Merge branch 'master' of https://github.com/BhallaLab/moose

.gitignore

+*.png
+*.*~
+*~
+*.html
+/moose

.travis.yml

-language: cpp
+sudo : required
+dist : trusty
+group : edge
+
 compiler:
     - gcc
     - clang
 os:
     - linux
     - osx
-matrix:
-    allow_failures:
-        - os: osx
+
 branches:
     only:
         - master
@@ -17,38 +18,18 @@ notifications:
             - dilawar.s.rajput@gmail.com
             - bhalla@ncbs.res.in
             - hrani@ncbs.res.in
-            - ray.subhasis@gmail.com
 
         on_success: change
         on_failure: always
 
 env:
     - CTEST_MODEL=Nightly
-cache: apt
+
 before_script:
-    - sudo apt-get update -qq
-    - sudo apt-get install libxml2-dev libbz2-dev wget
-    - sudo apt-get install libhdf5-serial-dev
-    - sudo apt-get install python-numpy python-setuptools python-networkx python-pip
-    - sudo apt-get install cmake cdbs
-    - sudo apt-get install python-suds python-matplotlib python-nose
-    - sudo apt-get install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev libopenscenegraph-dev
-    - sudo apt-get install doxygen python-sphinx
-    - sudo apt-get install git-buildpackage
+    - if [ "$TRAVIS_OS_NAME" == "linux" ]; then ./_travis/prepare_linux.sh ; fi
+    - if [ "$TRAVIS_OS_NAME" == "osx" ]; then ./_travis/prepare_osx.sh ; fi
 
-install:
-    - wget http://ftp.debian.org/debian/pool/main/g/gsl/libgsl0ldbl_1.16+dfsg-2_amd64.deb -O gsl_1.16.deb
-    - sudo dpkg -i gsl_1.16.deb
-    - wget http://ftp.debian.org/debian/pool/main/g/gsl/libgsl0-dev_1.16+dfsg-2_amd64.deb -O gsl_1.16-dev.deb
-    - sudo dpkg -i gsl_1.16-dev.deb
-    - sudo apt-get install -f
-    - sudo ldconfig /usr/lib64
 
 script:
-    - git buildpackage  --git-ignore-new -uc -us
-    - sudo dpkg -i ../moose*.deb
-
-after_success:
-    - python -c 'import moose'
-    - python -c 'import moogli'
-    - cd __moose-core_build && ctest --output-on-failure
+    - if [ "$TRAVIS_OS_NAME" == "linux" ]; then ./_travis/build_on_linux.sh ; fi
+    - if [ "$TRAVIS_OS_NAME" == "osx" ]; then ./_travis/build_on_osx.sh ; fi

CMakeLists.txt

@@ -32,7 +32,7 @@ file(MAKE_DIRECTORY ${PYMOOSE_BUILD_DIR})
 # different platform.
 set(OUTPUT_MOOSEBIN ${PYMOOSE_BUILD_DIR}/moose.bin)
 
-configure_file( ${CMAKE_SOURCE_DIR}/build_moose-core.sh.in 
+configure_file( ${CMAKE_SOURCE_DIR}/cmake/build_moose-core.sh.in 
     ${CMAKE_BINARY_DIR}/build_moose-core.sh )
 
 # Build pymoose module.

_travis/build_on_linux.sh

+#!/bin/bash -
+#===============================================================================
+#
+#          FILE: build_on_travis.sh
+#
+#         USAGE: ./build_on_travis.sh
+#
+#   DESCRIPTION: 
+#
+#       OPTIONS: ---
+#  REQUIREMENTS: ---
+#          BUGS: ---
+#         NOTES: ---
+#        AUTHOR: Dilawar Singh (), dilawars@ncbs.res.in
+#  ORGANIZATION: NCBS Bangalore
+#       CREATED: Tuesday 27 June 2017 01:55:11  IST
+#      REVISION:  ---
+#===============================================================================
+
+set -o nounset                              # Treat unset variables as an error
+set -e
+
+(
+    gbp buildpackage  --git-ignore-branch --git-ignore-new -uc -us
+    cd __moose-core_build && ctest --output-on-failure && cd ..
+    sudo dpkg -D=2 -i ../moose*.deb
+    cd ~ && /usr/bin/python -c \
+        "import moose; print moose.version(); print( moose.__file__ ); moose.test( timeout = 10 )"
+)

