[REVIEW]: ClassipyGRB: Machine Learning-Based Classification and Visualization of Gamma Ray Bursts using t-SNE #5923
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@wkerzendorf — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate! 👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting 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 the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible! |
Review checklist for @dfmConflict of interest
Code of Conduct
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Functionality
Documentation
Software paper
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@wkerzendorf — This is a ping to keep this on your radar. Please generate your checklist and start going through it ASAP! Thanks!! |
Review checklist for @wkerzendorfConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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Functionality Installing the software worked but subsequently running the examples did not: ---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[1], line 3
1 from ClassiPyGRB import SWIFT
2 swift = SWIFT(res=64)
----> 3 df = swift.obtain_data(name='GRB211211A')
File ~/miniconda/envs/joss_classipygrb/lib/python3.8/site-packages/ClassiPyGRB/_swift.py:174, in SWIFT.obtain_data(self, name, check_disk)
172 raise RuntimeError(f"Error from tables when trying to read: {e}. Try to re-install tables package.")
173 else:
--> 174 with resources.open_text(summary_tables, 'summary_general.txt') as file:
175 grb_names, ids = np.genfromtxt(file, delimiter="|", dtype=str, usecols=(0, 1), unpack=True,
176 autostrip=True)
177 if len(grb_names) == 0 or not isinstance(grb_names, (Sequence, Mapping, np.ndarray)):
File ~/miniconda/envs/joss_classipygrb/lib/python3.8/importlib/resources.py:126, in open_text(package, resource, encoding, errors)
124 if reader is not None:
125 return TextIOWrapper(reader.open_resource(resource), encoding, errors)
--> 126 _check_location(package)
127 absolute_package_path = os.path.abspath(package.__spec__.origin)
128 package_path = os.path.dirname(absolute_package_path)
File ~/miniconda/envs/joss_classipygrb/lib/python3.8/importlib/resources.py:82, in _check_location(package)
80 def _check_location(package):
81 if package.__spec__.origin is None or not package.__spec__.has_location:
---> 82 raise FileNotFoundError(f'Package has no location {package!r}')
FileNotFoundError: Package has no location <module 'ClassiPyGRB.summary_tables' (namespace)>There are also no automated ways to run the tests or descriptions of how to run tests. There are also no CI/CD workflows for this repository. The repository has a rudimentary contribution guidelines but without testing frameworks it might be hard to check if contributions break existing code. Documentation The Documentation also only exists of a single Paper The paper has several typos and I would suggest re-reading it carefully and employing a grammar checker. The paper does not make a complete State of the Field analysis but claims that have not previously been identified by other groups without giving specific references. The paper also often uses qualitative words such as _easy _ and fast without quantitative description of what makes it easy and or fast (these are just some examples). |
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@KenethGarcia — I wanted to check in to see if you've had an opportunity to look at any of the issues I opened or @wkerzendorf's comments above? It's useful to iteratively address comments as the review progresses. Let us know when you'll have a chance to work on this! |
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@dfm Thank you for reaching out! We appreciate your proactive approach to the ongoing review. Actually, we are addressing the issues you've opened, as well as carefully considering @wkerzendorf comments. We expect to answer the issues in the next days for further comments. Actually, there are minor updates in the GitHub repository, and we are implementing a conda installation with an updated catalogue of GRBs (up to 2023). |
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Dear @dfm and @wkerzendorf, We are writing to leave you with some updates on changes that have been made to ClassiPyGRB based on your comments and feedback: Regarding the comment about “Installation and cross-platform support”:We updated the installation tutorial by adding conda/mamba installation instructions. We conducted several hours of testing and environment validation to ensure a seamless and reliable installation process. Furthermore, we also remark that in previously installed tkinter/pytables OS, the requirements of creating the conda environment are unnecessary. About testing and CI workflows:We have implemented the following documentation for Test Running Procedure:
About the Statement of Need:We added a new section where we specify:
Thank you very much for your comments, we will be looking forward to any additional suggestions to this library. Best Regards |
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@KenethGarcia — Thanks for your work on this. I've now finished going through my checklist and opened some last small issues and one PR. Please take a look at those! After those are finished I'm happy to recommend acceptance. |
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@wkerzendorf — Can you also take a look at this again soon and try to go through your last checklist items? Thanks!! |
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Thank you @dfm for your comments! We will work around the current documentation and additional comments that you have submitted. Best Regards! |
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@wkerzendorf — Pinging you to keep this on your radar! Please try to get back to this ASAP. Many thanks! |
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Dear @dfm, As you request, we have added:
Thank you for the indications and we will stay in contact, Best regards, Keneth @editorialbot generate pdf |
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@editorialbot set v1.1.0 as version |
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Done! version is now v1.1.0 |
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@editorialbot set 10.5281/zenodo.10909942 as archive |
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Done! archive is now 10.5281/zenodo.10909942 |
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@KenethGarcia — Thank you!! Everything is looking good over here. I'm still waiting on a final word from @wkerzendorf, since the checklist isn't fully completed. I've sent several emails as well - hoping we hear back soon! |
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All looks good. I'm happy to accept. |
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Thanks @wkerzendorf!! |
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@editorialbot recommend-accept |
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👋 @openjournals/aass-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5230, then you can now move forward with accepting the submission by compiling again with the command |
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@wkerzendorf — Many thanks for your review here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!! @KenethGarcia — Your paper is now accepted and published in JOSS! ⚡🚀💥 |
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Thank you so much @dfm @wkerzendorf ! |
Submitting author: @KenethGarcia (Keneth Stiven Garcia Cifuentes)
Repository: https://github.com/KenethGarcia/ClassiPyGRB
Branch with paper.md (empty if default branch):
Version: v1.1.0
Editor: @dfm
Reviewers: @wkerzendorf, @dfm
Archive: 10.5281/zenodo.10909942
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