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Sign up[PRE REVIEW]: f90nml - A Python module for Fortran namelists #1472
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whedon
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May 22, 2019
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type:
What happens now? This submission is currently in a You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here. |
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whedon
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May 22, 2019
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PDF failed to compile for issue #1472 with the following error: /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-fc4c5c749ca9/lib/whedon.rb:115:in |
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danielskatz
commented
May 22, 2019
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marshallward
commented
May 23, 2019
Thank you @danielskatz, I've updated the doc to include a reference to the ISO document. (Not sure what else to cite here, since it's a pretty low level tool). I will direct @whedon in the next post. Also, I believe that @zbeekman may be a suitable referee for this paper, based on his contributions to the Fortran community. |
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marshallward
commented
May 23, 2019
@whedon generate pdf |
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PDF failed to compile for issue #1472 with the following error: Error producing PDF. l.300 ...hierarchical tree of \texttt{Namelists}\s Looks like we failed to compile the PDF |
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marshallward
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May 23, 2019
@whedon generate pdf |
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danielskatz
commented
May 23, 2019
Please see marshallward/f90nml#94 |
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danielskatz
commented
May 23, 2019
For submissions to JOSS, papers should talk a bit about the research use and users of the software - see https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain |
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marshallward
commented
May 23, 2019
Given that this is more of a Fortran tool rather than addressing a specific research activity, would you recommend submitting to a different journal? |
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FWIW (maybe not much!) I can see great value in research contexts for such a tool. Two immediate use cases jump to mind (although they are sort of two sides of the same coin):
1. Modernization & PortabilityNamelist files are better than old school "input deck" formatted input files, but they still are not as widely used (and easy to work with) as JSON and YAML. Research codes like NASA's FUN3D rely heavily on namelists for input files as do weather & climate codes like WRF. Increasingly these types of Engineering, Geoscience & Physics codes are needing to be integrated into workflows and analysis pipelines using other tools. As such, namelists are a poor choice of data format for both input files and outputs, as they are not easily generated or read by other tools. Increasingly research code inputs may need to be assimilated from more diverse sources, and analysis with tools like Jupyter notebooks or further processing of outputs is desired.
2. Mixed Language ProgrammingPython is often used as glue code in scientific and engineering software. For example Helios integrates components written in different languages, mostly Fortran and C++, and can swap in modular near-body CFD solvers for various rotorcraft and wind energy problems, including FUN3D, mentioned above. The glue code, and main driver application is written in python, but needs to generate namelist files to help talk to the Fortran based components. A framework like It is my (completely unsolicited and possibly worthless) opinion that, with suitable research, edits and references, that this f90nml joss article could be crafted into one that highlights the research uses, users and applications, and is appropriate for review. (But I haven't read the draft yet, this is based solely on my opinion and familiarity with the software.) |
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P.S. I'm on that list, but recently added, so you must scroll down to the 582nd row. Should the submission proceed, I hope my enthusiasm above is not mis-interpreted. I do not know, nor have I ever worked with or for the same company as @marshallward; I just appreciate the f90nml tool. |
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rgieseke
commented
May 23, 2019
Pymagicc (https://doi.org/10.21105/joss.00516) has used I'm at GitHub's satellite conference right now, where it was just announced that GitHub repos will display "Used by" other projects button. For |
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danielskatz
commented
May 23, 2019
I have no doubts about the usefulness of this software, I'm just trying to make sure if fits JOSS - I'll confer with other editors and be back soon |
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marshallward
commented
May 23, 2019
Thanks all for the kind feedback. I will modify the manuscript over the next day or so and try to consolidate some of the uses cases from these projects, including the ones linked by @rgieseke. (I was aware of a few via Google, but I'm surprised to see much more). |
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marshallward
commented
May 23, 2019
@whedon generate pdf |
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PDF failed to compile for issue #1472 with the following error: Error reading bibliography ./paper.bib (line 51, column 5): |
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marshallward
commented
May 23, 2019
@whedon generate pdf |
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marshallward
commented
May 23, 2019
@whedon generate pdf |
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marshallward
commented
May 23, 2019
@whedon generate pdf |
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danielskatz
commented
May 24, 2019
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danielskatz
commented
May 24, 2019
sorry, now I see you said so earlier. I'll assign you, but until we get a second reviewer, nothing will start, and your delay to next weekend is fine |
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danielskatz
commented
May 24, 2019
@whedon assign @danielskatz as editor |
whedon
assigned
danielskatz
May 24, 2019
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OK, the editor is @danielskatz |
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danielskatz
commented
May 24, 2019
whedon
assigned
danielskatz and
zbeekman
and unassigned
danielskatz
May 24, 2019
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OK, the reviewer is @zbeekman |
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danielskatz
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May 24, 2019
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I’m not against it but @rouson and I collaborate a lot so having both of us
as reviewers may be redundant or offer similar perspectives. I’ll be happy
to step aside for @rouson or review w/ him, but I wanted you
@danielskatz to be aware of this.
Happy either way so long as I can punt until after May 31.
…On Thu, May 23, 2019 at 8:25 PM Daniel S. Katz ***@***.***> wrote:
@whedon <https://github.com/whedon> assign @zbeekman
<https://github.com/zbeekman> as reviewer
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danielskatz
commented
May 24, 2019
Ok, let's see if Damian is available, or we will stick with you. In any case, we need another reviewer. Suggestions from @marshallward or @zbeekman ? |
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danielskatz
commented
May 24, 2019
@tclune, @kc9qey - would either of you be willing to review this submission to JOSS? (A JOSS review covers the short paper and the code repository, using this set of criteria) |
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danielskatz
commented
May 24, 2019
Thanks @tclune - with 2 reviewers now, we'll get going. |
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danielskatz
commented
May 24, 2019
whedon
assigned
danielskatz and
zbeekman
and unassigned
zbeekman and
danielskatz
May 24, 2019
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OK, @tclune is now a reviewer |
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danielskatz
commented
May 24, 2019
@whedon start review |
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OK, I've started the review over in #1474. Feel free to close this issue now! |
danielskatz
closed this
May 24, 2019
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rouson
commented
May 25, 2019
@danielskatz It sounds like you have enough reviewers. If not, another person I would recommend is Craig Rasmussen. I'm not sure if my tagging him here work, but here goes: @rasmussn. My experience with python is very limited so I'm probably not the best reviewer. |
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danielskatz
commented
May 25, 2019
Yes, we're all set, but thanks anyhow. |
whedon commentedMay 22, 2019
•
edited
Submitting author: @marshallward (Marshall Ward)
Repository: https://github.com/marshallward/f90nml
Version: v1.1
Editor: @danielskatz
Reviewers: @zbeekman, @tclune
Author instructions
Thanks for submitting your paper to JOSS @marshallward. Currently, there isn't an JOSS editor assigned to your paper.
@marshallward if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.
Editor instructions
The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type: