Joss-reviews: [REVIEW]: The SuiteSparse Matrix Collection Website Interface

Created on 8 Feb 2019  ·  67Comments  ·  Source: openjournals/joss-reviews

Submitting author: @ScottKolo (Scott Kolodziej)
Repository: https://github.com/ScottKolo/suitesparse-matrix-collection-website
Version: JOSS-1.0.2
Editor: @jedbrown
Reviewer: @dblarremore, @tkonolige
Archive: 10.6084/m9.figshare.7381076

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/965b1c7bba801c85e9341a3db9013ef8"><img src="http://joss.theoj.org/papers/965b1c7bba801c85e9341a3db9013ef8/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/965b1c7bba801c85e9341a3db9013ef8/status.svg)](http://joss.theoj.org/papers/965b1c7bba801c85e9341a3db9013ef8)

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

@dblarremore & @tkonolige, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @jedbrown know.

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

Review checklist for @dblarremore

Conflict of interest

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: JOSS-1.0.2
  • [x] Authorship: Has the submitting author (@ScottKolo) 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 @tkonolige

Conflict of interest

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: JOSS-1.0.2
  • [x] Authorship: Has the submitting author (@ScottKolo) 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)?
accepted published recommend-accept review
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picture whedon

All 67 comments

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

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whedon picture whedon on 8 Feb 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 8 Feb 2019

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

whedon picture whedon on 8 Feb 2019

@dblarremore @tkonolige :wave: Welcome and thanks for agreeing to review! The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the project repository). I'll be watching this thread if you have any questions.

jedbrown picture jedbrown on 8 Feb 2019

@ScottKolo I think https://doi.org/10.1007/978-1-5041-2940-4_9 is the correct doi for Matrix market: A web resource for test matrix collections. It would be great if you can add that.

I also see that there is no documentation for building, installing, and testing locally. I created an issue for it in your repository: ScottKolo/suitesparse-matrix-collection-website#5.

tkonolige picture tkonolige on 11 Feb 2019

@jedbrown I'm not sure about the example usage and functional documentation parts of the checklist. Does there need to be documentation on how to use the website? I think it is pretty straight forward.

tkonolige picture tkonolige on 12 Feb 2019

I don't think human "use" of the website needs separate documentation, but there appears to be an API used by several external packages and I don't immediately notice documentation of that API.

jedbrown picture jedbrown on 12 Feb 2019

I don't think human "use" of the website needs separate documentation, but there appears to be an API used by several external packages and I don't immediately notice documentation of that API.

We do include information about other interfaces to the Collection on the website itself on the Interfaces page. I also just added information in the repository README referencing the Interfaces page and also the URL routing feature, which might be considered an API.

The use of most of the website should be (we hope) easy enough to understand and figure out. We also include tooltips to help users with certain terminology:

image

Regarding the inner workings of things like UFget/ssget, we considered that somewhat out of scope for this paper as these interfaces were presented in Davis and Hu and are not strictly considered part of the web application. For example, these interfaces often provide the option to download a matrix, and that download URL is the same URL being used by the web application when you click the button on the website. The files are also not served by the Rails web application we've presented - they're being served by a file server. The way we see it, this is a "frontend" to access the "backend" presented in Davis and Hu.

ScottKolo picture ScottKolo on 13 Feb 2019

That all makes sense. I think you're good on the documentation front then.

@ScottKolo, @jedbrown should the release version listed here be bumped to match what is currently in the repository (now that some changes have been made)?

tkonolige picture tkonolige on 13 Feb 2019

Yeah, we'll ask for a tagged release at acceptance, and the version will be set at that time.

jedbrown picture jedbrown on 13 Feb 2019

Trivial: "applicaiton" typo in README.

Perhaps more useful: Possible change needed in installation instructions for OSX.
I tried to do the local installation, updated Ruby, and got all of that sorted out. On README line
bundle exec rake db:setup
I kept getting an error
PG::ConnectionBad: could not connect to server: No such file or directory
Is the server running locally and accepting
connections on Unix domain socket "/tmp/.s.PGSQL.5432"?
I eventually fixed this by (apparently) manually starting the server via the top answer here whose details are then described in detail here.
After that, my local installation was totally fine.

To recap, my experience required that I insert this line between the bundle install and bundle exec rake commands:
pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log start

Now, the question: is this worth inserting into the documentation? Are there files that could be modified by @ScottKolo or is this a sort of novice ruby user thing? (I am basically a test case for _user who does not know what he is doing with a local ruby installation_ so perhaps not an issue.) Curious to hear what you guys think.

dblarremore picture dblarremore on 20 Feb 2019

To recap, my experience required that I insert this line between the bundle install and bundle exec rake commands:
pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log start

After installing PostgreSQL, one needs to start it up so it's running in the background. You can do this a number of ways: manually start/stop, use the daemon, etc. After installing PostgreSQL from a package manager, it often spits out a line at the end about this (i.e. "run this magical incantation to start the daemon").

I'm happy to add whatever you think is helpful to the documentation. I might suggest the following additional call to pg_isready:

ruby -v                              # Check that Ruby 2.5+ is installed
pg_isready                           # Check that PostgreSQL database is ready
git clone https://github.com/ScottKolo/suitesparse-matrix-collection-website.git
cd suitesparse-matrix-collection-website
gem install bundler:1.16.6           # Dependency manager
bundle install --without production  # Download and install dependencies
bundle exec rake db:setup            # Generate and seed the database
bundle exec rails server             # Start the Ruby on Rails server application

Unfortunately, if pg_isready fails, it is not very informative regarding how to fix the problem.

I can add a line mentioning something about "PostgreSQL must be running - if it is not, try running pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log start."

My only concern is that the above command assumes the user's postgres installation directory and log file location.

ScottKolo picture ScottKolo on 20 Feb 2019

I like the idea to use pg_isready but how about putting this snippet above, under the bullet list that includes the need for ruby and postgreSQL? Then it would be filed in with the prep work and dependencies instead of with the installation itself.

What you wrote was really nice, so I tinkered with it a little, but maybe something like this? Happy for any modifications to this, since it's your README, but thought this might be useful:

After installing PostgreSQL, note that one needs to start it up so it's running in the background. The status can be checked using pg_isready. If this fails, the installation can be started manually, e.g. via pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log start, depending on the location of your installation. If PostgreSQL was installed from a package manager, it often spits out a line at the end about this (i.e. "run this magical incantation to start the daemon").

If you think this is an ok suggestion, and decide to put the pg_isready note above in the dependencies, it might also be appropriate to move the ruby -v check up there as well.

dblarremore picture dblarremore on 20 Feb 2019

With a little of my own wordsmithing, I have added information about starting PostgreSQL and installing Ruby to the README. Let me know if you think it's too much or not enough.

scottkolo/suitesparse-matrix-collection-website@384f0ad354c2d5be1b0351bb3aec5c9a0adc0955

ScottKolo picture ScottKolo on 21 Feb 2019
👍1

Looks great. Not overly verbose, but still thorough enough to capture users like me.

dblarremore picture dblarremore on 21 Feb 2019
👍1

Just following up - is there any further feedback or any actions required on our part? What are the next steps?

ScottKolo picture ScottKolo on 1 Mar 2019

@whedon generate pdf

jedbrown picture jedbrown on 7 Mar 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 7 Mar 2019

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

whedon picture whedon on 7 Mar 2019

@whedon check references

jedbrown picture jedbrown on 7 Mar 2019 
Attempting to check references...
whedon picture whedon on 7 Mar 2019

```Reference check summary:

OK DOIs

  • 10.1145/2049662.2049663 is OK

MISSING DOIs

INVALID DOIs

  • None
    ```
whedon picture whedon on 7 Mar 2019

Whedon is quite flaky about checking DOIs; they look fine in the paper. I made a PR for some bib formatting issues: https://github.com/ScottKolo/suitesparse-matrix-collection-website/pull/6
I think we'll be ready to archive and accept if that looks reasonable. Thanks for your patience.

jedbrown picture jedbrown on 8 Mar 2019

Whedon is quite flaky about checking DOIs

I think Whedon only checks DOIs for @article entries currently. I'll see if I can fix this.

arfon picture arfon on 8 Mar 2019

@whedon check references

arfon picture arfon on 8 Mar 2019 
Attempting to check references...
whedon picture whedon on 8 Mar 2019

```Reference check summary:

OK DOIs

  • 10.1145/2049662.2049663 is OK
  • 10.1007/978-1-5041-2940-4_9 is OK
  • 10.17616/R3WG6Z is OK

MISSING DOIs

INVALID DOIs

  • None
    ```
whedon picture whedon on 8 Mar 2019

I have checked all of the suggested DOIs - they are all incorrect. Here's a quick discussion about each of these references and why they (currently) lack DOIs:

MISSING DOIs

This is a tech report. The suggested DOI references a paper that predates it by 15 years.

This is a website for Clarivate Analytics' Data Citation Index. The suggested DOI leads to a cardiology journal (?).

This is a website describing the use of the UFL Sparse Matrix Collection via AWS. The suggested DOI points to a generic article on Database Services in AWS.

This article was published in the Mathematica Journal, but it does not seem to have any DOI associated with it. The suggested DOI is a broken link.

This article is currently a preprint on arXiv. The suggested DOI links to some prior work by the same authors.

This article is currently in review. The suggested DOI references work by similar authors almost 20 years ago.

This article is a preprint on arXiv. The suggested DOI points to an unrelated article in physics.

