[REVIEW]: Course Materials for Data Science in Practice

whedon commented 3 years ago

Submitting author: @TomDonoghue (Thomas Donoghue) Repository: https://github.com/DataScienceInPractice/Site Version: v1.1 Editor: @magsol Reviewer: @KiCh84, @krother Archive: 10.5281/zenodo.6568091

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Status

Status badge code:

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Markdown: [![status](https://jose.theoj.org/papers/19ab6fe3aec0080e3c8208eaeaf7a670/status.svg)](https://jose.theoj.org/papers/19ab6fe3aec0080e3c8208eaeaf7a670)

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

@KiCh84 & @krother, 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 @KiCh84

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: v1.1
[x] Authorship: Has the submitting author (@TomDonoghue) 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?
[x] 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 @krother

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: v1.1
[x] Authorship: Has the submitting author (@TomDonoghue) 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?
[x] 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 commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @KiCh84, @krother it looks like you're currently assigned to review this paper :tada:.

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whedon commented 3 years ago

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

OK DOIs

- 10.21105/jose.00032 is OK
- 10.5281/zenodo.2799972 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.05 s (773.3 files/s, 506834.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                29              0          24233           1333
Markdown                         5            159              0            278
YAML                             2              8             12             47
TeX                              1              1              0             39
make                             1             29             36             35
JSON                             2              0              0              8
-------------------------------------------------------------------------------
SUM:                            40            197          24281           1740
-------------------------------------------------------------------------------

Statistical information for the repository '4a32af834d93a6eba0263b8d' was
gathered on 2021/07/06.
No commited files with the specified extensions were found.

whedon commented 3 years ago

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

krother commented 2 years ago

@KiCh84 I created an issue for the missing release, so that the final paper refers to a defined state of the repository.

whedon commented 2 years ago

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

whedon commented 2 years ago

:wave: @KiCh84, please update us on how your review is going (this is an automated reminder).

krother commented 2 years ago

There are currently two issue that I found, and I have created GitHub issues for both.

TomDonoghue commented 2 years ago

Hey @krother - thanks a ton for the review! The things you brought up make total sense, I will fix them up soon.

@KiCh84 - have you had a chance to look at the project and do you have any issues / suggestions? If you have a timeline for adding any comments, I might try and group any updates together!

KiCh84 commented 2 years ago

Hey Tom ! I have been SWAMPED with things ( not only Professional ) , I think next week I should be able to get into it in more detail . I do apologize if there is any inconvenience caused by that :/

On Tue, Jul 27, 2021, 22:26 Tom @.***> wrote:

Hey @krother https://github.com/krother - thanks a ton for the review! The things you brought up make total sense, I will fix them up soon.

@KiCh84 https://github.com/KiCh84 - have you had a chance to look at the project and do you have any issues / suggestions? If you have a timeline for adding any comments, I might try and group any updates together!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/121#issuecomment-887811309, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASWZ3SHVCJWQJP7DK2BL763TZ4I6ZANCNFSM475BW2CQ .

voytek commented 2 years ago

@KiCh84 no, rush since it sounds like a lot's happening (sorry!) but I wanted to see if you had any additional comments or recommendations for us!

KiCh84 commented 2 years ago

Dear Bradley,

I am reading through the course material, and I just quickly wanted to check in and ask you about who the target audience is, for this wonderful course ? and I apologise heavily for the delay in the responses .

On Fri, Aug 6, 2021 at 7:43 PM Bradley Voytek @.***> wrote:

@KiCh84 https://github.com/KiCh84 no, rush since it sounds like a lot's happening (sorry!) but I wanted to see if you had any additional comments or recommendations for us!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/121#issuecomment-894415775, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASWZ3SEQNIVM7AWATCHWXU3T3QNK7ANCNFSM475BW2CQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email .

voytek commented 2 years ago

No worries! The target is undergraduate students with some Python experience, and some statistics.

We have a complementary paper for that class that outlines the general target—and our motivations—here.

