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[REVIEW]: AtomNeb: IDL Library for Atomic Data of Ionized Nebulae #898

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whedon opened this Issue Aug 17, 2018 · 59 comments

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whedon commented Aug 17, 2018

Submitting author: @danehkar (Ashkbiz Danehkar)
Repository: https://github.com/atomneb/AtomNeb-idl
Version: v0.0.2
Editor: @arfon
Reviewer: @mgalloy, @mdpiper
Archive: 10.5281/zenodo.2584420

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/7205fc05ec14970b77c4551c2fe6b0bf"><img src="http://joss.theoj.org/papers/7205fc05ec14970b77c4551c2fe6b0bf/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/7205fc05ec14970b77c4551c2fe6b0bf/status.svg)](http://joss.theoj.org/papers/7205fc05ec14970b77c4551c2fe6b0bf)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@mgalloy & @mdpiper, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

Please try and complete your review in the next two weeks

Review checklist for @mgalloy

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: v0.0.2
  • Authorship: Has the submitting author (@danehkar) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: 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

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @mdpiper

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: v0.0.2
  • Authorship: Has the submitting author (@danehkar) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: 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

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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whedon commented Aug 17, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mgalloy, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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For a list of things I can do to help you, just type:

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whedon commented Aug 17, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 17, 2018

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mdpiper commented Aug 20, 2018

Info for contributors (the last item in the Documentation checklist) isn't present, so I made a request in atomneb/AtomNeb-idl#1.

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mdpiper commented Aug 20, 2018

This package doesn't include unit tests (second-to-last item in the Documentation checklist). I've made a request for testing with atomneb/AtomNeb-idl#2.

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mdpiper commented Aug 24, 2018

The package isn't stamped with a release, so I created atomneb/AtomNeb-idl#3 to request one. This addresses the third item in the General checks checklist.

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mdpiper commented Aug 24, 2018

The package doesn't include API documentation (the fourth item in the Documentation checklist). I've requested this in atomneb/AtomNeb-idl#4.

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mdpiper commented Aug 30, 2018

I offered a PR (atomneb/AtomNeb-idl#5) to automatically locate the package data from the examples.

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mdpiper commented Aug 30, 2018

Created an issue (atomneb/AtomNeb-idl#6) to address package installation (the first item in the Functionality checklist).

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mdpiper commented Sep 6, 2018

My review of AtomNeb is complete. The library and its associated paper are appropriate for publication in JOSS, pending @danehkar's responses to the minor issues I've opened in the repository.

(@arfon I'll complete the open items in the review checklist once these issues have been addressed.)

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arfon commented Sep 7, 2018

Thanks @mdpiper!

@mgalloy - how are you getting along here?

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danehkar commented Sep 11, 2018

@mdpiper thank you for your review. I will solve those minor issues. did you also finish your review of proEQUIB?

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mgalloy commented Sep 11, 2018

Catching up after some travel. Added some comments on issues opened by @mdpiper.

I think it would also be useful to add a short sentence after the opening description of AtomNeb database in your README that indicates precisely how AtomNeb-idl relates to it. Does it contain the data, access them via the web, access data you have generated, etc.?

I should be able to start looking at proEQUIB shortly.

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arfon commented Nov 4, 2018

@danehkar - I think this review is waiting on you at this point?

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danehkar commented Nov 27, 2018

@mdpiper Info for contributors (the last item in the Documentation checklist) isn't present, so I made a request in atomneb/AtomNeb-idl#1.

I included CONTRIBUTING.md in the AtomNeb-idl repository that contains some guidelines for contributors. Now I closed the issue atomneb/AtomNeb-idl#1.

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danehkar commented Nov 27, 2018

@mdpiper I offered a PR (atomneb/AtomNeb-idl#5) to automatically locate the package data from the examples.

Thank you! I merged your PR into the repository. Now the package data are automatically located in the examples: atomneb/AtomNeb-idl/examples.

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danehkar commented Nov 27, 2018

@mdpiper Created an issue (atomneb/AtomNeb-idl#6) to address package installation (the first item in the Functionality checklist).

Thank you for your installation note suggestion. I added an installation note in README.md:

To install the AtomNeb database and its API library, simply add the path of this package directory to your IDL path. This package requires IDL version 7.1 or later. For more information about the path management in IDL, read the tips for customizing IDL program path provided by Harris Geospatial Solutions or the IDL library installation note by David Fanning in the Coyote IDL Library.

