diffpy · sbillinge · Aug 4, 2025 · Jul 30, 2025 · Jul 30, 2025 · ycexiao
diff --git a/...les/QPA-Quantitative phase analysis.ipynb → ...les/QPA-Quantitative phase analysis.ipynb b/...les/QPA-Quantitative phase analysis.ipynb → ...les/QPA-Quantitative phase analysis.ipynb
diff --git a/examples/crystal_3d_widget.ipynb → docs/examples/crystal_3d_widget.ipynb b/examples/crystal_3d_widget.ipynb → docs/examples/crystal_3d_widget.ipynb
diff --git a/examples/data/cime.dat → docs/examples/data/cime.dat b/examples/data/cime.dat → docs/examples/data/cime.dat
diff --git a/examples/data/cime.fhz → docs/examples/data/cime.fhz b/examples/data/cime.fhz → docs/examples/data/cime.fhz
diff --git a/examples/data/cpd-1a.prn → docs/examples/data/cpd-1a.prn b/examples/data/cpd-1a.prn → docs/examples/data/cpd-1a.prn
diff --git a/examples/data/pbso4-n.dat → docs/examples/data/pbso4-n.dat b/examples/data/pbso4-n.dat → docs/examples/data/pbso4-n.dat
diff --git a/examples/data/pbso4-x.dat → docs/examples/data/pbso4-x.dat b/examples/data/pbso4-x.dat → docs/examples/data/pbso4-x.dat
diff --git a/examples/single-crystal-data.ipynb → docs/examples/single-crystal-data.ipynb b/examples/single-crystal-data.ipynb → docs/examples/single-crystal-data.ipynb
diff --git a/.../structure-solution-multiprocessing.ipynb → .../structure-solution-multiprocessing.ipynb b/.../structure-solution-multiprocessing.ipynb → .../structure-solution-multiprocessing.ipynb
diff --git a/...tructure-solution-powder-cimetidine.ipynb → ...tructure-solution-powder-cimetidine.ipynb b/...tructure-solution-powder-cimetidine.ipynb → ...tructure-solution-powder-cimetidine.ipynb
diff --git a/...les/structure-solution-powder-pbso4.ipynb → ...les/structure-solution-powder-pbso4.ipynb b/...les/structure-solution-powder-pbso4.ipynb → ...les/structure-solution-powder-pbso4.ipynb
diff --git a/docs/source/api/pyobjcryst.example_package.rst b/docs/source/api/pyobjcryst.example_package.rst
diff --git a/docs/source/api/pyobjcryst.rst b/docs/source/api/pyobjcryst.rst
@@ -10,21 +10,206 @@
     :undoc-members:
     :show-inheritance:
 
-Subpackages
------------
-
-.. toctree::
-   pyobjcryst.example_package
 
 Submodules
 ----------
 
-|module|
---------
+pyobjcryst.atom module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.atom
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.crystal module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.crystal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.diffractiondatasinglecrystal module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.diffractiondatasinglecrystal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.fourier module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.fourier
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.general module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.general
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.globaloptim module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.globaloptim
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.globals module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.globals
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.indexing module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.indexing
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.io module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.io
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.lsq module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.lsq
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.molecule module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.molecule
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.polyhedron module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.polyhedron
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.powderpattern module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.powderpattern
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.pyobjcryst_app module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.pyobjcryst_app
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.radiation module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.radiation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.refineableobj module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.refineableobj
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.scatterer module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.scatterer
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.scatteringdata module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.scatteringdata
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.scatteringpower module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.scatteringpower
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.scatteringpowersphere module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.scatteringpowersphere
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.spacegroup module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.spacegroup
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.unitcell module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.unitcell
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.utils module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.version module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: pyobjcryst.version
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
-.. |module| replace:: pyobjcryst.example_submodule module
+pyobjcryst.zscatterer module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: pyobjcryst.example_submodule
+.. automodule:: pyobjcryst.zscatterer
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -50,6 +50,8 @@
     "sphinx.ext.intersphinx",
     "sphinx_rtd_theme",
     "sphinx_copybutton",
+    "nbsphinx",
+    "nbsphinx_link",
     "m2r",
 ]
 

