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diff --git a/master/.doctrees/src/saltproc.version.doctree b/master/.doctrees/src/saltproc.version.doctree index 404e02831..1eb8c8b51 100644 Binary files a/master/.doctrees/src/saltproc.version.doctree and b/master/.doctrees/src/saltproc.version.doctree differ diff --git a/master/_modules/index.html b/master/_modules/index.html index 527ee1a71..af3f2eb13 100644 --- a/master/_modules/index.html +++ b/master/_modules/index.html @@ -3,7 +3,7 @@ - Overview: module code — Saltproc 0.3.1.dev documentation + Overview: module code — Saltproc 0.4.dev documentation + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Contributing

+
+

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 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

+

Is something in the code not working? Consider making a bug report! In particular:

+
    +

  • 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.

    • +
+
+
+

Feature Requests

+

If you have an idea that could add to or improve SaltProc, and know how to implement it, consider making a Feature Request!

+
+
+

Discussion

+

If you

+
    +

  • have feedback or a feature idea that aren’t concrete/focused enough to go into a Feature Request Issue

    • +

  • want to show off cool work you have done with the software

    • +
+

please use our Discussions page!

+
+

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

+

Please use the provided pull request template. In particular:

+
    +

  • Make sure the test suite passes on your computer. To do so, run py.test saltproc in the repository directory. At a minumum, you must run the tests requring serpent locally as they are not tested by our CI

    • +

  • Describe your feature/change/fix in the release notes (located in doc/releasenotes) for the currently in-development release version. Use the descriptive comments and examples as reference.

    • +

  • Please reference relevant Github issues in your commit message using GH1234 or #1234.

    • +

  • Changes should be PEP8 compatible PEP8.

    • +

  • Keep style fixes to a separate commit to make your PR more readable.

    • +

  • Docstrings ideally follow the sphinx autodoc

    • +

  • 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.

    • +
+
+
+
+

More developer docs

+
    +

  • We are working on it.

    • +
+
+
+

Meta

+

Note, this contributing file was adapted from the one at the pandas repo. Thanks pandas!

+
+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: master + + +
+
+
Tags
+
v0.3.0
+
v0.4.0
+
+
+
Branches
+
master
+
+
+
+ + + \ No newline at end of file diff --git a/master/devguide/index.html b/master/devguide/index.html new file mode 100644 index 000000000..4af45ac71 --- /dev/null +++ b/master/devguide/index.html @@ -0,0 +1,150 @@ + + + + + + + Developer’s Guide — Saltproc 0.4.dev documentation + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Developer’s Guide

+

Welcome to the SaltProc developer’s guide. Here you’ll find +all the information you need to be an efficient and effective contributor +to SaltProc.

+
+

Note

+

The SaltProc developer’s guide is a work in progress. +Information contained within may change, so make sure to check the +release notes for updates!

+
+

If you’re new to software development, please familiarize yourself with the +git workflow before getting started. We’ll be using terminoigy +in this developer’s guide that relies on understanding it.

+
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: master + + +
+
+
Tags
+
v0.3.0
+
v0.4.0
+
+
+
Branches
+
master
+
+
+
+ + + \ No newline at end of file diff --git a/master/examples.html b/master/examples.html index a17dcf8ca..29bf057b0 100644 --- a/master/examples.html +++ b/master/examples.html @@ -4,7 +4,7 @@ - Examples — Saltproc 0.3.1.dev documentation + Examples — Saltproc 0.4.dev documentation + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Release Notes

+
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: master + + +
+
+
Tags
+
v0.3.0
+
v0.4.0
+
+
+
Branches
+
master
+
+
+
+ + + \ No newline at end of file diff --git a/master/releasenotes/template.html b/master/releasenotes/template.html new file mode 100644 index 000000000..de5e27527 --- /dev/null +++ b/master/releasenotes/template.html @@ -0,0 +1,155 @@ + + + + + + + Release notes for vx.x.x — Saltproc 0.4.dev documentation + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Release notes for vx.x.x

+
+

Note

+

These release notes are currently in production.

