Added periodic homog example + changes in process files for including zip and notebooks

doc/conf.py

@@ -24,8 +24,9 @@ sys.path.insert(0, os.path.abspath('..'))
 #sys.path.insert(0, os.path.abspath('../examples</'))
 
 sys.path.append(os.getcwd())
-import rstprocess
-rstprocess.process()
+import process_sources
+process_sources.process()
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -35,13 +36,17 @@ rstprocess.process()
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx',
-              'sphinx.ext.mathjax', 'sphinx.ext.napoleon']
+              'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'nbsphinx']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
+source_parsers = {
+   '.md': 'recommonmark.parser.CommonMarkParser',
+}
+
 # The suffix of source filenames.
-source_suffix = '.rst'#,'.txt']
+source_suffix = ['.rst','.md']#,'.txt']
 
 # The encoding of source files.
 #source_encoding = 'utf-8-sig'
@@ -58,9 +63,9 @@ copyright = u'2016, Jeremy Bleyer'
 # built documents.
 #
 # The short X.Y version.
-version = '1.0'
+version = 'master'
 # The full version, including alpha/beta/rc tags.
-release = '1.0'
+release = 'master'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -74,7 +79,7 @@ release = '1.0'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ['_build', '**.ipynb_checkpoints']
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -186,6 +191,7 @@ html_static_path = ['_static']
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'NumericaltoursofcontinuummechanicsusingFEniCSdoc'
 
+html_short_title = "Numerical tours of continuum mechanics using FEniCS"
 
 # -- Options for LaTeX output ---------------------------------------------
 
@@ -204,7 +210,7 @@ latex_elements = {
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', 'NumericaltoursofcontinuummechanicsusingFEniCS.tex', u'Numerical tours of continuum mechanics using FEniCS Documentation',
+  ('index', 'NumericaltoursofcontinuummechanicsusingFEniCS.tex', u'Numerical tours of continuum mechanics using FEniCS',
    u'Jeremy Bleyer', 'manual'),
 ]
 
@@ -216,6 +222,7 @@ latex_documents = [
 # not chapters.
 #latex_use_parts = False
 
+
 # If true, show page references after internal links.
 #latex_show_pagerefs = False
 
@@ -234,7 +241,7 @@ latex_documents = [
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'numericaltoursofcontinuummechanicsusingfenics', u'Numerical tours of continuum mechanics using FEniCS Documentation',
+    ('index', 'numericaltoursofcontinuummechanicsusingfenics', u'Numerical tours of continuum mechanics using FEniCS',
      [u'Jeremy Bleyer'], 1)
 ]
 
@@ -248,7 +255,7 @@ man_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'NumericaltoursofcontinuummechanicsusingFEniCS', u'Numerical tours of continuum mechanics using FEniCS Documentation',
+  ('index', 'NumericaltoursofcontinuummechanicsusingFEniCS', u'Numerical tours of continuum mechanics using FEniCS',
    u'Jeremy Bleyer', 'NumericaltoursofcontinuummechanicsusingFEniCS', 'One line description of project.',
    'Miscellaneous'),
 ]
@@ -264,3 +271,19 @@ texinfo_documents = [
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
+#nbsphinx_prolog = """
+#Go there: https://example.org/notebooks/{{ env.doc2path(env.docname, base=None) }}
+#
+#----
+#"""
+
+#{% set docname = env.doc2path(env.docname, base='doc') %}
+nbsphinx_prolog = r"""
+{% set docname = env.docname.split("/")[-1] %}
+.. role:: raw-html(raw)
+ :format: html
+.. nbinfo::
+ The corresponding files can be obtained from:
+
+ - Jupyter Notebook: :download:`{{docname+".ipynb"}}`
+ - Python script: :download:`{{docname+".py"}}`"""
\ No newline at end of file

doc/homogenization.rst

+.. Numerical tours of continuum mechanics using FEniCS documentation master file, created by
+   sphinx-quickstart on Wed Jun  8 21:25:10 2016.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Homogenization of heterogeneous materials
+=========================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 1
+
+   demo/periodic_homog_elas/periodic_homog_elas.ipynb
+
+
+

doc/index.rst

@@ -13,6 +13,7 @@ Contents:
 
    intro
    linear_problems
+   homogenization
    nonlinear_problems
    demo/reissner_mindlin/reissner_mindlin.rst
    tips_and_tricks

doc/nonlinear_problems.rst

@@ -10,7 +10,7 @@ Contents:
 .. toctree::
    :maxdepth: 1
 
-   demo/nonlinear_materials/vonMises_plasticity.py.rst
+   demo/2D_plasticity/vonMises_plasticity.py.rst
 
