[REVIEW]: PySHbundle: A Python software to convert GRACE Spherical Harmonic Coefficients to gridded mass change fields

[editorialbot]

Submitting author: @lsmvivek (Vivek Kumar Yadav)
Repository: https://github.com/GESS-research-group/pyshbundle
Branch with paper.md (empty if default branch):
Version: v0.3.0
Editor: @hugoledoux
Reviewers: @tsutterley, @MMesch
Archive: Pending

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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) by leaving comments 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

@tsutterley & @MMesch, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @hugoledoux know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @tsutterley

📝 Checklist for @MMesch

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.26 s (177.2 files/s, 82006.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          15            977           1433           1777
Markdown                        17            387              0           1106
Jupyter Notebook                 5              0          14443            710
YAML                             5             13              8            279
TeX                              1             14              0             77
TOML                             1              5              0             48
HTML                             1              2              0              9
XML                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            46           1398          15884           4007
-------------------------------------------------------------------------------

Commit count by author:

   185	Abhishek Mhamane
   182	Amin Shakya
   167	lsmvivek
    44	mn5hk
    37	Vivek
     7	vivek
     3	Walling9
     1	Bramha Dutt Vishwakarma

[editorialbot]

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

✅ OK DOIs

- 10.1007/s10712-022-09754-9 is OK
- 10.5281/zenodo.8075728 is OK
- 10.18419/opus-9193 is OK
- 10.1002/2017WR021150 is OK
- 10.1029/98JB02844 is OK
- 10.1029/2018GC007529 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: ggtools 1.1.7
- No DOI given, and none found for title: SHBUNDLE 2021
- No DOI given, and none found for title: GitHub - Strawpants/GRACE-filter: Contains softwar...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1199

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[tsutterley]

Review checklist for @tsutterley

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 https://github.com/GESS-research-group/pyshbundle?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@lsmvivek) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[MMesch]

Review checklist for @MMesch

I'm inlining comments as I'm progressing through the review

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy
  https://github.com/openjournals/joss/blob/master/COI.md 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
  https://joss.theoj.org/about#code_of_conduct.

General checks

• Repository: Is the source code for this software available at the
  https://github.com/GESS-research-group/pyshbundle?

  • a priori yes but completeness of the available source code will be checked later
  • this check could probably be automated by JOSS

• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved https://opensource.org/licenses/alphabetical software license?

  • GPL
  • this check could probably be automated by JOSS

• Contribution and authorship: Has the submitting author (@lsmvivek) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

  • a priori yes

• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort

  • As a rule of thumb, JOSS’ minimum allowable contribution should represent not less than three months of work for an individual. Some factors that may be considered by editors and reviewers when judging effort include:
  • Age of software (is this a well-established software project) / length of commit history.
    • first commit in Git Repo in 2022
    • regular contributions since 2022.
    • The original SHBundle code seems to be from 1994 as stated in the paper.
  • Number of commits.
    • 754 commits total
  • Number of authors.
    • three main contributors
  • Total lines of code (LOC). Submissions under 1000 LOC will usually be flagged those under 300 LOC will be desk rejected.
    • 4007
  • Whether the software has already been cited in academic papers.
    • probably not in the form of the python wrapper, at least I can't find any references but that's not unusual if this is the first article. The original software SHBundle has been cited. Google Scholar shows 44 results for the search term "shbundle stuttgart" and some of them at least reference the "parent" of this software.
  • Whether the software is sufficiently useful that it is likely to be cited by your peer group.
    • Can't fully judge on this at this point.

• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.

  • can't judge at this point

• Reproducibility: If the paper contains original results, results are entirely
  reproducible by reviewers. If the paper contains no original results, please check this item.

• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy
  https://joss.readthedocs.io/en/latest/policies.html?highlight=animal#joss-policies? If the paper contains no such data, please check this item.

  • doesn't apply

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, who the target audience is, and its relation to other work?
• 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
  https://pandoc.org/MANUAL.html#extension-citations?

Random

Repository

• The GitHub About section "Convert SH bundle matlab codes to python" is not very evocative and maybe even a bit misleading. I suggest updating to something closer to the README.md title.

Paper

[hugoledoux]

@MMesch @tsutterley just a reminder so that you don't forget this review

[tsutterley]

thanks @hugoledoux! back at work 😵‍💫

[tsutterley]

Some overall comments for PySHbundle for #7550:

I put together some issues (GESS-research-group/pyshbundle#132 GESS-research-group/pyshbundle#133 GESS-research-group/pyshbundle#134) that I found looking over the documentation. I still need to build an environment to run the programs themselves. I thought that the Theoretical Background page was really good.

Line-by-Line

• Line 18 All NASA satellite products have processing levels (see NASA Earthdata learn site)
• Line 18 I think "GRACE has transformed Geosciences" is a little strong. I might also rephrase the earlier portion of the sentence as "One of the major mechanisms of short term mass transport is the redistribution of water".
• Line 23 "The L2 spherical harmonic data are typically noisy, which necessitates the use of spectral filtering. The data also have to be corrected for known artifacts and contaminating geophysical signals, such as solid Earth processes in the case of isolating TWSA."
• Line 26 probably could be "most L3 users"
• Line 27 "The majority" and "most often use the off-the-shelf L3 products"
• Line 30 "called PySHbundle, was developed to ease the conversion of GRACE L2"
• Line 34 "The NASA/DLR GRACE and NASA/GFZ GRACE-FO twin satellite missions measure changes in the Earth's gravitational field by measuring their inter-satellite distance. Changes in the local gravity field affect the orbit of each satellite, which is recorded with the onboard ranging system."
• Line 42 this sentence starts in the middle??
• Line 42 Should note that the JPL mascons are created directly from the Level-1B satellite ranges
• Line 47 Might want to mention frommle2 from @strawpants instead of his GRACE-filter set of programs
• Line 51 "Spherical"
• Line 52 "while the latest release was from 2021"
• Line 71 Degree 1 isn't just poorly measured, it is inherently zero in a center-of-mass (CM) reference frame. Also "JPl"→"JPL" and "ITGZ"→"GFZ"

[lsmvivek]

@hugoledoux @tsutterley
I have addressed:

• The above issues
• The issues raised at: GESS-research-group#132, GESS-research-group#134

All changes are in joss-review-7550 branch

[strawpants]

Just noticed that frommle2 was mentioned in this thread. Most of the work has now moved to shxarray. So if you decide to mention it it's better to mention shxarray, because it's actively maintained.

thanks,
Roelof

[hugoledoux]

All changes are in joss-review-7550 branch

if that branch is only temporary and you'll merge soon it's fine. But if you want our bot to build the paper from that specific branch then I can change that in the details above this page. Let me know.

[lsmvivek]

if that branch is only temporary and you'll merge soon it's fine. But if you want our bot to build the paper from that specific branch then I can change that in the details above this page. Let me know.

Kindly suggest how do I implement the changes and issues raised by the reviewer's?

Looking at some other completed submissions, I believe the author's make the changes and merge it into the main branch (which is being used for review). I did not merge the changes yet for your input.

[hugoledoux]

okay all is fine, make some changes and then merge them.

I was just warning you that if you modify the paper and ask our bot to compile the PDF it will use the main branch.

[lsmvivek]

I was just warning you that if you modify the paper and ask our bot to compile the PDF it will use the main branch.

I have merged the branch joss-review-7550 branch, where I implemented the changes, into the main branch.

[hugoledoux]

@MMesch just a small reminder not to forget this review

[MMesch]

I started going through it in detail. Opened a first issue GESS-research-group/pyshbundle#138 and associated pr GESS-research-group/pyshbundle#137 .