[REVIEW]: PyGDH ("pigged"): Python Grid Discretization Helper #2744
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👋🏼 @kfhiga @JamieJQuinn @zhaowei0566 this is the review thread for the paper. All of our communications will happen here from now on. Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines. The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time. Please feel free to ping me (@melissawm) if you have any questions/concerns. |
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@melissawm <https://github.com/melissawm> @JamieJQuinn
<https://github.com/JamieJQuinn> @zhaowei0566
<https://github.com/zhaowei0566> Thank you all for your time!
Kenny
…On Mon, Oct 12, 2020 at 3:25 PM Melissa Weber Mendonça < ***@***.***> wrote:
👋🏼 @kfhiga <https://github.com/kfhiga> @JamieJQuinn
<https://github.com/JamieJQuinn> @zhaowei0566
<https://github.com/zhaowei0566> this is the review thread for the paper.
All of our communications will happen here from now on.
Both reviewers have checklists at the top of this thread with the JOSS
requirements. As you go over the submission, please check any items that
you feel have been satisfied. There are also links to the JOSS reviewer
guidelines.
The JOSS review is different from most other journals. Our goal is to work
with the authors to help them meet our criteria instead of merely passing
judgment on the submission. As such, the reviewers are encouraged to submit
issues and pull requests on the software repository. When doing so, please
mention openjournals/joss-reviews#2744 so that a link is created to this
thread (and I can keep an eye on what is happening). Please also feel free
to comment and ask questions on this thread. In my experience, it is better
to post comments/questions/suggestions as you come across them instead of
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Repo is on Bitbucket so couldn't link this repo directly. Added a few issues about installation on non-Debian systems. |
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👋 Hello all, just checking in to see if there's anything I can help you with. |
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Hi everyone and thanks for checking @melissawm. I've committed some changes
in response to the issues noted in the Bitbucket issue tracker. I should
probably have mentioned that here in case Bitbucket doesn't send
notifications on issue updates (sorry, still pretty new to this).
Thanks,
Kenny
…On Wed, Oct 28, 2020 at 10:52 AM Melissa Weber Mendonça < ***@***.***> wrote:
👋 Hello all, just checking in to see if there's anything I can help you
with.
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No problem! This is the first time I edit a submission that is not on github, so I'm new to this workflow as well. Glad to see things are ok, please ping me if there's any questions or comments. Thanks! |
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I'm happy to accept this with a few changes, mostly to the documentation: Documentation:
Code:
Otherwise I think this is a great package for an domain scientist who just wants some results without getting too deep into the nitty-gritty. As much as I feel I've torn apart the documentation (sorry!), it's a fantastic introduction for a new user, both to the software and to solving these kind of problems numerically. Similarly, the breadth of the provided examples in impressive and they seem to provide a comprehensive view of the problems solvable with pygdh. |
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Thank you for the detailed advice! I will get to work on these and let you
know when I've made the changes.
Kenny
…On Sat, Nov 14, 2020 at 5:32 AM Jamie J Quinn ***@***.***> wrote:
I'm happy to accept this with a few changes, mostly to the documentation:
*Documentation:*
- I found the SPHINX annotations distracting; I imagine they would be
very confusing to a new python user. Can these be removed from the examples
in the documentation? I think they're fine in the actual example code.
- I don't think the full source code for each example is required in
the documentation. It's easy enough for a user to grab the examples from
the repo. Additionally, it may help to shorten the length of the
documentation file (which may be intimidating for new users). Could the
full example code be removed from the end of each section?
- There's a statement at the end of page one of the documentation:
"*Users should be warned that although PyGDH has been successfully
used in past and ongoing research products andis anticipated to be useful
to others, it is still under development and should not be considered to be
well-tested, stablesoftware.*"
I would expect some users to read this and be unsure about whether the
results of code using pygdh can be trusted, however you've stated that the
numpy solvers are used, which are very mature and well-tested.
Additionally, you provide a number of examples with analytical comparisons
so in my opinion, the code is well validated, if not widely verified
through community use. Could this statement be reworded to reflect that the
code has been validated with test problems and uses a mature solver under
the hood?
- I'd suggest changing section 3.3.1 so that it doesn't look so much
like a full example. I personally followed that as if it were a functioning
example only to find out there were parts missing. Perhaps this section
could instead just describe the program structure without examples and then
use the working example in 3.4 to illustrate those. The initial paragraph
in 3.3.1 is sufficient in my opinion.
