Merge pull request openturns#3 from sofianehaddad/sh/fixes

Some fixes

.github/workflows/build.yml

@@ -11,7 +11,8 @@ jobs:
       - name: Build
         shell: bash -l {0}
         run: |
-          conda install -y openturns numpy pytest jupyter numpydoc sphinx nbsphinx jupyter_client ipython pandoc
+          conda install -y openturns numpy pytest numpydoc sphinx sphinx-gallery pandoc
+          conda install -c conda-forge sphinx_rtd_theme
           python setup.py install
           pytest
           sudo apt install -y texlive-latex-recommended texlive-fonts-recommended texlive-latex-extra

doc/conf.py

@@ -14,13 +14,13 @@
 import sys, os
 from distutils.version import LooseVersion
 import sphinx
+import sphinx_gallery
 import subprocess
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('../'))
-sys.path.append(os.path.abspath('sphinxext'))
 
 # -- General configuration ------------------------------------------------
 
@@ -31,42 +31,66 @@
     'sphinx.ext.autosummary',
     'sphinx.ext.coverage',
     'numpydoc',
-    'nbsphinx'
+    'sphinx_gallery.gen_gallery'
 ]
 
-nbsphinx_execute = 'never'
-# dont add .txt suffix to notebook
-html_sourcelink_suffix = ''
-tags.add('nbsphinx')
-extensions.append('IPython.sphinxext.ipython_console_highlighting')
+sphinx_gallery_conf = {
+    'examples_dirs': ['examples'],  # path to
+    # example scripts
+    'gallery_dirs': ['auto_example'],
+     'filename_pattern': '/plot_',
+    'run_stale_examples': True,
+    'show_signature': False,
+    # directory where function/class granular galleries are stored
+    'backreferences_dir'  : 'gen_modules/backreferences',
+
+    # Modules for which function/class level galleries are created.
+    'doc_module'          : ('openturns'),
+
+    # objects to exclude from implicit backreferences. The default option
+    # is an empty set, i.e. exclude nothing.
+    'exclude_implicit_doc': {},
+}
 
-autodoc_default_flags = ['members', 'inherited-members']
-intersphinx_mapping = {'python': ('http://openturns.github.io/openturns/1.18', 'openturns-objects.inv')}
-autosummary_generate = True
+if LooseVersion(sphinx.__version__) >= LooseVersion('1.8'):
+    autodoc_default_options = {'members': None, 'inherited-members': None, 'exclude-members': 'thisown'}
+else:
+    autodoc_default_flags =  ['members', 'inherited-members']
 
-numpydoc_show_class_members = True
-numpydoc_class_members_toctree = False
-
-# for equations
 try:
     import sphinx.ext.imgmath
     extensions.append('sphinx.ext.imgmath')
+    imgmath_latex_preamble = r'\usepackage{{{0}math_notations}}'.format(
+        os.path.dirname(__file__) + os.sep)
     imgmath_use_preview = True
     if subprocess.call('dvisvgm -V', shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0:
         imgmath_image_format = 'svg'
+    # embed image files inside html
+    imgmath_embed = True
 except ImportError:
     extensions.append('sphinx.ext.pngmath')
+    pngmath_latex_preamble = r'\usepackage{{{0}math_notations}}'.format(
+        os.path.dirname(__file__) + os.sep)
     # The next option is used for smart-alignment of math images on the text.
     # It only works when the preview-latex package is installed.
     # See http://sphinx-doc.org/latest/ext/math.html#confval-pngmath_use_preview
     pngmath_use_preview = True
 
+extensions.append('matplotlib.sphinxext.plot_directive')
+
+intersphinx_mapping = {'python': (
+    'http://openturns.github.io/openturns/1.18', 'openturns-objects.inv')}
+autosummary_generate = True
+
+numpydoc_show_class_members = True
+numpydoc_class_members_toctree = False
+
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
 # The suffix(es) of source filenames.
-source_suffix = '.rst'
+source_suffix = ['.rst']
 
 # The master toctree document.
 master_doc = 'index'
@@ -95,7 +119,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build','themes', 'sphinxext', '.ipynb_checkpoints']
+exclude_patterns = []
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None
@@ -126,8 +150,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 html_theme = 'openturns'
-if LooseVersion(sphinx.__version__) < LooseVersion('1.3'):
-    html_theme = 'default'
+html_sourcelink_suffix = ''
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -190,23 +213,21 @@
 \usepackage{amsfonts}
 \usepackage{amsmath}
 \usepackage{expdlist}
+\usepackage{math_notations}
+\usepackage{stackrel}
 \let\latexdescription=\description
 \def\description{\latexdescription{}{} \breaklabel}
 \DeclareMathOperator*{\argmin}{Argmin}
 '''
 
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-'papersize': 'a4paper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
 
-# Additional stuff for the LaTeX preamble.
-'preamble': latex_preamble,
-
-# Latex figure (float) alignment
-#'figure_align': 'htbp',
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    'papersize': 'a4paper',
+    # The font size ('10pt', '11pt' or '12pt').
+    'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    'preamble': latex_preamble,
 }
 
 # Grouping the document tree into LaTeX files. List of tuples

doc/examples/examples.rst

@@ -1,45 +1,10 @@
 Examples
 ========
 
-.. toctree::
-    :maxdepth: 1
-
-    basic.ipynb
-
-Example 1: Axial stressed beam
-------------------------------
-
-This example is a simple beam, restrained at one side and stressed by a traction load F at the other side.
-
-1- Problem statement
-````````````````````
-
-a- Inputs
-'''''''''
-
-- Stochastics variables:
+This section illustrates how to use the template.
 
-====== ======================== ==================
- Name  Description              Distribution
-====== ======================== ==================
-F      Traction load            Normal(75e3, 5e3)
-sigma  Axial stress             LogNormal(300, 30)
-====== ======================== ==================
 
-- Deterministic independent variables:
-
-======== ================================ =================
-Variable Description                      Value
-======== ================================ =================
-D        diameter                         20.0
-======== ================================ =================
-
-b- Output
-'''''''''
-
-Primary energy savings :math:`G`
-
-.. math::
-
-    G = \sigma_e -\frac{F}{\pi \frac{D^2}{4} }
 
+.. toctree::
+
+   ../auto_example/plot_basic

doc/examples/plot_basic.py

@@ -0,0 +1,31 @@
+"""
+Example : Using ottemplatepython module
+---------------------------------------
+"""
+# %%
+# This example aims to illustrate how to use the module.
+
+# %%
+# | Loading python modules
+
+# %%
+import openturns as ot
+from openturns.viewer import View
+import numpy as np
+import ottemplate
+from matplotlib import pylab as plt
+
+# %%
+# | Using the module to compute power
+print(ottemplate.MyClass(3).power(2))
+
+# %%
+# | Compute power using arrays
+array = np.linspace(-5, 5, 101)
+values = ottemplate.MyClass(array).power(2.0)
+
+# %%
+# | Use of graph objects
+graph = ot.Graph('Square function', 'x1', 'x2', True, '')
+graph.add(ot.Cloud(array, values))
+View(graph).show()

ottemplate/ottemplate.py

@@ -4,7 +4,7 @@
 class MyClass(object):
     """
     Class test
-    Applying power on
+    Applying power function
 
     Parameters
     ----------
@@ -28,4 +28,4 @@ def power(self, n):
         y : float
             The cube value.
         """
-        return np.power(self.value, n)
+        return np.power(self.value, n)