Update notebooks (#484)

* fixed default ipyparallel setup and sdInfo regressions

* updated stack (to update mpich and sphinx)

* updating stack to add imagesize

* removed errors from sphing doc generation

* Refactor the tutorial directory.

* simplified handling of hit remotes

* Added a Navier-Stokes driven cavity example.

* added Makefile targets for setting up remote src and bld caches

* fix Makefile for when lsb_release not present

* updated stack to fix pycgal fail

* fix mprans.PresInc numerical flux and Jacobian

* updated stack to fix pycgal build failure

* Added streamlines to NSE solution plots.

* updated stack and removed adjoint from PresInc

* updated hashdist that supports pushing xz archives

* updated stack and cleaned up CI support

* removed reference  to update_notebooks branch in Dockerfile

.hashdist_default

@@ -1,4 +1,5 @@
-95601061658628ad9da3be1a5538681ed1092634
+3b554016f6f539fdd2c713595f1c9ad8a3e9c179
+
 
 
 

.hashstack_default

@@ -1,4 +1,10 @@
-2ca88aa0ef486b86ad45191ea56c72ce641f8dda
+f107fbfbfb8f3a87607929c8ee3901bef3a1447a
+
+
+
+
+
+
 
 
 

.travis.yml

@@ -18,9 +18,6 @@ addons:
     - libssl-dev
 
 before_install:
-- wget https://dl.dropboxusercontent.com/u/26353144/hashdist_trusty.tgz
-- tar xzf hashdist_trusty.tgz 
-- mv .hashdist $HOME
 - pip install pyliblzma
 
 install:
@@ -30,6 +27,9 @@ install:
 - make hashdist
 - make stack
 - make stack/default.yaml
+- ./hashdist/bin/hit init-home
+- ./hashdist/bin/hit remote add https://dl.dropboxusercontent.com/u/26353144/hashdist_src --objects="source"
+- ./hashdist/bin/hit remote add https://dl.dropboxusercontent.com/u/26353144/hashdist_ubuntu_14_04 --objects="build"
 - FC=gfortran make install
 - export PATH=$PWD/linux2/bin:$PATH
 - export SSL_CERT_DIR=/etc/ssl/certs

Dockerfile

@@ -92,24 +92,20 @@ RUN useradd -m -s /bin/bash -N -u $NB_UID $NB_USER
 
 RUN mkdir /home/$NB_USER/.jupyter && \
     mkdir /home/$NB_USER/.local && \
-    mkdir /home/$NB_USER/.hashdist && \
     echo "cacert=/etc/ssl/certs/ca-certificates.crt" > /home/$NB_USER/.curlrc
 
-ADD https://dl.dropboxusercontent.com/u/26353144/hashdist_config_jovyan.yaml /home/$NB_USER/.hashdist/config.yaml
-
 RUN chown -R $NB_USER:users /home/$NB_USER
 
 USER jovyan
 
-RUN ls /home/$NB_USER/.hashdist && \
-    cat /home/$NB_USER/.hashdist/config.yaml
-
 WORKDIR /home/$NB_USER
 
-RUN cat /home/$NB_USER/.hashdist/config.yaml && \
-    git clone https://github.com/erdc-cm/proteus && \
+RUN git clone https://github.com/erdc-cm/proteus && \
     cd proteus && \
     make hashdist stack stack/default.yaml && \
+    ./hashdist/bin/hit init-home && \
+    ./hashdist/bin/hit remote add https://dl.dropboxusercontent.com/u/26353144/hashdist_src --objects="source" && \
+    ./hashdist/bin/hit remote add https://dl.dropboxusercontent.com/u/26353144/hashdist_debian_jessie --objects="build" && \
     cd stack && \
     ../hashdist/bin/hit build default.yaml -v
 

Makefile

@@ -120,6 +120,16 @@ hashdist:
 	@echo "No hashdist found.  Cloning hashdist from GitHub"
 	git clone https://github.com/hashdist/hashdist.git 
 	cd hashdist && git checkout ${HASHDIST_DEFAULT_VERSION}
+
+hashdist_src:
+	@echo "Trying to add hashdist source cache"
+	./hashdist/bin/hit remote add https://dl.dropboxusercontent.com/u/26353144/hashdist_src --objects="source"
+
+hashdist_bld:
+	@echo "Trying to add hashdist build cache for your arch"
+	HASHSTACK_BLD = $(shell lsb_release -ir | python -c "import sys; rel=dict((k.split(':')[0].split()[0],k.split(':')[1].strip().replace('.','_').lower()) for k in sys.stdin.readlines()); print '{Distributor}_{Release}'.format(**rel)")
+	./hashdist/bin/hit remote add https://dl.dropboxusercontent.com/u/26353144/hashdist_${HASHSTACK_BLD} --objects="build"
+
 stack: 
 	@echo "No stack found.  Cloning stack from GitHub"
 	git clone https://github.com/hashdist/hashstack.git stack
@@ -297,3 +307,8 @@ jupyter:
 	jupyter nbextension install --py --sys-prefix rise
 	jupyter nbextension enable --py --sys-prefix rise
 	jupyter dashboards quick-setup --sys-prefix
+	jupyter nbextension install --sys-prefix --py ipyparallel
+	jupyter nbextension enable --sys-prefix --py ipyparallel
+	jupyter serverextension enable --sys-prefix --py ipyparallel
+	ipython profile create mpi --parallel
+	echo "c.IPClusterEngines.engine_launcher_class = 'MPI'" >> ${HOME}/.ipython/profile_mpi/ipcluster_config.py

doc/Makefile

@@ -59,9 +59,7 @@ source/api/modules.rst:
 	sphinx-apidoc --output-dir=source/api ../proteus --separate -M
 