*Code:*
- The examples folder is very busy due to all the example code &
outputs being in one single folder. Can these be split into one folder per
example?
- I like the level of detail in what the code prints as it runs
however it could be clearer what is an info statement, a warning, or an
error. Could the difference between info, warnings and errors be made
clearer, e.g. replacing statements like '! example error" with "ERROR:
example error" and "INFO: creating domain"?
Otherwise I think this is a great package for an domain scientist who just
wants some results without getting too deep into the nitty-gritty. As much
as I feel I've torn apart the documentation (sorry!), it's a fantastic
introduction for a new user, both to the software and to solving these kind
of problems numerically. Similarly, the breadth of the provided examples in
impressive and they seem to provide a comprehensive view of the problems
solvable with pygdh.
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Thank the authors @kfhiga for sharing with the science community an open source code for studying time-dependent and nonlinear user-discretized equations on 0D, 1D, and simple 2D spatial domains using the finite volume method. This may be very useful for people, like me, working on unsteady aerodynamics. I don’t have questions about the technical stuff behind the code as they have been presented in the authors’ another publish work. The code is well written. I installed the code followings the steps using the code given in Downloads page and ran it successfully. The authors prepared a well-organized document. Thanks. I recommend to accept it with minor changes @melissawm
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Thank you all! Can I ask that you confirm (and tag me) once those suggestions have been made and both @zhaowei0566 and @JamieJQuinn are satisfied so we can move to acceptance? |
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Thank you, Wei and Melissa.
Wei thanks for the advice. I'll look into reducing the number of licensing
files, but if I remember correctly, the apparent redundancy was a
requirement from my institution as a condition for allowing the open source
release. I will look into the pip or conda packaging--another condition
from the U.S. Department of Energy is that we track the number of
downloads, which is done automatically on the Bitbucket download page, but
if pip or conda would handle that too, it would definitely be a possibility.
I'll let you know when I've completed the changes.
Thanks again,
Kenny
…On Mon, Nov 23, 2020 at 5:18 AM Melissa Weber Mendonça < ***@***.***> wrote:
Thank you all! Can I ask that you confirm (and tag me) once those
suggestions have been made and both @zhaowei0566
<https://github.com/zhaowei0566> and @JamieJQuinn
<https://github.com/JamieJQuinn> are satisfied so we can move to
acceptance?
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Hello, all! Any updates, @kfhiga ? |
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Sorry @melissawm, things are moving a bit slowly here. I hope to get all of
the revisions finished within the next couple of weeks. Thanks for checking
up.
Kenny
…On Mon, Dec 14, 2020 at 6:59 AM Melissa Weber Mendonça < ***@***.***> wrote:
Hello, all! Any updates, @kfhiga <https://github.com/kfhiga> ?
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Hello, all! I see that all boxes are ticked at the reviewer's checklists. Do you have any pending issues to resolve before we move on? Can @kfhiga @JamieJQuinn @zhaowei0566 confirm if we are ready to go? :) |
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Hi @melissawm, sorry, still working on this, hope to have it finished this
week!
Thanks for checking:
Kenny
…On Mon, Dec 21, 2020 at 7:03 AM Melissa Weber Mendonça < ***@***.***> wrote:
Hello, all! I see that all boxes are ticked at the reviewer's checklists.
Do you have any pending issues to resolve before we move on? Can @kfhiga
<https://github.com/kfhiga> @JamieJQuinn <https://github.com/JamieJQuinn>
@zhaowei0566 <https://github.com/zhaowei0566> confirm if we are ready to
go? :)
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Hello @melissawm <https://github.com/melissawm> @JamieJQuinn
<https://github.com/JamieJQuinn> @zhaowei0566
<https://github.com/zhaowei0566>,
Thank you again for all of your suggestions. I believe that I've addressed
the recommendations and have committed the changes.
If accepted, I'd like to update the documentation with a link to the
article, along with acknowledgments for all of you, before making a final
commit, if possible. I'd then like to package that release or a later
release for pip and possibly conda and Debian, assuming that my management
clears this (I'm supposed to track download counts, so this might be a
concern).
I wasn't able to remove the redundant license files since I needed to meet
multiple specific requirements (for pip, from my management, etc.).