 
 

doc/rstprocess.py → doc/process_sources.py

@@ -19,9 +19,11 @@
 import sys
 import os
 import shutil
+import zipfile
 
 # extensions of files which must be copied with the demo when building docs
 file_extensions = [".png",".gif", ".geo", ".xml", ".msh", ".pdf"]
+zipfile_extensions = [".geo", ".msh", ".xml", ".py", ".ipynb"]
 
 def process():
     """Copy demo rst files (C++ and Python) from the DOLFIN source tree
@@ -36,7 +38,7 @@ def process():
 
     # Directories to scan
     subdirs = ["../examples"]
-
+    retval = os.getcwd()
     # Iterate over subdirectories containing demos
     for subdir in subdirs:
 
@@ -55,28 +57,51 @@ def process():
                 if not os.path.isdir(version_path):
                     continue
 
-                # Build list of rst files in demo source directory
-                rst_files = [f for f in os.listdir(version_path) if os.path.splitext(f)[1] == ".rst" ]
-
                 # Create directory in documentation tree for demo
-                demo_dir = os.path.join('./demo/', demo, version)
+                demo_dir = os.path.join('./demo/', demo)
                 if not os.path.exists(demo_dir):
                     os.makedirs(demo_dir)
 
+                ipynb_files =  [f for f in os.listdir(version_path) if f.endswith("ipynb") ]
+                for f in ipynb_files:
+                    ff = os.path.join(path, f)
+                    shutil.copy(ff, demo_dir)
+                    ret = os.system("jupyter-nbconvert --to script %s --output %s" % (ff,  os.path.join("../../doc",demo_dir, os.path.splitext(f)[0])))
+                    if not ret == 0:
+                        raise RuntimeError("Unable to convert ipynb file to a .py ({})".format(f))
+
+                # Build list of rst files in demo source directory
+                rst_files = [f for f in os.listdir(version_path) if f.endswith("rst") ]
+
                 # Copy rst files into documentation demo directory and process with Pylit
                 for f in rst_files:
                     shutil.copy(os.path.join(version_path, f), demo_dir)
 
                     # Run pylit on cpp.rst and py.rst files (file with 'double extensions')
-                    if os.path.splitext(os.path.splitext(f)[0])[1] in (".py"):
+                    if "py" in f.split("."):
                         rst_file = os.path.join(demo_dir, f)
                         command = pylit_parser + " " + rst_file
                         ret = os.system("python "+command)
                         if not ret == 0:
                             raise RuntimeError("Unable to convert rst file to a .py ({})".format(f))
 
+
+
                 tocopy_files = [f for f in os.listdir(version_path) if os.path.splitext(f)[1] in file_extensions ]
                 for f in tocopy_files:
                     source = os.path.join(version_path, f)
                     print("Copying {} to {}".format(source, demo_dir))
                     shutil.copy(source, demo_dir)
+
+                for f in ipynb_files + rst_files:
+                    cwd = os.getcwd()
+                    os.chdir(demo_dir)
+                    files = os.listdir(".")
+                    zip_files = []
+                    for ff in files:
+                        if any([ff.endswith(ext) for ext in zipfile_extensions]):
+                            zip_files.append(ff)
+                    with zipfile.ZipFile(f.split(".")[0]+".zip", 'w') as myzip:
+                        for a in zip_files:
+                            myzip.write(a, compress_type=zipfile.ZIP_DEFLATED)
+                    os.chdir(cwd)

examples/nonlinear_materials/vonMises_plasticity.py.rst → examples/2D_plasticity/vonMises_plasticity.py.rst

