Migration into main

docs/source/examples/distanceprinter.py → docs/examples/distanceprinter.py

@@ -47,9 +47,9 @@ def _addPairContribution(self, bnds, sumscale):
 
 
 def get_pyobjcryst_sphalerite():
-    from pyobjcryst import loadCrystal
+    from pyobjcryst.crystal import create_crystal_from_cif
 
-    crst = loadCrystal("datafiles/sphalerite.cif")
+    crst = create_crystal_from_cif("datafiles/sphalerite.cif")
     return crst
 
 

docs/source/examples/parallelPDF.py → docs/examples/parallelPDF.py

@@ -38,9 +38,9 @@
 if opts.pyobjcryst:
     # use pyobjcryst if requested by the user
     from numpy import pi
-    from pyobjcryst import loadCrystal
+    from pyobjcryst.crystal import create_crystal_from_cif
 
-    menthol = loadCrystal(mentholcif)
+    menthol = create_crystal_from_cif(mentholcif)
     for sc in menthol.GetScatteringComponentList():
         sp = sc.mpScattPow
         sp.Biso = sp.Biso or 8 * pi**2 * Uisodefault

docs/source/api/diffpy.srreal.rst

@@ -10,21 +10,142 @@
     :undoc-members:
     :show-inheritance:
 
-Subpackages
------------
-
-.. toctree::
-   diffpy.srreal.example_package
-
 Submodules
 ----------
 
-|module|
---------
+diffpy.srreal.atomradiitable module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.atomradiitable
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+diffpy.srreal.attributes module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.attributes
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.bondcalculator module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.bondcalculator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.bvparameterstable module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.bvparameterstable
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.bvscalculator module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.bvscalculator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.eventticker module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.eventticker
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.overlapcalculator module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.overlapcalculator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.overlapcalculator module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.overlapcalculator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.pairquantity module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.pairquantity
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.parallel module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.parallel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.pdfbaseline module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.pdfbaseline
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.pdfcalculator module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.pdfcalculator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.pdfenvelope module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.pdfenvelope
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.peakprofile module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.peakprofile
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.peakwidthmodel module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.peakwidthmodel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srreal.scatteringfactortable module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srreal.scatteringfactortable
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
-.. |module| replace:: diffpy.srreal.example_submodule module
+diffpy.srreal.sfaverage module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.srreal.example_submodule
+.. automodule:: diffpy.srreal.sfaverage
     :members:
     :undoc-members:
     :show-inheritance:

docs/source/examples.rst

@@ -1,4 +1,22 @@
-.. _examples:
+.. _developers-guide-examples:
 
+===================
 Examples
-########
+===================
+
+.. This creates the links from the filenames within README to pages.
+.. _compareC60PDFs_objcryst.py: examples/compareC60PDFs_objcryst.html
+.. _compareC60PDFs.py: examples/compareC60PDFs.html
+.. _distanceprinter.py: examples/distanceprinter.html
+.. _parallelPDF.py: examples/parallelPDF.html
+
+
+Files
+-----
+
+.. toctree::
+
+   examples/compareC60PDFs_objcryst.rst
+   examples/compareC60PDFs.rst
+   examples/distanceprinter.rst
+   examples/parallelPDF.rst

docs/source/examples/compareC60PDFs.rst

@@ -0,0 +1,7 @@
+.. _compareC60PDFs.rst:
+
+==========================
+compareC60PDFs.py
+==========================
+
+.. literalinclude:: ../../examples/compareC60PDFs.py

docs/source/examples/compareC60PDFs_objcryst.rst

@@ -0,0 +1,7 @@
+.. _compareC60PDFs_objcryst.py:
+
+==========================
+compareC60PDFs_ObjCryst.py
+==========================
+
+.. literalinclude:: ../../examples/compareC60PDFs_objcryst.py

docs/source/examples/distanceprinter.rst

@@ -0,0 +1,7 @@
+.. _distanceprinter.py:
+
+===========================
+distanceprinter.py
+===========================
+
+.. literalinclude:: ../../examples/distanceprinter.py

