Joss-reviews: [REVIEW]: matador: a Python library for analysing, curating and performing high-throughput density-functional theory calculations

Created on 11 Aug 2020  ·  82Comments  ·  Source: openjournals/joss-reviews

Submitting author: @ml-evs (Matthew L Evans)
Repository: https://github.com/ml-evs/matador
Version: 0.9.9
Editor: @jgostick
Reviewers: @mkhorton, @srmnitc
Archive: 10.5281/zenodo.4095078

:warning: JOSS reduced service mode :warning:

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

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4d0eea9bea4362dec4cb6d62ebccc913"><img src="https://joss.theoj.org/papers/4d0eea9bea4362dec4cb6d62ebccc913/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4d0eea9bea4362dec4cb6d62ebccc913/status.svg)](https://joss.theoj.org/papers/4d0eea9bea4362dec4cb6d62ebccc913)

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

@mkhorton, 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/joss-reviews/invitations

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

Conflict of interest

  • [x] 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

General checks

  • [x] Repository: Is the source code for this software available at the repository url?
  • [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • [x] Contribution and authorship: Has the submitting author (@ml-evs) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

  • [x] Installation: Does installation proceed as outlined in the documentation?
  • [x] Functionality: Have the functional claims of the software been confirmed?
  • [x] 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

  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • [x] 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

  • [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • [x] 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 @srmnitc

Conflict of interest

  • [x] 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

General checks

  • [x] Repository: Is the source code for this software available at the repository url?
  • [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • [x] Contribution and authorship: Has the submitting author (@ml-evs) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

  • [x] Installation: Does installation proceed as outlined in the documentation?
  • [x] Functionality: Have the functional claims of the software been confirmed?
  • [x] 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

  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • [x] 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

  • [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • [x] 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?
Python Shell accepted published recommend-accept review
Source
picture whedon

All 82 comments

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

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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 picture whedon on 11 Aug 2020

PDF failed to compile for issue #2563 with the following error:

Can't find any papers to compile :-(

whedon picture whedon on 11 Aug 2020

@whedon generate pdf from branch joss

ml-evs picture ml-evs on 11 Aug 2020 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon picture whedon on 11 Aug 2020

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 11 Aug 2020

@whedon commands

ml-evs picture ml-evs on 11 Aug 2020

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
whedon picture whedon on 11 Aug 2020

Thanks for initiating this review! I've been implementing a few more features since I submitted, so the version to review should be changed to v0.9.8. Is that a problem?

ml-evs picture ml-evs on 11 Aug 2020

@whedon add @srmnitc as reviewer

jgostick picture jgostick on 11 Aug 2020

OK, @srmnitc is now a reviewer

whedon picture whedon on 11 Aug 2020

Tagging the other author here, @ajm143.

ml-evs picture ml-evs on 12 Aug 2020

I'm just getting started on the code review. For the record, I want to add the same note as in the pre-review thread that I know @ml-evs in the context of another project. This project is OPTIMADE, a consortium of research groups and organizations in the computational materials field working on a common REST API standard. I don't believe this to be a conflict for the purposes of this review.

mkhorton picture mkhorton on 31 Aug 2020

I'm just getting started on the code review. For the record, I want to add the same note as in the pre-review thread that I know @ml-evs in the context of another project. This project is OPTIMADE, a consortium of research groups and organizations in the computational materials field working on a common REST API standard. I don't believe this to be a conflict for the purposes of this review.

Thanks @mkhorton --- just to confirm we are part of the same consortium but haven't worked together directly.

ml-evs picture ml-evs on 31 Aug 2020

Hi @mkhorton and @srmnitc
How is the review coming along? I see many 'unchecked' check boxes in the list above...are you having any difficulties with this software?

jgostick picture jgostick on 8 Sep 2020

Hi @jgostick, no major issues, just a few integration tests not running. Need to re-compile a dependency (castep) first :-)

For @ml-evs, only comment for testing is to add a note about test_requirements.txt in the testing instructions.

mkhorton picture mkhorton on 8 Sep 2020

For @ml-evs, only comment for testing is to add a note about test_requirements.txt in the testing instructions.

Good spot, thanks. Let me know if there's any trouble with CASTEP and/or the integration tests.

ml-evs picture ml-evs on 8 Sep 2020

@jgostick No problems here too. Sorry, I just got delayed with other things and did not yet check the code. I plan to go through this week.

srmnitc picture srmnitc on 9 Sep 2020

Hi @ml-evs, I have finished my first round of review. Overall, matador looks quite nice and the documentation looks very good. Thanks! I only have minor points that I have raised on the repo. The major one is just with the jupyter notebooks as a lot of them seem to not run on a binder instance. I would not say this would prevent me from checking the examples section on the checklist, but I think it would be great if you could take a look. Another one is with the statement of need in the paper. I think the advantages of matador are clearly described, but what exactly is the research question that matador answers/or helps to answer? Once again, it is not a major issue, maybe @jgostick could decide if the current state is enough. Thanks for the time and effort in developing matador.

srmnitc picture srmnitc on 13 Sep 2020

Hi @ml-evs, I have finished my first round of review. Overall, matador looks quite nice and the documentation looks very good. Thanks! I only have minor points that I have raised on the repo. The major one is just with the jupyter notebooks as a lot of them seem to not run on a binder instance. I would not say this would prevent me from checking the examples section on the checklist, but I think it would be great if you could take a look. Another one is with the statement of need in the paper. I think the advantages of matador are clearly described, but what exactly is the research question that matador answers/or helps to answer? Once again, it is not a major issue, maybe @jgostick could decide if the current state is enough. Thanks for the time and effort in developing matador.

Hi @srmnitc, thanks so much for taking the time to review matador. I'll address your comments in more detail in the issues you have raised (I broadly agree with all of them).

Referring specifically to your final point, in the introduction to the paper we outline the research question that _we_ use the code for, namely job management and analysis for high-throughput crystal structure prediction, but the matador library itself should be generally useful to anyone using CASTEP. I'll have a go at making this clearer in the paper and the documentation and invite you to comment further in the specific issue.

ml-evs picture ml-evs on 14 Sep 2020
👍1

So I actually am having issues compiling CASTEP (which usually never gives me issues) to be able to fully run the integration tests. My apologies for this, I'll try and get this sorted ASAP. The specific error I'm seeing is:

Error: Type mismatch between actual argument at (1) and actual argument at (2)

in case anyone in this thread has suggestions.

mkhorton picture mkhorton on 16 Sep 2020

So I actually am having issues compiling CASTEP (which usually never gives me issues) to be able to fully run the integration tests. My apologies for this, I'll try and get this sorted ASAP. The specific error I'm seeing is:

Error: Type mismatch between actual argument at (1) and actual argument at (2)

in case anyone in this thread has suggestions.

That looks like the classic Fortran compiler error when the code is missing an implicit none, but I'd be surprised if that was the case... I assume this is with gfortran (and perhaps a more recent one?) I've certainly compiled CASTEP with gfortran 8 with no problems in the recent past. Perhaps you could post your compiler/arch and the error dump I can try to be more helpful (here or elsewhere)?

ml-evs picture ml-evs on 16 Sep 2020

Yes, I apologize. It wasn't very helpful of me to include that error without system details! This is the gfortran from gcc version 10.2.0 (Homebrew GCC 10.2.0) on macOS 10.15.6 with any necessary dependencies installed via homebrew, e.g. cmake, openmpi.

The integration tests aside, I have otherwise completed my review of matador. Matador is a toolbox for running, storing, analyzing and retrieving data generated from first-principles materials modeling techniques. The code is cleanly separated with the intent of each module well-defined and includes a nice CLI interface, robust integration especially with CASTEP (for launching pre-defined workflows, ingesting ('scraping') contents of directories, running jobs via HPC interfaces and the like and storing and retrieving documents via MongoDB). Plotting functionality is particularly impressive and well structured. The code also includes some basic transformations ("swaps"), phase diagram functionality, and fingerprinting (including a very nice PXRD class). Documentation is good with clean docstrings throughout.

While there are clearly several modules still in development or with placeholder code, the existent code as-is easily passes the threshold for publication and features currently described are functional and useful, and passes all the criteria for a JOSS publication.

mkhorton picture mkhorton on 23 Sep 2020
👍1

Thanks for the constructive review @mkhorton.

I should be able to find the time to address @srmnitc's remaining comments this week, in this PR https://github.com/ml-evs/matador/pull/125.

ml-evs picture ml-evs on 30 Sep 2020

@whedon generate pdf

srmnitc picture srmnitc on 13 Oct 2020

PDF failed to compile for issue #2563 with the following error:

Can't find any papers to compile :-(

whedon picture whedon on 13 Oct 2020

@ml-evs Just an update. Seems like work is in progress on the PR. Once merged, it should allow me to check off the remaining points!

srmnitc picture srmnitc on 13 Oct 2020

@whedon generate pdf from branch joss

ml-evs picture ml-evs on 14 Oct 2020 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon picture whedon on 14 Oct 2020

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

whedon picture whedon on 14 Oct 2020

Gah, just noticed another typo... this should now be the final proof.

ml-evs picture ml-evs on 14 Oct 2020

@whedon generate pdf from branch joss

ml-evs picture ml-evs on 14 Oct 2020 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon picture whedon on 14 Oct 2020

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

whedon picture whedon on 14 Oct 2020

@whedon generate pdf from branch joss

ml-evs picture ml-evs on 14 Oct 2020 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon picture whedon on 14 Oct 2020

@whedon check references

ml-evs picture ml-evs on 14 Oct 2020

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

whedon picture whedon on 14 Oct 2020

@jgostick @ml-evs With some issues now fixed, I am able to check all the boxes in the review. With that, I would like to recommend matador for publication. It is a well-written module with very helpful examples and documentation. @jgostick thanks for inviting me to review and @ml-evs thanks for your efforts in fixing all the issues!

srmnitc picture srmnitc on 15 Oct 2020
🎉1

@jgostick @ml-evs With some issues now fixed, I am able to check all the boxes in the review. With that, I would like to recommend matador for publication. It is a well-written module with very helpful examples and documentation. @jgostick thanks for inviting me to review and @ml-evs thanks for your efforts in fixing all the issues!

Thanks @srmnitc, your review of the examples on Binder and careful reading of the paper were especially helpful. I have merged the paper into master and will re-trigger Whedon.

ml-evs picture ml-evs on 15 Oct 2020

@whedon generate pdf

ml-evs picture ml-evs on 15 Oct 2020

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

whedon picture whedon on 15 Oct 2020

@whedon check references

ml-evs picture ml-evs on 15 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10/f4mfm4 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10/bdfg3f is OK
- 10/f5xrnj is OK
- 10/gdq6h4 is OK
- 10/f9wbtg is OK
- 10/d7spb8 is OK
- 10/drbjhg is OK
- 10.5281/zenodo.2628066 is OK
- 10.5281/zenodo.3904495 is OK
- 10.1021/acs.chemmater.0c02054 is OK
- 10/ggj45f is OK
- 10/f9jxbz is OK
- 10.1103/PhysRevLett.95.216401 is OK
- 10/ggrmgf is OK
- 10.21105/joss.00717 is OK
- 10/gg5vsq is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 15 Oct 2020

Hi @ml-evs There are a few things left to do:

Here is a list of what to do next:

  • [ ] Double check authors and affiliations (including ORCIDs)
  • [ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • [ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
  • [ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
jgostick picture jgostick on 15 Oct 2020

Hi @jgostick,

  • [x] Double check authors and affiliations (including ORCIDs)

ORCIDs in the paper are correct, though I don't see them rendering in the preview.

  • [x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.

v0.9.9 has just been released https://github.com/ml-evs/matador/releases/tag/0.9.9

  • [x] Archive the release on Zenodo/figshare/etc and post the DOI here.

