search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
721 stars 38 forks source link

[PRE REVIEW]: PyGMI - a python package for geoscience modelling and interpretation #6472

Closed editorialbot closed 3 months ago

editorialbot commented 8 months ago

Submitting author: !--author-handle-->@Patrick-Cole<!--end-author-handle-- (Patrick Cole) Repository: https://github.com/Patrick-Cole/pygmi Branch with paper.md (empty if default branch): Version: v3.2.8.0 Editor: !--editor-->@boisgera<!--end-editor-- Reviewers: @AnkitBarik, @AlexanderJuestel Managing EiC: Kristen Thyng

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b5e69e8e0d634e313e7b0037cadc950f"><img src="https://joss.theoj.org/papers/b5e69e8e0d634e313e7b0037cadc950f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b5e69e8e0d634e313e7b0037cadc950f/status.svg)](https://joss.theoj.org/papers/b5e69e8e0d634e313e7b0037cadc950f)

Author instructions

Thanks for submitting your paper to JOSS @Patrick-Cole. Currently, there isn't a JOSS editor assigned to your paper.

@Patrick-Cole if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
editorialbot commented 8 months ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 8 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.33 s (458.0 files/s, 200041.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          95          12898          15863          34254
reStructuredText                 2            108              0           1043
HTML                            45              3              0            919
TeX                              1             17              0            208
TOML                             1              6              0             71
Markdown                         1              9              0             34
CSV                              1              0              0             27
DOS Batch                        1              1              0             22
YAML                             1              1              4             18
XML                              2              0              0             16
-------------------------------------------------------------------------------
SUM:                           150          13043          15867          36612
-------------------------------------------------------------------------------

Commit count by author:

   952  Patrick
    86  pcole@geoscience.org.za
     6  Janine-Cole
     2  Patrick Cole
     1  Marinda
editorialbot commented 8 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1190/1.1439386 is OK
- 10.1016/j.cageo.2005.03.002 is OK
- 10.1016/j.cageo.2006.02.016 is OK
- 10.1186/s40623-015-0228-9 is OK
- 10.1109/36.3001 is OK
- 10.1190/1.1444531 is OK
- 10.1785/0220190313 is OK
- 10.2113/econgeo.107.2.209 is OK
- 10.1190/1.1988183 is OK
- 10.1190/1.1543203 is OK
- 10.1109/PROC.1981.11918 is OK
- 10.1071/EG08028 is OK
- 10.1190/1.1444942 is OK

MISSING DOIs

- No DOI given, and none found for title: Multiresolution Segmentation: An Optimization Appr...
- No DOI given, and none found for title: Potential Theory in Gravity and Magnetic Applicati...
- No DOI given, and none found for title: GDAL/OGR Geospatial Data Abstraction software Libr...
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: Joint modelling of gravity and magnetic fields - a...

INVALID DOIs

- None
editorialbot commented 8 months ago

Paper file info:

📄 Wordcount for paper.md is 925

✅ The paper includes a Statement of need section

editorialbot commented 8 months ago

License info:

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

editorialbot commented 8 months ago

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

kthyng commented 8 months ago

Hi @Patrick-Cole and thanks for your submission! We have a backlog of submissions so I will add this to our waitlist. In the meantime, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them. Thanks for your patience.

Patrick-Cole commented 8 months ago

Hi,

I chose reviewers on the list based on geophysics, python and earth sciences, but honestly, I am not fussy.

Matt Hall leouieda TobbeTripitaka Haipeng Li margauxmouchene

kthyng commented 7 months ago

@fraukewiese Could you edit this submission?

kthyng commented 7 months ago

@editorialbot invite @fraukewiese as editor

editorialbot commented 7 months ago

Invitation to edit this submission sent!

kthyng commented 7 months ago

@fraukewiese might you be able to edit this submission?

fraukewiese commented 6 months ago

Hi, sorry for the late response. The submission does not fit to my area of expertise, so I need to reject.

kthyng commented 6 months ago

@martinfleis Could you edit this submission?

kthyng commented 6 months ago

@editorialbot invite @martinfleis as editor

editorialbot commented 6 months ago

Invitation to edit this submission sent!

boisgera commented 6 months ago

Hi @kthyng,

If @martinfleis was not available, you could consider inviting me as editor. Geoscience is not my area of expertise, but I belong to a "School of Mines" so many of my colleagues would be great potential reviewers.

kthyng commented 6 months ago

A volunteer! I will most definitely take you up on this!

kthyng commented 6 months ago

@editorialbot assign @boisgera as editor

editorialbot commented 6 months ago

Assigned! @boisgera is now the editor

boisgera commented 5 months ago

I am following several leads internally for reviewers ; I've been recently given a list of people that would be great for this by the head of the Geostats team. I am contacting some of them right now.

boisgera commented 4 months ago

Still following the lead for reviewers in my institution. Great discussion with two of them very recently ; one element of feedback that I have is that they are wary of the magnitude of the work (given that the code base has > 30k loc) ; they need a moment to consider if they go for it or not.

boisgera commented 4 months ago

Still following the lead for reviewers in my institution. Great discussion with two of them very recently ; one element of feedback that I have is that they are wary of the magnitude of the work (given that the code base has > 30k loc) ; they need a moment to consider if they go for it or not.

And ... I failed to convince them. Contacting new potential reviewers right now.

boisgera commented 4 months ago

A new potential reviewer declined after evaluation of the paper. He didn't feel that he had enough expertise on many of the project features (and also, lack of time).

I am going back to the list of potential rewievers.

kthyng commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

editorialbot commented 4 months ago

Five most similar historical JOSS papers:

GemGIS - Spatial Data Processing for Geomodeling Submitting author: @AlexanderJuestel Handling editor: @crvernon (Active) Reviewers: @omshinde, @kanishkan91 Similarity score: 0.7138

planetMagFields: A Python package for analyzing and plotting planetary magnetic field data Submitting author: @AnkitBarik Handling editor: @dfm (Active) Reviewers: @athulpg007, @kjg136 Similarity score: 0.7106

emg3d: A multigrid solver for 3D electromagnetic diffusion Submitting author: @prisae Handling editor: @jedbrown (Active) Reviewers: @akelbert, @emersodb, @lukeolson Similarity score: 0.7085

GeoBO: Python package for Multi-Objective Bayesian Optimisation and Joint Inversion in Geosciences Submitting author: @sebhaan Handling editor: @hugoledoux (Active) Reviewers: @npetra, @sgkang Similarity score: 0.7000

Geodata-Harvester: A Python package to jumpstart geospatial data extraction and analysis Submitting author: @sebhaan Handling editor: @hugoledoux (Active) Reviewers: @lukasbeuster, @martibosch Similarity score: 0.6969

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

kthyng commented 4 months ago

@boisgera Maybe some of the authors of these similar papers could be relevant?

boisgera commented 4 months ago

@boisgera Maybe some of the authors of these similar papers could be relevant?

Yes, thank you @kthyng!

I was pushing for reviewers coming from my institution so far because I thought that it was worth introducing some new people to JOSS reviews. I also think that it would be beneficial to these researchers (so far the people which have accepted to review for JOSS on my demand like the process a lot better than the classic review process).

But it's now likely that I'll have to contact external reviewers already familiar with JOSS. I have sent today e-mails to the last 2 "obvious" potential reviewers internally and if its doesn't pan out, the authors on your liste are next!

kthyng commented 4 months ago

I like your plan @boisgera!

boisgera commented 4 months ago

But it's now likely that I'll have to contact external reviewers already familiar with JOSS. I have sent today e-mails to the last 2 "obvious" potential reviewers internally and if its doesn't pan out, the authors on your liste are next!

Started to reach out for JOSS paper authors.

boisgera commented 4 months ago

@editorialbot add @AnkitBarik as reviewer

editorialbot commented 4 months ago

@AnkitBarik added to the reviewers list!

AnkitBarik commented 3 months ago

@editorialbot generate checklist

editorialbot commented 3 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

AnkitBarik commented 3 months ago

@editorialbot commands

editorialbot commented 3 months ago

Hello @AnkitBarik, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
AnkitBarik commented 3 months ago

@editorialbot generate my checklist

editorialbot commented 3 months ago

Checklists can only be created once the review has started in the review issue

boisgera commented 3 months ago

Hi @kthyng, @AnkitBarik,

I am discussing with a potential 2nd reviewer who wanted to reach for a colleague first. Hopefully we will be able to start the review soon!

boisgera commented 3 months ago

@editorialbot add @AlexanderJuestel as reviewer

editorialbot commented 3 months ago

@AlexanderJuestel added to the reviewers list!

boisgera commented 3 months ago

@editorialbot start review

editorialbot commented 3 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7019.