@@ -14,7 +14,7 @@ von Mises material. The structure response is computed using an iterative
 predictor-corrector return mapping algorithm embedded in a Newton-Raphson global
 loop for restoring equilibrium. Due to the simple expression of the von Mises criterion,
 the return mapping procedure is completely analytical (with linear isotropic
-hardening). The corresponding file can be obtained from :download:`vonMises_plasticity.py`.
+hardening). The corresponding sources can be obtained from :download:`vonMises_plasticity.zip`.
 Another implementation of von Mises plasticity can also be found at
 https://bitbucket.org/fenics-apps/fenics-solid-mechanics.
 

examples/elasticity/2D_elasticity.py.rst

@@ -15,7 +15,7 @@ Introduction
 In this first numerical tour, we will show how to compute a small strain solution for
 a 2D isotropic linear elastic medium, either in plane stress or in plane strain,
 in a tradtional displacement-based finite element formulation. The corresponding
-file can be obtained from :download:`2D_elasticity.py`.Extension to 3D
+file can be obtained from :download:`2D_elasticity.py`. Extension to 3D
 is straightforward and an example can be found in the :ref:`ModalAnalysis` example.
 
 We consider here the case of a cantilever beam modeled as a 2D medium of dimensions

examples/periodic_homog_elas/hexag_incl.geo

+// Gmsh project created on Mon Sep 14 09:33:57 2015
+a = 1.;
+R = 0.2;
+t = Pi/3;
+b = Sin(t)*a;
+bR = Sin(t)*R;
+c = a*Cos(t);
+cR = R*Cos(t);
+
+d = 1.;
+
+nx = 80;
+nR = R*nx;
+ns = nx-2*nR;
+
+Point(1) = {0, 0, 0, d};
+Point(2) = {a, 0, 0, d};
+Point(3) = {a+c, b, 0, d};
+Point(4) = {c, b, 0, d};
+Point(5) = {R,0,0,d};
+Point(6) = {a-R,0,0,d};
+Point(7) = {a+cR,bR,0,d};
+Point(8) = {a+c-cR,b-bR,0,d};
+Point(9) = {a+c-R,b,0,d};
+Point(10) = {c+R,b,0,d};
+Point(11) = {c-cR,b-bR,0,d};
+Point(12) = {cR,bR,0,d};
+
+Line(1) = {1, 5};
+Line(2) = {5, 6};
+Line(3) = {6, 2};
+Line(4) = {2, 7};
+Line(5) = {7, 8};
+Line(6) = {8, 3};
+Line(7) = {3, 9};
+Line(8) = {9, 10};
+Line(9) = {10, 4};
+Line(10) = {4, 11};
+Line(11) = {11, 12};
+Line(12) = {12, 1};
+Circle(13) = {5, 1, 12};
+Circle(14) = {7, 2, 6};
+Circle(15) = {9, 3, 8};
+Circle(16) = {11, 4, 10};
+Line Loop(17) = {13, -11, 16, -8, 15, -5, 14, -2};
+Plane Surface(18) = {17};
+Line Loop(19) = {1, 13, 12};
+Plane Surface(20) = {19};
+Line Loop(21) = {3, 4, 14};
+Plane Surface(22) = {21};
+Line Loop(23) = {7, 15, 6};
+Plane Surface(24) = {23};
+Line Loop(25) = {10, 16, 9};
+Plane Surface(26) = {25};
+
+Transfinite Line{1,3,4,6,7,9,10,12} = nR;
+Transfinite Line{2,5,8,11} = ns;
+Transfinite Line{14,16} = 2*nR;
+Transfinite Line{13,15} = nR;
+
+Periodic Line{1} = {9};
+Periodic Line{2} = {8};
+Periodic Line{3} = {7};
+Periodic Line{4} = {12};
+Periodic Line{5} = {11};
+Periodic Line{6} = {10};
+
+Physical Line(1) = {1,2,3};
+Physical Line(2) = {4,5,6};
+Physical Line(3) = {7,8,9};
+Physical Line(4) = {10,11,12};
+
+Physical Surface(0) = {18};
+Physical Surface(1) = {20,22,24,26};
+