Updating dev

.github/workflows/draft-pdf.yml

@@ -1,4 +1,5 @@
-on: [push]
+name: Build JOSS paper, only on dispatch
+on: [workflow_dispatch]
 
 jobs:
   paper:

.github/workflows/manual_publish.yml

@@ -0,0 +1,49 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# assumming this is being done in a repo with trusted publishing permissions in pypi
+
+# There is an automated runner which should upload a new PyPi package but it often fails due to API BS.
+# This is here so one doesn't have to republish everything
+
+name: manually publish pypi package (for touble shooting)
+
+on: workflow_dispatch
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+        id-token: write
+    steps: 
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.11'
+    - uses: mpi4py/setup-mpi@v1
+    - name: Install dependencies
+      run: |
+        python --version
+        python -m pip install --upgrade pip
+        pip install .
+        pip install build
+    - name: Patch Numba
+      run : |
+        bash .github/workflows/patch.sh
+    - name: Build package
+      run: python -m build
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+      #with:
+      #  user: __token__
+      #  password: ${{ secrets.PYPI_API_TOKEN }}

CITATION.cff

@@ -0,0 +1,110 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: 'MC/DC: Monte Carlo Dynamic Code'
+message: >-
+  a pure python high performance Monte Carlo neutronics
+  package
+type: software
+authors:
+  - name: >-
+      Center for Exascale Monte Carlo Neutron Transport
+      (CEMeNT)
+    website: 'https://cement-psaap.github.io/'
+  - given-names: Ilham
+    family-names: 'Variansyah '
+    email: variansi@oregonstate.edu
+    affiliation: Oregon State University
+    orcid: 'https://orcid.org/0000-0003-3426-7160'
+  - given-names: Joanna Piper
+    family-names: Morgan
+    email: morgajoa@oregonstate.edu
+    affiliation: Oregon State University
+    orcid: 'https://orcid.org/0000-0003-1379-5431'
+  - given-names: Samuel
+    family-names: Pasmann
+    orcid: 'https://orcid.org/0000-0003-1391-1471'
+  - given-names: Kayla
+    family-names: Clements
+    email: clemekay@oregonstate.edu
+    affiliation: Oregon State University
+    orcid: 'https://orcid.org/0000-0003-3358-5618'
+  - given-names: Braxton
+    family-names: Cuneo
+    email: bcuneo@seattleu.edu
+    affiliation: Seattle University
+    orcid: 'https://orcid.org/0000-0002-6493-0990'
+  - given-names: Alexander
+    family-names: Mote
+    email: motea@oregonstate.edu
+    orcid: 'https://orcid.org/0000-0001-5099-0223'
+    affiliation: Oregon State University
+  - given-names: Caleb
+    family-names: Shaw
+    email: cashaw4@ncsu.edu
+    affiliation: North Carolina State University
+  - given-names: Jordan
+    family-names: Northrop
+    email: northj@oregonstate.edu
+    affiliation: Oregon State Universtiy
+    orcid: 'https://orcid.org/0000-0003-0420-9699'
+  - given-names: Rohan
+    family-names: Pankaj
+    orcid: 'https://orcid.org/0009-0005-0445-9323'
+  - given-names: 'Ryan G. '
+    family-names: McClarren
+    email: rmcclarr@nd.edu
+    affiliation: University of Notre Dame
+    orcid: 'https://orcid.org/0000-0002-8342-6132'
+  - given-names: Todd S.
+    family-names: Palmer
+    email: palmerts@oregonstate.edu
+    affiliation: Oregon State Univeristy
+    orcid: 'https://orcid.org/0000-0003-3310-5258'
+  - given-names: Lizhong
+    family-names: Chen
+    email: chenliz@oregonstate.edu
+    affiliation: Oregon State University
+    orcid: 'https://orcid.org/0000-0001-5890-7121'
+  - given-names: Dmitriy Y.
+    family-names: Anistratov
+    email: anistratov@ncsu.edu
+    affiliation: North Carolina State University
+  - given-names: C. T.
+    family-names: Kelley
+    email: ctk@ncsu.edu
+    affiliation: North Carolina State University
+  - given-names: 'Camille  '
+    family-names: Palmer
+    email: palmecam@oregonstate.edu
+    orcid: 'https://orcid.org/0000-0002-7573-4215'
+    affiliation: Oregon State University
+  - given-names: Kyle E.
+    family-names: Niemeyer
+    email: niemeyek@oregonstate.edu
+    orcid: 'https://orcid.org/0000-0003-4425-7097'
+    affiliation: Oregon State University
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.10576604
+    description: Zenodo Archive
+  - type: doi
+    value: 10.21105/joss.06415
+    description: Paper description of MC/DC
+repository-code: 'https://github.com/CEMeNT-PSAAP/MCDC'
+url: 'https://cement-psaapgithubio.readthedocs.io/en/latest/'
+abstract: >-
+  MC/DC is a performant, scalable, and machine-portable
+  Python-based Monte Carlo neutron transport software
+  currently developed in the Center for Exascale Monte Carlo
+  Neutron Transport (CEMeNT).
+keywords:
+  - monte carlo
+  - numba
+  - gpu
+  - neutron transport
+  - radiation transport
+license: BSD-3-Clause
+version: 0.9.1
+date-released: '2024-04-08'

