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[REVIEW]: ApplNumComp: An Open Access Introductory Course for Applied Numerical Computing #143

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whedon opened this issue Oct 11, 2021 · 34 comments
Open
41 of 44 tasks

[REVIEW]: ApplNumComp: An Open Access Introductory Course for Applied Numerical Computing #143

whedon opened this issue Oct 11, 2021 · 34 comments
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@kyleniemeyer @ThomasA @sconde
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@whedon
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whedon commented Oct 11, 2021 •
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Submitting author: @ashleefv (Ashlee N. Ford Versypt)
Repository: https://github.com/ashleefv/ApplNumComp
Branch with paper.md (empty if default branch):
Version: v1.1
Editor: @kyleniemeyer
Reviewers: @sconde, @ThomasA
Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/c94d50fd10727c68b3b678ed042cb794"><img src="https://jose.theoj.org/papers/c94d50fd10727c68b3b678ed042cb794/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/c94d50fd10727c68b3b678ed042cb794/status.svg)](https://jose.theoj.org/papers/c94d50fd10727c68b3b678ed042cb794)

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

@sconde & @ThomasA, 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/jose-reviews/invitations

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

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source for this learning module available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
  • Version: Does the release version given match the repository release (v1.1)?
  • Authorship: Has the submitting author (@ashleefv) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

  • A statement of need: Do the authors clearly state the need for this module and who the target audience is?
  • Installation instructions: Is there a clearly stated list of dependencies?
  • Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

  • Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
  • Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
  • Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
  • Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
  • Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Does the paper clearly state the need for this module and who the target audience is?
  • Description: Does the paper describe the learning materials and sequence?
  • Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
  • Could someone else teach with this module, given the right expertise?
  • Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @ThomasA

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source for this learning module available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
  • Version: Does the release version given match the repository release (v1.1)?
  • Authorship: Has the submitting author (@ashleefv) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

  • A statement of need: Do the authors clearly state the need for this module and who the target audience is?
  • Installation instructions: Is there a clearly stated list of dependencies?
  • Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

  • Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
  • Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
  • Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
  • Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
  • Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Does the paper clearly state the need for this module and who the target audience is?
  • Description: Does the paper describe the learning materials and sequence?
  • Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
  • Could someone else teach with this module, given the right expertise?
  • Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
@whedon whedon mentioned this issue Oct 11, 2021
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@whedon
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whedon commented Oct 11, 2021

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

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/jose-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/jose-reviews:

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

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@whedon
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whedon commented Oct 11, 2021

Wordcount for paper.md is 1077

@whedon
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whedon commented Oct 11, 2021 

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.18260/1-2--32072 is OK
- 10.22369/issn.2153-4136/9/1/3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented Oct 11, 2021 

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.14 s (553.1 files/s, 67170.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        28            447              0           2080
MATLAB                          21            136            329           1779
Qt                               2              0              0           1601
Python                          15            178            200           1181
TeX                              6            130             87            730
Jupyter Notebook                 5              0            420             90
HTML                             1             17             12             55
-------------------------------------------------------------------------------
SUM:                            78            908           1048           7516
-------------------------------------------------------------------------------


Statistical information for the repository '6d2c3ae50c994dd5b553e539' was
gathered on 2021/10/11.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ashlee Ford Versypt              2          1598             20          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Ashlee Ford Versypt        1578           98.7          0.0                9.19

@whedon
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whedon commented Oct 11, 2021

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@kyleniemeyer
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👋 @ashleefv @sconde, @ThomasA the actual review will take place in this issue. Thanks!

@ThomasA
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ThomasA commented Oct 24, 2021

@kyleniemeyer I somehow did not manage to accept the invite for the review repository. At least I cannot check the boxes in this review issue. Can you resend the invite?

@kyleniemeyer
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@whedon re-invite @ThomasA as reviewer

@whedon
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whedon commented Oct 25, 2021

The reviewer already has a pending invite.

