[REVIEW]: AMAT: A Python package for rapid conceptual design of aerocapture and atmospheric Entry, Descent, and Landing (EDL) missions in a Jupyter environment

[whedon]

Submitting author: @athulpg007 (Athul Pradeepkumar Girija)
Repository: https://github.com/athulpg007/AMAT
Version: v2.2.3
Editor: @jbytecode
Reviewer: @astrojuanlu, @helgee
Archive: 10.5281/zenodo.5650129

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

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Markdown: [![status](https://joss.theoj.org/papers/57c18b7854b74d83e75250857716e229/status.svg)](https://joss.theoj.org/papers/57c18b7854b74d83e75250857716e229)

Reviewers and authors:

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Reviewer instructions & questions

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

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Review checklist for @astrojuanlu

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@athulpg007) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @helgee

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@athulpg007) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @astrojuanlu, @helgee it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1142

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/AERO.2010.5447017 is OK
- 10.1109/AERO.2002.1035313 is OK
- 10.17226/13117 is OK
- 10.2514/6.2003-2172 is OK
- 10.2514/1.2589 is OK
- 10.2514/1.A34121 is OK
- 10.2514/1.A34056 is OK
- 10.2514/1.A34719 is OK
- 10.2514/1.A34529 is OK
- 10.2514/1.A33997 is OK
- 10.2514/6.2007-605 is OK
- 10.2514/1.A34703 is OK
- 10.2514/1.13095 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=4.75 s (40.4 files/s, 20854.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            75          11312             75          41553
JavaScript                      11           2144           2126           8152
Jupyter Notebook                63              0          14124           5419
Python                          18           1973           3746           3902
SVG                              1              0              0           2671
CSS                              4            164             34            641
TeX                              1             25              0            196
Markdown                         2             96              0            179
reStructuredText                14            138            144            167
DOS Batch                        1              8              1             26
make                             1              4              7              9
YAML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                           192          15864          20257          62918
-------------------------------------------------------------------------------


Statistical information for the repository 'd5800a3257896aa4b39ed359' was
gathered on 2021/09/09.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Athul P. Girija                 30         46315          25145          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Athul P. Girija           29348           63.4          8.8               13.79

[jbytecode]

Dear @astrojuanlu and @helgee,

Thank you for accepting our invitation. Here is the review issue. There are 20 check items for each reviewer. Whenever you finish the corresponding item, you can check it. You can interact with the authors and the editor. Please do not hesitate to ask me if you have difficulties.

Thank you in advance!

[astrojuanlu]

I did a first pass, and opened athulpg007/AMAT#3 and athulpg007/AMAT#4 accordingly. In addition, I didn't see automated tests or contribution instructions, so for now I left those checkboxes unchecked. I still have to go over the rest.

[athulpg007]

I have addressed athulpg007/AMAT/#/3 and athulpg007/AMAT/#/4.

Also addressed athulpg007/AMAT/#/5

I will add some tests and contribution instructions later today. Thanks!

[athulpg007]

Added some tests and contribution instructions. Sorry for my late response.

[jbytecode]

@athulpg007 thank you for adding tests. It is also a good practice to add a GitHub action that performs the tests after a commit so people can see the latest changes don't break the package.

[athulpg007]

@jbytecode thanks for the comment, I will set up the GitHub action as suggested.

[whedon]

👋 @astrojuanlu, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @helgee, please update us on how your review is going (this is an automated reminder).

[athulpg007]

License has been updated to GPL-v3-or-later. Updated up header text from some files with the old CC-BY-SA-4.0 license text to reflect the new license. If this issue if resolved, I will close athulpg007/AMAT/#3.

Removed pandas and jupyterlab from setup.py Listed package and readthedocs build dependencies in docs/requirements.txt. See if this resolves athulpg007/AMAT/#5

Added GitHub action to perform tests after a commit.

[jbytecode]

Added GitHub action to perform tests after a commit.

Great! Thank you. @athulpg007

[helgee]

Quick note @athulpg007: I have verified that the Linux installation instructions are valid for macOS as well.

[helgee]

I have concluded my review and I am happy to accept this submission 🎉

[jbytecode]

@helgee thank you for your valuable review and recommendation of an accept

[athulpg007]

@helgee thank for your time and valuable review. I added Linux/MacOS to the Linux installation instructions.