Thanks for the kind words, and I hope this clarifies!

voytek commented 2 years ago

Just checking back in on this @KiCh84!

voytek commented 2 years ago

Checking in again, @krother, @KiCh84

labarba commented 2 years ago

@whedon check repository

whedon commented 2 years ago

Wordcount for paper.md is 1030

whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (665.8 files/s, 436407.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                29              0          24233           1333
Markdown                         5            159              0            278
YAML                             2              8             12             47
TeX                              1              1              0             39
make                             1             29             36             35
JSON                             2              0              0              8
-------------------------------------------------------------------------------
SUM:                            40            197          24281           1740
-------------------------------------------------------------------------------

Statistical information for the repository '6efd259c0298602ec2e996f3' was
gathered on 2021/10/01.
No commited files with the specified extensions were found.

labarba commented 2 years ago

@openjournals/dev — hi folks! I'm a little confused about the stats on this repo. What does it mean when the stats list 24k lines under "comment" for Jupyter Notebook? The repo has a lot of material that is not picked up by the stats tool?

arfon commented 2 years ago

@openjournals/dev — hi folks! I'm a little confused about the stats on this repo. What does it mean when the stats list 24k lines under "comment" for Jupyter Notebook? The repo has a lot of material that is not picked up by the stats tool?

It looks like cloc is detecting 29 notebooks which seems about right. As for the actual LOC within, it's entirely possible that this tool doesn't know how to calculate LOC properly (i.e., is getting confused about what is code in a notebook).

Is there other material that you think it should be detecting?

labarba commented 2 years ago

Is there other material that you think it should be detecting?

I don't know! It just threw me off when I looked at the loc and saw a small-ish number, then pulled the repo and saw all those Jupyter notebooks with code and all.

xuanxu commented 2 years ago

I suspect the stats tool is counting as 'Comments' every cell in the notebooks with cell_type: "markdown" (as opposed to cell_type: code)

magsol commented 2 years ago

Hi @KiCh84! 👋 We'd like to get this review wrapped up. Is there anything you need to finish your review?

magsol commented 2 years ago

Hi @krother! 👋 Is your review complete? It looks like there are still just a couple items you haven't checked off yet. We'd love to get this review wrapped up soon, so please let me know if there is anything else you need.

krother commented 2 years ago

@magsol I created a couple of issues in the repository yet. The two related to the checkboxes are: the lack of a version number (not a big deal on my end). The other is that there are two different licenses in the repo and the paper, I believe this needs to be fixed.

KiCh84 commented 2 years ago

Hi !! I've joined a new job and it's hectic there for me till I get a bit comfortable with the tasks , so have not had the time 😭.

On Tue, Oct 12, 2021, 22:09 Shannon @.***> wrote:

Hi @KiCh84 https://github.com/KiCh84! 👋 We'd like to get this review wrapped up. Is there anything you need to finish your review?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/121#issuecomment-941439019, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASWZ3SE4VJ4RHCOHUZEH2ELUGSIXDANCNFSM475BW2CQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

voytek commented 2 years ago

I felt like we were so close here! Any new updates? Anything we can do / respond to in the meantime?

voytek commented 2 years ago

Hello?

magsol commented 2 years ago

@voytek Have you had a chance to read through the issues that @krother mentioned in his last comment?

@KiCh84 Any chance of wrapping things up here?

voytek commented 2 years ago

Yeah, we can implement those changes pretty quickly. But we were waiting for all reviewers' comments. Should we just proceed?

cc @TomDonoghue

TomDonoghue commented 2 years ago

I'll go ahead and come back to this and address everything currently noted (within the next week or so), so that we get as much as possible ready and done here, then it'll just be any last new review items that come up & last checks.

magsol commented 2 years ago

Hi folks! Where are we with this review? @krother @KiCh84 there are still unchecked items on both your lists, are those outstanding or have they been addressed yet? @TomDonoghue @voytek how does the feedback so far look?

KiCh84 commented 2 years ago

Those are outstanding from my end , i really do not know when i will have the time to review all of it because of the current work situation , seems to be madness on my side of things for sure :(

On Sun, Nov 21, 2021, 21:25 Shannon @.***> wrote:

Hi folks! Where are we with this review? @krother https://github.com/krother @KiCh84 https://github.com/KiCh84 there are still unchecked items on both your lists, are those outstanding or have they been addressed yet? @TomDonoghue https://github.com/TomDonoghue @voytek https://github.com/voytek how does the feedback so far look?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/121#issuecomment-974890058, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASWZ3SB3HTU2D5DBQJGIFFTUNFIS7ANCNFSM475BW2CQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

magsol commented 2 years ago

Hi all! Touching base again.

@KiCh84 has your work situation improved at all? Any sort of timeline to completing the review? Or do we need to look for other reviewers?

@krother It looks like you're -almost- finished with the review; just a couple more items to check off. Are these items you can finish, or do you need feedback from the authors?

