[REVIEW]: The MTPy software package for magnetotelluric data analysis and visualisation #1358

whedon · Mar 31, 2019

Submitting author: @alkirkby (Alison Kirkby)
Repository: https://github.com/MTgeophysics/mtpy
Version: v1.0
Editor: @lheagy
Reviewer: @JKutt
Archive: 10.5281/zenodo.2698634

Status

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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) 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

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

Make sure you're logged in to your GitHub account
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 @lheagy know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @JKutt

Conflict of interest

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

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?
Version: v1.0
Authorship: Has the submitting author (@alkirkby) 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)?

whedon · Mar 31, 2019

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

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whedon · Mar 31, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Mar 31, 2019

PDF failed to compile for issue #1358 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: date (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/lib/whedon.rb:69:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

lheagy · Mar 31, 2019

👋 Many thanks @JKutt for being willing to review! Above there is a checklist to help guide your review. Please feel free to open issues on the target repository with comments or suggestions for improvement in the submission and link them here by mentioning openjournals/joss-reviews#1358 in the issue text.

The author @alkirkby mentioned that she will fix the images in the paper on monday.

Please let me know if you have any questions!

alkirkby · Mar 31, 2019

@whedon generate pdf

whedon · Mar 31, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Mar 31, 2019

PDF failed to compile for issue #1358 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: date (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/lib/whedon.rb:69:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-96d847bd9060/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

alkirkby · Mar 31, 2019

@whedon generate pdf

whedon · Mar 31, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Mar 31, 2019

👉 Check article proof 📄 👈

alkirkby · Mar 31, 2019

@whedon generate pdf

whedon · Mar 31, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Mar 31, 2019

👉 Check article proof 📄 👈

JKutt · Apr 2, 2019

Hi @lheagy, I managed to complete my review! I had a bit of a stumble at first getting things running but after following the Linux install more thoroughly I managed to get it going. Once up and running everything went quite smooth! A lot of good stuff in here. I found a few things and created an issue for one but the others already exist (e.g. error with print statements due to python 2 vs. 3).

alkirkby · Apr 3, 2019

Hey @JKutt, thanks for the review! We're glad you managed to install MTPy in the end, but we are tidying up some of the issues at the moment to make it easier for users.
I was wondering if you could let me know the issue numbers for the issues you mentioned above? I can't find anything in the issues page about print statements with python 2 vs 3, for example. I need to go through the issues page as some of the issues were resolved but never closed.

lheagy · Apr 4, 2019

Many thanks for your speedy review @JKutt! @alkirkby: it looks they are issues

alkirkby · Apr 5, 2019

Great thanks @lheagy. I've checked both those issues - #78 has been addressed and I have now addressed #77.

JKutt · Apr 5, 2019

Hi @alkirkby the "print" statements issue was brought up in MTgeophysics/mtpy#63

alkirkby · Apr 8, 2019

Hi @JKutt, Fei tells me that the print statements issue was resolved, are you able to specify where in MTPy you're encountering these issues?

JKutt · Apr 12, 2019

Hi @JKutt, Fei tells me that the print statements issue was resolved, are you able to specify where in MTPy you're encountering these issues?

@alkirkby sorry for the late reply, missed this one. I can't quite remember off the top of my head but it was in places where "print" is used instead of "print()"

zhang01GA · Apr 18, 2019

Hi @JKutt and @alkirkby:
Two weeks ago, I did fix one new print issue in mtpy/imaging/plotstrike.py
MTgeophysics/mtpy@c4b6f3d

Today, I applied 2to3 to every *.py script in mtpy. But had not found any print statement issue.
All active print statement has been changed to print() in the refactoring long time ago.
(some py2 prints may exist in commented out # lines. But they are not active).

Please let me know. Thanks

lheagy · Apr 23, 2019

Thanks @zhang01GA! @JKutt, would you mind taking another look when you have a chance?

JKutt · Apr 25, 2019

Thanks @zhang01GA! @JKutt, would you mind taking another look when you have a chance?

All seems good now! No issues second time around.

lheagy · May 1, 2019

👋 @JKutt: it looks like the box for automated-tests is still un-checked. Do you have any other comments wrt testing? or can this be ticked off? Thanks!

JKutt · May 1, 2019

👋 @JKutt: it looks like the box for automated-tests is still un-checked. Do you have any other comments wrt testing? or can this be ticked off? Thanks!

@lheagy darn, I missed that one! Apologies. No concern on the testing, simply missed ticking it off. Should be good now!

whedon · May 1, 2019


OK DOIs

- 10.1111/j.1365-246x.2005.02779.x is OK
- 10.1111/j.1365-246X.2004.02281.x is OK
- 10.1111/j.1365-246X.2004.02203.x is OK
- 10.1029/JB092iB01p00633 is OK
- 10.1190/1.1442813 is OK
- 10.1111/j.1365-246X.2011.05347.x is OK
- 10.1016/j.cageo.2014.01.010 is OK
- 10.1016/J.CAGEO.2014.07.013 is OK
- 10.1190/1.1438799 is OK
- 10.1111/j.1365-246X.1962.tb02992.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

alkirkby · May 1, 2019

Hi @lheagy, okay great!

@zhang01GA is looking into the documentation issue and will link the user guide from the main page. I've just fixed the doi issue. Nearly there!

alkirkby · May 2, 2019

Hi @lheagy, @zhang01GA has now fixed the documentation issue and has added a link to the user guide to the front page.

lheagy · May 3, 2019

Excellent, thanks @alkirkby!

Please take a look at the pdf proof below. If everything looks good, then please make a new release and archive the software on zenodo or similar and ensure that the title and author list match those in the paper. Then, please post the new version number and doi here.

lheagy · May 3, 2019

@whedon generate pdf

whedon · May 3, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · May 3, 2019

👉 Check article proof 📄 👈

alkirkby · May 10, 2019

Great thanks @lheagy,
I've just created a release and archived the software: DOI: 10.5281/zenodo.2698634
We are now just awaiting final sign-off of the proof. We'll let you know when it's ready to go!

alkirkby · May 21, 2019

Hi @lheagy,
We have just obtained final approval of the proof so are ready to go ahead with the next stage of the process!

alkirkby · May 21, 2019

version number is 1.0

lheagy · May 21, 2019

@whedon set 10.5281/zenodo.2698634 as archive

whedon · May 21, 2019

OK. 10.5281/zenodo.2698634 is the archive.

lheagy · May 21, 2019

@whedon set 1.0 as version

whedon · May 21, 2019

OK. 1.0 is the version.

lheagy · May 21, 2019

@whedon check references

whedon · May 21, 2019

Attempting to check references...

whedon · May 21, 2019


OK DOIs

- 10.1111/j.1365-246x.2005.02779.x is OK
- 10.1111/j.1365-246X.2004.02281.x is OK
- 10.1111/j.1365-246X.2004.02203.x is OK
- 10.1029/JB092iB01p00633 is OK
- 10.1190/1.1442813 is OK
- 10.1111/j.1365-246X.2011.05347.x is OK
- 10.1016/j.cageo.2014.01.010 is OK
- 10.1016/J.CAGEO.2014.07.013 is OK
- 10.1190/1.1438799 is OK
- 10.1111/j.1365-246X.1962.tb02992.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

lheagy · May 21, 2019

@whedon set v1.0 as version

whedon · May 21, 2019

OK. v1.0 is the version.

lheagy · May 21, 2019

👋 @alkirkby, excellent! Would you mind updating the title in the zenodo archive to match the title of the paper: "The MTPy software package for magnetotelluric data analysis and visualisation". After that, we are good to go!

alkirkby · May 21, 2019

@lheagy, ok no worries, done.

lheagy · May 21, 2019

Many thanks @JKutt for your speedy review! and congratulations @alkirkby and team on your submission 🎉

👋 @openjournals/joss-eics, this submission is ready to be accepted!

danielskatz · May 22, 2019

Thanks to @JKutt for reviewing and @lheagy for editing!

danielskatz · May 22, 2019

@whedon accept

whedon · May 22, 2019

Attempting dry run of processing paper acceptance...

whedon · May 22, 2019


OK DOIs

- 10.1111/j.1365-246x.2005.02779.x is OK
- 10.1111/j.1365-246X.2004.02281.x is OK
- 10.1111/j.1365-246X.2004.02203.x is OK
- 10.1029/JB092iB01p00633 is OK
- 10.1190/1.1442813 is OK
- 10.1111/j.1365-246X.2011.05347.x is OK
- 10.1016/j.cageo.2014.01.010 is OK
- 10.1016/J.CAGEO.2014.07.013 is OK
- 10.1190/1.1438799 is OK
- 10.1111/j.1365-246X.1962.tb02992.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · May 22, 2019

Check final proof 👉 openjournals/joss-papers#709

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#709, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz · May 22, 2019

@alkirkby - I see a couple of reference problems that I've tried to fix via MTgeophysics/mtpy#82

One is opening quotes that were backwards, and the other is an underscore that caused a URL to not work right. I'm sure my fix will work for the quotes, but I'm not sure it will work for the URL. Can you accept the PR, and see if paper will compile? If not, we can try to fix the underscore in the URL another way.

whedon assigned lheagy Mar 31, 2019

whedon added the review label Mar 31, 2019

whedon referenced this issue Mar 31, 2019
Closed
[PRE REVIEW]: The MTPy software package for magnetotelluric data analysis and visualisation #1355

This was referenced Apr 1, 2019

Closed

Generalizing language to include if use on a Mac is working MTgeophysics/mtpy#77

Closed

Installation confusion MTgeophysics/mtpy#78

whedon assigned JKutt May 6, 2019

lheagy added the accepted label May 21, 2019

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[REVIEW]: The MTPy software package for magnetotelluric data analysis and visualisation #1358

Comments

whedon commented Mar 31, 2019 • edited

Status

Reviewer instructions & questions

Review checklist for @JKutt

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon assigned lheagy Mar 31, 2019

whedon added the review label Mar 31, 2019

whedon referenced this issue Mar 31, 2019

[PRE REVIEW]: The MTPy software package for magnetotelluric data analysis and visualisation #1355

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This was referenced Apr 1, 2019

Generalizing language to include if use on a Mac is working MTgeophysics/mtpy#77

Installation confusion MTgeophysics/mtpy#78

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whedon commented Mar 31, 2019 •

edited

lheagy commented Mar 31, 2019 •

edited