Now I closed the issue atomneb/AtomNeb-idl#6.

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mdpiper commented Nov 28, 2018

@danehkar With your recent updates, I've marked as complete a few more items on the checklist.

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labarba commented Jan 19, 2019

👋 @danehkar — We haven't heard from you in a while. What's your status? Are you able to work on this revision soon?

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danehkar commented Jan 25, 2019

@labarba I am currently working on those issues. Hopefully, I will resolve them in a month. Thank you for your patience.

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danehkar commented Feb 19, 2019

The package doesn't include API documentation (the fourth item in the Documentation checklist). I've requested this in atomneb/AtomNeb-idl#4.

@mdpiper The documentation is now hosted at https://atomneb.github.io/AtomNeb-idl/doc/

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danehkar commented Feb 20, 2019

This package doesn't include unit tests (second-to-last item in the Documentation checklist). I've made a request for testing with atomneb/AtomNeb-idl#2.

@mdpiper I added mgunit in the folder test_mgunit for automated tests.

To test, you can download AtomNeb-idl with its dependencies as follows

git clone --recursive https://github.com/atomneb/AtomNeb-idl.git

You need to unpack rc_o_iii_SSB17.fits.tar.gz in atomic-data-rc:

tar -xvf rc_o_iii_SSB17.fits.tar.gz

To run the test, you need to run the following command:

idl test_all.pro

There should not be any errors in test-results.html.

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mgalloy commented Feb 20, 2019

I ran the tests and confirm they all passed. One note: I had to go get mgutlibtestcase__define.pro — it is not part of mgunit. I would add it to the test_mgunit directory, possibly renaming to atomnebuttestcase__define.pro.

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danehkar commented Feb 21, 2019

I ran the tests and confirm they all passed. One note: I had to go get mgutlibtestcase__define.pro — it is not part of mgunit. I would add it to the test_mgunit directory, possibly renaming to atomnebuttestcase__define.pro.

Thank you for testing. I will copy mgutlibtestcase__define.proto the test_mgunit directory, and rename it to atomnebuttestcase__define.pro.

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danehkar commented Feb 21, 2019

@arfon I would like to rename the title of this submission (898) from AtomNeb: Atomic Data for Ionized Nebulae to AtomNeb: IDL Library for Atomic Data of Ionized Nebulae since I am working on a similar python package, and I want to distinguish between them. I will upload the revised paper of this IDL library soon.

@arfon arfon changed the title [REVIEW]: AtomNeb: Atomic Data for Ionized Nebulae [REVIEW]: AtomNeb: IDL Library for Atomic Data of Ionized Nebulae Feb 21, 2019

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arfon commented Feb 21, 2019

@arfon I would like to rename the title of this submission (898) from AtomNeb: Atomic Data for Ionized Nebulae to AtomNeb: IDL Library for Atomic Data of Ionized Nebulae since I am working on a similar python package, and I want to distinguish between them. I will upload the revised paper of this IDL library soon.

OK, no problem. I've updated the issue title here.

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whedon commented Feb 27, 2019

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danehkar commented Mar 1, 2019

@mgalloy Thank you very much for your test and review of this package. I look forward to @mdpiper's comments.

@arfon Thank you for regenerating the article proof. It looks fine.

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mdpiper commented Mar 1, 2019

@danehkar With your recent updates, I've marked off the last three items on my checklist, completing my review. One minor issue, which I defer to @arfon, is the version on the software (v0.0.1) doesn't quite follow semantic versioning. If this isn't an issue for JOSS, it isn't for me either.

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arfon commented Mar 2, 2019

@danehkar With your recent updates, I've marked off the last three items on my checklist, completing my review. One minor issue, which I defer to @arfon, is the version on the software (v0.0.1) doesn't quite follow semantic versioning. If this isn't an issue for JOSS, it isn't for me either.

We can update the version at the end of the review if needed. Just let me know what version you're reviewing.

Also, we don't insist on using semantic versioning.

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danehkar commented Mar 4, 2019

Considering Semantic Versioning (MAJOR.MINOR.PATCH), the code did not have any MAJOR change such as incompatible API changes, and any MINOR changes (e.g. adding a new functionality) since it was submitted. It has some changes in comments for documentation, so I changed the PATCH version from v0.0.1 to v0.0.2. I added an MGUnit tester, while the program functions were not changed, so there are no major or minor changes.