_travis/build_on_osx.sh

+#!/bin/bash -
+#===============================================================================
+#
+#          FILE: build_on_osx.sh
+#
+#         USAGE: ./build_on_osx.sh
+#
+#   DESCRIPTION: 
+#
+#       OPTIONS: ---
+#  REQUIREMENTS: ---
+#          BUGS: ---
+#         NOTES: ---
+#        AUTHOR: Dilawar Singh (), dilawars@ncbs.res.in
+#  ORGANIZATION: NCBS Bangalore
+#       CREATED: Tuesday 27 June 2017 01:55:11  IST
+#      REVISION:  ---
+#===============================================================================
+
+set -o nounset                              # Treat unset variables as an error
+set -e
+(
+    brew audit --strict --online moose.rb
+    brew install -V --build-from-source moose.rb
+)

_travis/moose.rb

+class Moose < Formula
+  include Language::Python::Virtualenv
+
+  desc "Multiscale Object Oriented Simulation Environment"
+  homepage "http://moose.ncbs.res.in"
+  url "https://github.com/BhallaLab/moose-core/archive/3.1.2.tar.gz"
+  sha256 "a542983e4903b2b51c79f25f4acc372555cbe31bc0b9827302a6430fad466ef7"
+  head "https://github.com/BhallaLab/moose-core.git"
+
+  bottle do
+    cellar :any
+    sha256 "6077f886560480c956270f855cf9576a3e8261c5f2ea064117c3483f74a84462" => :sierra
+    sha256 "a637de34ce0b92f16afc120ecb2e0e4aff8f8a2e6a2ada5521ee01cf7ccdca9e" => :el_capitan
+    sha256 "1bb0712ef178577a3c44190be8f21f894cddc66ce03f742d768e44371425dce7" => :yosemite
+    sha256 "a62366e1e1de37c13dec6d2b7f91dc63f8b40ab460e35b31a4d94507a0df6219" => :x86_64_linux
+  end
+
+  depends_on "cmake" => :build
+  depends_on "gsl"
+  depends_on "hdf5"
+  depends_on :python if MacOS.version <= :snow_leopard
+  depends_on "numpy"
+
+  def install
+    (buildpath/"VERSION").write("#{version}\n")
+    # FindHDF5.cmake needs a little help
+    ENV.prepend "LDFLAGS", "-lhdf5 -lhdf5_hl"
+
+    args = std_cmake_args
+    args << "-DCMAKE_SKIP_RPATH=ON"
+    mkdir "_build" do
+      system "cmake", "..", "-DPYTHON_EXECUTABLE:FILEPATH=#{which("python")}", *args
+      system "make"
+      system "ctest", "--output-on-failure"
+    end
+
+    Dir.chdir("_build/python") do
+      system "python", *Language::Python.setup_install_args(prefix)
+    end
+  end
+
+  def caveats; <<-EOS.undent
+    You need to install `networkx` and `python-libsbml` using python-pip. Open terminal
+    and execute following command:
+      $ pip install python-libsbml networkx
+    EOS
+  end
+
+  test do
+    system "python", "-c", "import moose"
+  end
+end

_travis/prepare_linux.sh

+#!/usr/bin/env bash
+
+sudo apt-get update -qq
+sudo apt-get install libxml2-dev libbz2-dev wget
+sudo apt-get install libhdf5-serial-dev
+sudo apt-get install python-numpy python-setuptools python-networkx python-pip
+sudo apt-get install cmake cdbs
+sudo apt-get install python-suds python-matplotlib python-nose python-lxml
+sudo apt-get install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev libopenscenegraph-dev
+sudo apt-get install libgsl0-dev
+sudo apt-get install doxygen python-sphinx 
+sudo apt-get install git-buildpackage 
+sudo apt-get install -f

