[REVIEW]: From Maps to Models - Tutorials for structural geological modeling using GemPy and GemGIS

[whedon]

Submitting author: !--author-handle-->@AlexanderJuestel<!--end-author-handle-- (Alexander Jüstel) Repository: https://github.com/cgre-aachen/gemgis_data Branch with paper.md (empty if default branch): Version: 1.0.0 Editor: !--editor-->@acocac<!--end-editor-- Reviewers: @BenjMy, @jwagemann Archive:

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/5e6ad1eedf43a1175c41e188b2881941"><img src="https://jose.theoj.org/papers/5e6ad1eedf43a1175c41e188b2881941/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/5e6ad1eedf43a1175c41e188b2881941/status.svg)](https://jose.theoj.org/papers/5e6ad1eedf43a1175c41e188b2881941)

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

@BenjMy & @jwagemann, 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/jose-reviews/invitations

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

Review checklist for @BenjMy

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• [x] Repository: Is the source for this learning module available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
• [x] Version: 1.0.0
• [x] Authorship: Has the submitting author (@AlexanderJuestel) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• [x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• [x] Installation instructions: Is there a clearly stated list of dependencies?
• [x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

• [x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
• [x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• [x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• [x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• [x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
• [x] Description: Does the paper describe the learning materials and sequence?
• [x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
• [x] Could someone else teach with this module, given the right expertise?
• [x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @jwagemann

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• [x] Repository: Is the source for this learning module available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
• [x] Version: 1.0.0
• [x] Authorship: Has the submitting author (@AlexanderJuestel) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• [x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• [x] Installation instructions: Is there a clearly stated list of dependencies?
• [x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

• [x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
• [x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• [x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• [x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• [x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
• [x] Description: Does the paper describe the learning materials and sequence?
• [x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
• [x] Could someone else teach with this module, given the right expertise?
• [x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[jwagemann]

Hi @AlexanderJuestel , thank you for the great revisions to the tutorial. It is now much clearer and also easier to follow for a reader / learner.

Before I can tick all boxes, I have some small suggestions for improvement:

• Version: I still see a version mismatch - last release of the repo was on 29 December 2022 with v.0.0.1?
• README needs to be updated:
  • Target audience: there is a spelling mistake ‘Lectures’ and it should read ‘Lecturers’
  • List of dependencies on README:
    • Would be good to list the packages together with their versions used
  • The outline seems to be slightly different from the outline here, correct?
• Links on the outline needs to be updated:
  • Try to make it ‘browsable’ via nbviewer: https://nbviewer.org/github/cgre-aachen/gemgis_data/blob/main/notebooks/00_introduction_to_structural_modeling.ipynb#installation-of-gempy-and-gemgis
  • You have to use relative paths for the notebook links: If I want to open a notebook under 2 or 3, I get referred back to Github
• Binder seems to reflect a different organisation of the notebooks. When I open the Binder image, it is not easy for me to find the notebooks outline as described on the repo. Try to make it for learners easy to get started. Best would be to have the starting notebook right in the home directory of the binder image and from this notebook, learners can navigate themselves through the course content.

I did not revise the paper, as it seems that it has not been updated, correct? The only version I found was from 1 December 2022.

[AlexanderJuestel]

@jwagemann thanks for checking some boxes! Let me get back to your comments right away!

• I would suggest a bumping of the version and a new release once the paper is ready for publication. Would that be okay with you?