Thanks again for your help, and please let me know if you need further
changes. This was my first time going through a peer-review process for
software and I thought that it was a great learning experience.
Kenny
…On Mon, Dec 21, 2020 at 7:20 AM Kenneth Higa ***@***.***> wrote:
Hi @melissawm, sorry, still working on this, hope to have it finished this
week!
Thanks for checking:
Kenny
On Mon, Dec 21, 2020 at 7:03 AM Melissa Weber Mendonça <
***@***.***> wrote:
> Hello, all! I see that all boxes are ticked at the reviewer's checklists.
> Do you have any pending issues to resolve before we move on? Can @kfhiga
> <https://github.com/kfhiga> @JamieJQuinn <https://github.com/JamieJQuinn>
> @zhaowei0566 <https://github.com/zhaowei0566> confirm if we are ready to
> go? :)
>
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> You are receiving this because you were mentioned.
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@melissawm I'm happy accepting this. @kfhiga thatnks for your work addressing our concerns; this is a great piece of software! Cheers, |
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Thank you, @JamieJQuinn <https://github.com/JamieJQuinn>, and thank you for
all of your advice on improving the package! Hope you're all having a nice
holiday break.
Best regards,
Kenny
…On Fri, Dec 25, 2020 at 5:35 AM Jamie J Quinn ***@***.***> wrote:
@melissawm <https://github.com/melissawm> I'm happy accepting this.
@kfhiga <https://github.com/kfhiga> thatnks for your work addressing our
concerns; this is a great piece of software!
Cheers,
Jamie
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Thanks for taking care of my comments. I don't have any further. I recommend to accept the present version. Congratulations! @kfhiga @melissawm |
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Hello, @kfhiga - it seems like this DOI link is broken, can you check to see what's happening? Thanks! |
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Hello @melissawm <https://github.com/melissawm>,
Sorry for the inconvenience. I got in touch with Dryad, and turns out
that they prefer to have software-only archives go directly to Zenodo
rather than through their data curation process (where my submission
got stuck).
Here's the new DOI:
10.5281/zenodo.4556303
or hyperlink:
https://doi.org/10.5281/zenodo.4556303
Thank you!
Kenny
…On Mon, Feb 22, 2021 at 5:13 AM Melissa Weber Mendonça < ***@***.***> wrote:
Hello, @kfhiga <https://github.com/kfhiga> - it seems like this DOI link
is broken, can you check to see what's happening? Thanks!
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Sorry for the delay, thanks for the information. I'll go through with acceptance. |
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@whedon set 10.5281/zenodo.4556303 as archive |
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OK. 10.5281/zenodo.4556303 is the archive. |
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@whedon set 0.4.3 as version |
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OK. 0.4.3 is the version. |
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@whedon accept |
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👋 @openjournals/joss-eics, this paper is ready to be accepted and published. Check final proof 👉 openjournals/joss-papers#2123 If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2123, then you can now move forward with accepting the submission by compiling again with the flag |
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@whedon accept deposit=true |
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Congratulations to @kfhiga (Kenneth Higa) and co-authors!! And thanks to @JamieJQuinn and @zhaowei0566 for reviewing, and @melissawm for editing! |
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Thank you everyone @JamieJQuinn <https://github.com/JamieJQuinn>
@zhaowei0566 <https://github.com/zhaowei0566> @melissawm
<https://github.com/melissawm>! This was my first time submitting an
article specifically for software, and it was a great experience. The open
and automated review and publishing process was really great to see too.
Thanks again!
Kenny
…On Tue, Mar 2, 2021 at 8:59 AM Daniel S. Katz ***@***.***> wrote:
Congratulations to @kfhiga <https://github.com/kfhiga> (Kenneth Higa) and
co-authors!!
And thanks to @JamieJQuinn <https://github.com/JamieJQuinn> and
@zhaowei0566 <https://github.com/zhaowei0566> for reviewing, and
@melissawm <https://github.com/melissawm> for editing!
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Submitting author: @kfhiga (Kenneth Higa)
Repository: https://bitbucket.org/berkeleylab/esdr-pygdh/
Version: 0.4.3
Editor: @melissawm
Reviewer: @JamieJQuinn, @zhaowei0566
Archive: 10.5281/zenodo.4556303
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