Merge pull request #197 from yardasol/remove-pyne

Remove pyne

.github/workflows/cache-dependencies.yml

@@ -144,5 +144,8 @@ jobs:
           pip install .
           cd ../
 
+      - name: Install SaltProc
+        run: pip install .
+
       - name: Check packages
         run: conda list

.github/workflows/deploy-docs.yml

@@ -23,7 +23,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
             fetch-depth: 0
 
@@ -56,6 +56,9 @@ jobs:
         run: mamba env update -n saltproc-doc-env -f doc/doc-environment.yml
         if: steps.dependencies-cache.outputs.cache-hit != 'true'
 
+      - name: Install SaltProc
+        run: pip install .
+
       - name: Check packages
         run: conda list
 

.github/workflows/test-saltproc.yml

@@ -41,6 +41,7 @@ jobs:
         with:
           miniforge-variant: Mambaforge # mamba is faster than base conda
           miniforge-version: latest
+          channels: conda-forge
           activate-environment: saltproc-env
           use-mamba: true
           use-only-tar-bz2: true

doc/devguide/style.rst

@@ -3,4 +3,7 @@
 Style Guide
 ===========
 
-Coming soon!
+Style for Python code must follow PEP8_.
+
+.. _PEP8: https://www.python.org/dev/peps/pep-0008/
+

doc/devguide/tests.rst

@@ -3,4 +3,16 @@
 Test Suite
 ==========
 
-Coming soon!
+The SaltProc test suite uses the JEFF 3.1.2 library for Serpent2 integration
+tests, and the ENDF/B VII.1 library for OpenMC integration tests. You can
+obtain the JEFF 3.1.2 library by running the `process_j312.bash` script
+under `scripts/xsdata`, and you can obtain the ENDF/B VII.1 library
+for OpenMC from `this`_ link, which you can also find on
+`openmc.org <openmc.org/official-data-libraries/>`_. The test suite
+requires the `pytest`_ package.
+
+.. _this: https://anl.box.com/shared/static/9igk353zpy8fn9ttvtrqgzvw1vtejoz6.xz
+.. _pytest: https://docs.pytest.org
+
+Whenever a new feature or function is added, a test should also be added
+for that feature.

doc/doc-environment.yml

@@ -3,16 +3,16 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - pyne>=0.5.11=nomoab_noopenmc*
+  - numpy
   - openmc
-  - numpy>=1.14.0
   - pytables
   - networkx
-  - pydotplus
+  - pydot
+  - jsonschema
   - sphinx
   - sphinx_rtd_theme
-  - jsonschema
   - pip:
-      - sphinx-multiversion
-      - sphinxcontrib-apidoc
-      - sphinx-jsonschema
+    - serpentTools
+    - sphinx-multiversion
+    - sphinxcontrib-apidoc
+    - sphinx-jsonschema

doc/index.rst

@@ -11,10 +11,10 @@ calculations. It couples directly with depletion-capable transport solvers to en
 calculations.
 
 **SaltProc** welcomes your contributions. It already relies on many libraries
-in the Scientific Python ecosystem including `pyne`_, `numpy`_, `matplotlib`_,
+in the Scientific Python ecosystem including `openmc`_, `numpy`_, `matplotlib`_,
 `networkx`_, and `pydot`_.
 
-.. _pyne: http://pyne.io/
+.. _openmc: http://openmc.org/
 .. _numpy: http://numpy.org
 .. _matplotlib: http://matplotlib.org
 .. _networkx: http://networkx.github.io

doc/installation.rst

@@ -3,24 +3,24 @@ Installation
 
 SaltProc has the following dependencies:
 
-  #. `Python`_ (>=3.5)
-  #. `Serpent`_ (>=2.1.31)
-  #. `PyNE`_ (>=0.5.11)
-  #. `OpenMC`_ (>=0.13.0)
-  #. `NumPy`_ (>=1.14.0)
+  #. `python`_ (>=3.5)
+  #. `serpent`_ (>=2.1.31)
+  #. `serpentTools`_
+  #. `openmc`_ (>=0.13.0)
+  #. `numpy`_ (>=1.14.0)
   #. `PyTables`_
-  #. `NetworkX`_
-  #. `PyDotPlus`_
+  #. `networkx`_
+  #. `pydot`_
   #. `jsonschema`_
 
-.. _Serpent: http://montecarlo.vtt.fi
-.. _PyNE: http://pyne.io
-.. _OpenMC: https://openmc.org/
-.. _Python: http://python.org
-.. _NumPy: http://numpy.org
+.. _serpent: http://montecarlo.vtt.fi
+.. _serpentTools: https://serpent-tools.readthedocs.io/en/master/index.html
+.. _openmc: https://openmc.org/
+.. _python: http://python.org
+.. _numpy: http://numpy.org
 .. _PyTables: http://pytables.org
-.. _NetworkX: http://networkx.github.io
-.. _PyDotPlus: https://pydotplus.readthedocs.io/
+.. _networkx: http://networkx.github.io
+.. _pydot: https://github.com/pydot/pydot
 .. _pytest: https://docs.pytest.org
 .. _pytest documentation: https://docs.pytest.org/en/latest/how-to/usage.html
 .. _sphinx: https://www.sphinx-doc.org
@@ -36,7 +36,6 @@ Optional Dependencies:
   #. `pytest`_ (for testing)
   #. `sphinx`_ and `sphinx-rtd-theme`_ (for building documentation)
   #. `matplotlib`_
-  #. `ViTables`_
 
