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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
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‎.hashdist_default‎

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‎.hashstack_default‎

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‎.shippable-profile.yaml‎

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‎.travis.yml‎

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

‎.travisprofile.yml‎

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‎Dockerfile‎

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

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

‎doc/Makefile‎

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

‎doc/source/_templates/layout.html‎

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

‎doc/source/conf.py‎

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# General information about the project.
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project = u'Proteus'
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copyright = u'2016, The Proteus Team'
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copyright = u'2017, The Proteus Team'
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# The version info for the project you're documenting, acts as replacement for
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#mathjax_path = "https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
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mathjax_pth = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-MML-AM_CHTM"

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