@ThomasA please accept the invite by clicking this link: https://github.com/openjournals/jose-reviews/invitations

@whedon
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whedon commented Oct 25, 2021

👋 @ThomasA, please update us on how your review is going (this is an automated reminder).

@whedon
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whedon commented Oct 25, 2021

👋 @sconde, please update us on how your review is going (this is an automated reminder).

@labarba
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labarba commented Nov 2, 2021

Hi everyone! Could we have a little update? When do you think you could tick off a few more items of your checklist, @sconde @ThomasA ?

@ThomasA
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ThomasA commented Nov 23, 2021

Sorry, I have been swamped by work lately. Have been working on #138 tonight. I hope to complete this one within the next couple of days.

@sconde
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sconde commented Nov 28, 2021

[ ] A statement of need: Do the authors clearly state the need for this module and who the target audience is?

ashleefv/ApplNumComp#2

@sconde
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sconde commented Nov 28, 2021

  • Installation instructions: Is there a clearly stated list of dependencies?

ashleefv/ApplNumComp#3

@sconde
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sconde commented Nov 28, 2021

  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

ashleefv/ApplNumComp#4

@kyleniemeyer
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Hi @ashleefv, sorry for the delay here—checking back on this now. I see that @sconde left some issues related to the review, have you been able to address those yet?

@ThomasA have you had a chance to work on your review?

@ashleefv
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ashleefv commented Feb 19, 2022 via email

@kyleniemeyer
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Hi @ashleefv, have you been able to make progress on the submission?

@ashleefv
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ashleefv commented Apr 9, 2022 via email

@ThomasA
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ThomasA commented Apr 9, 2022

I am terribly sorry I have not been very responsive. I have been quite overwhelmed at work due to my team being severely decimated.
I should be able to finish this review over Easter.

@ashleefv
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ashleefv commented May 16, 2022 via email

@kyleniemeyer
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Sorry for the (major) delay here - I checked in with @ThomasA via email and he will complete his review soon

@labarba
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labarba commented Dec 30, 2022

@ashleefv – an update that we are reaching out to the reviewers via other channels. Will keep trying to get this to the finish line!

@sconde
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sconde commented Dec 30, 2022

  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

@ashleefv This issue still needs to be resolved.

@sconde
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sconde commented Dec 30, 2022 •
edited

  • Version: Does the release version given match the repository release (v1.1)?

@ashleefv, does the release version need to be updated to reflect the changes you've made?

@ashleefv
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ashleefv commented Dec 30, 2022 via email

@kyleniemeyer
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@ashleefv I realize that I haven't done a great job shepherding this review along—hopefully we can get this wrapped up "soon".

Like JOSS, JOSE reviews are not meant to be monolithic, requiring a response to both reviewers after the reviews are complete in the traditional manner.

Instead, recognizing the software-adjacent nature of the work, as reviewers provide comments and raise issues one-by-one, they can be addressed along the way, in a more continuous and conversational way in here.

(It's also easier for a second reviewer to just give a thumbs up if you have already addressed things raised here.)

So, please do work on addressing those issues if you can.

@ThomasA
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ThomasA commented Jan 6, 2023

  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

ashleefv/ApplNumComp#4

I second this issue

@ThomasA
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ThomasA commented Jan 6, 2023

Regarding the statement of need, I find it well described in the paper while it is not that clear in the repository documentation as such (looking at the README.md).

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ThomasA commented Jan 6, 2023

Regarding "telling the story", I think the paper does this somewhat, but the author's additional paper https://doi.org/10.18260/1-2--32072 referenced therein seems to do this even more so. I think it is fine that interested readers can go there for more information.

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ThomasA commented Jan 6, 2023

Aside from the few remarks above, I think this looks like an excellent and coherent collection of introductory educational material for the topics the module covers.
I apologise for the insanely long time I took to get around to completing this review.

@sconde
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sconde commented Feb 8, 2023

All that remains is the community guidelines @ashleefv

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sconde commented Mar 13, 2023

@ashleefv, any update on the guidelines?

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