+
+
+

Summary

+
+
+

Dependency Changes

+
+
+

New Features

+
+
+

Bug Fixes

+
+
+

Script Changes

+
+
+

Python API Changes

+
+
+

Contributors

+

The following people contributed code to this release of SaltProc:

+
+
+

Reviewers

+

The following people reviewed code for this release of SaltProc:

+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: master + + +
+
+
Tags
+
v0.3.0
+
v0.4.0
+
+
+
Branches
+
master
+
+
+
+ + + \ No newline at end of file diff --git a/master/releasenotes/v0.3.0.html b/master/releasenotes/v0.3.0.html new file mode 100644 index 000000000..41c564ce2 --- /dev/null +++ b/master/releasenotes/v0.3.0.html @@ -0,0 +1,196 @@ + + + + + + + Release notes for v0.3.0 — Saltproc 0.4.dev documentation + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Release notes for v0.3.0

+

This release of SaltProc adds several new features, including a refactor of depcode, updated documentation, and installation guides. Make sure you apply this bug fix in your Serpent2 code if you haven’t already.

+
+

New Features

+
    +

  • Complete refactor of the code into object-oriented python.

    • +

  • Adds a Sparging system package – contained in the sparger and separator modules – that calculates removal efficiencies for various target isotopes (i.e. Xe, Kr, H).

    • +

  • Adds a script for creating a Serpent2 compatible cross section library

    • +

  • Refactors the depcode module by making Depcode a purley abstract class; add the DepcodeSerpent class which is an instance of Depcode

    • +
+
+
+

Bug Fixes

+ +
+
+

Commit list

+ +
+
+

Contributors

+
    +

  • @yardasol

    • +

  • @mehmeturkmen

    • +

  • @andrewryh

    • +

  • @jbae11

    • +
+

Full Changelog: https://github.com/arfc/saltproc/compare/v0.2.0…v0.3.0

+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: master + + +
+
+
Tags
+
v0.3.0
+
v0.4.0
+
+
+
Branches
+
master
+
+
+
+ + + \ No newline at end of file diff --git a/master/releasenotes/v0.4.0.html b/master/releasenotes/v0.4.0.html new file mode 100644 index 000000000..2e4b4f82b --- /dev/null +++ b/master/releasenotes/v0.4.0.html @@ -0,0 +1,293 @@ + + + + + + + Release notes for v0.4.0 — Saltproc 0.4.dev documentation + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Release notes for v0.4.0

+
+

Note

+

These release notes are currently in production.

+
+
+

Summary

+

This version of SaltProc refactors the code in preparation for supporting OpenMC.

+
+
+

Dependency Changes

+
    +

  • Saltproc now requires the following packages

    + +
    • +
+
+
+

New Features

+ +
+
+

Bug Fixes

+ +
+
+

Script Changes

+
    +

  • The following scripts have been renamed:

    +
      +

    • process_j312.sh → process_j312.bash

      • +
    +
    • +
+
+
+

Python API Changes

+
    +

  • New tests for previously untested functions in simulation.py:

    +
      +

    • test_check_switch_geo_trigger

      • +

    • test_store_after_repr

      • +

    • test_store_mat_data

      • +

    • test_store_run_init_info

      • +

    • test_store_run_step_info

      • +
    +
    • +

  • The following class methods have been added/(re)moved:

    +
      +

    • App.check_restart() → Simulation.check_restart()

      • +

    • Simulation.switch_to_next_geometry → DepcodeSerpent.switch_to_next_geometry

      • +

    • Simulation.runsim_no_reproc → test/integration_tests/test_no_reproc_run.py::runsim_no_reproc