ScottKolo picture ScottKolo on 8 Mar 2019

@whedon generate pdf

ScottKolo picture ScottKolo on 8 Mar 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 8 Mar 2019

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

whedon picture whedon on 8 Mar 2019

Yeah, the DOI checker is very buggy. References look good to me now. Can you fix one spelling error "constrainted", tag a release (annotated tag preferred), and archive on Zenodo or similar?

jedbrown picture jedbrown on 8 Mar 2019

@whedon generate pdf

ScottKolo picture ScottKolo on 8 Mar 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 8 Mar 2019

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

whedon picture whedon on 8 Mar 2019

One last nitpick: Is there any way to prevent line breaks in the middle of URLs?

image

ScottKolo picture ScottKolo on 8 Mar 2019

I would consider dropping the https:// part because it's arguably clutter given that full links are embedded. and/or using a tt font:

[`https://sparse.tamu.edu/Mycielski`](https://sparse.tamu.edu/Mycielski)
jedbrown picture jedbrown on 8 Mar 2019

@whedon generate pdf

ScottKolo picture ScottKolo on 8 Mar 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 8 Mar 2019

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

whedon picture whedon on 8 Mar 2019

@whedon generate pdf

ScottKolo picture ScottKolo on 8 Mar 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 8 Mar 2019

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

whedon picture whedon on 8 Mar 2019

Okay, I have tagged release at JOSS-1.0.2.
https://github.com/ScottKolo/suitesparse-matrix-collection-website/releases/tag/JOSS-1.0.2

We have archived the code for this release using figshare: https://figshare.com/articles/SuiteSparse_Matrix_Collection_Website/7381076

Does all of that look correct?

ScottKolo picture ScottKolo on 8 Mar 2019

Author list on the figshare appears to be missing Yifan Hu, who was on the paper. Can you fix the author lists to match in content and order?

jedbrown picture jedbrown on 9 Mar 2019

Fixed. The Figshare DOI is https://doi.org/10.6084/m9.figshare.7381076

The title now matches, as do the authors and author order.

ScottKolo picture ScottKolo on 9 Mar 2019

@whedon set JOSS-1.0.2 as version

jedbrown picture jedbrown on 9 Mar 2019

OK. JOSS-1.0.2 is the version.

whedon picture whedon on 9 Mar 2019

@ScottKolo Is it intended that https:// appears in exactly one of the URLs?

jedbrown picture jedbrown on 9 Mar 2019

Yes. We removed it for most as you suggested, since it wasn’t helpful in those contexts, but left it when we referenced its deployment location.

ScottKolo picture ScottKolo on 9 Mar 2019
👍1

@whedon set 10.6084/m9.figshare.7381076 as archive

jedbrown picture jedbrown on 9 Mar 2019

OK. 10.6084/m9.figshare.7381076 is the archive.

whedon picture whedon on 9 Mar 2019

Over to you, @openjournals/joss-eics.

jedbrown picture jedbrown on 9 Mar 2019

@whedon accept

arfon picture arfon on 10 Mar 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 10 Mar 2019

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/543

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/543, 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 10 Mar 2019

```Reference check summary:

OK DOIs

  • 10.1145/2049662.2049663 is OK
  • 10.1007/978-1-5041-2940-4_9 is OK
  • 10.17616/R3WG6Z is OK

MISSING DOIs

INVALID DOIs

  • None
    ```
whedon picture whedon on 10 Mar 2019

@ScottKolo - the paper currently looks a little peculiar with both the figures being right at the start. This PR moves them into the body of the paper: https://github.com/ScottKolo/suitesparse-matrix-collection-website/pull/7

arfon picture arfon on 10 Mar 2019

@whedon accept

arfon picture arfon on 10 Mar 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 10 Mar 2019

```Reference check summary:

OK DOIs

  • 10.1145/2049662.2049663 is OK
  • 10.1007/978-1-5041-2940-4_9 is OK
  • 10.17616/R3WG6Z is OK

MISSING DOIs

INVALID DOIs

  • None
    ```
whedon picture whedon on 10 Mar 2019

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/544

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/544, 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 10 Mar 2019

@whedon accept deposit=true

arfon picture arfon on 10 Mar 2019 
Doing it live! Attempting automated processing of paper acceptance...
whedon picture whedon on 10 Mar 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 :point_right: https://github.com/openjournals/joss-papers/pull/545
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01244
  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 10 Mar 2019

@dblarremore, @tkonolige - many thanks for your reviews and to @jedbrown for editing this submission ✨

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

arfon picture arfon on 10 Mar 2019

: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](http://joss.theoj.org/papers/10.21105/joss.01244/status.svg)](https://doi.org/10.21105/joss.01244)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01244">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01244/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01244/status.svg
   :target: https://doi.org/10.21105/joss.01244

This is how it will look in your documentation:

DOI

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whedon picture whedon on 10 Mar 2019
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