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Software report:
github.com/AlDanial/cloc v 1.90 T=0.04 s (849.0 files/s, 266823.1 lines/s)
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Language files blank comment code
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Fortran 77 21 22 2558 5473
Python 7 585 742 1618
TeX 1 17 0 278
Markdown 3 77 0 270
C/C++ Header 2 1 0 258
Bourne Shell 3 4 2 17
make 1 4 0 17
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SUM: 38 710 3302 7931
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Commit count by author:
85 Jakob Stegmann
50 stegmaja
5 Jordan Barber
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.48550/arXiv.2405.02912 is OK
- 10.1093/mnras/stac2192 is OK
- 10.1103/PhysRevD.106.023014 is OK
- 10.1093/mnras/stab287 is OK
- 10.3847/1538-4357/ab8461 is OK
- 10.1093/mnras/sty2848 is OK
- 10.1093/mnras/sty1999 is OK
- 10.3847/1538-4357/aacea4 is OK
- 10.3847/1538-4365/aa6fb6 is OK
- 10.1186/s40668-016-0019-0 is OK
- 10.1146/annurev-astro-081915-023315 is OK
- 10.1093/mnras/stu2396 is OK
- 10.1126/science.1223344 is OK
- 10.1046/j.1365-8711.2002.05038.x is OK
- 10.1046/j.1365-8711.2000.03426.x is OK
MISSING DOIs
- No DOI given, and none found for title: TRES: TRiple Evolution Simulation package
- No DOI given, and none found for title: MOBSE: Massive Objects in Binary Stellar Evolution
INVALID DOIs
- None
Paper file info:
š Wordcount for paper.md
is 576
ā
The paper includes a Statement of need
section
License info:
ā
License found: MIT License
(Valid open source OSI approved license)
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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ā ļø Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.
@stegmaja ā Thanks for your submission! All the suitable JOSS editors are currently working at capacity so I'm going to "waitlist" this review until an editor with the relevant expertise is available to take it on. Thanks for your patience!
One thing I'd like to clarify off the bat: I think that the code in the mobse
directory is not part of this review, right? I think that this submission just covers the Python code.
Also: while this submission waits in the queue, you might want to take a look at the JOSS review criteria especially the testing and installation/packaging. I think that these elements look like they could use some work before the review starts!
@dfm - Thank you very much! Indeed, mobse
shall not be part of the review because it is essentially copied from the MOBSE gitlab repository (https://gitlab.com/mobse/source-code). I added an instalment instruction using the new yml file and will swiftly upload a test instruction.
@editorialbot assign me as editor
Assigned! @warrickball is now the editor
Hi @stegmaja, I'll start looking for reviewers. If there's anyone you have in mind who isn't a conflict of interest, let me know.
I'll also re-iterate @dfm's point above:
Also: while this submission waits in the queue, you might want to take a look at the JOSS review criteria especially the testing and installation/packaging. I think that these elements look like they could use some work before the review starts!
I just installed tse
and, though it worked, several points already came up:
README.md
says to navigate to mobse
to run make mobse
. It should say "Navigate to the mobse/src
directory." (as in compile.sh
).conda
steps. I didn't and the program seemed to run correctly (though without tests I can't be sure).data
folder, nor could I find a description of its contents.While I continue finding reviewers, we also need to resolve the open source status of MOBSE. I note that MOBSE is MIT-licensed, which appears consistent with TSE's licence. But MOBSE appears to be derived from (and indeed has a lot of identical code to) the original BSE, which as far as I can tell was (and still is) distributed without any licence. In it's current state, I don't think that part of the repo can be included in our review.
There are theoretically two ways to resolve this.
git clone https://gitlab.com/mobse/source-code mobse
before the existing instructions.The second option is reasonably straightforward and much more feasible than the first.
Hi @stegmaja, I'll start looking for reviewers. If there's anyone you have in mind who isn't a conflict of interest, let me know.
I'll also re-iterate @dfm's point above:
Also: while this submission waits in the queue, you might want to take a look at the JOSS review criteria especially the testing and installation/packaging. I think that these elements look like they could use some work before the review starts!
I just installed
tse
and, though it worked, several points already came up:
- The installation part of the
README.md
says to navigate tomobse
to runmake mobse
. It should say "Navigate to themobse/src
directory." (as incompile.sh
).- It isn't clear why it's necessary to run the
conda
steps. I didn't and the program seemed to run correctly (though without tests I can't be sure).- I couldn't find a description of the terminal output.
- Nothing mentioned that a CSV file would be created in the
data
folder, nor could I find a description of its contents.
Dear @warrickball,
thank you very much for serving as an editor to my code! Regarding your first points:
README.md
like you suggested.conda
steps are to ensure that the user has all the required packages installed. While most of them are indeed standard and already installed for most users, I don't think that is the case for the gala
package needed to (optionally) evolve the triples inside a Galactic potential.I will add a description of 3. and 4. shortly.
Regarding your second comment about MOBSE: There are two minor changes I did to the mobse package in mobse/src/evolve.f
and mobse/src/mobse.f
to allow compatibility between my code and MOBSE, without actually changing the physics. Now I also highlight this in the README.md
file. From that perspective would you think it is the most straightforward and user-friendly approach to only keep those two modified files in the repo but adding the rest of MOBSE with git clone ...
like you suggested?
Best regards
Jakob
Edit: 3. and 4. are also added.
Thanks for addressing these early issues. I've found two reviewers, so I'll start the proper review shortly but make a few remarks here.
Regarding your second comment about MOBSE: There are two minor changes I did to the mobse package in mobse/src/evolve.f and mobse/src/mobse.f to allow compatibility between my code and MOBSE, without actually changing the physics. Now I also highlight this in the README.md file. From that perspective would you think it is the most straightforward and user-friendly approach to only keep those two modified files in the repo but adding the rest of MOBSE with git clone ... like you suggested?
One possibility is to include a patch file and instructions on how to apply it when installing it. You could possibly even bundle a script to download, patch and install MOBSE in the appopriate place.
To be more concrete, here's how I started a patch file that I think has the desired effect.
$ git clone https://github.com/stegmaja/TSE
$ git clone git@gitlab.com:mobse/source-code.git mobse
$ cd TSE
$ diff -ruN ../mobse/src mobse/src > test.patch
$ cd ../mobse
$ patch -p1 < ../TSE/test.patch
patching file src/evolve.f
patching file src/mobse.f
So you could include the equivalent of test.patch
in this repo and apply it as part of the installation. It turns out you can also do something similar with git
. In particular, replacing the last step with
$ git apply ../TSE/test.patch
worked for me.
While experimenting, I also noticed that mobse/input/const_mobse.h
also differ. I presume that doesn't matter.
The conda steps are to ensure that the user has all the required packages installed.
That's fair though bear in mind that not all Python users have Conda, and the implication is that TSE requires Conda, which doesn't seem to be the case.
@editorialbot add @rieder as reviewer
@rieder added to the reviewers list!
@editorialbot add @katiebreivik as reviewer
@katiebreivik added to the reviewers list!
@editorialbot start review
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7102.
Submitting author: !--author-handle-->@stegmaja<!--end-author-handle-- (Jakob Stegmann) Repository: https://github.com/stegmaja/TSE Branch with paper.md (empty if default branch): Version: v2.0 Editor: !--editor-->@warrickball<!--end-editor-- Reviewers: @rieder, @katiebreivik Managing EiC: Dan Foreman-Mackey
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