Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[REVIEW]: cppduals: a nestable vectorized templated dual number library for C++11 #1487

Closed
whedon opened this issue Jun 5, 2019 · 109 comments
Assignees
Labels

Comments

@whedon
Copy link
Collaborator

@whedon whedon commented Jun 5, 2019

Submitting author: @tesch1 (Michael Tesch)
Repository: https://gitlab.com/tesch1/cppduals
Version: v0.1.2
Editor: @danielskatz
Reviewer: @StewMH, @mdavezac
Archive: 10.5281/zenodo.3528307

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/a6291c0d8c548ceed6728072eb5a3438"><img src="http://joss.theoj.org/papers/a6291c0d8c548ceed6728072eb5a3438/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/a6291c0d8c548ceed6728072eb5a3438/status.svg)](http://joss.theoj.org/papers/a6291c0d8c548ceed6728072eb5a3438)

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

@StewMH & @mdavezac, 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 @danielskatz know.

Please try and complete your review in the next two weeks

Review checklist for @StewMH

Conflict of interest

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: v0.1.2
  • Authorship: Has the submitting author (@tesch1) 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)?

Review checklist for @mdavezac

Conflict of interest

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: v0.1.2
  • Authorship: Has the submitting author (@tesch1) 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

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Jun 5, 2019

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

⭐️ Important ⭐️

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
@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Jun 5, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Jun 5, 2019

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Jun 5, 2019

👋 @StewMH, @mdavezac - thanks for agreeing to review this submission. Your job, as stated in the first comment in this issue, is to go through the paper and the software repository, and check off the boxes in your list as you've done so. When you find something that is a problem, if it's brief, you can mention it here, and if it's less brief or an action for the submitter, open an issue in the software repository and mention this issue in it.

If you have any questions or problems, please tell me.

@StewMH

This comment has been minimized.

Copy link

@StewMH StewMH commented Jun 5, 2019

Hi @tesch1,

I tried compiling this with GCC 7.3 and got this error:

In file included from /home/smh/joss/cppduals/duals/dual_eigen:389:0,
                 from /home/smh/joss/cppduals/tests/sandbox.cpp:20:
/home/smh/joss/cppduals/duals/arch/AVX/ComplexDual.h: In function ‘Packet Eigen::internal::pset1(const typename Eigen::internal::unpacket_traits<Packet>::type&) [with Packet = Eigen::internal::Packet2cdf; typename Eigen::internal::unpacket_traits<Packet>::type = std::complex<duals::dual<float> >]’:
/home/smh/joss/cppduals/duals/arch/AVX/ComplexDual.h:157:21: error: ‘_mm256_set_m128’ was not declared in this scope
   return Packet2cdf(_mm256_set_m128(v,v));
                     ^~~~~~~~~~~~~~~
/home/smh/joss/cppduals/duals/arch/AVX/ComplexDual.h:157:21: note: suggested alternative: ‘_mm256_set_epi8’
   return Packet2cdf(_mm256_set_m128(v,v));
                     ^~~~~~~~~~~~~~~
                     _mm256_set_epi8

I think you need a workaround here. See e.g. opencv/opencv#8080 for a similar issue.

I didn't have any luck compiling it with Clang on Ubuntu either, so far.

Also, it's Apache-licensed but you have MPL-licensed files:
https://gitlab.com/tesch1/cppduals/blob/master/duals/arch/AVX/Dual.h

@tesch1

This comment has been minimized.

Copy link

@tesch1 tesch1 commented Jun 6, 2019

Hi,

Thanks for reviewing!

Ah yeah, the "older gcc missing avx primitive". Just checked in an update/workaround. Does it compile for you now?

Also, did you run into the same error(s) under clang, or was there something else?

Regarding the licenses, yes, there are some files that were modified from Eigen, so retain the Eigen license. These are only included with #include <duals/dual_eigen>. An upcoming update will clarify this in the README.

@mdavezac

This comment has been minimized.

Copy link

@mdavezac mdavezac commented Jun 6, 2019

@tesch1, have you considered dual licensing the non-eigen parts with MPL as well as Apache? That way, users can pick a format where the whole product is covered under a single license.

@tesch1

This comment has been minimized.

Copy link

@tesch1 tesch1 commented Jun 6, 2019

Oh yes, that's a great idea. I'll do that. I picked Apache+LLVM because libc++ uses it, and wanted to be broadly compatible with that, but dual-licensing is even better.

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Jun 10, 2019

👋 Any news on this from the authors or reviewers?

@StewMH

This comment has been minimized.

Copy link

@StewMH StewMH commented Jun 10, 2019

Hi,

I have got past the missing avx primitive with GCC. Now the compilation runs for a while but fails with an ICE probably related to out-of-memory, at least on my VM. I can try a more powerful bare-metal machine, the VM only has 2G of RAM.

Cheers,
Stewart

@mdavezac

This comment has been minimized.

Copy link

@mdavezac mdavezac commented Jun 10, 2019

An issue has been filed in the original repo.

