphfuncy
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.morphs.morphshift module
+diffpy.morph.morphs.morphchain module
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.morphs.morphshift
+.. automodule:: diffpy.morph.morphs.morphchain
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.morph.morphs.morphresolution module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.morph.morphs.morphresolution
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.morph.morphs.morphstretch module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.morph.morphs.morphstretch
     :members:
     :undoc-members:
     :show-inheritance:
@@ -59,34 +75,34 @@ diffpy.morph.morphs.morph module
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.morphs.morphrgrid module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+diffpy.morph.morphs.morphsqueeze module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.morphs.morphrgrid
+.. automodule:: diffpy.morph.morphs.morphsqueeze
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.morphs.morphsmear module
+diffpy.morph.morphs.morphrgrid module
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.morphs.morphsmear
+.. automodule:: diffpy.morph.morphs.morphrgrid
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.morphs.morphstretch module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+diffpy.morph.morphs.morphishape module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.morphs.morphstretch
+.. automodule:: diffpy.morph.morphs.morphishape
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.morphs.morphscale module
+diffpy.morph.morphs.morphsmear module
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.morphs.morphscale
+.. automodule:: diffpy.morph.morphs.morphsmear
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/doc/source/api/diffpy.morph.rst → docs/source/api/diffpy.morph.rst b/doc/source/api/diffpy.morph.rst → docs/source/api/diffpy.morph.rst
@@ -14,8 +14,8 @@ Subpackages
 .. toctree::
     :titlesonly:
 
-    diffpy.morph.morphs
     diffpy.morph.morph_helpers
+    diffpy.morph.morphs
 
 Submodules
 ----------
@@ -36,18 +36,18 @@ diffpy.morph.morph_api module
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.refine module
-^^^^^^^^^^^^^^^^^^^^^^^^^^
+diffpy.morph.tools module
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.refine
+.. automodule:: diffpy.morph.tools
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.tools module
-^^^^^^^^^^^^^^^^^^^^^^^^^
+diffpy.morph.morphpy module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.tools
+.. automodule:: diffpy.morph.morphpy
     :members:
     :undoc-members:
     :show-inheritance:
@@ -60,10 +60,10 @@ diffpy.morph.morph_io module
     :undoc-members:
     :show-inheritance:
 
-diffpy.morph.log module
-^^^^^^^^^^^^^^^^^^^^^^^
+diffpy.morph.refine module
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.log
+.. automodule:: diffpy.morph.refine
     :members:
     :undoc-members:
     :show-inheritance:
@@ -75,3 +75,11 @@ diffpy.morph.morphapp module
     :members:
     :undoc-members:
     :show-inheritance:
+
+diffpy.morph.log module
+^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.morph.log
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/conf.py → docs/source/conf.py b/doc/source/conf.py → docs/source/conf.py
@@ -24,7 +24,8 @@
 except Exception:
     fullversion = "No version found. The correct version will appear in the released version."  # noqa: E501
 
-# Import modules referenced in documentation (resolves `WARNING: autodoc: failed to import module`)
+# Import modules referenced in documentation
+# (resolves `WARNING: autodoc: failed to import module`)
 autodoc_mock_imports = [
     "diffpy.utils",
 ]

diff --git a/doc/source/images/ex_tutorial_bar.png → docs/source/images/ex_tutorial_bar.png b/doc/source/images/ex_tutorial_bar.png → docs/source/images/ex_tutorial_bar.png
diff --git a/doc/source/images/ex_tutorial_temp.png → docs/source/images/ex_tutorial_temp.png b/doc/source/images/ex_tutorial_temp.png → docs/source/images/ex_tutorial_temp.png
diff --git a/doc/source/images/qs_tutorial_morphed.png → docs/source/images/qs_tutorial_morphed.png b/doc/source/images/qs_tutorial_morphed.png → docs/source/images/qs_tutorial_morphed.png
diff --git a/doc/source/images/qs_tutorial_scaled.png → docs/source/images/qs_tutorial_scaled.png b/doc/source/images/qs_tutorial_scaled.png → docs/source/images/qs_tutorial_scaled.png
diff --git a/doc/source/images/qs_tutorial_unmorphed.png → docs/source/images/qs_tutorial_unmorphed.png b/doc/source/images/qs_tutorial_unmorphed.png → docs/source/images/qs_tutorial_unmorphed.png
diff --git a/doc/source/index.rst → docs/source/index.rst b/doc/source/index.rst → docs/source/index.rst
diff --git a/doc/source/license.rst → docs/source/license.rst b/doc/source/license.rst → docs/source/license.rst
diff --git a/doc/source/morphpy.rst → docs/source/morphpy.rst b/doc/source/morphpy.rst → docs/source/morphpy.rst
diff --git a/doc/source/quickstart.rst → docs/source/quickstart.rst b/doc/source/quickstart.rst → docs/source/quickstart.rst
diff --git a/doc/source/release.rst → docs/source/release.rst b/doc/source/release.rst → docs/source/release.rst
diff --git a/doc/source/tutorialfiles.rst → docs/source/tutorialfiles.rst b/doc/source/tutorialfiles.rst → docs/source/tutorialfiles.rst
diff --git a/doc/source/tutorials.rst → docs/source/tutorials.rst b/doc/source/tutorials.rst → docs/source/tutorials.rst
diff --git a/requirements/test.txt → requirements/tests.txt b/requirements/test.txt → requirements/tests.txt