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[REVIEW]: SEP: Source Extractor as a library #58
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/ cc @openjournals/joss-reviewers - would anyone be willing to review this submission? If you would like to review this submission then please comment on this thread so that others know you're doing a review (so as not to duplicate effort). Something as simple as Reviewer instructions
Any questions, please ask for help by commenting on this issue! 🚀 |
I will do this one. |
I'm a bit uncertain about the license part. The repo has a licenses directory that contains 3 licenses, two as .md and one as .txt. Is the fact that some of these are in .md ok for JORS? Also, the readme states "The license for all parts of the code derived from SExtractor is LGPLv3. The license for code not derived from SExtractor is MIT. The license for the library as a whole is therefore LGPLv3. The license for each file is explicitly stated at the top of each file and the full text of the licenses can be found in licenses." which is fairly clear, but it's not clear to me why the licenses file then contains the contains the BSD license as well. |
Re versions: The repo talks about version 1.0 as not yet released, discusses 0.60 as the most recent release, and also points to a software archive that contains version 0.30. The paper says that there is no software archive yet. If this JOSS submission is for version 0.60, there needs to be a software archive that contains the code from version 0.60. |
I feel like the original reference |
Thanks for the review! License: I removed the copy of the BSD license and corrected the file extensions of the MIT license to versions: I updated the link in the readme to point to the v0.6.0 zenodo archive. (v1.0.0 will be the next release of SEP which will remove deprecated features; it has not yet been released though). citation: I added the Bertin & Arnouts (1996) citation to the paper. |
Ah, now I remember why the BSD license was there. One file I could change MIT -> BSD to simply things overall; I just had a slight preference for MIT, so I started with that. |
so the readme should be changed to say this (not the details, but just that there is some BSD code too) |
@arfon, how/when does the paper get regenerated? |
@danielskatz - I currently have to do this. @whedon is gaining those super-powers soon. |
Do we need a updated paper compiling? |
yes please |
@danielskatz here you go: 10.21105.joss.00058.pdf |
re a statement of need in the paper: the repo readme probably should have a little of the paper content to explain what source extractor is and who might want to use it. This could also potentially go in docs/index.srt The license info in docs/index.srt might need to be updated? It would also be useful if the docs contained a simple tutorial/test - just one input, the code needed to do an analysis, and a correct output to compare against. |
re Community guidelines - the answers to the following are currently no. Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support Perhaps some more can be added to the README? or to a CONTRIBUTING file? |
Installation failed on my mac: tmp3:~ dsk$ pip install --no-deps sep ... [lots of cc's, with a fair number of warnings]
Command "/usr/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/bp/2p2fmtrx0w100fzhrllbvy1w0000gn/T/pip-build-DagS36/sep/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /var/folders/bp/2p2fmtrx0w100fzhrllbvy1w0000gn/T/pip-BGrAfD-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/bp/2p2fmtrx0w100fzhrllbvy1w0000gn/T/pip-build-DagS36/sep/ I assume this permission error is something easy to fix, but I'm unclear why others would not have the same issue, which makes me think that either there's something odd on my system (which is possible) or this is common and should be addressed in the documentation. |
@danielskatz this is really useful feedback, but in my role as self-appointed derail police please consider filing a ticket against the target repo bug tracker and linking to this issue instead of pasting the body of error messages into this thread. |
responding in the other issue: openjournals/joss#163 |
@whedon commands |
Here are some things you can ask me to do:
🚧 Important 🚧 This is all quite new. Please make sure you check the top of the issue after running a @whedon command (you might also need to refresh the page to see the issue update). |
@whedon assign @danielskatz as reviewer |
OK, the reviewer is @danielskatz |
Thanks for the excellent feedback @danielskatz!
|
Note that you should go to http://sep.readthedocs.io/en/latest to see the latest docs build. I'm planning to do a new release soon, at which point the docs changes will be visible at the default url http://sep.readthedocs.io. |
Thanks - this enables me to check another box and succeed in the install. However, there are still some issues: ./test.py gives me an error: the first line seems to be looking for a file that doesn't exist. |
The |
I have pytest installed (via pip). Perhaps I need to do something with my path? |
ok, resolved - not sure if this should be part of the docs or not. Now that I have this working, I get 20 successes and 1 failure: tmp3:sep dsk$ ./test.py test.py F.................... =================================== FAILURES ===================================
test.py:90: /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/testing/utils.py:1181: in assert_allclose comparison = <function compare at 0x10e1b21b8>
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/testing/utils.py:644: AssertionError |
This is a bug that is fixed on master (you have the master version of the tests, but the release version of the library). I'm planning to release a new version with the fix soon, but want to address any remaining issues here first. |
Is it worth updating the paper for the new version? I think that would be best, but if not, I will approve this one. |
I agree. I'll do the release and post here after the paper is updated (including a new zenodo DOI). |
I updated the repository (particularly codemeta.json) with the DOI for the new version (v1.0.0). @arfon If you regenerate the paper, will it reflect the changes in codemeta.json? |
Currently no. That would be very nice if it did 😁 Would you mind adding the DOI link to this issue too? |
SEP v1.0.0 DOI: http://dx.doi.org/10.5281/zenodo.159035 |
@danielskatz by the looks of the checklist I think we're good to accept here. Can you confirm? |
No, I want to check this new version first. On Oct 4, 2016, at 17:31, Arfon Smith <notifications@github.commailto:notifications@github.com> wrote: @danielskatzhttps://github.com/danielskatz by the looks of the checklist I think we're good to accept here. Can you confirm? — |
I'm happy with the code now. I see two possible issues still, however: 1 - in the paper, I see "Software Archive: PENDING" This should be updated to http://dx.doi.org/10.5281/zenodo.159035 Otherwise, I'm happy to accept this. |
👍 I can do these two things.
🎉 |
@whedon commands |
Here are some things you can ask me to do:
🚧 Important 🚧 This is all quite new. Please make sure you check the top of the issue after running a @whedon command (you might also need to refresh the page to see the issue update). |
@danielskatz many thanks for the thorough review! @kbarbary your paper is now accepted into JOSS. Your DOI is http://dx.doi.org/10.21105/joss.00058 🎉 🚀 💥 |
Thanks @arfon and thanks @danielskatz for the review; it improved the package! |
Submitting author: @kbarbary (Kyle Barbary)
Repository: https://github.com/kbarbary/sep
Version: v1.0.0
Editor: @arfon
Reviewer: @danielskatz
Archive: http://dx.doi.org/10.5281/zenodo.159035
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Reviewer questions
Conflict of interest
General checks
Functionality
Documentation
Software paper
Paper PDF: 10.21105.joss.00058.pdf
paper.md
file include a list of authors with their affiliations?The text was updated successfully, but these errors were encountered: