Trac November 2021

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#2577: CactusTutorial.ipynb contains code only suitable or tutorial server
by Roland Haas 19 Nov '21

19 Nov '21

#2577: CactusTutorial.ipynb contains code only suitable or tutorial server Reporter: Roland Haas Status: new Milestone: Version: development version Type: bug Priority: major Component: EinsteinToolkit Virtual Machine The tutorial notebook is intended for both use inside of the tutorial server $and docker image$ as well as users' own jupyer notebook server in their account and finally as a read-only, offline version. The current notebook contains instances of code that will fail or do dangerous things on a user’s laptop. Namley: ```python import scrolldown ``` will fail unless a Python module `scrolldown` is available. This should be encased in a `try:... except ModuleNotFoundError` block. And ```shell cd ~/ rm -fr ~/Cactus tar xzf ~etuser/Cactus.tar.gz ``` which is very dangerous since it will remove any `Cactus` directory in a user’s $HOME which is a bad thing to do for offline use where users may want to use a different directory $eg GW150914 or so$. The tarbal will also only exist on the notebook server and thus `tar` will fail on private jupyter notebook servers or in offline use. This can confuse potential new users that expect to be able to enter each command in the notebook and thus be able to run Cactus. This cell should be protect by some bash-level if statements that check if it is being run on the notebook server and a comment that this cell will only be used on the notebook server added to the cell as a shell comment $so that it cannot be lost$. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2577/cactustutorialipy…

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#2551: include RePriMand in the ET
by Roland Haas 19 Nov '21

19 Nov '21

#2551: include RePriMand in the ET Reporter: Roland Haas Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Roland Haas): Applied as git hash [b786700](https://bitbucket.org/einsteintoolkit/manifest/commits/b786700100b… "einsteintoolkit.bib: add Kastaun:2020uxr" of [manifest](https://bitbucket.org/einsteintoolkit/manifest) -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2551/include-reprimand…

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#2551: include RePriMand in the ET
by Wolfgang Kastaun 19 Nov '21

19 Nov '21

#2551: include RePriMand in the ET Reporter: Roland Haas Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Wolfgang Kastaun): ``` @article{Kastaun:2020uxr, author = "Kastaun, Wolfgang and Kalinani, Jay Vijay and Ciolfi, Riccardo", title = "{Robust Recovery of Primitive Variables in Relativistic Ideal Magnetohydrodynamics}", eprint = "2005.01821", archivePrefix = "arXiv", primaryClass = "gr-qc", doi = "10.1103/PhysRevD.103.023018", journal = "Phys. Rev. D", volume = "103", number = "2", pages = "023018", year = "2021" } ``` ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2551/include-reprimand…

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#2551: include RePriMand in the ET
by Roland Haas 19 Nov '21

19 Nov '21

#2551: include RePriMand in the ET Reporter: Roland Haas Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Roland Haas): Once RePrimAnd is compiled by default $or also before if you like, I can always enable its build on Jenkins$ you could set up a "repo push" $the default$ [web-hook](https://bitbucket.org/einsteintoolkit/tickets/admin/addon/admin/b… to contact [https://einsteintoolkit.org/hooks/repo\_changed.php?secret=XXX](https://ein… to send commit messages to [commits@einsteintoolkit.org](mailto:commits@einsteintoolkit.org) where XXX is to be found in [https://bitbucket.org/einsteintoolkit/www/src/master/hooks/repo\_changed.ph… $or thereabouts, look for the variable `$secret`$. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2551/include-reprimand…

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#2551: include RePriMand in the ET
by Roland Haas 19 Nov '21

19 Nov '21

#2551: include RePriMand in the ET Reporter: Roland Haas Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Roland Haas): It’s not super important $since RePrimAnd is not yet compiled by default$ you may consider to hook yourself up to the ET commits mailing list $like the ET thorns do$ by setting up [commits@einsteintoolkit.org](mailto:commits@einsteintoolkit.org) as the recipient of push event emails in [https://github.com/GITHUB\_USER\_NAME/REPO\_NAME/settings/notifications/edi… . -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2551/include-reprimand…

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#2538: Inclusion of kuibit
by Roland Haas 19 Nov '21

19 Nov '21

#2538: Inclusion of kuibit Reporter: Gabriele Bozzola Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Roland Haas): It’s not super important $since kuibit is analysis not ET thorn$ you may consider to hook yourself up to the ET commits mailing list $like the ET thorns do$ by setting up [commits@einsteintoolkit.org](mailto:commits@einsteintoolkit.org) as the recipient of push event emails in [https://github.com/GITHUB\_USER\_NAME/REPO\_NAME/settings/notifications/edi… . -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2538/inclusion-of-kuib…

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#2538: Inclusion of kuibit
by Gabriele Bozzola 19 Nov '21

19 Nov '21

#2538: Inclusion of kuibit Reporter: Gabriele Bozzola Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Gabriele Bozzola): > Usually the suggested citations are secondary publications or publications that describe specific aspects that not all users will use. I see. Without `numpy`, `scipy`, and `h5py`, `kuibit` would not exist. Therefore, I personally always cite them, and I would recommend anyone that uses `kuibit` to do the same. $\`matplotlib\` is not as important in `kuibit`: you can use 95 % of the available features without it and use your preferred plotting library instead$ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2538/inclusion-of-kuib…

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#2538: Inclusion of kuibit
by Roland Haas 19 Nov '21

19 Nov '21

#2538: Inclusion of kuibit Reporter: Gabriele Bozzola Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Roland Haas): Applied as git hash [ab8dab7](https://bitbucket.org/einsteintoolkit/manifest/commits/ab8dab7695d… "einsteintoolkit.bib: add Harris:2020xlr, Virtanen:2019joe for numpy and scipy" of [manifest](https://bitbucket.org/einsteintoolkit/manifest) and git hash [bef96ab](https://bitbucket.org/einsteintoolkit/manifest/commits/bef96ab37f9… "einsteintoolkit.bib: add Kuibit main citation" of [manifest](https://bitbucket.org/einsteintoolkit/manifest) -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2538/inclusion-of-kuib…

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#2538: Inclusion of kuibit
by Roland Haas 19 Nov '21

19 Nov '21

#2538: Inclusion of kuibit Reporter: Gabriele Bozzola Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Roland Haas): Thank you. You can certainly add the scipy and numpy citations as suggested ones. If you do list citations for kuibit’s dependencies $typically not done, those dependenicies would have their own list$ you may also consider the matplotlib citation $which they actually request, [https://matplotlib.org/3.1.1/citing.html](https://matplotlib.org/3.1.1/citi…): ```tex @Article{Hunter:2007, Author = {Hunter, J. D.}, Title = {Matplotlib: A 2D graphics environment}, Journal = {Computing in Science \& Engineering}, Volume = {9}, Number = {3}, Pages = {90--95}, abstract = {Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.}, publisher = {IEEE COMPUTER SOC}, doi = {10.1109/MCSE.2007.55}, year = 2007 } ``` though the entry itself already exists in einsteintoolkit.bib. Usually the suggested citations are secondary publications or publications that describe specific aspects that not all users will use. Independent of this, adding the numpy and scipy entries \(with or without suggested-for$ to einsteintoolkit.bib seems like a good idea. Thanks for looking them up. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2538/inclusion-of-kuib…

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#2538: Inclusion of kuibit
by Gabriele Bozzola 19 Nov '21

19 Nov '21

#2538: Inclusion of kuibit Reporter: Gabriele Bozzola Status: open Milestone: ET_2021_11 Version: development version Type: enhancement Priority: major Component: Comment (by Gabriele Bozzola): You can use this citation key: ```tex @article{Bozzola:2021hus, requested-for = {kuibit}, author = "Bozzola, Gabriele", title = "{kuibit: Analyzing Einstein Toolkit simulations with Python}", eprint = "2104.06376", archivePrefix = "arXiv", primaryClass = "gr-qc", doi = "10.21105/joss.03099", journal = "J. Open Source Softw.", volume = "6", number = "60", pages = "3099", year = "2021" } ``` `kuibit` relies upon `numpy`, `scipy`, and `h5py` ``` @article{Harris:2020xlr, suggested-for = {kuibit}, author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J. van der Walt and Ralf Gommers and Pauli Virtanen and David Cournapeau and Eric Wieser and Julian Taylor and Sebastian Berg and Nathaniel J. Smith and Robert Kern and Matti Picus and Stephan Hoyer and Marten H. van Kerkwijk and Matthew Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and Warren Weckesser and Hameer Abbasi and Christoph Gohlke and Travis E. Oliphant}, title = "{Array programming with NumPy}", eprint = "2006.10256", archivePrefix = "arXiv", primaryClass = "cs.MS", doi = "10.1038/s41586-020-2649-2", journal = "Nature", volume = "585", number = "7825", pages = "357--362", year = "2020" } @article{Virtanen:2019joe, suggested-for = {kuibit}, author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and {van der Walt}, St{\'e}fan J. and Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C J and Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and {VanderPlas}, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R. and Archibald, Anne M. and Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and {van Mulbregt}, Paul and {SciPy 1.0 Contributors}}, title = "{SciPy 1.0--Fundamental Algorithms for Scientific Computing in Python}", eprint = "1907.10121", archivePrefix = "arXiv", primaryClass = "cs.MS", doi = "10.1038/s41592-019-0686-2", journal = "Nature Meth.", volume = "17", pages = "261", year = "2020" } ``` Unfortunately, h5py does not have a recommended citation. ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2538/inclusion-of-kuib…

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Trac November 2021