The 0.9.9 release is archived at http://doi.org/10.5281/zenodo.4095078

  • [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.

Author list matches, but the title of the archive is just the package name, which seems to be okay looking at other accepted JOSS papers?

ml-evs picture ml-evs on 16 Oct 2020

@whedon set 10.5281/zenodo.4095078 as archive

jgostick picture jgostick on 23 Oct 2020

OK. 10.5281/zenodo.4095078 is the archive.

whedon picture whedon on 23 Oct 2020

@whedon check references

jgostick picture jgostick on 23 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10/f4mfm4 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10/bdfg3f is OK
- 10/f5xrnj is OK
- 10/gdq6h4 is OK
- 10/f9wbtg is OK
- 10/d7spb8 is OK
- 10/drbjhg is OK
- 10.5281/zenodo.2628066 is OK
- 10.5281/zenodo.3904495 is OK
- 10.1021/acs.chemmater.0c02054 is OK
- 10/ggj45f is OK
- 10/f9jxbz is OK
- 10.1103/PhysRevLett.95.216401 is OK
- 10/ggrmgf is OK
- 10.21105/joss.00717 is OK
- 10/gg5vsq is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 23 Oct 2020

@whedon generate pdf

jgostick picture jgostick on 23 Oct 2020

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

whedon picture whedon on 23 Oct 2020

@whedon set 0.9.9 as the version

jgostick picture jgostick on 23 Oct 2020

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

@whedon commands
whedon picture whedon on 23 Oct 2020

@whedon set 0.9.9 as version

jgostick picture jgostick on 23 Oct 2020

OK. 0.9.9 is the version.

whedon picture whedon on 23 Oct 2020

@whedon accept

jgostick picture jgostick on 23 Oct 2020 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 23 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10/f4mfm4 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10/bdfg3f is OK
- 10/f5xrnj is OK
- 10/gdq6h4 is OK
- 10/f9wbtg is OK
- 10/d7spb8 is OK
- 10/drbjhg is OK
- 10.5281/zenodo.2628066 is OK
- 10.5281/zenodo.3904495 is OK
- 10.1021/acs.chemmater.0c02054 is OK
- 10/ggj45f is OK
- 10/f9jxbz is OK
- 10.1103/PhysRevLett.95.216401 is OK
- 10/ggrmgf is OK
- 10.21105/joss.00717 is OK
- 10/gg5vsq is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 23 Oct 2020

PDF failed to compile for issue #2563 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:77:in doi_citation': undefined methodencode' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:64:in make_citation' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:50:inblock in generate_citations'
from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:in each' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:ineach'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:43:in generate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/compilers.rb:246:incrossref_from_markdown'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/compilers.rb:21:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:100:incompile'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:88:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
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:indispatch'
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-d14a699185fb/bin/whedon:131:in 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

'

whedon picture whedon on 23 Oct 2020

Hi @mkhorton congrats! This one took a while, but it's all good now. An editor in chief will now come and make the acceptance final (and hopefully sort out the messy error message whedon produced above! I just compiled the pdf, so I don't understand why it's complaining).

jgostick picture jgostick on 23 Oct 2020

Thanks @jgostick, please keep me in mind if you need reviewers in this area.

Thanks again to @mkhorton and @srmnitc for their time and thoughtful reviews.

Regarding the whedon error, the tidier traceback is:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:77:in `doi_citation': undefined method `encode' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:64:in `make_citation' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:50:in `block in generate_citations'
from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:in `each' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:in `each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:43:in `generate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/compilers.rb:246:in `crossref_from_markdown'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/compilers.rb:21:in `generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:100:in `compile'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:88:in `compile' 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-d14a699185fb/bin/whedon:131: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 `

I can't see weird characters that would be missing an encode method in my bib file, but I can try fixing some dodgy indentation that crept in, though I assume I will not be able to retrigger the accept command myself!

