diff --git a/CITATION b/CITATION deleted file mode 100644 index 1136d81e2..000000000 --- a/CITATION +++ /dev/null @@ -1,17 +0,0 @@ -If you use pyro, we appreciate you citing the latest code paper: - -@article{pyro:2019, -author = {Harpole, Alice and Zingale, Michael and Hawke, Ian and Chegini, Taher}, -doi = {10.21105/joss.01265}, -journal = {The Journal of Open Source Software}, -number = {34}, -pages = {1265}, -title = {pyro : a framework for hydrodynamics explorations and prototyping}, -volume = {4}, -year = {2019} -} - -You should also cite the Zenodo DOI for the code release. A bibtex -entry for the latest release can be found here: - -https://doi.org/10.5281/zenodo.2575565 diff --git a/CITATION.md b/CITATION.md new file mode 100644 index 000000000..2d3bee035 --- /dev/null +++ b/CITATION.md @@ -0,0 +1,46 @@ +If you use pyro, please cite the pyro JOSS paper *and* the latest Zenodo DOI. + +## JOSS + +The pyro JOSS paper is at: https://joss.theoj.org/papers/10.21105/joss.01265 + +You can cite it as: + +```bibtex +@article{pyro_joss, + doi = {10.21105/joss.01265}, + url = {https://doi.org/10.21105/joss.01265}, + year = {2019}, + publisher = {The Open Journal}, + volume = {4}, + number = {34}, + pages = {1265}, + author = {Alice Harpole and Michael Zingale and Ian Hawke and Taher Chegini}, + title = {pyro: a framework for hydrodynamics explorations and prototyping}, + journal = {Journal of Open Source Software} +} +``` + +## Astronomy and Computing + +You can also additionally cite the paper from *Astronomy and Computing*: + +```bibtex +@article{pyro_ac, + author = {{Zingale}, M.}, + title = "{pyro: A teaching code for computational astrophysical hydrodynamics}", + journal = {Astronomy and Computing}, + year = 2014, + month = {oct}, + volume = 6, + pages = {52-62}, + doi = {10.1016/j.ascom.2014.07.003} +} +``` + +## Zenodo + +The latest pyro Zenodo record is at https://doi.org/10.5281/zenodo.2575564 + + + diff --git a/docs/Makefile b/docs/Makefile index db840c4cc..7b0dbd771 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -18,4 +18,5 @@ help: # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile ./document_problems.py + curl -L -H 'Accept: application/x-bibtex' https://zenodo.org/api/records/2575564 > source/zenodo.bibtex.txt @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/source/ack.rst b/docs/source/ack.rst index f1a8fb876..bf8071366 100644 --- a/docs/source/ack.rst +++ b/docs/source/ack.rst @@ -1,44 +1,5 @@ Acknowledgments =============== -The current pyro developers are listed in the `.zenodo.json` file that -is used for releases. - -You are free to use this code and the accompanying notes in your -classes. Please credit "pyro development team" for the code, and -*please send a note to the pyro-help e-mail list describing how you -use it, so we can keep track of it (and help justify the development -effort).* - -If you use pyro in a publication, please cite it using this bibtex -citation:: - - @article{pyro, - doi = {10.21105/joss.01265}, - url = {https://doi.org/10.21105/joss.01265}, - year = {2019}, - publisher = {The Open Journal}, - volume = {4}, - number = {34}, - pages = {1265}, - author = {Alice Harpole and Michael Zingale and Ian Hawke and Taher Chegini}, - title = {pyro: a framework for hydrodynamics explorations and prototyping}, - journal = {Journal of Open Source Software} - } - pyro benefited from numerous useful discussions with Ann Almgren, John Bell, and Andy Nonaka. - - -History -======= - -The original pyro code was written in 2003-4 to help developer -Zingale understand these methods for himself. It was originally written -using the Numeric array package and handwritten C extensions for the -compute-intensive kernels. It was ported to numarray when that -replaced Numeric, and continued to use C extensions. This version -"pyro2" was resurrected beginning in 2012 and rewritten for numpy -using f2py, and brought up to date. Most recently we've dropped -f2py and are using numba for the compute-intensive kernels. - diff --git a/docs/source/citing.rst b/docs/source/citing.rst new file mode 100644 index 000000000..9dc9e24f8 --- /dev/null +++ b/docs/source/citing.rst @@ -0,0 +1,17 @@ +Citing pyro +=========== + +You are free to use this code and the accompanying notes in your +classes. Please credit "pyro development team" for the code, and +*please make a post to the pyro github discussions describing how you +use it, so we can keep track of it (and help justify the development +effort).* + +.. mdinclude:: ../../CITATION.md + +The bibtex for the latest version is included below (updated automatically): + +.. literalinclude:: ./zenodo.bibtex.txt + :language: bibtex + + diff --git a/docs/source/conf.py b/docs/source/conf.py index 252642120..247091d9d 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -47,6 +47,7 @@ 'sphinx_copybutton', 'sphinx_math_dollar', 'sphinx-prompt', + 'sphinx_mdinclude', 'IPython.sphinxext.ipython_console_highlighting', 'sphinx.ext.githubpages'] diff --git a/docs/source/history.rst b/docs/source/history.rst new file mode 100644 index 000000000..7943377f2 --- /dev/null +++ b/docs/source/history.rst @@ -0,0 +1,12 @@ +History +======= + +The original pyro code was written in 2003-4 to help developer +Zingale understand these methods for himself. It was originally written +using the Numeric array package and handwritten C extensions for the +compute-intensive kernels. It was ported to numarray when that +replaced Numeric, and continued to use C extensions. This version +"pyro2" was resurrected beginning in 2012 and rewritten for numpy +using f2py, and brought up to date. Most recently we've dropped +f2py and are using numba for the compute-intensive kernels. + diff --git a/docs/source/index.rst b/docs/source/index.rst index 5dfa8a232..b71eb3623 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -90,7 +90,9 @@ new ideas. :hidden: help + history ack + citing .. toctree:: :maxdepth: 1 diff --git a/requirements.txt b/requirements.txt index b65955f6d..954d2cfd0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,6 +14,7 @@ sphinxcontrib-bibtex sphinx-math-dollar sphinx-copybutton sphinx-prompt +sphinx-mdinclude importlib-metadata prettytable codespell