[REVIEW]: dolfin-adjoint 2018.1: automated adjoints for FEniCS and Firedrake

whedon commented 5 years ago

Submitting author: @sebastkm (Sebastian Mitusch) Repository: https://bitbucket.org/dolfin-adjoint/pyadjoint Version: 2018.1.1 Editor: @Kevin-Mattheus-Moerman Reviewers: @chrisrichardson, @IgorBaratta Archive: 10.5281/zenodo.3247690

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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

@chrisrichardson, @IgorBaratta, 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 @Kevin-Mattheus-Moerman know.

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

Review checklist for @chrisrichardson

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS 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] Version: 2018.1.1
[x] Authorship: Has the submitting author (@sebastkm) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @IgorBaratta

Conflict of interest
[x] 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

[x] I confirm that I read and will adhere to the JOSS 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] Version: 2018.1.1
[x] Authorship: Has the submitting author (@sebastkm) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 5 years ago

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

: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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

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

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

Kevin-Mattheus-Moerman commented 5 years ago

@whedon add @IgorBaratta as reviewer

whedon commented 5 years ago

OK, @IgorBaratta is now a reviewer

Kevin-Mattheus-Moerman commented 5 years ago

@sebastkm, @chrisrichardson, @IgorBaratta, this is where the review process takes place. Let me know if you have any questions (Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations, which will enable you to tick the boxes at the top of this review issue).

IgorBaratta commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- http://doi.org/10.1137/120873558 is OK

MISSING DOIs

- https://doi.org/10.1145/2998441 may be missing for title: Firedrake: automating the finite element method by composing abstractions
- https://doi.org/10.1145/2566630 may be missing for title: Unified form language: A domain-specific language for weak formulations of partial differential equations

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 5 years ago

@sebastkm can you check the above DOI's? Thank you

Kevin-Mattheus-Moerman commented 5 years ago

@chrisrichardson, @IgorBaratta thanks for your review efforts. I can see several unticked boxes above. Are you opening issues on the project repository for these (if so please link to them here as well so we can easily keep track of progress)? If not could you summarize your concerns/issues here so @sebastkm knows what to work on? Thanks!

IgorBaratta commented 5 years ago

@Kevin-Mattheus-Moerman , I'm almost finishing my review. I've opened 1 issue and created 1 PR for a small fix.

So far everything looks pretty good. I hope to go through all the boxes above by Friday.

IgorBaratta commented 5 years ago

@Kevin-Mattheus-Moerman All boxes are now ticked, and from my side, this is good to go. Just need to update the pdf to reflect the changes in the doi.

Kevin-Mattheus-Moerman commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

PDF failed to compile for issue #1292 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 16 0 16 0 0 30 0 --:--:-- --:--:-- --:--:-- 30 Error reading bibliography ./references.bib (line 30, column 1): unexpected "d" expecting space, ",", white space or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

sebastkm commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

Kevin-Mattheus-Moerman commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1137/120873558 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1145/2998441 is OK
- 10.1145/2566630 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 5 years ago

@chrisrichardson thanks again for agreeing to review this work. Can you summarize where we stand at this point? What should @sebastkm be working on? If you have opened issues on the project repository can you link to them here? Thanks!

labarba commented 5 years ago

Looks like the first reviewer gave a recommendation to accept.

👋 @chrisrichardson — We're waiting for you to complete the review. Can you give us a status update? When do you think you might finish? Thanks!

Kevin-Mattheus-Moerman commented 5 years ago

Thanks @chrisrichardson for ticking those final boxes.

Kevin-Mattheus-Moerman commented 5 years ago

@wedon generate pdf

sebastkm commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

labarba commented 5 years ago

What's the status here, @Kevin-Mattheus-Moerman?

Kevin-Mattheus-Moerman commented 5 years ago

@labarba thanks for the reminder. I think this looks good and I'll proceed with the final steps.

Kevin-Mattheus-Moerman commented 5 years ago

@sebastkm at this point can you please do the following:

[x] Minor suggestion, in your paper please consider using [www.dolfin-adjoint.org](www.dolfin-adjoint.org) such that it renders as a hyperlink.
[x] Can you archive a copy of the reviewed software in ZENODO? Can you list the DOI of the archived version here when you have it?
[x] Can you provide the version tag for the reviewed/archived package?

Kevin-Mattheus-Moerman commented 5 years ago

@sebastkm :point_up: any luck processing these last steps? Let me know if you have questions.

sebastkm commented 5 years ago

Done! The DOI is: 10.5281/zenodo.3247690 The version tag is 2018.1.1

Kevin-Mattheus-Moerman commented 5 years ago

@whedon set 10.5281/zenodo.3247690 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3247690 is the archive.

Kevin-Mattheus-Moerman commented 5 years ago

@whedon set 2018.1.1 as version

whedon commented 5 years ago

OK. 2018.1.1 is the version.

Kevin-Mattheus-Moerman commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

Kevin-Mattheus-Moerman commented 5 years ago

@sebastkm some final points:

[x] Can you update the ZENODO meta data such that the archive title matches the JOSS paper title?
[x] Did you see my minor suggestion to use this (rather than just www.dolfin-adjoint.org) in your paper such that the website renders as a hyperlink: [www.dolfin-adjoint.org](www.dolfin-adjoint.org).

sebastkm commented 5 years ago

The updated joss paper is on a branch (or tag) 2018.1.1. The one on master-branch is outdated at the moment. I could also update the master branch version, if it is not possible to use the 2018.1.1 version.

I've updated the ZENODO meta data now.

Kevin-Mattheus-Moerman commented 5 years ago

@sebastkm yes updating the master branch version would be easiest if that is okay. I think that is where @whedon builds the paper from.

sebastkm commented 5 years ago

Done

sebastkm commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

Kevin-Mattheus-Moerman commented 5 years ago

Thanks @sebastkm :rocket:

Kevin-Mattheus-Moerman commented 5 years ago

@openjournals/joss-eics This submission is ready to be accepted

openjournals / joss-reviews