[REVIEW]: EZyRB: Easy Reduced Basis method

whedon commented 6 years ago

Submitting author: @mtezzele (Marco Tezzele) Repository: https://github.com/mathLab/EZyRB Version: v0.2.0 Editor: @arfon Reviewer: @dlagrava, @ziotom78 Archive: 10.5281/zenodo.1216303

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/5863039d479498779b88e165e1682725"><img src="http://joss.theoj.org/papers/5863039d479498779b88e165e1682725/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/5863039d479498779b88e165e1682725/status.svg)](http://joss.theoj.org/papers/5863039d479498779b88e165e1682725)

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

@dlagrava & @ziotom78, 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 @arfon know.

Review checklist for @dlagrava

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: Does the release version given match the GitHub release (v0.2.0)?
[x] Authorship: Has the submitting author (@mtezzele) 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?
[ ] 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 @ziotom78

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: Does the release version given match the GitHub release (v0.2.0)?
[x] Authorship: Has the submitting author (@mtezzele) 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 6 years ago

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @dlagrava, 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 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

ziotom78 commented 6 years ago

@mtezzele Here are a few comments:

A few minor fixes in the PDF:
- Second sentence: "In the first one constructs…" it would be nice to have a comma: "In the first, one constructs…"
- Consider this page to understand how to properly cite bibliographical entries. E.g., write "…for a new parameter [see for example @cite1;@cite2]", separating entries with a semicolon ";", so that there will not be multiple parentesis.
- Citation Chinestra, Huerta, Rozza, Wilcox in the "References" section is incomplete (no book title)
You should create a GitHub release marked 0.2.0 at https://github.com/mathLab/EZyRB/releases, so in the future people will be able to download the code used for this review.

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

PDF failed to compile for issue #661 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 13 0 13 0 0 269 0 --:--:-- --:--:-- --:--:-- 270 Error reading bibliography ./paper.bib (line 37, column 5): 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

ndem0 commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

mtezzele commented 6 years ago

@ziotom78 thanks for the suggestions. @ndem0 made all the fixes.

ziotom78 commented 6 years ago

@mtezzele @ndem0 thank you for the prompt response! Everything seems to have been fixed, except the URL to Chinesta's book: it looks like it has a spurious https://dx.doi.org/ at the beginning of it.

Might you please add the link to the arXiv entry for the paper by Salmoiraghi et al? Meanwhile, I'll play with EZyRB, I just installed it on my computer.

ndem0 commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

ndem0 commented 6 years ago

@ziotom78 I fixed both the wrong doi and arXiv link missing, now the paper should be ok!

dlagrava commented 6 years ago

@mtezzele a couple of typos on the paper.md:

since its structure can interact with several simulation software by simply providing the output file of the simulations
As an example, ...

Thanks.

mtezzele commented 6 years ago

@dlagrava typos fixed. Thanks!

ziotom78 commented 6 years ago

I created ticket #68 on EZyRB's website, as there is no clear indication of the supported Python version. (I discovered that EZyRB does not support Python 3.6 by trial and error, although I later realized that setup.py indicates that in the metadata.)

ndem0 commented 6 years ago

@ziotom78 Thanks for the segnalation, I added in the README file the supported Python version.

ziotom78 commented 6 years ago

@ndem0 thanks! @arfon, everything looks fine to me now.

mtezzele commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

arfon commented 6 years ago

@dlagrava, @ziotom78 - can you both confirm we're good to accept here now?

ziotom78 commented 6 years ago

@arfon for me it's ok

dlagrava commented 6 years ago

@arfon I am really sorry, I finished this yesterday, but I have been very busy. For me all is good here.

ndem0 commented 6 years ago

@arfon We have upload the package and this is the DOI for all the versions: 10.5281/zenodo.1216303

arfon commented 6 years ago

@whedon set 10.5281/zenodo.1216303 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1216303 is the archive.

arfon commented 6 years ago

@ziotom78 @dlagrava - many thanks for your reviews here ✨

@ndem0 - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00661 :zap: :rocket: :boom:

whedon commented 6 years ago

: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 snippet:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00661/status.svg)](https://doi.org/10.21105/joss.00661)

This is how it will look in your documentation:

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:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://www.flipcause.com/secure/cause_pdetails/Mjk3Nzk=

ndem0 commented 6 years ago

@arfon @ziotom78 @dlagrava Many thanks for the efforts!

openjournals / joss-reviews