 $(BUILDDIR)/capi/html/files.html:
-	-mkdir -p build/html/capi
 	doxygen
-	cp doxygenIndexRedirect.html build/html/capi/html/index.html
 
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml

doc/source/_templates/layout.html

@@ -2,7 +2,7 @@
 
 {% set theme_css_files = [] %}
 {% if theme_bootstrap_version == "3" %}
-  {% set bootstrap_version, bootstrap_additional_css, navbar_version = "3.3.4", "theme", "" %}
+  {% set bootstrap_version, bootstrap_additional_css, navbar_version = "3.3.6", "theme", "" %}
   {% set bs_span_prefix = "col-md-" %}
 {% else %}
   {% set bootstrap_version, bootstrap_additional_css, navbar_version = "2.3.2", "responsive", "-2" %}
@@ -104,12 +104,12 @@
      style="height:1in;"> A Python toolkit for computational methods and simulation</p>
     <div class="btn-group" role="group">
       <a class="btn btn-success"
-          href="https://github.com/erdc-cm/proteus/archive/v1.2.0.tar.gz">
+          href="https://github.com/erdc-cm/proteus/archive/1.2.0.tar.gz">
             <span class="glyphicon glyphicon-download"></span> Download
       </a>
       <button type="button" class="btn btn-success dropdown-toggle" data-toggle="dropdown"><span class="caret"></span></button>
       <ul class="dropdown-menu">
-        <li><a https://github.com/erdc-cm/proteus/archive/v1.2.0.tar.gz">Version 1.2.0</a></li>
+        <li><a https://github.com/erdc-cm/proteus/archive/1.2.0.tar.gz">Version 1.2.0</a></li>
       </ul>
     </div>
   </div>

doc/source/conf.py

@@ -97,7 +97,7 @@ def linkcode_resolve(domain, info):
 
 # General information about the project.
 project = u'Proteus'
-copyright = u'2016, The Proteus Team'
+copyright = u'2017, The Proteus Team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -452,5 +452,4 @@ def linkcode_resolve(domain, info):
 
 graphviz_output_format = 'svg'
 
-#mathjax_path = "https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
 mathjax_pth = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-MML-AM_CHTM"

proteus/AnalysisTools.py

@@ -1,6 +1,6 @@
 import numpy as np
 from scipy import signal as sn
-from pylab import *
+#from pylab import *
 import collections as cll
 import csv
 from proteus import WaveTools as WT

proteus/Context.py

@@ -6,23 +6,24 @@
 It also alows declaring input options to the user context that can be
 set from the command line.
 
-Example (set the global context from an object):
+Example (set the global context from an object)::
 
-#create a simple context class
-globalSettings = {"nnx":11, "T":10.0, "g"=9.8}
-MyContext = namedtuple("MyContext",globalSettings.keys())
-#set the global  context  object
-proteus.Context.set(MyContext._make(globalSettings.values())
+  #create a simple context class
+  globalSettings = {"nnx":11, "T":10.0, "g"=9.8}
+  MyContext = namedtuple("MyContext",globalSettings.keys())
+  #set the global  context  object
+  proteus.Context.set(MyContext._make(globalSettings.values())
 
-Example (set the global context from a module):
+Example (set the global context from a module)::
 
-import globalSettingsModule
-proteus.Context.setFromModule(globalSettingsModule)
+  import globalSettingsModule
+  proteus.Context.setFromModule(globalSettingsModule)
 
-Example (use the global context):
+Example (use the global context)::
+
+  ct = proteus.Context.get()
+  nnx = ct.nnx
 
-ct = proteus.Context.get()
-nnx = ct.nnx
 """
 from collections import  namedtuple
 from .Profiling import logEvent
@@ -57,16 +58,18 @@ def Options(optionsList=None):
     """Construct an o
     from proteus.LinearAlgebraToptions object (named tuple)
     
-    :param optionsList: An iteratble of options tuples. Each option is a 3-tuple,
-    with the first entry the option name string, the second entry the default value,
-    and the third entry a help string
+    :param optionsList: An iteratble of options tuples. Each option is
+                        a 3-tuple, with the first entry the option
+                        name string, the second entry the default
+                        value, and the third entry a help string
+
+    Example::
 
-    Example:
+      opts=Context.Options([("nnx", 11, "number of mesh nodes in x-direction"),
+                            ("nny", 21, "number of mesh nodes in y-direction"])
+      nnx = opts.nnx
+      nny = opts.nny
 
-    opts=Context.Options([("nnx", 11, "number of mesh nodes in x-direction"),
-                          ("nny", 21, "number of mesh nodes in y-direction"])
-    nnx = opts.nnx
-    nny = opts.nny
     """
     import ast, sys
     global contextOptionsString

proteus/Domain.cpp

@@ -509,7 +509,7 @@ void PiecewiseLinearComplexDomain::writeAsymptote(const char* filename)
 }
 // void PiecewiseLinearComplex::getBoundingBox(vector<double> & v)
 // {}		  
-void PiecewiseLinearComplex::writePoly(const char* filename)
+void PiecewiseLinearComplexDomain::writePoly(const char* filename)
 {
   if(!filename)
     {