ml-evs picture ml-evs on 23 Oct 2020

@whedon generate pdf

ml-evs picture ml-evs on 23 Oct 2020

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

whedon picture whedon on 23 Oct 2020

Hmmm, I guess that was just a one-time glitch? the PDF generated just fine for me above as well.

jgostick picture jgostick on 23 Oct 2020

@whedon accept

arfon picture arfon on 26 Oct 2020 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 26 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10/f4mfm4 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10/bdfg3f is OK
- 10/f5xrnj is OK
- 10/gdq6h4 is OK
- 10/f9wbtg is OK
- 10/d7spb8 is OK
- 10/drbjhg is OK
- 10.5281/zenodo.2628066 is OK
- 10.5281/zenodo.3904495 is OK
- 10.1021/acs.chemmater.0c02054 is OK
- 10/ggj45f is OK
- 10/f9jxbz is OK
- 10.1103/PhysRevLett.95.216401 is OK
- 10/ggrmgf is OK
- 10.21105/joss.00717 is OK
- 10/gg5vsq is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 26 Oct 2020

PDF failed to compile for issue #2563 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:77:in doi_citation': undefined methodencode' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:64:in make_citation' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:50:inblock in generate_citations'
from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:in each' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:ineach'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/bibtex_parser.rb:43:in generate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/compilers.rb:246:incrossref_from_markdown'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/compilers.rb:21:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:100:incompile'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:88:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
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:indispatch'
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-d14a699185fb/bin/whedon:131:in 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

'

whedon picture whedon on 26 Oct 2020

@ml-evs - could you merge this PR which modifies the DOIs to the more standard format? https://github.com/ml-evs/matador/pull/132

arfon picture arfon on 26 Oct 2020

@ml-evs - could you merge this PR which modifies the DOIs to the more standard format? ml-evs/matador#132

Hi @arfon, done. Was ShortDOI the problem?

ml-evs picture ml-evs on 26 Oct 2020

Hi @arfon, done. Was ShortDOI the problem?

Yes, our system currently doesn't support these (although it looks like we should!)

arfon picture arfon on 27 Oct 2020

@whedon accept

arfon picture arfon on 27 Oct 2020 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 27 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1524/zkri.220.5.567.65075 is OK
- 10.1016/j.cpc.2014.02.013 is OK
- 10.1021/jacs.8b04183 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.1088/0953-8984/21/39/395502 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.2628066 is OK
- 10.5281/zenodo.3904495 is OK
- 10.1021/acs.chemmater.0c02054 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.commatsci.2016.10.015 is OK
- 10.1103/PhysRevLett.95.216401 is OK
- 10.1595/205651320X15742491027978 is OK
- 10.21105/joss.00717 is OK
- 10.1088/1742-6596/371/1/012062 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 27 Oct 2020

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1868

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1868, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

whedon picture whedon on 27 Oct 2020

@whedon accept deposit=true

arfon picture arfon on 27 Oct 2020 
Doing it live! Attempting automated processing of paper acceptance...
whedon picture whedon on 27 Oct 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon picture whedon on 27 Oct 2020

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1869
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02563
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

whedon picture whedon on 27 Oct 2020

@mkhorton, @srmnitc - many thanks for your reviews here and to @jgostick for editing this submission ✨

@ml-evs - your paper is now accepted into JOSS :zap::rocket::boom:

arfon picture arfon on 27 Oct 2020
🎉1

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.02563/status.svg)](https://doi.org/10.21105/joss.02563)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02563">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02563/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02563/status.svg
   :target: https://doi.org/10.21105/joss.02563

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

whedon picture whedon on 27 Oct 2020

Great, thanks @arfon for getting it over the last hurdle!

ml-evs picture ml-evs on 27 Oct 2020
Was this page helpful?
0 / 5 - 0 ratings

Related issues

whedon picture whedon  ·  10Comments
whedon picture whedon  ·  12Comments
whedon picture whedon  ·  12Comments
whedon picture whedon  ·  12Comments
whedon picture whedon  ·  9Comments