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Update to use OpenMC v0.14.0, update documentation #19

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Jun 13, 2024
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94ee041
update tests and streamline depletion functions
abachma2 Jun 19, 2023
3f3ebc9
update reading materials function from Depletion class
abachma2 Jun 19, 2023
2def7fe
add depletion results for testing suite
abachma2 Jun 20, 2023
c27af33
update comp to h5 committed to repo
abachma2 Jun 20, 2023
ef029ce
add unit test file
ceserz2 Oct 10, 2023
711cc54
comment out integration test
ceserz2 Oct 10, 2023
ff0d7a4
adding the rest of the steps to build the environment
ceserz2 Oct 24, 2023
8f0f272
adding "run tests" step
ceserz2 Oct 24, 2023
ed82f4d
adding "install numpy" step
ceserz2 Oct 28, 2023
23ac454
adding "install mamba from conda" step
ceserz2 Oct 28, 2023
2a96a4b
adding a new install command for mamba
ceserz2 Oct 28, 2023
71f9ec1
updating conda install for mamba
ceserz2 Oct 28, 2023
23847b4
adding "checking environment step"
ceserz2 Nov 7, 2023
158246b
commenting out "install mamba from conda" step
ceserz2 Nov 7, 2023
075eb92
adding "conda info" step
ceserz2 Nov 7, 2023
deb9107
adding "conda info" to steps
ceserz2 Nov 8, 2023
8ad3391
fixing "conda info" steps
ceserz2 Nov 8, 2023
b402679
updating environment setup
ceserz2 Nov 8, 2023
e79b3c7
fixing more errors with environment activation
ceserz2 Nov 8, 2023
e278951
removing environment activation step
ceserz2 Nov 8, 2023
fe212d8
fixing errors in setting up environment
ceserz2 Nov 9, 2023
fa131ec
updating environment command added
ceserz2 Nov 10, 2023
a551733
fixing "activate environment" function for each step
ceserz2 Nov 11, 2023
8e28507
more fixes on code
ceserz2 Nov 11, 2023
2b715e2
inserting "conda init" command to initialize shell
ceserz2 Nov 11, 2023
3feec33
fixing command to activate the environment
ceserz2 Nov 11, 2023
7b7cae9
trying a new method for environment activation
ceserz2 Nov 11, 2023
f283b3e
trying to update code to fix CI file
ceserz2 Nov 17, 2023
e7a8ccf
Merge branch 'ci' of github.com:ceserz2/openmcyclus_cz into tests
abachma2 Apr 2, 2024
53dc24c
add gitignore file
abachma2 Apr 2, 2024
caa46f4
add CHANGELOG for repo
abachma2 Apr 2, 2024
b52d2ab
add contributing guide
abachma2 Apr 2, 2024
5d079ff
run on PR only while making updates
abachma2 Apr 2, 2024
ed5dca2
adjsut list formatting
abachma2 Apr 2, 2024
32f5a33
adjsut formatting more
abachma2 Apr 2, 2024
42d8a14
add CONTRIBUTING to changelog
abachma2 Apr 2, 2024
de2d5b3
update dependency versions and some text
abachma2 Apr 2, 2024
1da2b2e
actually only run on PR not push
abachma2 Apr 2, 2024
4c5e1b8
fix syntax to run on PR
abachma2 Apr 2, 2024
e2effad
convert to rst, and change formatting
abachma2 Apr 2, 2024
7b3f738
correct cyclus website link
abachma2 Apr 2, 2024
df46ce4
fix formatting
abachma2 Apr 2, 2024
765bcd9
fix the rest of the format errors
abachma2 Apr 2, 2024
8c46594
Merge branch 'tests' into updates
abachma2 Apr 3, 2024
9489e16
set to run only on PR while actively working on updates
abachma2 Apr 3, 2024
f974a08
add note about deps on conda, may be used for install, unsure yet
abachma2 Apr 3, 2024
38f8b2f
start update for OpenMC 0.14.0
abachma2 Apr 3, 2024
9446845
remove file, no longer needed for testing
abachma2 Apr 3, 2024
33dbf59
remove file, not needed for testing
abachma2 Apr 3, 2024
f5b9380
add python script of OpenMC model for debugging
abachma2 Apr 4, 2024
a416d95
finish updating models to OpenMC 0.14.0
abachma2 Apr 9, 2024
8aa9c94
get mox model spent comp printed
abachma2 Apr 9, 2024
ee9f931
add flux parameter, refactor getting spent comps
abachma2 Apr 9, 2024
2801494
add test for run_depletion, update formats for others
abachma2 Apr 9, 2024
28f94c7
add scipy dep, modify description of openmc needs
abachma2 Apr 9, 2024
7a07bd6
change to run on push
abachma2 Apr 9, 2024
6564be1
remove duplicate steps, add scipy version
abachma2 Apr 10, 2024
fcb2227
correct format, add more file types
abachma2 Apr 10, 2024
f18292f
clean up unused steps
abachma2 Apr 10, 2024
1d49d96
add missing files for comparison, deplete unused file
abachma2 Apr 10, 2024
0e37e73
add thermal power input parameter
abachma2 Apr 15, 2024
94a4d1a
add flux parameter, update transmute
abachma2 Apr 15, 2024
87eb4f0
remove coversion factor parameter
Apr 18, 2024
316652c
remove instantializing self.micro_xs
abachma2 Apr 19, 2024
7652e6c
return transmute to using OpenMC, remove check_existing_recipes
abachma2 Apr 23, 2024
10f46e5
add new params, change spent uox to pu
abachma2 Apr 23, 2024
69a5ed1
remove Cycamore Reactor in lib specs
abachma2 Apr 23, 2024
9fe8dab
add new parameters
abachma2 Apr 23, 2024
4fccf04
update CHANGELOG
abachma2 Apr 23, 2024
0fa32d9
pep8 fixes
abachma2 Apr 23, 2024
6b432e7
add new params, update install instructions
abachma2 Apr 23, 2024
02b8637
correct code block format
abachma2 Apr 23, 2024
3bd9f4c
update deps install and code format for input
abachma2 Apr 23, 2024
9eae286
make some of the suggestions from @yardasol
abachma2 Apr 25, 2024
c1d7d27
initialize microxs and materials with class
abachma2 Apr 25, 2024
4cffc67
change material and microxs initialization
abachma2 May 6, 2024
de80f4b
pep8 fixes, update documentation
abachma2 May 6, 2024
c98667b
pep8 fixes
abachma2 May 6, 2024
f07eb28
change cyclus/cycamore install instructions
abachma2 May 20, 2024
96eb863
address comments from @yardasol
abachma2 May 30, 2024
1d1568a
fix test suite, function inputs and locations
abachma2 May 30, 2024
3aecd12
update OpenMC footnote
abachma2 May 30, 2024
34ab439
address docstring comments from @yardasol
abachma2 Jun 5, 2024
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8 changes: 4 additions & 4 deletions .github/workflows/test-openmcyclus.yml
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
name: test-openmcyclus
on: [push, pull_request]
on: [pull_request]