• The paper was updated a couple of times. I have attached the latest build of the paper from 3 weeks ago (https://github.com/cgre-aachen/gemgis_data/actions/runs/4689904821)

• The spelling mistake was fixed in https://github.com/cgre-aachen/gemgis_data/commit/0256472d714cc8feff01da62a74b4add4890d21e

• The main dependencies and their tested versions were added in https://github.com/cgre-aachen/gemgis_data/commit/5b635a267102045174fb2ab788fa7205e66c84e0

• I adapted the outline and added NBViewer links to the notebooks linked in the readme in https://github.com/cgre-aachen/gemgis_data/commit/cc91fd46b19c9972937f15553114b82947555547

I will work on the relative paths tomorrow and post an update as soon as possible :)

paper.zip

[jwagemann]

Hi @AlexanderJuestel , thanks for you swift response. I think you have to activate the command @whedon generate pdf to regenerate your pdf in the JOSE format. I had a look at the md file and I ticked the remaining boxes.

@acocac All good on my side, after Alex changed the paths of the notebooks. I can't tick the box with the version, but I am happy as Alex proposed, to change the version to 1.0.0 once the paper will be published.

[AlexanderJuestel]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[AlexanderJuestel]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[AlexanderJuestel]

Good morning @acocac and @jwagemann,

I changed the links according to the recommendations of @jwagemann in https://github.com/cgre-aachen/gemgis_data/commit/2c4666f2b68bbaa80cba0f75795cc693d3ff9582. To be honest, I did not know NBViewer before and this adds a lot of value to everything! Thanks for the hint!

If you are fine with everything now, I would create a 1.0.0 release and the submission would be ready for publication from my side :)

[AlexanderJuestel]

@whedon check references

[whedon]

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

OK DOIs

- 10.5281/zenodo.4569086 is OK
- 10.5194/gmd-12-1-2019 is OK
- 10.21105/joss.01450 is OK
- 10.5281/zenodo.4572994 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/j.pepi.2008.06.013 is OK
- 10.1007/978-94-011-2556-7_11 is OK
- 10.1130/GES02455.1 is OK
- 10.1007/BF02775087 is OK
- 10.1007/978-1-4615-9630-1 is OK
- 10.21105/joss.03709 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[acocac]

If you are fine with everything now, I would create a 1.0.0 release and the submission would be ready for publication from my side :)

@jwagemann, only a last item in your checklist, can you confirm if everything is ok with the version? thank you

[AlexanderJuestel]

If there are no further comments, I will release the final version so @jwagemann can check her last box

[AlexanderJuestel]

I have created a 1.0.0 release: https://github.com/cgre-aachen/gemgis_data/releases/tag/v1.0.0

The Zenodo integration failed right now. I am working on a fix!

[AlexanderJuestel]

@acocac, do you think we can proceed with the publication of the article these days?

Cheers Alex

[acocac]

@acocac, do you think we can proceed with the publication of the article these days?

Cheers Alex

Hi @AlexanderJuestel, I'm trying to follow the editorial procedure of JOSE. Please @jwagemann confirm all is ok with the version and complete the checklist 🙏

[AlexanderJuestel]

@acocac it seems like @jwagemann has checked all the boxes :)

[acocac]

@acocac it seems like @jwagemann has checked all the boxes :)

Hi @AlexanderJuestel glad to hear the checklist is complete! Congrats for the hardwork 🚀

Let me proceed with the publication between today evening and tomorrow. Thanks for your understanding.

[acocac]

@whedon check repository

[whedon]

Wordcount for paper.md is 2694

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.60 s (128.9 files/s, 116232.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                51              0          62289           5731
Markdown                        10            168              0            426
QML                              1              3              0            240
XML                              8              0              0            221
TeX                              1             14              0            168
YAML                             4             13              9             82
Python                           2             16             16             30
-------------------------------------------------------------------------------
SUM:                            77            214          62314           6898
-------------------------------------------------------------------------------

Statistical information for the repository 'cb55e0469da4b2c5a46e4381' was
gathered on 2023/05/15.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
AlexanderJuestel                 5            65              3          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
AlexanderJuestel             62           95.4          0.1                8.06

[acocac]

I have created a 1.0.0 release: https://github.com/cgre-aachen/gemgis_data/releases/tag/v1.0.0

The Zenodo integration failed right now. I am working on a fix!