diff --git a/docs/source/examples/Quantitative-phase-analysis.nblink b/docs/source/examples/Quantitative-phase-analysis.nblink
@@ -1,3 +1,3 @@
 {
-    "path": "../../../../examples/QPA-Quantitative phase analysis.ipynb"
+    "path": "../../examples/QPA-Quantitative phase analysis.ipynb"
 }
diff --git a/docs/source/examples/crystal_3d_widget.nblink b/docs/source/examples/crystal_3d_widget.nblink
@@ -1,3 +1,3 @@
 {
-    "path": "../../../../examples/crystal_3d_widget.ipynb"
+    "path": "../../examples/crystal_3d_widget.ipynb"
 }
diff --git a/docs/source/examples/index.rst → docs/source/examples/examples.rst b/docs/source/examples/index.rst → docs/source/examples/examples.rst
diff --git a/docs/source/examples/structure-solution-multiprocessing.nblink b/docs/source/examples/structure-solution-multiprocessing.nblink
@@ -1,3 +1,3 @@
 {
-    "path": "../../../../examples/structure-solution-multiprocessing.ipynb"
+    "path": "../../examples/structure-solution-multiprocessing.ipynb"
 }
diff --git a/docs/source/examples/structure-solution-powder-cimetidine.nblink b/docs/source/examples/structure-solution-powder-cimetidine.nblink
@@ -1,3 +1,3 @@
 {
-    "path": "../../../../examples/structure-solution-powder-cimetidine.ipynb"
+    "path": "../../examples/structure-solution-powder-cimetidine.ipynb"
 }
diff --git a/docs/source/examples/structure-solution-powder-pbso4.nblink b/docs/source/examples/structure-solution-powder-pbso4.nblink
@@ -1,3 +1,3 @@
 {
-    "path": "../../../../examples/structure-solution-powder-pbso4.ipynb"
+    "path": "../../examples/structure-solution-powder-pbso4.ipynb"
 }
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -32,7 +32,7 @@ was developed by V. Favre-Nicolin as part of the development of the
 Further developments including the ability to index and refine
 powder patterns, solve and display crystal structures, using the
 global optimisation and least squares algorithms (see the
-:doc:`examples/index`) are provided by Vincent Favre-Nicolin (ESRF).
+:doc:`examples/examples`) are provided by Vincent Favre-Nicolin (ESRF).
 
 For a complete list of contributors, see
 https://github.com/diffpy/pyobjcryst/graphs/contributors and
@@ -63,15 +63,15 @@ Usage & notebooks
   * etc..
 
   The functionality is similar to what is available in `Fox <http://fox.vincefn.net>`_.
-  See the :doc:`examples/index`:
+  See the :doc:`examples/examples`:
 
   * :doc:`3D Crystal structure display <examples/crystal_3d_widget>`
   * :doc:`Solving the cimetidine structure from its powder pattern <examples/structure-solution-powder-cimetidine>`
   * :doc:`Solving the PbSO4 structure from its X and N powder patterns <examples/structure-solution-powder-pbso4>`
   * :doc:`Meta-structure solution using multi-processing <examples/structure-solution-multiprocessing>`
   * :doc:`Quantitative phase analysis (QPA) <examples/Quantitative-phase-analysis>`
 
-The **API documentation** can be found in :doc:`api/modules`.
+The **API documentation** can be found in :doc:`api/pyobjcryst`.
 
 You can also read the
 `documentation of the underlying ObjCryst++ library <https://vincefn.net/ObjCryst/annotated.html>`_.
@@ -89,11 +89,11 @@ Table of contents
    :maxdepth: 2
 
    getting-started
+   Examples <examples/examples>
    Package API <api/pyobjcryst>
    release
    license
 
-=======
 Indices
 =======
 

diff --git a/requirements/docs.txt b/requirements/docs.txt
@@ -1,5 +1,7 @@
 sphinx
 sphinx_rtd_theme
 sphinx-copybutton
+nbsphinx
+nbsphinx-link
 doctr
 m2r