fix: remove nbsphinx_link dependency

Author: ycexiao

docs/source/conf.py

@@ -17,6 +17,7 @@
 import time
 from importlib.metadata import version
 from pathlib import Path
+import shutil
 
 # Attempt to import the version dynamically from GitHub tag.
 try:
@@ -34,6 +35,15 @@
 # abbreviations
 ab_authors = "Billinge Group members"
 
+# Include notebooks at build time.
+root_dir = Path(__file__).resolve().parents[1]
+external_nb_dir = root_dir / 'examples'
+for f in external_nb_dir.glob("*.ipynb"):
+    dest = Path(__file__).parent / 'examples' / f.name
+    if dest.exists():
+        dest.unlink()
+    shutil.copy(f, dest)
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -50,8 +60,7 @@
     "sphinx.ext.intersphinx",
     "sphinx_copybutton",
     "nbsphinx",
-    "nbsphinx_link",
-    "m2r2",
+    "m2r",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -63,7 +72,7 @@
 source_suffix = [".rst", ".md"]
 
 # The encoding of source files.
-# source_encoding = 'utf-8-sig'
+# source_encoding = eutf-8-sig'
 
 # The master toctree document.
 master_doc = "index"

docs/source/examples/Quantitative-phase-analysis.nblink

@@ -4,17 +4,16 @@ Example notebooks
 
 Several examples available in the pyobjcryst repository:
 
-
 :doc:`3D Crystal structure display <crystal_3d_widget>`
-=======================================================
+================================================================
 
 Example of importing a CIF file from a file or the
 `Crystallography Open Database <http://crystallography.net/cod/>`_
 and displaying it in a widget using
 `3dmol.js <https://3dmol.csb.pitt.edu/>`_.
 
 :doc:`Solving the cimetidine structure from its powder pattern <structure-solution-powder-cimetidine>`
-======================================================================================================
+===============================================================================================================
 
 In this example, a powder pattern is used to solve the crystal
 structure of Cimetidine. This covers all the steps: loading the
@@ -23,7 +22,7 @@ the spacegroup, profile fitting, and solving the structure
 using a global optimisation algorithm.
 
 :doc:`Solving the PbSO4 structure from its X and N powder patterns <structure-solution-powder-pbso4>`
-=====================================================================================================
+==============================================================================================================
 
 In this example, two powder patterns (X-ray and neutron) are used to solve
 the crystal structure of PbSO4. This covers all the steps: loading the
@@ -32,14 +31,14 @@ the spacegroup, profile fitting for the two patterns, and solving the
 structure using a global optimisation algorithm.
 
 :doc:`Meta-structure solution using multi-processing <structure-solution-multiprocessing>`
-==========================================================================================
+===================================================================================================
 
 This is a more advanced example where 8 different spacegroups are
 tested in parallel to determine which one is correct. The solutions
 can then be compared and displayed individually.
 
 :doc:`Quantitative phase analysis (QPA) <Quantitative-phase-analysis>`
-======================================================================
+===============================================================================
 
 Example of QPA based on the data available from the `1999 Round Robin
 <https://www.iucr.org/__data/iucr/powder/QARR/samples.htm>`_,

docs/source/examples/crystal_3d_widget.nblink

@@ -2,6 +2,6 @@ sphinx
 pydata-sphinx-theme
 sphinx-copybutton
 nbsphinx
-nbsphinx-link
 doctr
 m2r
+ipykernel