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Merged
merged 8 commits into from
Jul 28, 2025
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style: use numpy docstring and fix documentation rendering #125

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2e89a68
chore: remove example files
ycexiao Jul 25, 2025
18ac7ed
chore: use correct path to example python file
ycexiao Jul 26, 2025
f51ac3e
chore: use correct path to CHANGELOG.rst
ycexiao Jul 26, 2025
de50055
fix: use numpy-style docstring
ycexiao Jul 26, 2025
5fe0ee4
[pre-commit.ci] auto fixes from pre-commit hooks
pre-commit-ci[bot] Jul 26, 2025
b36e3d3
chore: use `Parameters` instead of `Arguments`
ycexiao Jul 28, 2025
ae7697e
Merge branch 'fix-docstring' of github.com:ycexiao/diffpy.srfit into …
ycexiao Jul 28, 2025
6e882b9
chore: fix pre-commit
ycexiao Jul 28, 2025
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2 changes: 1 addition & 1 deletion CHANGELOG.rst
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Expand Up @@ -9,7 +9,7 @@ Release notes


Version 3.0.0 – 2019-03-14
==========================
--------------------------

**Added:**

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31 changes: 0 additions & 31 deletions docs/source/api/diffpy.srfit.example_package.rst
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23 changes: 9 additions & 14 deletions docs/source/api/diffpy.srfit.rst
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Expand Up @@ -14,17 +14,12 @@ Subpackages
-----------

.. toctree::
diffpy.srfit.example_package

Submodules
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There seems to be no submodules in diffpy.srfit.

----------

|module|
--------

.. |module| replace:: diffpy.srfit.example_submodule module

.. automodule:: diffpy.srfit.example_submodule
:members:
:undoc-members:
:show-inheritance:
diffpy.srfit.equation
diffpy.srfit.equation.literals
diffpy.srfit.equation.visitors
diffpy.srfit.fitbase
diffpy.srfit.interface
diffpy.srfit.pdf
diffpy.srfit.sas
diffpy.srfit.structure
diffpy.srfit.util
2 changes: 1 addition & 1 deletion docs/source/conf.py
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"sphinx.ext.intersphinx",
"sphinx_rtd_theme",
"sphinx_copybutton",
"m2r",
"m2r2",
]

# Add any paths that contain templates here, relative to this directory.
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coreshellnp.py
========================

.. literalinclude:: ../../../examples/coreshellnp.py
.. literalinclude:: ../../examples/coreshellnp.py
2 changes: 1 addition & 1 deletion docs/source/examples/crystalpdf.rst
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crystalpdf.py
========================

.. literalinclude:: ../../../examples/crystalpdf.py
.. literalinclude:: ../../examples/crystalpdf.py
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crystalpdfall.py
========================

.. literalinclude:: ../../../examples/crystalpdfall.py
.. literalinclude:: ../../examples/crystalpdfall.py
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crystalpdfobjcryst.py
========================

.. literalinclude:: ../../../examples/crystalpdfobjcryst.py
.. literalinclude:: ../../examples/crystalpdfobjcryst.py
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crystalpdftwodata.py
========================

.. literalinclude:: ../../../examples/crystalpdftwodata.py
.. literalinclude:: ../../examples/crystalpdftwodata.py
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crystalpdftwophase.py
========================

.. literalinclude:: ../../../examples/crystalpdftwophase.py
.. literalinclude:: ../../examples/crystalpdftwophase.py
2 changes: 1 addition & 1 deletion docs/source/examples/debyemodel.rst
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debyemodel.py
========================

.. literalinclude:: ../../../examples/debyemodel.py
.. literalinclude:: ../../examples/debyemodel.py
2 changes: 1 addition & 1 deletion docs/source/examples/debyemodelII.rst
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debyemodelII.py
========================

.. literalinclude:: ../../../examples/debyemodelII.py
.. literalinclude:: ../../examples/debyemodelII.py
2 changes: 1 addition & 1 deletion docs/source/examples/ellipsoidsas.rst
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ellipsoidsas.py
========================

.. literalinclude:: ../../../examples/ellipsoidsas.py
.. literalinclude:: ../../examples/ellipsoidsas.py
2 changes: 1 addition & 1 deletion docs/source/examples/gaussiangenerator.rst
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gaussiangenerator.py
========================