@StewMH, I think I clicked on your checkboxes rather than mine at some point... I tried to undo the damage, but I do apologized if I made a mess of things 😊

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Jun 13, 2019

@tesch1 - please let us know when you have worked on the issues in https://gitlab.com/tesch1/cppduals/issues/4

@tesch1

This comment has been minimized.

Copy link

@tesch1 tesch1 commented Jun 15, 2019

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Jun 17, 2019

@whedon remind @tesch1 in 2 weeks

@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Jun 17, 2019

Reminder set for @tesch1 in 2 weeks

@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Jul 1, 2019

👋 @tesch1, please update us on how things are progressing here.

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Jul 7, 2019

👋 @tesch1, please update us on how things are progressing here.

2 similar comments
@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Jul 12, 2019

👋 @tesch1, please update us on how things are progressing here.

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Jul 19, 2019

👋 @tesch1, please update us on how things are progressing here.

@tesch1

This comment has been minimized.

Copy link

@tesch1 tesch1 commented Jul 19, 2019

@whedon generate pdf from branch paper-3

@StewMH - did you ever get it to compile? Some Eigen constructs can be quite demanding on compiler memory, especially in newer (> 3.3.7) versions.

I've updated https://gitlab.com/tesch1/cppduals/issues/4 and merged changes into the master branch (which is currently building).

Regarding licensing, have changed everything to MPL-2 for simplicity's sake.

@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Jul 19, 2019

Attempting PDF compilation from custom branch paper-3
. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Jul 19, 2019

@tesch1

This comment has been minimized.

Copy link

@tesch1 tesch1 commented Jul 19, 2019

@danielskatz It would appear that whedon does not correctly use custom branches from gitlab when generating pdfs (or I did the syntax wrong above?)

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Jul 19, 2019

What didn't work? It looks like whedon generated a PDF. Is it not from the right branch?

@tesch1

This comment has been minimized.

Copy link

@tesch1 tesch1 commented Jul 19, 2019

It is not from the right branch.

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Nov 5, 2019

Thanks - once the submission is accepted (hopefully in another 10 min or so), the DOI for the JOSS article will be shown here. You can certainly add this to the zenodo metadata.

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Nov 5, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Nov 5, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Nov 5, 2019

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Nov 5, 2019

There seem to be some issue in a couple of bib entries - can you merge https://gitlab.com/tesch1/cppduals/merge_requests/18 which I think should fix them?

@tesch1

This comment has been minimized.

Copy link

@tesch1 tesch1 commented Nov 5, 2019

Merged

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Nov 5, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Nov 5, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Nov 5, 2019

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Nov 5, 2019

@whedon accept

@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Nov 5, 2019

Attempting dry run of processing paper acceptance...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Nov 5, 2019


OK DOIs

- 10.1145/2503210.2503219 is OK
- 10.1007/978-1-4613-0075-5 is OK
- 10.5281/zenodo.2677671 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Nov 5, 2019

Check final proof 👉 openjournals/joss-papers#1087

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1087, 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

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Nov 5, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Nov 5, 2019
@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Nov 5, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Nov 5, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Nov 5, 2019

🚨🚨🚨 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 👉 openjournals/joss-papers#1088
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01487
  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...

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Nov 5, 2019

Thanks to @StewMH and @mdavezac for reviewing!

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Nov 5, 2019

@tesch1 - you can see the DOI above (https://doi.org/10.21105/joss.01487). It's not quite working for me yet, which could be a backlog in registering new DOIs, or it could be due to a server in my location - Once it works, I will close this issue and we will be done.

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Nov 5, 2019

Ah, now the DOI resolves, but I don't yet see https://www.theoj.org/joss-papers/joss.01487/10.21105.joss.01487.pdf working.

@tesch1

This comment has been minimized.

Copy link

@tesch1 tesch1 commented Nov 5, 2019

Thanks to @StewMH and @mdavezac for reviewing!

I second that, Thanks gentlemen!! Also thank you, @danielskatz !

@danielskatz

This comment has been minimized.

@tesch1

This comment has been minimized.

Copy link

@tesch1 tesch1 commented Nov 5, 2019

@danielskatz nope, 404

@danielskatz

This comment has been minimized.

Copy link

@danielskatz danielskatz commented Nov 5, 2019

@arfon, any thoughts on this?

@mdavezac

This comment has been minimized.

Copy link

@mdavezac mdavezac commented Nov 5, 2019

Congrats, @tesch1! 🍾

@arfon

This comment has been minimized.

Copy link
Member

@arfon arfon commented Nov 5, 2019

@arfon, any thoughts on this?

Looks like there's an issue with GitHub Pages right now: https://www.githubstatus.com/incidents/42hkbtl63nmn

@arfon

This comment has been minimized.

Copy link
Member

@arfon arfon commented Nov 5, 2019

OK, looks like the PDF URL is resolving now.

@danielskatz danielskatz closed this Nov 5, 2019
@whedon

This comment has been minimized.

Copy link
Collaborator Author

@whedon whedon commented Nov 5, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.01487/status.svg)](https://doi.org/10.21105/joss.01487)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01487">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01487/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01487/status.svg
   :target: https://doi.org/10.21105/joss.01487

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:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
6 participants
You can’t perform that action at this time.