docs/source/examples/parallelPDF.rst

@@ -0,0 +1,7 @@
+.. _parallelPDF.py:
+
+===========================
+parallelPDF.py
+===========================
+
+.. literalinclude:: ../../examples/parallelPDF.py

news/fix-docstring.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: Fix documentation rendering.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

requirements/pip.txt

@@ -0,0 +1,2 @@
+setuptools
+numpy

setup.py

@@ -17,14 +17,26 @@
 
 
 def get_boost_libraries():
-    base_lib = "boost_python"
-    major, minor = str(sys.version_info[0]), str(sys.version_info[1])
-    tags = [f"{major}{minor}", major, ""]
-    mttags = ["", "-mt"]
-    candidates = [base_lib + tag for tag in tags for mt in mttags] + [base_lib]
-    for lib in candidates:
-        if find_library(lib):
-            return [lib]
+    major, minor = sys.version_info[:2]
+    candidates = [
+        f"boost_python{major}{minor}",
+        f"boost_python{major}",
+        "boost_python",
+    ]
+
+    conda_prefix = os.environ.get("CONDA_PREFIX")
+    if conda_prefix:
+        libdir = os.path.join(conda_prefix, "lib")
+        for name in candidates:
+            so = f"lib{name}.so"
+            if os.path.isfile(os.path.join(libdir, so)):
+                return [name]
+
+    # fallback to ldconfig
+    for name in candidates:
+        found = find_library(name)
+        if found:
+            return [name]
     raise RuntimeError("Cannot find a suitable Boost.Python library.")
 
 
@@ -111,11 +123,11 @@ def create_extensions():
 
 
 # Extensions not included in pyproject.toml
-setup_args = dict(
-    ext_modules=[],
-)
+def ext_modules():
+    if set(sys.argv) & {"build_ext", "bdist_wheel", "install"}:
+        return create_extensions()
+    return []
 
 
 if __name__ == "__main__":
-    setup_args["ext_modules"] = create_extensions()
-    setup(**setup_args)
+    setup(ext_modules=ext_modules())

src/diffpy/srreal/atomradiitable.py

@@ -35,7 +35,10 @@ class CovalentRadiiTable(AtomRadiiTable):
     def _standardLookup(self, smbl):
         """Return covalent atom radius in Angstroms.
 
-        smbl -- string symbol of an element
+        Attributes
+        ----------
+        smbl
+            string symbol of an element
 
         Return float.  Raise ValueError for unknown element symbol.
         """

src/diffpy/srreal/bondcalculator.py

@@ -58,9 +58,13 @@ def _init_kwargs(self, **kwargs):
 def _call_kwargs(self, structure=None, **kwargs):
     """Return sorted bond distances in the specified structure.
 
-    structure    -- structure to be evaluated, an instance of diffpy Structure
-                    or pyobjcryst Crystal.  Reuse the last structure when None.
-    kwargs       -- optional parameter settings for this calculator
+    Attributes
+    ----------
+    structure
+        structure to be evaluated, an instance of diffpy Structure
+        or pyobjcryst Crystal.  Reuse the last structure when None.
+    kwargs
+        optional parameter settings for this calculator
 
     Return a sorted numpy array.
     """

src/diffpy/srreal/bvscalculator.py

@@ -75,9 +75,13 @@ def _init_kwargs(self, **kwargs):
 def _call_kwargs(self, structure=None, **kwargs):
     """Return bond valence sums at each atom site in the structure.
 
-    structure    -- structure to be evaluated, an instance of diffpy Structure
-                    or pyobjcryst Crystal.  Reuse the last structure when None.
-    kwargs       -- optional parameter settings for this calculator
+    Attributes
+    ----------
+    structure
+        structure to be evaluated, an instance of diffpy Structure
+        or pyobjcryst Crystal.  Reuse the last structure when None.
+    kwargs
+        optional parameter settings for this calculator
 
     Return an array of calculated valence sums.
     See valences for the expected values.