From 720bc206ace7794737557b569da5230b30e70071 Mon Sep 17 00:00:00 2001 From: Sparks29032 Date: Wed, 2 Jul 2025 09:22:04 -0500 Subject: [PATCH 1/3] Add new api-documentation --- doc/source/api/diffpy.morph.morph_helpers.rst | 10 ++-- doc/source/api/diffpy.morph.morphs.rst | 60 ++++++++++++------- doc/source/api/diffpy.morph.rst | 28 +++++---- 3 files changed, 61 insertions(+), 37 deletions(-) diff --git a/doc/source/api/diffpy.morph.morph_helpers.rst b/doc/source/api/diffpy.morph.morph_helpers.rst index e8889166..f986593b 100644 --- a/doc/source/api/diffpy.morph.morph_helpers.rst +++ b/doc/source/api/diffpy.morph.morph_helpers.rst @@ -1,6 +1,6 @@ :tocdepth: -1 -diffpy.morph.morph_helpers package +diffpy.morph.morph-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 b/doc/source/api/diffpy.morph.morphs.rst index c4b55150..2baaa24e 100644 --- a/doc/source/api/diffpy.morph.morphs.rst +++ b/doc/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 b/doc/source/api/diffpy.morph.rst index 01046993..0c2381a8 100644 --- a/doc/source/api/diffpy.morph.rst +++ b/doc/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: From 92d2a20fad8c38f1cd5ce28b0be97193078dbd5e Mon Sep 17 00:00:00 2001 From: Sparky <59151395+Sparks29032@users.noreply.github.com> Date: Wed, 2 Jul 2025 09:24:36 -0500 Subject: [PATCH 2/3] Update diffpy.morph.morph_helpers.rst --- doc/source/api/diffpy.morph.morph_helpers.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/api/diffpy.morph.morph_helpers.rst b/doc/source/api/diffpy.morph.morph_helpers.rst index f986593b..4651f506 100644 --- a/doc/source/api/diffpy.morph.morph_helpers.rst +++ b/doc/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 From e11bfba8920cc5cfd1e20a6c62eb69dc0da0701f Mon Sep 17 00:00:00 2001 From: Sparks29032 Date: Wed, 2 Jul 2025 09:29:47 -0500 Subject: [PATCH 3/3] Plural from scikit-package change --- {doc => docs}/Makefile | 0 {doc => docs}/make.bat | 0 {doc => docs}/manual/Makefile | 0 {doc => docs}/manual/README.txt | 0 {doc => docs}/manual/acknowledgements.texinfo | 0 {doc => docs}/manual/disclaimer.texinfo | 0 {doc => docs}/manual/images/aspirin_smear.png | Bin {doc => docs}/manual/images/aspirin_stretch.png | Bin {doc => docs}/manual/images/ex_tutorial_bar.png | Bin .../manual/images/ex_tutorial_download.png | Bin {doc => docs}/manual/images/ex_tutorial_params.png | Bin .../manual/images/ex_tutorial_shape_download.png | Bin .../images/ex_tutorial_shape_sphere_zoomed.png | Bin {doc => docs}/manual/images/ex_tutorial_stretch.png | Bin {doc => docs}/manual/images/ex_tutorial_temp.png | Bin {doc => docs}/manual/images/morph_ex1.png | Bin {doc => docs}/manual/images/morph_ex2.png | Bin {doc => docs}/manual/images/nacl_example.agr | Bin {doc => docs}/manual/images/nacl_example.png | Bin {doc => docs}/manual/images/pdfmorph_example.agr | 0 {doc => docs}/manual/images/pdfmorph_example.png | Bin {doc => docs}/manual/images/pdfmorph_example.xcf | Bin {doc => docs}/manual/images/pdfmorph_smear.png | Bin {doc => docs}/manual/images/pdfmorph_smear2.png | Bin {doc => docs}/manual/images/pdfmorph_stretch.png | Bin .../manual/images/qs_tutorial_download.png | Bin {doc => docs}/manual/images/qs_tutorial_morphed.png | Bin {doc => docs}/manual/images/qs_tutorial_scaled.png | Bin .../manual/images/qs_tutorial_unmorphed.png | Bin {doc => docs}/manual/make.bat | 0 {doc => docs}/manual/pdfmorph.pdf | Bin {doc => docs}/manual/pdfmorph.texinfo | 0 {doc => docs}/manual/redistribution.texinfo | 0 {doc => docs}/source/_static/.placeholder | 0 .../source/api/diffpy.morph.morph_helpers.rst | 0 {doc => docs}/source/api/diffpy.morph.morphs.rst | 0 {doc => docs}/source/api/diffpy.morph.rst | 0 {doc => docs}/source/conf.py | 3 ++- {doc => docs}/source/images/ex_tutorial_bar.png | Bin {doc => docs}/source/images/ex_tutorial_temp.png | Bin {doc => docs}/source/images/qs_tutorial_morphed.png | Bin {doc => docs}/source/images/qs_tutorial_scaled.png | Bin .../source/images/qs_tutorial_unmorphed.png | Bin {doc => docs}/source/index.rst | 0 {doc => docs}/source/license.rst | 0 {doc => docs}/source/morphpy.rst | 0 {doc => docs}/source/quickstart.rst | 0 {doc => docs}/source/release.rst | 0 {doc => docs}/source/tutorialfiles.rst | 0 {doc => docs}/source/tutorials.rst | 0 requirements/{test.txt => tests.txt} | 0 51 files changed, 2 insertions(+), 1 deletion(-) rename {doc => docs}/Makefile (100%) rename {doc => docs}/make.bat (100%) rename {doc => docs}/manual/Makefile (100%) rename {doc => docs}/manual/README.txt (100%) rename {doc => docs}/manual/acknowledgements.texinfo (100%) rename {doc => docs}/manual/disclaimer.texinfo (100%) rename {doc 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doc/source/api/diffpy.morph.morphs.rst rename to docs/source/api/diffpy.morph.morphs.rst diff --git a/doc/source/api/diffpy.morph.rst b/docs/source/api/diffpy.morph.rst similarity index 100% rename from doc/source/api/diffpy.morph.rst rename to docs/source/api/diffpy.morph.rst diff --git a/doc/source/conf.py b/docs/source/conf.py similarity index 98% rename from doc/source/conf.py rename to docs/source/conf.py index 9ac22a75..64a5c046 100644 --- a/doc/source/conf.py +++ b/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 b/docs/source/images/ex_tutorial_bar.png similarity index 100% rename from doc/source/images/ex_tutorial_bar.png rename to docs/source/images/ex_tutorial_bar.png diff --git a/doc/source/images/ex_tutorial_temp.png b/docs/source/images/ex_tutorial_temp.png similarity index 100% rename from doc/source/images/ex_tutorial_temp.png rename to docs/source/images/ex_tutorial_temp.png diff --git a/doc/source/images/qs_tutorial_morphed.png b/docs/source/images/qs_tutorial_morphed.png similarity index 100% rename from doc/source/images/qs_tutorial_morphed.png rename to docs/source/images/qs_tutorial_morphed.png diff --git a/doc/source/images/qs_tutorial_scaled.png b/docs/source/images/qs_tutorial_scaled.png similarity index 100% rename from doc/source/images/qs_tutorial_scaled.png rename to docs/source/images/qs_tutorial_scaled.png diff --git a/doc/source/images/qs_tutorial_unmorphed.png b/docs/source/images/qs_tutorial_unmorphed.png similarity index 100% rename from doc/source/images/qs_tutorial_unmorphed.png rename to docs/source/images/qs_tutorial_unmorphed.png diff --git a/doc/source/index.rst b/docs/source/index.rst similarity index 100% rename from doc/source/index.rst rename to docs/source/index.rst diff --git a/doc/source/license.rst b/docs/source/license.rst similarity index 100% rename from doc/source/license.rst rename to docs/source/license.rst diff --git a/doc/source/morphpy.rst b/docs/source/morphpy.rst similarity index 100% rename from doc/source/morphpy.rst rename to docs/source/morphpy.rst diff --git a/doc/source/quickstart.rst b/docs/source/quickstart.rst similarity index 100% rename from doc/source/quickstart.rst rename to docs/source/quickstart.rst diff --git a/doc/source/release.rst b/docs/source/release.rst similarity index 100% rename from doc/source/release.rst rename to docs/source/release.rst diff --git a/doc/source/tutorialfiles.rst b/docs/source/tutorialfiles.rst similarity index 100% rename from doc/source/tutorialfiles.rst rename to docs/source/tutorialfiles.rst diff --git a/doc/source/tutorials.rst b/docs/source/tutorials.rst similarity index 100% rename from doc/source/tutorials.rst rename to docs/source/tutorials.rst diff --git a/requirements/test.txt b/requirements/tests.txt similarity index 100% rename from requirements/test.txt rename to requirements/tests.txt