.. literalinclude:: ../../../examples/gaussiangenerator.py
.. literalinclude:: ../../examples/gaussiangenerator.py
2 changes: 1 addition & 1 deletion docs/source/examples/gaussianrecipe.rst
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gaussianrecipe.py
========================

.. literalinclude:: ../../../examples/gaussianrecipe.py
.. literalinclude:: ../../examples/gaussianrecipe.py
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interface.py
========================

.. literalinclude:: ../../../examples/interface.py
.. literalinclude:: ../../examples/interface.py
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npintensity.py
========================

.. literalinclude:: ../../../examples/npintensity.py
.. literalinclude:: ../../examples/npintensity.py
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npintensityII.py
========================

.. literalinclude:: ../../../examples/npintensityII.py
.. literalinclude:: ../../examples/npintensityII.py
2 changes: 1 addition & 1 deletion docs/source/examples/nppdfcrystal.rst
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nppdfcrystal.py
========================

.. literalinclude:: ../../../examples/nppdfcrystal.py
.. literalinclude:: ../../examples/nppdfcrystal.py
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nppdfobjcryst.py
========================

.. literalinclude:: ../../../examples/nppdfobjcryst.py
.. literalinclude:: ../../examples/nppdfobjcryst.py
2 changes: 1 addition & 1 deletion docs/source/examples/nppdfsas.rst
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nppdfsas.py
========================

.. literalinclude:: ../../../examples/nppdfsas.py
.. literalinclude:: ../../examples/nppdfsas.py
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simplepdf.py
========================

.. literalinclude:: ../../../examples/simplepdf.py
.. literalinclude:: ../../examples/simplepdf.py
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simplepdftwophase.py
========================

.. literalinclude:: ../../../examples/simplepdftwophase.py
.. literalinclude:: ../../examples/simplepdftwophase.py
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simplerecipe.py
========================

.. literalinclude:: ../../../examples/simplerecipe.py
.. literalinclude:: ../../examples/simplerecipe.py
6 changes: 3 additions & 3 deletions docs/source/extending.rst
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Expand Up @@ -180,7 +180,7 @@ external program before or after interfacing with SrFit. An example of a
customized Profile is the ``SASProfile`` class in the
``diffpy.srfit.sas.sasprofile`` module:

.. literalinclude:: ../../../src/diffpy/srfit/sas/sasprofile.py
.. literalinclude:: /../../src/diffpy/srfit/sas/sasprofile.py
:pyobject: SASProfile

The ``__init__`` method sets the ``xobs``, ``yobs`` and ``dyobs`` attributes of
Expand Down Expand Up @@ -218,7 +218,7 @@ to keep the restraint cost comparable to the residual of a single data point.
``Restraint`` whose penalty is the root-mean-square deviation from the expected
and calculated BVS of a structure.

.. literalinclude:: ../../../src/diffpy/srfit/structure/bvsrestraint.py
.. literalinclude:: ../../src/diffpy/srfit/structure/bvsrestraint.py
:pyobject: BVSRestraint

Note that the penalty scaling is optional (selected by the `scaled` flag) and
Expand All @@ -230,7 +230,7 @@ restrainable object. A ``BVSRestraint`` is used to restrain a ``SrRealParSet``,
which is a ``ParameterSet`` wrapper base class for SrReal-compatible
structures. The restraint is applied with the ``restrainBVS`` method.

.. literalinclude:: ../../../src/diffpy/srfit/structure/srrealparset.py
.. literalinclude:: ../../src/diffpy/srfit/structure/srrealparset.py
:pyobject: SrRealParSet.restrainBVS

The purpose of the method is to create the custom ``Restraint`` object,
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@@ -1,3 +1,5 @@
:tocdepth: -1

.. index:: release notes

.. mdinclude:: ../../../CHANGELOG.md
.. include:: ../../CHANGELOG.rst
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diffpy.structure uses include and has a better title hierarchy

23 changes: 23 additions & 0 deletions news/fix-docstring.rst
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@@ -0,0 +1,23 @@
**Added:**

* No news added: Fix the docstring in this repo

**Changed:**

* <news item>

**Deprecated:**

* <news item>

**Removed:**

* <news item>

**Fixed:**

* <news item>

**Security:**

* <news item>
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