README.md

@@ -4,6 +4,7 @@
 
 [![Build](https://github.com/CEMeNT-PSAAP/MCDC/actions/workflows/mpi_numba_reg.yml/badge.svg)](https://github.com/CEMeNT-PSAAP/MCDC/actions/workflows/mpi_numba_reg.yml)
 [![ReadTheDocs](https://readthedocs.org/projects/cement-psaapgithubio/badge/?version=latest&style=flat)](https://cement-psaapgithubio.readthedocs.org/en/latest/ )
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06415/status.svg)](https://doi.org/10.21105/joss.06415)
 [![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
 
@@ -108,18 +109,21 @@ You can find specifics on how to run these tests locally [here](https://github.c
 
 To provide proper attribution to MC/DC, please cite
 ```
-@inproceedings{var_mc23_mcdc,
-    Booktitle = {International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering},
-    title = {Development of {MC/DC}: a performant, scalable, and portable Python-based {M}onte {C}arlo neutron transport code},
-    year = {2023},
-    author = {Ilham Variansyah and Joanna Piper Morgan and Kyle E. Niemeyer and Ryan G. McClarren},
-    address = {Niagara Falls, Ontario, Canada},
-    doi={10.48550/arXiv.2305.07636},
-}
+    @article{morgan2024mcdc,
+        title = {Monte {Carlo} / {Dynamic} {Code} ({MC}/{DC}): {An} accelerated {Python} package for fully transient neutron transport and rapid methods development},
+        author = {Morgan, Joanna Piper and Variansyah, Ilham and Pasmann, Samuel L. and Clements, Kayla B. and Cuneo, Braxton and Mote, Alexander and Goodman, Charles and Shaw, Caleb and Northrop, Jordan and Pankaj, Rohan and Lame, Ethan and Whewell, Benjamin and McClarren, Ryan G. and Palmer, Todd S. and Chen, Lizhong and Anistratov, Dmitriy Y. and Kelley, C. T. and Palmer, Camille J. and Niemeyer, Kyle E.},
+        journal = {Journal of Open Source Software},
+        volume = {9},
+        number = {96},
+        year = {2024},
+        pages = {6415},
+        url = {https://joss.theoj.org/papers/10.21105/joss.06415},
+        doi = {10.21105/joss.06415},
+    }
 ```
 which should render something like this
 
-Variansyah, Ilham, J. P. Morgan, K. E. Niemeyer, and R. G. McClarren. 2023. “Development of MC/DC: a performant, scalable, and portable Python-based Monte Carlo neutron transport code.” In *International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering*, Niagara Falls, Ontario, Canada. DOI. [10.48550/arXiv.2305.07636](https://doi.org/10.48550/arXiv.2305.07636)
+Morgan et al. (2024). Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development. Journal of Open Source Software, 9(96), 6415. https://doi.org/10.21105/joss.06415.
 
 ## License