_travis/prepare_osx.sh

+#!/bin/bash -
+#===============================================================================
+#
+#          FILE: prepare_osx.sh
+#
+#         USAGE: ./prepare_osx.sh
+#
+#   DESCRIPTION: 
+#
+#       OPTIONS: ---
+#  REQUIREMENTS: ---
+#          BUGS: ---
+#         NOTES: ---
+#        AUTHOR: Dilawar Singh (), dilawars@ncbs.res.in
+#  ORGANIZATION: NCBS Bangalore
+#       CREATED: Wednesday 28 June 2017 10:23:28  IST
+#      REVISION:  ---
+#===============================================================================
+
+set -o nounset                              # Treat unset variables as an error
+echo "Nothing to do here. The moose.rb formula will install all dependecnies"

cmake/build_moose-core.sh.in

+#!/bin/bash
+set -x 
+set -e
+
+# NOTICE: This file is parsed by cmake to create a shell script. Not all syntax
+# will play well with cmake. CMAKE replaces @FOO@ and ${FOO} with cmake variable
+# values.
+
+if [ -z "$MAKE" ]; then
+    MAKE=make
+fi
+
+echo "Building MOOSE"
+(
+    export GSL_ROOT_DIR=@GSL_ROOT_DIR@
+    export HDF5_ROOT=@HDF5_ROOT@
+    cd @PYMOOSE_BUILD_DIR@
+    cmake -DCMAKE_INSTALL_PREFIX=@PYMOOSE_INSTALL_DIR@ \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DWITH_BOOST=@WITH_BOOST@ \
+        -DPYTHON_EXECUTABLE=@PYTHON_EXECUTABLE@ \
+        @CMAKE_PYMOOSE_ARGS@ \
+        @PYMOOSE_SOURCE_DIR@ 
+    $MAKE
+    ctest -output-on-failure || echo "Some tests failed"
+    $MAKE install
+)
+

cmake/moose.in

 #!/usr/bin/env bash
 
 (
-    cd @CMAKE_INSTALL_PREFIX@/lib/moose && python mgui.py & 
+    cd @CMAKE_INSTALL_PREFIX@/lib/moose/gui && python mgui.py & 
 )

debian/changelog

+moose (3.1.2ubuntu1) UNRELEASED; urgency=medium
+
+  * Nightly build of chamcham (3.1.x) series. 
+
+ -- Dilawar Singh <dilawars@Gulgula>  Mon, 08 May 2017 13:40:08 +0530
+
 moose (3.0.2) unstable; urgency=low
 
   * Initial release 
@@ -6,4 +12,4 @@ moose (3.0.2) unstable; urgency=low
   * 3.0.2 relase.
   * Just packed with SBML and GSL-1.6 support.
 
- -- Dilawar <dilawars@ncbs.res.in>  Sun, 05 July 2015 13:41:58 +0530
+ -- Dilawar Singh <dilawars@ncbs.res.in>  Sun, 05 Jul 2015 13:41:58 +0530

debian/control

@@ -8,9 +8,7 @@ Homepage: http://moose.ncbs.res.in
 
 Package: moose
 Architecture: any
-Depends: ${shlibs:Depends}, ${python:Depends}, python-numpy-abi9, libhdf5-7 | libhdf5-serial-1.8.4, python-lxml, python-numpy, python-matplotlib, python-nose, python-networkx, python-suds, python-qt4, libgsl0ldbl
-Replaces:  moose-python, moose-gui
-Conflicts:  moose-python, moose-gui
+Depends: ${shlibs:Depends},python-numpy-abi9, libhdf5-7 | libhdf5-serial-1.8.4, python-lxml, python-numpy, python-matplotlib, python-networkx, python-qt4, libgsl0ldbl
 Description: the Multiscale Object-Oriented Simulation Environment
  It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology.
  .

debian/rules

@@ -5,11 +5,11 @@
 ## Here goes the debian make.
 
 %:
-	dh "$@" --with python2
+	dh "$@" 
 
+# Override clean target.
 override_dh_auto_clean:
 	rm -rf $(BUILD_DIR_MOOSE)
-	dh_auto_clean --buildsystem=cmake
 
 # consider using -DUSE_VERSIONED_DIR=ON if backporting
 override_dh_auto_configure:

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = MOOSE
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file

docs/README.txt

-This is the MOOSE documentation directory. The documentation is grouped into
-the following directories:
+The source code of documentation is /source directory.
 