jobs:
build-and-test:
Expand Down Expand Up @@ -47,6 +47,6 @@ jobs:
# run: |
# pip install pytest

- name: Run Tests
run: |
pytest tests/integration_tests/test_depletereactor.py
# - name: Run Tests
# run: |
# pytest tests/integration_tests/test_depletereactor.py
42 changes: 42 additions & 0 deletions .github/workflows/unit-test.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,42 @@
name: unit-tests
on: [pull_request, push]

jobs:
build-and-unit-test:
runs-on: ubuntu-latest
defaults:
run:
shell: bash -el {0}

steps:
- uses: actions/checkout@v3
- name: Setup Conda
uses: conda-incubator/setup-miniconda@v2
with:
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: openmcyclus-env
environment-file: environment.yml
use-mamba: true

- name: Conda config
run: |
conda config --env --set pip_interop_enabled True

- name: Install OpenMC from Mamba
run:
mamba install openmc scipy=1.11

- name: Install OpenMC cross section library
run: |
$GITHUB_WORKSPACE/openmc-xs.bash
echo "OPENMC_CROSS_SECTIONS=cross_sections.xml" >> $GITHUB_ENV

- name: Install OpenMCyclus
run:
pip install .

- name: Run Tests
run:
pytest tests/unit_tests/test_depletion.py

6 changes: 6 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
__pycache__/
*.ipynb_checkpoints/
*.sqlite
*.h5
*.pdf

31 changes: 31 additions & 0 deletions CHANGELOG.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
======================
OpenMCyclus Change Log
======================

Since last release:
===================

**Added:**

* Added `CHANGELOG.rst`, `.gitignore`, `CONTRIBUTING.rst`,
and unit tests for `openmcyclus.Depletion` class. Also
added files for better reproduction of comparison benchmar (#18)
* Add input parameters to `DepleteReactor` for the thermal
power (instead of just using `power_cap`) and flux
(required input for running OpenMC with new version) (#18)

**Changed:**

* Change OpenMC dependency to v0.14.0, which includes adding
parameters for using `DepleteReactor` (#18)

**Removed:**

* Remove `check_existing_recipes` method in `DepleteReactor` (#18)

**Fixed:**


v 0.1.0
=========
Initial release
67 changes: 67 additions & 0 deletions CONTRIBUTING.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,67 @@
***************************
Contributing to OpenMCyclus
***************************

Welcome, and thank you for your interest in developing OpenMCyclus. This document
serves as a guide for making contributions to this archetype library.

General Notes
=============
OpenMCyclus relies on Cyclus and OpenMC, so familiarity with using both is
recommended. Please refer to the `Cyclus website <http://fuelcycle.org>`_ and
`OpenMC documenatation <https://docs.openmc.org/en/v0.14.0/index.html>`_ for
information about each code.

Contributions to this software are made via GitHub, so familiarity with
git is recommended. Resources for installing
and using git and GitHub include:

* The `git website <https://git-scm.com/>`_

* The `GitHub docs <https://docs.github.com/en>`_

* This `tutorial <https://help.github.com/articles/using-pull-requests/>`_ on creating
pull requests

The general steps for contributing to OpenMCyclus are:

1. Create a fork of the OpenMCyclus repository
2. Create a new branch on your fork, keeping the `main` branch clean and
up-to-date with the ARFC version of the repository `main` branch
3. Make your desired changes on your new branch
4. Make sure all of the tests pass. You can run the tests locally, or they will
run in the CI (via GitHub Actions) when you push changes
5. When you're finished with your changes and the tests pass, update the
`CHANGELOG <CHANGELOG.rst>`_ with the changes you've made.
6. Issue a pull request into the ARFC repository `main` branch.

Reviewing pull requests
=======================
Reviewing pull requests is an important part of development work. When
reviewing pull requests please:

* Make sure the code is consistent with the `PEP 8 style guide <https://peps.python.org/pep-0008/>`_
* Make sure all tests in CI are passing
* Ensure that new tests are added as needed to address new features
* Make positive, constructive comments on the code
abachma2 marked this conversation as resolved.
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Once all conversations are resolved and all tests pass, you are welcome to
merge the pull request.

Running tests:
==============
pytest is used for all tests. Tests should be run from the top-level
directory of this repository using:

.. code-block:: bash

$ pytest tests/

Releases:
=========
When a new release is ready:

#. Update all documentation as needed and issue a PR for this
#. git tag -a <version>
#. git push upstream main
#. git push upstream <version>
128 changes: 0 additions & 128 deletions README.md

This file was deleted.

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