@arfon Please update Version from v0.0.1 to v0.0.2.

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arfon commented Mar 4, 2019

@whedon set v0.0.2 as version

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whedon commented Mar 4, 2019

OK. v0.0.2 is the version.

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arfon commented Mar 4, 2019

@whedon generate pdf

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whedon commented Mar 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 4, 2019

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arfon commented Mar 4, 2019

@danehkar - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

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danehkar commented Mar 6, 2019

@arfon I did the proof correction in the paper. You can check it here: 799. Please regenerated the final pdf for the paper. I also made an archive of the reviewed software in Zenodo here: https://doi.org/10.5281/zenodo.2584420

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arfon commented Mar 6, 2019

@whedon generate pdf

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whedon commented Mar 6, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 6, 2019

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arfon commented Mar 6, 2019

@whedon set 10.5281/zenodo.2584420 as archive

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whedon commented Mar 6, 2019

OK. 10.5281/zenodo.2584420 is the archive.

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arfon commented Mar 6, 2019

@whedon accept

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whedon commented Mar 6, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Mar 6, 2019

Check final proof 👉 openjournals/joss-papers#539

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#539, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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whedon commented Mar 6, 2019


OK DOIs

- 10.1086/498148 is OK
- 10.1051/0004-6361/200911712 is OK
- 10.1088/0004-637X/744/2/99 is OK
- 10.1051/0004-6361/201323152 is OK
- 10.1051/aas:2000139 is OK
- 10.1086/191479 is OK
- 10.1093/mnras/272.2.369 is OK
- 10.1051/aas:1998319 is OK
- 10.1093/mnras/272.1.41 is OK
- 10.1111/j.1745-3933.2012.01300.x is OK
- 10.1093/mnrasl/slt049 is OK
- 10.1051/0004-6361/201116511 is OK
- 10.1051/0004-6361/201116511e is OK
- 10.1093/mnras/stx1189 is OK
- 10.1093/mnras/stt1116 is OK
- 10.1093/mnras/stu203 is OK
- 10.3847/0004-6256/151/2/38 is OK
- 10.1017/pasa.2018.1 is OK
- 10.21105/joss.00899 is OK
- 10.1086/316190 is OK
- 10.1086/319184 is OK
- 10.1046/j.1365-8711.2003.06371.x is OK
- 10.1111/j.1365-2966.2005.09381.x is OK
- 10.1086/524378 is OK
- 10.1051/0004-6361:20010923 is OK
- 10.1051/0004-6361/201015362 is OK

MISSING DOIs

- https://doi.org/10.1051/0004-6361:20020263 may be missing for title: Recombination coefficients for O II lines at nebular temperatures and densities
- https://doi.org/10.1016/0032-0633(92)90127-a may be missing for title: Total and effective radiative recombination coefficients
- https://doi.org/10.1117/12.959819 may be missing for title: FITS - a Flexible Image Transport System

INVALID DOIs

- None
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arfon commented Mar 6, 2019

@danehkar - could you check those potentially missing DOIs and see if they are the correct ones for some of your references?

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danehkar commented Mar 6, 2019

@arfon Those references with missing DOI are from Astronomy & Astrophysics and Astronomy and Astrophysics Supplement:
1994A&A...282..999S
1991A&A...251..680P
1981A&AS...44..363W
These two journals (Astronomy & Astrophysics and Astronomy and Astrophysics Supplement) did not assign any Digital Object Identifier (DOI) to their publications prior to 2001, and they still have not assigned any DOI to their papers published before 2001.

Those DOI identified by the robot whedon are NOT related to these 3 references:

I confirm that the references in paper.bib are correct, as they are BibTex entries from adsabs.harvard.edu.

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arfon commented Mar 6, 2019

@whedon accept deposit=true

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whedon commented Mar 6, 2019

Doing it live! Attempting automated processing of paper acceptance...

@whedon whedon added the accepted label Mar 6, 2019

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whedon commented Mar 6, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#540
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00898
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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arfon commented Mar 6, 2019

@mgalloy, @mdpiper - many thanks for your reviews here

@danehkar - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Mar 6, 2019

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whedon commented Mar 6, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.00898/status.svg)](https://doi.org/10.21105/joss.00898)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00898">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00898/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00898/status.svg
   :target: https://doi.org/10.21105/joss.00898

This is how it will look in your documentation:

DOI

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