compare data output for mcnp.py

.travis.yml

@@ -1,53 +1,41 @@
+sudo: required
 language: python
 python:
   # We don't actually use the Travis Python, but this keeps it organized.
   - "2.7"
-  - "3.4"
+#  - "3.4"
+#  - "3.5"
+services:
+  - docker
 before_install:
-  - sudo apt-get update -qq
-  - sudo apt-get install -y gfortran
+  - sudo docker pull pynedist/pyne-ubuntu
 install:
-  # You may want to periodically update this, although the conda update
-  # conda line below will keep everything up-to-date.  We do this
-  # conditionally because it saves us some downloading if the version is
-  # the same.
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no 
-  - conda config --add channels pyne
-  - conda config --add channels cyclus
-  - conda update -q conda
-  - conda install conda-build jinja2 setuptools binstar patchelf nose
-  # Useful for debugging any issues with conda
-  - conda info -a
-
-  # download CI repo
-  - wget https://github.com/pyne/pyne-ci/archive/master.zip -O pyne-ci.zip
-  - unzip -j pyne-ci.zip "*/pyne/*" -d conda-recipe
-
-  # Replace dep1 dep2 ... with your dependencies
-  #- conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION dep1 dep2 ...
-  #- source activate test-environment
-  - conda build --no-test conda-recipe
-  - conda install pyne --use-local
-
+# copy the git repo being tested into the docker instance
+   - sudo docker run pynedist/pyne-ubuntu /bin/sh -c "cd /root/opt/"
+   - commit_id=$(sudo docker ps -l | tail -n1 | awk '{print $1}')
+   - sudo docker cp ../pyne $commit_id:/root/opt/pyne
+#   - sudo docker run pynedist/pyne-ubuntu /bin/sh -c "cd /root/opt/ ; git clone https://github.com/pyne/pyne"
+   - commit_id=$(sudo docker ps -l | tail -n1 | awk '{print $1}')
+   - sudo docker commit $commit_id pynedist/pyne-ubuntu
+   - sudo docker run pynedist/pyne-ubuntu /bin/sh -c "cd /root/opt/pyne/ ; python setup.py install --user -- -DMOAB_LIBRARY=/root/opt/moab/lib/libMOAB.so -DMOAB_INCLUDE_DIR=/root/opt/moab/include"
+   - commit_id=$(sudo docker ps -l | tail -n1 | awk '{print $1}')
+   - sudo docker commit $commit_id pynedist/pyne-ubuntu
 script:
-  - cd tests
-  #- nosetests
-  - ./travis-run-tests.sh
-
-  # Build the pyne-amalgamation test program 
-  - git clone https://github.com/pyne/pyne-amalgamation.git
-  - cd ..
-  - python amalgamate.py
-  - mv pyne.h pyne.cpp tests/pyne-amalgamation
-  - cd tests
-  - BASE=/home/travis/miniconda make -C pyne-amalgamation
-
-
+   - sudo docker run -e LD_LIBRARY_PATH="/root/.local/lib/" pynedist/pyne-ubuntu /bin/bash -c "cd /root/opt/pyne ; /root/.local/bin/nuc_data_make" 
+   - commit_id=$(sudo docker ps -l | tail -n1 | awk '{print $1}')
+   - sudo docker commit $commit_id pynedist/pyne-ubuntu
+   - sudo docker run -e LD_LIBRARY_PATH="/root/.local/lib/:/root/.local/lib/python2.7/site-packages/PyTAPS-1.4-py2.7-linux-x86_64.egg/:/root/opt/moab/lib" -e PYTHONPATH="/root/.local/lib/python2.7/site-packages/PyTAPS-1.4-py2.7-linux-x86_64.egg/" pynedist/pyne-ubuntu /bin/bash -c "cd /root/opt/pyne/tests ; ./travis-run-tests.sh"
+   - sudo docker run pynedist/pyne-ubuntu /bin/bash -c "cd /root/opt/pyne/tests ; git clone https://github.com/pyne/pyne-amalgamation.git"
+   - commit_id=$(sudo docker ps -l | tail -n1 | awk '{print $1}')
+   - sudo docker commit $commit_id pynedist/pyne-ubuntu
+   - sudo docker run pynedist/pyne-ubuntu /bin/bash -c "cd /root/opt/pyne/ ; python amalgamate.py"
+   - commit_id=$(sudo docker ps -l | tail -n1 | awk '{print $1}')
+   - sudo docker commit $commit_id pynedist/pyne-ubuntu
+   - sudo docker run pynedist/pyne-ubuntu /bin/bash -c "cd /root/opt/pyne/ ; mv pyne.h pyne.cpp tests/pyne-amalgamation"
+   - commit_id=$(sudo docker ps -l | tail -n1 | awk '{print $1}')
+   - sudo docker commit $commit_id pynedist/pyne-ubuntu
+# need to add amalgamate test
+   - sudo docker run -e LIBS="/root/opt/moab/lib:/root/.local/lib" pynedist/pyne-ubuntu /bin/bash -c "cd /root/opt/pyne/tests/pyne-amalgamation ; make BASE=$LIBS all"
+   - commit_id=$(sudo docker ps -l | tail -n1 | awk '{print $1}')
+   - sudo docker commit $commit_id pynedist/pyne-ubuntu
+

amalgamate.py

@@ -29,6 +29,8 @@
     'src/nucname.cpp',
     'src/rxname.h',
     'src/rxname.cpp',
+    'src/_atomic_data.h',
+    'src/_atomic_data.cpp',
     'src/data.h',
     'src/data.cpp',
     #'src/dagmc_bridge.cpp',

cmake/PyneMacros.cmake

@@ -20,22 +20,22 @@ get_filename_component (Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
 
 if (Fortran_COMPILER_NAME MATCHES "gfortran.*")
   # gfortran
-  set (CMAKE_Fortran_FLAGS_RELEASE "-funroll-all-loops -fno-f2c -O3 -c -fpic -fdefault-real-8 -fdefault-double-8")
-  set (CMAKE_Fortran_FLAGS_DEBUG   "-fno-f2c -O0 -g -fdefault-real-8 -fdefault-double-8")
+  set (CMAKE_Fortran_FLAGS_RELEASE "-funroll-all-loops -c -fpic -fdefault-real-8 -fdefault-double-8")
+  set (CMAKE_Fortran_FLAGS_DEBUG   "-c -fpic -fdefault-real-8 -fdefault-double-8")
 elseif (Fortran_COMPILER_NAME MATCHES "ifort.*")
   # ifort (untested)
-  set (CMAKE_Fortran_FLAGS_RELEASE "-f77rtl -O3 -r8")
+  set (CMAKE_Fortran_FLAGS_RELEASE "-f77rtl -O2 -r8")
   set (CMAKE_Fortran_FLAGS_DEBUG   "-f77rtl -O0 -g -r8")
 elseif (Fortran_COMPILER_NAME MATCHES "g77")
   # g77
-  set (CMAKE_Fortran_FLAGS_RELEASE "-funroll-all-loops -fno-f2c -O3 -m32")
+  set (CMAKE_Fortran_FLAGS_RELEASE "-funroll-all-loops -fno-f2c -O2 -m32")
   set (CMAKE_Fortran_FLAGS_DEBUG   "-fno-f2c -O0 -g -m32")
 else (Fortran_COMPILER_NAME MATCHES "gfortran.*")
   message ("CMAKE_Fortran_COMPILER full path: " ${CMAKE_Fortran_COMPILER})
   message ("Fortran compiler: " ${Fortran_COMPILER_NAME})
-  message ("No optimized Fortran compiler flags are known, we just try -O2...")
-  set (CMAKE_Fortran_FLAGS_RELEASE "-O2")
-  set (CMAKE_Fortran_FLAGS_DEBUG   "-O0 -g")
+  message ("No optimized Fortran compiler flags are known, we just try -fpic...")
+  set (CMAKE_Fortran_FLAGS_RELEASE "-fpic")
+  set (CMAKE_Fortran_FLAGS_DEBUG   "-fpic")
 endif (Fortran_COMPILER_NAME MATCHES "gfortran.*")
 
 macro( add_lib_to_pyne _name _source )

docs/devsguide/index.rst

@@ -15,6 +15,7 @@ work builds upon past work well.
     :maxdepth: 1
 
     style_guide
+    new_devs_guide
     testing
     doc
     release

docs/devsguide/index.rst 2

@@ -0,0 +1,34 @@
+.. Github Setup documentation master file, created by
+   sphinx-quickstart on Fri May  1 16:50:13 2015.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Github Setup's documentation!
+========================================
+**Installing Github**
+
+Go to https://help.github.com/articles/set-up-git/ and follow the directions.
+The download should include the latest Github visual interface as well as a 
+Bash shell terminal if your computer does not already have one.
+Note that the visual interface is not needed and any shell can be used.
+
+**Pushing Code and Documentation to Github**
+
+Follow this tutorial: https://help.github.com/articles/pushing-to-a-remote/.
+This tutorial covers how to push changes to local and remote repositories as 
+well as how to fork directories and initiate pull requests.
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

docs/devsguide/new_dev_guide.rst

@@ -0,0 +1,133 @@
+*********************
+New Developer's Guide
+*********************
+=================
+Setting up Github
+=================
+Before you start using GitHub, you have to make Git available on your computer.
+Even if it’s already installed, it’s probably a good idea to update to the 
+latest version. You can either install it as a package or via another installer, 
+or download the source code and compile it yourself.
+
+For download of Git visit `here <http://git-scm.com/downloads>`__
+
+-----------------
+Installing on Mac
+-----------------
+On Mavericks (10.9) or above you can do this simply by trying to run git from 
+the Terminal the very first time. If you don’t have it installed already, it 
+will prompt you to install it. You might be prompted to install command line 
+developer tools if Xcode isn’t installed on your computer. If you want a more up 
+to date version, you can also install it via a binary installer. An OSX Git 
+installer is maintained and available for download at the `Git website 
+<http://git-scm.com/download/mac.>`__.
+
+---------------------
+Installing on Windows
+---------------------
+There are also a few ways to install Git on Windows. The most official build is 
+available for download on the Git `website <http://git-scm.com/download/win>`__ 
+and the download will start automatically. Note that this is a project called 
+Git for Windows (also called msysGit), which is separate from Git itself; for 
+more information on it, go to http://msysgit.github.io/.
+
+-------------------
+Installing on Linux
+-------------------
+If you want to install Git on Linux via a binary installer, you can generally do 
+so through the basic package-management tool that comes with your distribution. 
+If you’re on Fedora for example, you can use yum:
+
+$ sudo yum install git
+
+If you’re on a Debian-based distribution like Ubuntu, try apt-get:
+
+$ sudo apt-get install git
+
+For more options, there are instructions for installing on several different 
+Unix flavors on the Git website, at http://git-scm.com/download/linux.
+
+==================================
+Connecting Github account to Git
+==================================
+More detailed steps go here 
+‘Github<https://help.github.com/categories/bootcamp/>’
+
+#. In your computer's terminal, tell Git your name so your commits will be 
+properly labeled. Type everything after the $ here:
+
+$ git config --global user.name "YOUR NAME"
+
+#. Tell Git the email address that will be associated with your Git commits. The 
+email you specify should be the same one found in your email settings on Github. 
+To keep your email address hidden click 'here 
+<https://help.github.com/articles/keeping-your-email-address-private/>'_ 
+
+$ git config --global user.email "YOUR EMAIL ADDRESS"
+
+==================================
+Installing from Source
+==================================
+NOTE: Might have to install pip, home-brew, and other programs to correctly 
+install.
+      Also, installing PyNE isn’t the same as cloning the repository.
+
+PyNE's `website <http://pyne.io/install/index.html>`__ will lead you through the 
+installation. 
+
+To contribute to the project, 
+
+#. Fork PyNE’s `Github repository <https://github.com/pyne/pyne>`__
+ (Pull requests can be done on Github by comparing original to your forked 
+repository). 
+
+#. On Github, copy the HTTPS(recommended) link on your the page of your forked 
+version that is located on the right side of the page. 
+
+#. To keep things organized, it would be best to make a directory somewhere that 
+is going to keep these files (Use “cd” to navigate to desired location and use 
+“mkdir DESIRED NAME OF FOLDER” to make the directory and then go inside it). 
+Make that directory your working directory and then enter ::
+
+	$ git clone https://github.com/pyne/pyne.git
+
+#. The PyNE files are now ready for your manipulations. Everything seen on the 
+PyNE website is given to you. You can easily contribute by editing the contents 
+of the folders, submitting these changes to your repository, and making a pull 
+request to PyNE through Github’s website (click on the Pull Requests tab on the 
+right side of the GitHub page and then submit a New Pull Request).
+
+==================================
+Signing up for list hosts 
+==================================
+Writing effective code isn’t easy. Thankfully, the PyNE developers can always be 
+contacted on the listhost at [email protected]. Another way to get help 
+is going to https://groups.google.com/forum/#!forum/pyne-users and joining the 
+group to post. 
+
+================
+Getting Practice 
+================
+Novices to open-source projects can get still beneficially contribute to PyNE.  
+To do so, go to PyNE’s ‘GitHub page <https://github.com/pyne/pyne>’ and, on the 
+right hand side of the page, click on Issues. Once on this page, click on the 
+“low hanging pinoli” label to display issues beginners can solve.
+
+.. figure:: lhp.png :width: 700px
+    :align: center
+    :height: 340px
+
+Also, if you were wondering, “low hanging pinoli” is a pine pun for low hanging 
+pine fruit to call newbies. 
+
+==================================
+Adding and Updating Documentation 
+==================================
+To contribute, you can edit the text file in any program that allows you to edit 
+text(Vim,textedit, Nano, etc) and doesn’t invisibly add characters to the 
+file(like Word). The only important part is to write the file in a manner that’s 
+considered reStructuredText (check out http://sphinx-doc.org/rest.html). Then, 
+Sphinx will do everything else under the hood as described `here 
+<http://pyne.io/devsguide/website.html>`__. Finally, commit these changes to 
+your forked version and submit a pull request (through GitHub or the command 
+line). 

docs/devsguide/style_guide.rst

@@ -7,9 +7,9 @@ PyNE is a polyglot project about a technical subject with many independent devel
 and users. To keep our heads on straight we have adopted the following styles and
 conventions.  We use these throughout the code base to ensure consistency.
 
-* `Python Style Guide <style_guide.rst#python-style-guide>`__
-* `Cython Style Guide <style_guide.rst#cython-style-guide>`__
-* `C++ Style Guide <style_guide.rst#cc-style-guide>`__
+* `Python Style Guide <style_guide.html#python-style-guide>`__
+* `Cython Style Guide <style_guide.html#cython-style-guide>`__
+* `C++ Style Guide <style_guide.html#cc-style-guide>`__
 
 ----------------------------------
 Rules to Write By

docs/devsguide/website.rst

@@ -12,6 +12,8 @@ Building the website/documentation requires the following:
    #. `sphinxcontrib-bibtex <https://pypi.python.org/pypi/sphinxcontrib-bibtex/>`_
    #. `PrettyTable <https://code.google.com/p/prettytable/>`_
    #. `Cloud Sphinx Theme <https://pythonhosted.org/cloud_sptheme/cloud_theme.html>`_
+   #. `jupyter <http://jupyter.org/>`_
+
 
 -----------------------------------
 Procedure for modifying the website

docs/install/conda.rst

@@ -14,10 +14,12 @@ option when installing conda.
 --------------------------
 Binary Package (For Users)
 --------------------------
-Binary distributions of the latest release (0.4) of pyne
-can be installed by running the command::
+Binary distributions of the latest release for mac and linux (64-bit) 
+using the conda package manager can be installed by running the command::
 
-    conda install -c https://conda.binstar.org/pyne pyne
+    conda install -c cyclus -c pyne pyne=VERSION
+
+where VERSION should be replaced with the version number to be installed.
 
 A windows 32-bit binary is also available on conda via the same command but
 it is highly experimental and likely broken. Conda binaries do not have 
@@ -43,4 +45,4 @@ cd to the conda-recipes directory and run::
     conda install $(conda build --output pyne)
     nuc_data_make
 
-You should now be able to update the conda package that lives on binstar.
+You should now be able to update the conda package that lives on binstar.

docs/install/linux_source.rst

@@ -28,13 +28,15 @@ Optional Depenendencies:
 Most of the dependencies are readily available through package managers.  Once
 all the dependencies are installed, PyNE can be installed. Download and unzip
 the source (`zip`_, `tar`_) or checkout a verison from the PyNE repository
-(`Github`_).  Then run the following commands from the unzipped directory::
+(`Github`_).  Then run the following commands from the directory above the
+unzipped directory::
 
     cd pyne/
     python setup.py install --user
     scripts/nuc_data_make
 
 The ``setup.py`` command compiles and installs the PyNE source code.
+Note that this command must be done in the top PyNE directory.
 The ``nuc_data_make`` builds and installs a database of nuclear data.
 Unfortunately, this must be done as a second step because most nuclear 
 data is under some form of license restriction or export control which 

docs/install/ubuntu.rst

@@ -4,6 +4,6 @@
 Ubuntu build script
 =================================
 
-A script for installing PyNE and all its dependencies from scratch on Ubuntu
-14.04 - 14.10 is found `here
-<https://github.com/pyne/install_scripts/blob/master/ubuntu_15.04.sh>`_
+Scripts for installing PyNE and all its dependencies from scratch on Ubuntu
+14.04 - 15.04 are found `here
+<https://github.com/pyne/install_scripts/>`_.

docs/sphinxext/notebook_sphinxext.py

@@ -12,11 +12,7 @@
 from docutils.parsers.rst.roles import set_classes
 from docutils.transforms import misc
 
-try:
-    from IPython.nbconver.exporters import html
-except ImportError:
-    from IPython.nbconvert import html
-
+from nbconvert import HTMLExporter
 
 class Notebook(Directive):
     """Use nbconvert to insert a notebook into the environment.
@@ -47,7 +43,7 @@ def run(self):
         nb_path = utils.relative_path(None, nb_path)
 
         # convert notebook to html
-        exporter = html.HTMLExporter(template_file='full')
+        exporter = HTMLExporter(template_file='full')
         output, resources = exporter.from_filename(nb_path)
         header = output.split('<head>', 1)[1].split('</head>',1)[0]
         body = output.split('<body>', 1)[1].split('</body>',1)[0]