@AlexanderJuestel Any updates on the issue for archiving v1.0.0 in Zenodo?

[AlexanderJuestel]

@acocac, I uploaded the repository manually. You can find it at: 10.5281/zenodo.7938495

[acocac]

@whedon set 10.5281/zenodo.7938495 as archive

[whedon]

OK. 10.5281/zenodo.7938495 is the archive.

[acocac]

@whedon set 1.0.0 as version

[whedon]

OK. 1.0.0 is the version.

[acocac]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[acocac]

@whedon check references

[whedon]

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

OK DOIs

- 10.5281/zenodo.4569086 is OK
- 10.5194/gmd-12-1-2019 is OK
- 10.21105/joss.01450 is OK
- 10.5281/zenodo.4572994 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/j.pepi.2008.06.013 is OK
- 10.1007/978-94-011-2556-7_11 is OK
- 10.1130/GES02455.1 is OK
- 10.1007/BF02775087 is OK
- 10.1007/978-1-4615-9630-1 is OK
- 10.21105/joss.03709 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[acocac]

@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

- 10.5281/zenodo.4569086 is OK
- 10.5194/gmd-12-1-2019 is OK
- 10.21105/joss.01450 is OK
- 10.5281/zenodo.4572994 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/j.pepi.2008.06.013 is OK
- 10.1007/978-94-011-2556-7_11 is OK
- 10.1130/GES02455.1 is OK
- 10.1007/BF02775087 is OK
- 10.1007/978-1-4615-9630-1 is OK
- 10.21105/joss.03709 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:wave: @openjournals/jose-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/jose-papers/pull/119

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/jose-papers/pull/119, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[acocac]

Hi @labarba, this paper is ready to be published.

@BenjMy @jwagemann, thanks for volunteering your time to review this submission!

@AlexanderJuestel and collaborators, congrats on having this published 🚀

[acocac]

@AlexanderJuestel this is just to let you know @labarba who leads the rest of the publication according to her JOSE EiC role got sick recently. Apologies for inconvenience. Thanks for your understanding.

[AlexanderJuestel]

@acocac, any update on when @labarba may finish the review?

Still best wishes to her in the meantime! Cheers Alex

[labarba]

@AlexanderJuestel Thank you for your patience. I'm coming out of COVID with already a week-long backlog. I'm also editor-in-chief of another journal. My response times are longer than two weeks.

[acocac]

Dear @AlexanderJuestel, fyi, Lorena confirmed me today there's still a backlog on publishing the final papers. We appreciate your patience.

[AlexanderJuestel]

Hello @acocac, just wondering if there were any news since it has been another four weeks already.

Cheers Alex

[acocac]

Hello @acocac, just wondering if there were any news since it has been another four weeks already.

Cheers Alex

@labarba we wondered if you have updates to proceed with the publication of this submission 🙏

[labarba]

Hi everybody! 👋 Thank you all for your patience. I looked over the paper, and see that the citations need fixing. @AlexanderJuestel – Please have a look a the Markdown citation format we use.

[labarba]

From our docs:

Citations

Citations to entries in paper.bib should be in rMarkdown format.

For a quick reference, the following citation commands can be used:

• @author:2001 -> "Author et al. (2001)"
• [@author:2001] -> "(Author et al., 2001)"
• [@author1:2001; @author2:2001] -> "(Author1 et al., 2001; Author2 et al., 2002)"

[AlexanderJuestel]

@whedon generate pdf

[editorialbot]

My name is now @editorialbot

[AlexanderJuestel]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[AlexanderJuestel]

@labarba I have fixed the citation commands in the manuscript and also adapted the rules for capitalization in titles in the bibtex file.

Let me know if there is anything else.

Cheers Alex

[labarba]

Ah, yes. Some links are broken too. Have a look at the bottom of page 7.

[AlexanderJuestel]

Thanks for pointing that out, @labarba. The links should be fixed now!