      • +

    • Simulation.store_run_step_info

      • +

    • Simulation.store_run_init_info

      • +

    • (new) → Depcode.switch_to_next_geometry

      • +

    • (new) → Depcode.read_depcode_info

      • +

    • (new) → Depcode.read_repcode_step_param

      • +

    • DepcodeSerpent.sss_meta_zzz → DepcodeSerpent.convert_nuclide_name_serpent_to_zam

      • +

    • DepcodeSerpent.get_tra_or_dec → DepcodeSerpent.create_nuclide_name_map_zam_to_serpent

      • +

    • DepcodeSerpent.read_depcode_template → DepcodeSerpent.read_plaintext_file

      • +
    +
    • +

  • Updated input file structure:

    +
      +

    • App.depcode_inp dictionary

      +
        +

      • (new) → App.depcode_inp['codename']

        • +

      • App.exec_path

        • +

      • App.template_file

        • +

      • App.neutron_pop → App.depcode_inp['npop']

        • +

      • App.active_cycles

        • +

      • App.inactive_cycles

        • +

      • App.geo_file → App.depcode_inp['geo_file_paths']

        • +
      +
      • +

    • App.simulation_inp dictionary:

      +
        +

      • (new) → App.simulation['sim_name']

        • +

      • App.db_file → App.simulation['db_name']

        • +

      • App.restart_flag

        • +

      • App.adjust_geo

        • +
      +
      • +

    • App.reactor_inp dictionary

      +
        +

      • (new) → App.reactor_inp['volume']

        • +

      • (new) → App.reactor_inp['mass_flowrate']

        • +

      • App.power_levels

        • +

      • App.depl_hist → App.reactor_inp['dep_step_length_cumulative']

        • +
      +
      • +
    +
    • +

  • The following class attributes have been added/(re)moved:

    +
      +

    • Depcode class:

      +
        +

      • template_path → template_inputfile_path

        • +

      • input_path → iter_inputfile

        • +

      • geo_file → geo_files

        • +
      +
      • +

    • Simulation class:

      +
        +

      • h5_file → db_path

        • +

      • (new) → restart_flag

        • +

      • (new) → adjust_geo

        • +

      • iter_matfile → (removed)

        • +
      +
      • +
    +
    • +

  • The signatures for the following class methods have changed to better make use of object data encapsulation:

    +
      +

    • Depcode.read_dep_comp

      • +

    • Depcode.write_depcode_input

      • +

    • Depcode.write_mat_file

      • +

    • DepcodeSerpent.read_depcode_template

      • +

    • DepcodeSerpent.create_nuclide_map_serpent_to_zam

      • +
    +
    • +
+
+
+

Contributors

+

The following people contributed code to this release of SaltProc:

+ +
+
+

Reviewers

+

The following people reviewed code for this release of SaltProc:

+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: master + + +
+
+
Tags
+
v0.3.0
+
v0.4.0
+
+
+
Branches
+
master
+
+
+
+ + + \ No newline at end of file diff --git a/master/search.html b/master/search.html index 47c8a573e..df58fe49a 100644 --- a/master/search.html +++ b/master/search.html @@ -3,7 +3,7 @@ - Search — Saltproc 0.3.1.dev documentation + Search — Saltproc 0.4.dev documentation @@ -30,7 +30,7 @@ Saltproc
- 0.3.1.dev + 0.4.dev
@@ -45,6 +45,8 @@
  • Installation
  • Examples
  • SaltProc API
    • +
  • Release Notes
    • +
  • Developer’s Guide
  • How to cite
    • diff --git a/master/searchindex.js b/master/searchindex.js index fb8ee328e..d0e220935 100644 --- a/master/searchindex.js +++ b/master/searchindex.js @@ -1 +1 @@ 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\ No newline at end of file diff --git a/master/src/index.html b/master/src/index.html index 5e05e6ed9..4721877b0 100644 --- a/master/src/index.html +++ b/master/src/index.html @@ -4,7 +4,7 @@ - SaltProc API — Saltproc 0.3.1.dev documentation + SaltProc API — Saltproc 0.4.dev documentation