[jbytecode]

@astrojuanlu sorry for pinging, how is your review going? Could you please update your status? Thank you in advance.

[jbytecode]

@astrojuanlu 👋👋👋 - could you please update your status and continue your reviewing? Please give a response and set a deadline if you are busy nowadays as we are a little bit ahead of normal reviewing timings. thank you in advance.

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/AERO.2010.5447017 is OK
- 10.1109/AERO.2002.1035313 is OK
- 10.2514/6.2003-2172 is OK
- 10.2514/1.2589 is OK
- 10.2514/1.A34121 is OK
- 10.2514/1.A34056 is OK
- 10.2514/1.A34719 is OK
- 10.2514/1.A34529 is OK
- 10.2514/1.A33997 is OK
- 10.2514/6.2007-605 is OK
- 10.2514/1.A34703 is OK
- 10.2514/1.13095 is OK

MISSING DOIs

- 10.17226/13117 may be a valid DOI for title: Vision and Voyages for Planetary Science in the Decade 2013-2022

INVALID DOIs

- None

[jbytecode]

@athulpg007 could you please

• correct the missing DOI issue as Whedon suggested above?
• or apply the pull request that I sent.

Thank you

[jbytecode]

@whedon set v2.2.3 as version

[whedon]

OK. v2.2.3 is the version.

[athulpg007]

@jbytecode applied pull request to correct missing DOI. Thank you for the edit.

[athulpg007]

@whedon check references

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/AERO.2010.5447017 is OK
- 10.1109/AERO.2002.1035313 is OK
- 10.17226/13117 is OK
- 10.2514/6.2003-2172 is OK
- 10.2514/1.2589 is OK
- 10.2514/1.A34121 is OK
- 10.2514/1.A34056 is OK
- 10.2514/1.A34719 is OK
- 10.2514/1.A34529 is OK
- 10.2514/1.A33997 is OK
- 10.2514/6.2007-605 is OK
- 10.2514/1.A34703 is OK
- 10.2514/1.13095 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jbytecode]

@whedon check references

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/AERO.2010.5447017 is OK
- 10.1109/AERO.2002.1035313 is OK
- 10.17226/13117 is OK
- 10.2514/6.2003-2172 is OK
- 10.2514/1.2589 is OK
- 10.2514/1.A34121 is OK
- 10.2514/1.A34056 is OK
- 10.2514/1.A34719 is OK
- 10.2514/1.A34529 is OK
- 10.2514/1.A33997 is OK
- 10.2514/6.2007-605 is OK
- 10.2514/1.A34703 is OK
- 10.2514/1.13095 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jbytecode]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[jbytecode]

@whedon set 10.5281/zenodo.5650129 as archive

[whedon]

OK. 10.5281/zenodo.5650129 is the archive.

[jbytecode]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/AERO.2010.5447017 is OK
- 10.1109/AERO.2002.1035313 is OK
- 10.17226/13117 is OK
- 10.2514/6.2003-2172 is OK
- 10.2514/1.2589 is OK
- 10.2514/1.A34121 is OK
- 10.2514/1.A34056 is OK
- 10.2514/1.A34719 is OK
- 10.2514/1.A34529 is OK
- 10.2514/1.A33997 is OK
- 10.2514/6.2007-605 is OK
- 10.2514/1.A34703 is OK
- 10.2514/1.13095 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2732

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2732, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03710 joss-papers#2735
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03710
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

Congratulations @athulpg007 on your article's publication in JOSS!

Many thanks to @astrojuanlu and @helgee for reviewing this, and @jbytecode for editing.

[whedon]

🎉🎉🎉 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](https://joss.theoj.org/papers/10.21105/joss.03710/status.svg)](https://doi.org/10.21105/joss.03710)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03710">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03710/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03710/status.svg
   :target: https://doi.org/10.21105/joss.03710

This is how it will look in your documentation:

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[athulpg007]

Dear @kyleniemeyer @jbytecode @astrojuanlu @helgee,

Thank you all for your efforts!

I added my name to the reviewer list, and made a small donation to support the journal.