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

[whedon]

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

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Markdown: [![status](https://jose.theoj.org/papers/c94d50fd10727c68b3b678ed042cb794/status.svg)](https://jose.theoj.org/papers/c94d50fd10727c68b3b678ed042cb794)

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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:

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✨ 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

• [x] As the reviewer I confirm that I have read the JOSE 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 JOSE code of conduct.

General checks

• [x] Repository: Is the source for this learning module available at the repository url?
• [x] 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)?
• [x] Authorship: Has the submitting author (@ashleefv) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• [x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• [x] Installation instructions: Is there a clearly stated list of dependencies?
• [x] 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!)

• [x] 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.)
• [x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• [x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• [x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• [x] 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

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

Review checklist for @ThomasA

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSE 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 JOSE code of conduct.

General checks

• [x] Repository: Is the source for this learning module available at the repository url?
• [x] 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)
• [x] Version: Does the release version given match the repository release (v1.1)?
• [x] Authorship: Has the submitting author (@ashleefv) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• [x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• [x] Installation instructions: Is there a clearly stated list of dependencies?
• [x] 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!)

• [x] 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.)
• [x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• [x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• [x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• [x] 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

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

[whedon]

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 :tada:.

:warning: JOSS reduced service mode :warning:

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.

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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 😿

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[whedon]

Wordcount for paper.md is 1077

[whedon]

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]

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]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[kyleniemeyer]

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

[ThomasA]

@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]

@whedon re-invite @ThomasA as reviewer

[whedon]

The reviewer already has a pending invite.

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

[whedon]

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

[whedon]

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

[labarba]

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]

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]

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

https://github.com/ashleefv/ApplNumComp/issues/2

[sconde]

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

https://github.com/ashleefv/ApplNumComp/issues/3

[sconde]

• 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

https://github.com/ashleefv/ApplNumComp/issues/4

[kyleniemeyer]

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]

Other deadlines have delayed me in addressing the reviewer's comments, but I have received them.

Ashlee N. Ford Versypt, Ph.D. (she, her, hers) Associate Professor Department of Chemical and Biological Engineering University at Buffalo, The State University of New York 507 Furnas Hall, Buffalo, NY 14260 @.*** http://www.cbe.buffalo.edu/fordversypt

---

From: Kyle Niemeyer @.> Sent: Friday, February 11, 2022 3:55 PM To: openjournals/jose-reviews @.> Cc: Ashlee Ford Versypt @.>; Mention @.> Subject: Re: [openjournals/jose-reviews] [REVIEW]: ApplNumComp: An Open Access Introductory Course for Applied Numerical Computing (#143)

Hi @ashleefvhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fashleefv&data=04%7C01%7Cashleefv%40buffalo.edu%7C46d0b3c359c74c9b404308d9eda0da59%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637802097386928025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=4yUFChAf9j75f242P8MitRTjA97NsCsgGTSnH45hADw%3D&reserved=0, sorry for the delay here—checking back on this now. I see that @scondehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsconde&data=04%7C01%7Cashleefv%40buffalo.edu%7C46d0b3c359c74c9b404308d9eda0da59%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637802097386928025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=F9YL%2BeFUb0K9%2BPUKHYMXzq2kqOCiwoV8p9Riz%2Fcib9Q%3D&reserved=0 left some issues related to the review, have you been able to address those yet?

@ThomasAhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FThomasA&data=04%7C01%7Cashleefv%40buffalo.edu%7C46d0b3c359c74c9b404308d9eda0da59%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637802097386928025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=QFldKaXs7R8F6x4407TWXzxlU4iJqTa1Eh8VN8HB0FM%3D&reserved=0 have you had a chance to work on your review?

— Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopenjournals%2Fjose-reviews%2Fissues%2F143%23issuecomment-1036615021&data=04%7C01%7Cashleefv%40buffalo.edu%7C46d0b3c359c74c9b404308d9eda0da59%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637802097386928025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2FuPdEcXPTvWYys%2F7Zxy0a6nLoLHMv6ZPo5gULCf%2FRQI%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADAP4NQ5MJBABBRXGGA2WSTU2VZUPANCNFSM5FYZDWRQ&data=04%7C01%7Cashleefv%40buffalo.edu%7C46d0b3c359c74c9b404308d9eda0da59%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637802097386928025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=JQ%2FSzRfz9TzsLeY66C8FA7K1EEI2eia4qNa8Z2JNjNE%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cashleefv%40buffalo.edu%7C46d0b3c359c74c9b404308d9eda0da59%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637802097386928025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Xf5eTyJkv5%2FwE%2BBfIbPX%2FnI%2FUVvafN0JVhVwuj%2B9uvQ%3D&reserved=0 or Androidhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cashleefv%40buffalo.edu%7C46d0b3c359c74c9b404308d9eda0da59%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637802097386928025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=k3EBNVhcnPJdEffl8hLTaqJ23JM02cejPHHcYIE9iog%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

[kyleniemeyer]

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

[ashleefv]

Part of my delay was also hoping I'd get comments back from more than 1 reviewer. So far only one has shared the feedback on this review forum. The other said in Nov. that they were working on it, but I haven't seen the critique.

On Apr 6, 2022 12:49 PM, Kyle Niemeyer @.***> wrote:

Hi @ashleefvhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fashleefv&data=04%7C01%7Cashleefv%40buffalo.edu%7C3859a88b38aa45b973cd08da17ed6868%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637848605689459397%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=zJK8HKoZXLbla5TzthQgs%2BLRDKlHokL%2F7mJVhuINFnM%3D&reserved=0, have you been able to make progress on the submission?

— Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopenjournals%2Fjose-reviews%2Fissues%2F143%23issuecomment-1090485739&data=04%7C01%7Cashleefv%40buffalo.edu%7C3859a88b38aa45b973cd08da17ed6868%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637848605689459397%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=J2qYpnEgaEjAZtJWjGGIlo%2BFk9JYedJdGw834qMQoyU%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADAP4NS3PVR4CONL3SRBYO3VDW6BJANCNFSM5FYZDWRQ&data=04%7C01%7Cashleefv%40buffalo.edu%7C3859a88b38aa45b973cd08da17ed6868%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637848605689459397%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=2Q%2BA7CP9ddfneFgbgdhIrKqbWw94uGZHFOu%2FNyJr0qc%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

[ThomasA]

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]

Any updates on the review?

Ashlee N. Ford Versypt, Ph.D. (she, her, hers) Associate Professor, Department of Chemical and Biological Engineering Core Faculty, Institute for Computational and Data Sciences Affiliated Faculty, Department of Engineering Education University at Buffalo, The State University of New York 507 Furnas Hall, Buffalo, NY 14260 @.*** http://www.cbe.buffalo.edu/fordversypt

---

From: Thomas Arildsen @.> Sent: Saturday, April 9, 2022 7:37 AM To: openjournals/jose-reviews @.> Cc: Ashlee Ford Versypt @.>; Mention @.> Subject: Re: [openjournals/jose-reviews] [REVIEW]: ApplNumComp: An Open Access Introductory Course for Applied Numerical Computing (#143)

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.

— Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopenjournals%2Fjose-reviews%2Fissues%2F143%23issuecomment-1093944427&data=04%7C01%7Cashleefv%40buffalo.edu%7C85d910bd5d0347f174ce08da1a1d4e6a%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637851010423250586%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2FI7ythWQVileEN9%2FeONjFNWEKhJvjfxnVTom2KBeSh4%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADAP4NWLXSCMCCSIU5VHWK3VEFTW7ANCNFSM5FYZDWRQ&data=04%7C01%7Cashleefv%40buffalo.edu%7C85d910bd5d0347f174ce08da1a1d4e6a%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637851010423250586%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=fTiiGjhjNXf1ByPTgPyc6WUQ9ZjYFaX3v2bEhcDM8k8%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

[kyleniemeyer]

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

[labarba]

@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]

• 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]

• [ ] 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]

I haven't made any changes in response to the first reviewer because I never got a second reviewer comments.

On Dec 30, 2022 3:41 PM, Sidafa Conde @.***> wrote:

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

@ashleefvhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fashleefv&data=05%7C01%7Cashleefv%40buffalo.edu%7C2121e46e64fd449cff7c08daeaaea105%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638080333016424451%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lg0Mf3jnhpTj3mkmZwDwuzz3JlmhHyCor%2FplvZnIEVo%3D&reserved=0, does the release version need to be updated to reflect the changes you've made?

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[kyleniemeyer]

@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]

• 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]

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).