Merge pull request #28 from vincefn/master

Merge doc changes + small issue with polyhedra + small fixes for powder pattern plotting

Author: vincefn

.readthedocs.yaml

@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: doc/manual/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: doc/requirements.txt

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Release notes
 
+## Version X.Y.Z
+
+### Fixed
+
+- Fix access to PRISM_TETRAGONAL_DICAP, PRISM_TRIGONAL, 
+  ICOSAHEDRON and TRIANGLE_PLANE.
+
+
 ## Version 2.2.1 -- 2021-11-28
 
 - Add quantitative phase analysis with PowderPattern.qpa(), including

doc/manual/source/conf.py

@@ -5,6 +5,7 @@
 import sys, os
 import time
 import sphinx_py3doc_enhanced_theme
+
 # Requires sphinx >= 0.6
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -50,6 +51,7 @@
 # built documents.
 sys.path.insert(0, os.path.abspath('../../..'))
 from setup import versiondata
+
 fullversion = versiondata.get('DEFAULT', 'version')
 # The short X.Y version.
 version = ''.join(fullversion.split('.post')[:1])
@@ -111,8 +113,10 @@
 # documentation.
 #
 html_theme_options = {
-    'collapsiblesidebar' : 'true',
-    'navigation_with_keys' : 'true',
+    'collapsiblesidebar': 'true',
+    'navigation_with_keys': 'true',
+    'body_min_width': '40%',
+    'body_max_width': '800px',
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -183,18 +187,17 @@
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'pyobjcrystdoc'
 
-
 # -- Options for LaTeX output --------------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-# 'papersize': 'letterpaper',
+    # The paper size ('letterpaper' or 'a4paper').
+    # 'papersize': 'letterpaper',
 
-# The font size ('10pt', '11pt' or '12pt').
-# 'pointsize': '10pt',
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
 
-# Additional stuff for the LaTeX preamble.
-# 'preamble': '',
+    # Additional stuff for the LaTeX preamble.
+    # 'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples

doc/manual/source/examples/index.rst

@@ -39,7 +39,7 @@ 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>`_,

doc/manual/source/index.rst

@@ -12,7 +12,7 @@ Crystallographic Library
 Authors
 ================
 
-pyobjcryst was written as part of the DANSE_ open-source project by
+`pyobjcryst` was written as part of the DANSE_ open-source project by
 Christopher Farrow, Pavol Juhás, and Simon J.L. Billinge.
 The sources are now maintained as a part of the DiffPy-CMI complex
 modeling initiative at the Brookhaven National Laboratory.
@@ -23,29 +23,41 @@ global optimisation and least squares algorithms (see the
 :doc:`examples/index`) are provided by Vincent Favre-Nicolin (ESRF).
 
 For a complete list of contributors, see
-https://github.com/diffpy/pyobjcryst/graphs/contributors.
+https://github.com/diffpy/pyobjcryst/graphs/contributors and
+https://github.com/diffpy/libobjcryst/graphs/contributors.
 
 .. _DANSE: http://danse.us/
 
 ======================================
 Installation
 ======================================
 
+`pyobjcryst` and `libobjcryst` conda packages can be easily installed under
+Linux and macOS using channel `conda-forge` or `diffpy` channels,
+e.g.:
+
+  * `conda install -c diffpy libobjcryst pyobjcryst`
+  * `conda install -c conda-forge libobjcryst pyobjcryst`
+
 See the `README <https://github.com/diffpy/pyobjcryst#requirements>`_
-file included with the distribution.
+file included with the distribution for more details.
 
 ======================================
 Usage
 ======================================
 
-pyobjcryst can be used in different ways:
+`pyobjcryst` can be used in different ways:
 
-* as a backend library to manage crystal structures description in an application
+* **as a backend library** to manage crystal structures description in an application
   like `DiffPy-CMI <https://www.diffpy.org/products/diffpycmi/index.html>`_
-* in python scripts or notebooks, allowing to display crystal structures,
-  index and refine powder diffraction patterns, solve crystal structures
-  from diffraction data using global optimisation algorithms, etc.. The
-  functionality is similar to what is available in `Fox <http://fox.vincefn.net>`_.
+* **in python scripts or notebooks**, allowing to:
+
+  * display crystal structures,
+  * index and refine powder diffraction patterns
+  * solve crystal structures from diffraction data using global optimisation algorithms
+  * etc..
+
+  The functionality is similar to what is available in `Fox <http://fox.vincefn.net>`_.
   See the :doc:`examples/index`:
 
   * :doc:`3D Crystal structure display <examples/crystal_3d_widget>`

doc/requirements.txt

@@ -0,0 +1,5 @@
+sphinx_py3doc_enhanced_theme
+m2r2
+nbsphinx
+nbsphinx-link
+numpy

src/extensions/zpolyhedron_ext.cpp

@@ -59,10 +59,10 @@ void wrap_zpolyhedron()
         .value("CUBE", CUBE)
         .value("ANTIPRISM_TETRAGONAL", ANTIPRISM_TETRAGONAL)
         .value("PRISM_TETRAGONAL_MONOCAP", PRISM_TETRAGONAL_MONOCAP)
-        .value("PRISM_TETRAGONAL_DICAP ", PRISM_TETRAGONAL_DICAP)
-        .value("PRISM_TRIGONAL ", PRISM_TRIGONAL)
+        .value("PRISM_TETRAGONAL_DICAP", PRISM_TETRAGONAL_DICAP)
+        .value("PRISM_TRIGONAL", PRISM_TRIGONAL)
         .value("PRISM_TRIGONAL_TRICAPPED", PRISM_TRIGONAL_TRICAPPED)
-        .value("ICOSAHEDRON ", ICOSAHEDRON)
-        .value("TRIANGLE_PLANE ", TRIANGLE_PLANE)
+        .value("ICOSAHEDRON", ICOSAHEDRON)
+        .value("TRIANGLE_PLANE", TRIANGLE_PLANE)
         ;
 }

src/pyobjcryst/__init__.py

@@ -17,7 +17,7 @@
 
 Objects are wrapped according to their header file in the ObjCryst source.
 
-See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).
+See the online ObjCryst++ documentation (https://vincefn.net/ObjCryst/).
 
 Modules
 

src/pyobjcryst/powderpattern.py

@@ -121,7 +121,7 @@ def plot(self, diff=None, hkl=None, figsize=(9, 4), fontsize_hkl=6, reset=False,
             plt.figure(figsize=figsize)
         plt.plot(x, obs, 'k', label='obs', linewidth=1)
         plt.plot(x, calc, 'r', label='calc', linewidth=1)
-        m = self.GetMaxSinThetaOvLambda() * self.GetWavelength()
+        m = min(1, self.GetMaxSinThetaOvLambda() * self.GetWavelength())
         mtth = np.rad2deg(np.arcsin(m)) * 2
         if plot_diff:
             diff = calc - obs - obs.max() / 20
@@ -191,8 +191,7 @@ def _do_plot_hkl(self, nb_max=100, fontsize_hkl=None):
         calc = self.GetPowderPatternCalc()
         x = np.rad2deg(self.GetPowderPatternX())
         # Clear previous text (assumes only hkl were printed)
-        plt.gca().texts = []
-        iphase = 0
+        plt.gca().texts.clear()
         for ic in range(self.GetNbPowderPatternComponent()):
             c = self.GetPowderPatternComponent(ic)
             if isinstance(c, PowderPatternDiffraction) is False: