Completely refactored and changed after latest Teddy's release (0.2.0)

.cache/v/cache/lastfailed

@@ -0,0 +1 @@
+{}

.gitignore

@@ -1,6 +1,10 @@
 *.pyc
 *~
 *.DS_Store
+*.h5
 _build/
 auto_examples/
 gen_api/
+saltproc.egg-info/
+.ipynb_checkpoints/
+saltproc/data/saltproc_*

.travis.yml

@@ -1,8 +1,11 @@
 language: python
 python:
-  - 2.7
-  - 3.6
-
+  - 3.5
+branches:
+  only:
+    - develop
+    - master
+
 # Setup anaconda
 install:
   - sudo apt-get install libhdf5-serial-dev
@@ -14,22 +17,22 @@ install:
   - sudo apt-get install liblapack-dev
   - sudo apt-get install git
   - sudo apt-get update
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
-  # Useful for debugging any issues with conda
+  - conda create -n pyne-env python=3.5
+  - conda init bash
+  - eval "$(conda shell.bash hook)"
+  - conda activate pyne-env
   - conda info -a
-  - conda install -c anaconda h5py
   - conda install -c conda-forge pyne
   - conda install -c anaconda pytest
+  - conda install -c conda-forge networkx
+  - conda install -c conda-forge pydotplus
 
 # run
 script:
-  - pytest ./saltproc/tests/saltproc_test.py
+  - pytest --ignore saltproc/tests/integration_tests saltproc -vv

CITATION.md

@@ -0,0 +1,63 @@
+## Citations
+
+The information below should help you to properly cite SaltProc where
+appropriate. Up-to-date citations will be added as they are produced.
+
+### Software Citation
+
+If you use the SaltProc software, we ask that you cite the version of SaltProc
+that you used:
+
+
+#### Version 0.2
+```tex
+
+@article{rykhlevskii_saltproc_2018,
+author = "Andrei Rykhlevskii, Jin Whan Bae, Kathryn Huff",
+title = "{arfc/saltproc: Code for online reprocessing simulation of molten salt
+reactor with external depletion solver SERPENT}",
+year = "2018",
+month = "7",
+publisher = "zenodo",
+url = "http://dx.doi.org/10.5281/zenodo.1306628	"
+}
+```
+
+If you use any of our published results or methods, please also cite the
+relevant paper(s) below.  
+
+
+### Method and Results Citations
+
+   The Molten Salt Breeder Reactor (MSBR) results should be cited :
+
+```tex
+@article{rykhlevskii_modeling_2019,
+	title = {Modeling and simulation of online reprocessing in the thorium-fueled molten salt breeder reactor},
+	volume = {128},
+	issn = {0306-4549},
+	url = {"http://dx.doi.org/10.1016/j.anucene.2019.01.030"},
+	journal = {Annals of Nuclear Energy},
+	author = {Rykhlevskii, Andrei and Bae, Jin Whan and Huff, Kathryn D.},
+	month = jun,
+	year = {2019},
+	pages = {366--379}
+}
+```
+
+   Transatomic Power MSR results should be cited :
+
+```tex
+@techreport{rykhlevskii_milestone_2019,
+	address = {Urbana, IL},
+	type = {Milestone {Report}},
+	title = {Milestone 2.1 {Report}: {Demonstration} of {SaltProc}},
+	url = {"http://dx.doi.org/10.5281/zenodo.3355649"},
+	institution = {University of Illinois at Urbana-Champaign},
+	author = {Rykhlevskii, Andrei and Huff, Kathryn},
+	month = jun,
+	year = {2019},
+	doi = {10.5281/zenodo.3355649},
+	pages = {1--23}
+}
+```

CONTRIBUTING.md

@@ -0,0 +1,90 @@
+### Thanks for Your Help!
+
+Contributing is so kind of you. In SaltProc, all contributions, bug reports,
+bug fixes, documentation improvements, enhancements and ideas are welcome.
+
+The [GitHub "issues" tab](https://github.com/arfc/saltproc/issues)
+contains some issues labeled "Difficulty:1-Beginner". Those are open issues
+that would be a good quick way to get started. Browse them to see if you want
+to get started on one.
+
+#### Bug Reports
+
+  - Please include a short but detailed, self-contained Python snippet or
+    explanation for reproducing the problem.
+
+  - Explain what the expected behavior was, and what you saw instead.
+
+##### Instructions for setting up a development environment
+
+The SaltProc is compatible with Python >=3.5. Anaconda is the recommended
+distribution to use to work on SAltProc; we will assume that if you want to use
+another distribution or your own set up, you can translate the instructions.
+
+You can download Anaconda at https://www.continuum.io/Downloads for the full
+install. You can also download a mini Anaconda install for a bare-bones
+install -- this is good for a build server or if you don't have much space.
+The mini Anaconda installs are available at https://conda.io/miniconda.html.
+
+Once your Anaconda package is installed and available, create a Python 3.6
+environment in Anaconda --
+
+- conda create -q -n saltproc-test-environment python=3.6 scipy numpy matplotlib pytest pytables flake8
+
+Each of these commands will take a bit of time -- give it a few minutes
+to download and install the packages and their dependences. Once complete,
+switch to each and install additional packages needed to run and test.
+
+Activate the 3.6 environment and install pyne, networkx and pydotplus
+
+ - source activate saltproc-test-environment
+ - conda install -c conda-forge pyne networkx pydotplus
+
+##### Setup Serpent Monte Carlo code environment
+
+The SaltProc assumes that Serpent directory is added in ``$PATH`` as follows:
+
+  - export PATH="/path/to/serpent/executable:$PATH"
+
+##### Run the tests
+
+Tests are automatically detected and run with pytest. Start in the root
+directory where you have cloned the saltproc repository and run in development
+environment
+
+ - source active saltproc-test-environment
+ - py.test saltproc
+
+##### Run style tests with flake8
+
+Adherance to style checks in flake8 is encouraged though not strictly
+enforced. While you should not feel compelled to fix existing failures,
+please do not add additional flake8 issues.
+
+  - run flake8 from the root of the pyrk working directory to get all flake8 issues
+  - run flake8 and provide a filename to just run checks on that file
+
+##### Pull Requests
+
+  - **Make sure the test suite passes** on your computer. To do so, run
+    `py.test saltproc` in the repository directory.
+  - Please reference relevant Github issues in your commit message using
+    `GH1234` or `#1234`.
+  - Changes should be PEP8 compatible [PEP8](http://www.python.org/dev/peps/pep-0008/).
+  - Keep style fixes to a separate commit to make your PR more readable.
+  - Docstrings ideally follow the [sphinx autodoc](https://pythonhosted.org/an_example_pypi_project/sphinx.html#function-definitions)
+  - Write tests.
+  - When writing tests, please make sure they are in a `tests` directory.
+  - When you start working on a PR, start by creating a new branch pointing at the latest
+    commit on github master.
+  - The SaltProc copyright policy is detailed in the
+    [LICENSE](https://github.com/arfc/saltproc/blob/master/LICENSE).
+
+#### More developer docs
+
+* We are working on it.
+
+
+#### Meta
+Note, this contributing file was adapted from the one at the
+[pandas](https://github.com/pydata/pandas) repo. Thanks pandas!