 
 
@@ -46,18 +45,9 @@ Clone the source from the SaltProc repository from `GitHub`_.
 
    git clone [email protected]:arfc/saltproc.git
 
-Note on installing OpenMC
--------------------------
-The ``conda-forge`` build of OpenMC 0.13.0 cannot be installed alongside the ``conda-forge`` build of PyNE due to a conflict in the pinned HDF5 versions required by those builds. Since both are dependencies, users will need to pick one to install from source. We recommend users install OpenMC from source as it has a more active community and a step-by-step guide on how to install it from source on most machines. For Ubuntu users, consider using the `ubuntu-nuclear-software-installer`_
-script to install OpenMC from source.
-
-.. _ubuntu-nuclear-software-installer: https://github.com/yardasol/ubuntu-nuclear-software-installer
-
-Otherwise, all of the dependencies are readily available through the `conda package manager`_.
-
 .. note:: We recommend using the `mamba`_ CLI tool to install packages quickly. SaltProc has a compltex package dependency structure which can result is long environment solve times in the default ``conda`` solver. ``mamba`` is a reimplementation of ``conda`` in ``C++`` and we have found it is significantly faster.
 
-You can download the required ones using ``conda`` on the provided ``environment.yml``
+You can download the required packages using ``conda`` on the provided ``environment.yml``
 file in the repository:
 
 .. code-block:: bash

doc/io_formats/depcode_input.rst

@@ -366,23 +366,6 @@ OpenMC-specific properties
     ``null``
 
 
-``dilute_initial``
-~~~~~~~~~~~~~~~~~~
-
-  :description:
-    Initial atom density to add for nuclides that are zero in initial
-    condition.
-
-  :type:
-    ``number``
-
-  :minimum:
-    0
-
-  :default:
-    1000
-
-
 ``fission_yield_mode``
 ~~~~~~~~~~~~~~~~~~~~~~
 

doc/io_formats/saltproc_input.rst

@@ -90,6 +90,39 @@ Required properties are as follows: ``proc_input_file``, ``dot_input_file``, ``o
     ``null``
 
 
+.. _rebuild_saltproc_results_property:
+
+``rebuild_saltproc_results``
+---------------------
+
+  :description:
+    Flag to reconstruct the ``saltproc_results.h5`` files from the stepwise
+    depletion simulation results.
+
+
+  :type:
+    ``boolean``
+
+  :default:
+    ``false``
+
+
+.. _run_without_reprocessing_property:
+
+``run_without_reprocessing``
+---------------------
+
+  :description:
+    Flag to run SaltProc with no material reprocessing.
+
+
+  :type:
+    ``boolean``
+
+  :default:
+    ``false``
+
+
 .. _depcode_property:
 
 ``depcode``

doc/overview.rst

@@ -44,7 +44,7 @@ Molten Salt Reactors. It performs following major functions:
 The code logic flow is the following:
 
   1. Runs the transport-depletion code (:meth:`saltproc.depcode.Depcode.run_depcode()`)
-  2. Parses through the output `*_dep.m` file and creates PyNE Material object
+  2. Parses through the output `*_dep.m` file and creates Materialflow object
      for each burnable material.
   3. Processes Fuel (:meth:`saltproc.app.reprocess_materials()` and :meth:`saltproc.app.refill_materials()`):
 

doc/releasenotes/v0.5.0.rst

@@ -15,6 +15,8 @@ Release notes for v0.5.0
 
 
 .. _openmc: https://github.com/openmc-dev/openmc
+.. _serpentTools: https://github.com/CORE-GATECH-GROUP/serpent-tools
+.. _pytables: https://github.com/PyTables/PyTables
 .. _@yardasol: https://github.com/yardasol
 
 
@@ -39,15 +41,15 @@ Dependency Changes
   Describe any new/removed/modified package dependencies
 
 
-- ``SaltProc`` now optionally requires the following package:
+- ``SaltProc`` now requires the following package:
 
   - (new) → `openmc`_
+  - (new) → `serpentTools`_
+  - (formality) → `pytables`_
 
-- ``pyne>=0.5.11`` → ``pyne>=0.5.11=nomoab_noopenmc*``
+- ``pyne>=0.5.11`` →  (removed)
 
-- ``pydotplus`` →  (removed)
-
-- (new) → ``pydot``
+- ``pydotplus`` →  ``pydot``
 
 
 
@@ -210,6 +212,10 @@ Python API Changes
     - (new) → ``timestep_units``
     - (new) → ``timestep_type``
 
+  - (new) → ``Results`` 
+
+    - New class for reading the `saltproc_results.h5` file
+
   - ``Simulation``
 
     -  ``core_number`` →  (removed)
@@ -250,4 +256,10 @@ The following people reviewed code for this release of SaltProc:
 ..
   `@gh_username <https://github.com/gh_uname>`_
 
+- `@smpark7 <https://github.com/smpark7>`_
+- `@LukeSeifert <https://github.com/LukeSeifert>`_
+- `@munkm <https://github.com/munkm>`_
+- `@abachma2 <https://github.com/abachma2>`_
+
+
 

environment.yml

@@ -3,12 +3,12 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - pyne>=0.5.11=nomoab_noopenmc*
-  - numpy>=1.14.0
+  - numpy
   - pytables
   - networkx
   - pydot
   - pytest
   - jsonschema
   - pip:
+    - serpentTools
     - argparse==1.4.0