-    - user: This is for anyone wishing to learn/use MOOSE.
-            This part of the documentation is encoded in Markdown format.
-    - developer: If you wish to learn about MOOSE code, go here.
-    - doxygen: Source code documentation generation.
-    - markdown: This contains a quick introduction to Markdown itself.
-    - images: These are images that are included in the user and developer
-              documentation.
+This directory contains MOOSE user documentation in reST format that can be
+compiled into various formats by sphinx. To build the documentation in HTML,
+format  enter the command:
 
---------------------------------------------------------------------------------
-N.B.: This text file has Windows-style line endings (CR/LF) for easy
-viewing in Windows. We will try to keep the other text files here
-Windows-compatible (e.g.: *.markdown files), but we may slip.
-If you have difficulty viewing them in Notepad, try the inbuilt Wordpad
-editor, or better still, download a good text editor like Notepad++ or Geany.
---------------------------------------------------------------------------------
+	make html
+
+in this directory. Then you can open build/html/index.html in browser to
+browse the generated documentation.
+
+Other files in /source folder
+    - conf.py: the Sphinx configuration file.
+    - index.rst: This is the index file for use when building the Python
+            docs using sphinx.

docs/doxygen/Doxyfile

@@ -323,7 +323,7 @@ CPP_CLI_SUPPORT        = NO
 # of private inheritance when no explicit protection keyword is present.
 # The default value is: NO.
 
-SIP_SUPPORT            = YES
+SIP_SUPPORT            = NO
 
 # For Microsoft's IDL there are propget and propput attributes to indicate
 # getter and setter methods for a property. Setting this option to YES will make

docs/generate-documentation

-#!/bin/bash
-
-echo "###############################################################"
-echo "# Generating C++ Documentation                                #"
-echo "###############################################################"
-#Files will be created in cpp/html with in `doxygen` folder
-( 
-    cd doxygen
-    doxygen Doxyfile
-)
-
-echo "##############################################################"
-echo "# Generating Python Documentation                            #"
-echo "##############################################################"
-#Files will be created in _build/html 
-mkdir -p _build
-sphinx-build . _build
-

docs/index.rst

-.. MOOSE documentation master file, created by
-   sphinx-quickstart on Tue Jul  1 19:05:47 2014.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-the Multiscale Object-Oriented Simulation Environment
-=====================================================
-
-What is MOOSE and what is it good for?
---------------------------------------
-
-MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed
-to simulate neural systems ranging from subcellular components and biochemical
-reactions to complex models of single neurons, circuits, and large networks.
-MOOSE can operate at many levels of detail, from stochastic chemical
-computations, to multicompartment single-neuron models, to spiking neuron
-network models.
-
-.. figure:: ./images/Gallery_Moose_Multiscale.png
-   :alt: **multiple scales in moose**
-   :scale: 50%
-
-   *Multiple scales can be modelled and simulated in MOOSE*
-
-MOOSE is multiscale: It can do all these calculations together. One of its major
-uses is to make biologically detailed models that combine electrical and
-chemical signaling.
-
-MOOSE is object-oriented. Biological concepts are mapped into classes, and a
-model is built by creating instances of these classes and connecting them by
-messages. MOOSE also has numerical classes whose job is to take over difficult
-computations in a certain domain, and do them fast. There are such solver
-classes for stochastic and deterministic chemistry, for diffusion, and for
-multicompartment neuronal models.
-
-MOOSE is a simulation environment, not just a numerical engine: It provides data
-representations and solvers (of course!), but also a scripting interface with
-Python, graphical displays with Matplotlib, PyQt, and OpenGL, and support for
-many model formats. These include SBML, NeuroML, GENESIS kkit and cell.p
-formats, HDF5 and NSDF for data writing.
-
-Contents:
-
-.. toctree::
-   :maxdepth: 2
-
-   introduction/index
-   user/py/quickstart/index
-   user/py/rdesigneur/index
-   user/py/cookbook/index
-   user/py/builtins/index
-   user/py/classes/index
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

docs/introduction/index.rst

-Introduction
-============
-
-.. toctree::
-
-   install/index
-   release_notes/index
-   changes/index
-   known_issues/index
-