@TomDonoghue @voytek Any feedback for the reviewers?

KiCh84 commented 2 years ago

Hi ! Could you give me till end of Feb ? That would be awesome , if that's possible!

On Sun, Jan 16, 2022, 17:00 Shannon @.***> wrote:

Hi all! Touching base again.

@KiCh84 https://github.com/KiCh84 has your work situation improved at all? Any sort of timeline to completing the review? Or do we need to look for other reviewers?

@krother https://github.com/krother It looks like you're -almost- finished with the review; just a couple more items to check off. Are these items you can finish, or do you need feedback from the authors?

@TomDonoghue https://github.com/TomDonoghue @voytek https://github.com/voytek Any feedback for the reviewers?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/121#issuecomment-1013902066, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASWZ3SDNHUQMKLCGM6CXKRLUWLTQLANCNFSM475BW2CQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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krother commented 2 years ago

@magsol on my side, the two issues https://github.com/DataScienceInPractice/Site/issues/5 and https://github.com/DataScienceInPractice/Site/issues/6 are still open.

magsol commented 2 years ago

Thanks for the update, @krother .

@TomDonoghue @voytek Would you have a chance soon to look into those two remaining issues? If we can knock those out, then by that point hopefully we'll have heard back from @KiCh84 .

krother commented 2 years ago

@magsol both issues I mentioned above have been resolved. From my side, everything is clear now :sun_with_face:

magsol commented 2 years ago

Excellent, thank you so much @krother!

At this point, I think we're just waiting on @KiCh84's completed review.

TomDonoghue commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

TomDonoghue commented 2 years ago

Hey all! I have come back around to this and done a round of edits on the project. As well as responding to current reviewer comments, I fixed up a couple things on the site (including fixing up the project section), and also make some minor updates to the paper (re-generated version available above).

Thank you to @krother for reviewing this work, and for suggesting some helpful comments! I believe I have updated everything related to your review, but please let me know if I missed anything.

@KiCh84 - is there anything else you need from us to help you finish the review? I see that you've checked off most of the comments - please let us know if you have any comments or suggestions for helping to get the remaining topics checked off.

@magsol - thanks for keeping track of this, and sorry I was a little slow at getting back to it recently. I believe we have currently done everything on our side, and are just waiting on the final reviewer checks - please let us know if there is anything else we can do to finish this one up!

magsol commented 2 years ago

@KiCh84 I hate to bug you on this, but: it looks like the remaining items on your reviewer checklist are pretty straightforward and wouldn't take long for you to verify. Would you mind taking a look sometime this week to see if everything checks out? Thank you so much!!

TomDonoghue commented 2 years ago

Just wanted to check back in here, since I think we're hopefully quite close, and it would be really nice to finish this.

@KiCh84 - do you know if / when you'll be able to finish the review here? @magsol - in the mean time, is there anything else we can do to help get this finished up?

magsol commented 2 years ago

Hi @TomDonoghue , thanks for checking in on things.

@KiCh84: we're waiting for you at this point! If you can't finish in the next week ish, please let me know, as we'd really like to get this over the finish line ASAP.

voytek commented 2 years ago

Anything next here?

magsol commented 2 years ago

@KiCh84 Hi there 👋 We're waiting on your review to wrap things up here! Please let me know ASAP with either a timetable for wrapping this up, or let me know if we need to find a replacement reviewer. Thank you!

KiCh84 commented 2 years ago

Hi Shannon , It looks you might have to find a replacement reviewer . There's just too many things on my plate currently and would be unable to give it the attention it deserves . I apologize heavily for this :(

On Mon, May 16, 2022, 20:50 Shannon @.***> wrote:

@KiCh84 https://github.com/KiCh84 Hi there 👋 We're waiting on your review to wrap things up here! Please let me know ASAP with either a timetable for wrapping this up, or let me know if we need to find a replacement reviewer. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/121#issuecomment-1128018040, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASWZ3SE6JXEMJK6RJLGJCWTVKKKFTANCNFSM475BW2CQ . You are receiving this because you were mentioned.Message ID: @.***>

TomDonoghue commented 2 years ago

Okay... @magsol - can you clarify what happens now and what the expected timeline is? It's already a year since this started review, and it was a year before that that we actually submitted this project...

magsol commented 2 years ago

@TomDonoghue At this point, I think it'd be easiest for me to go through the outstanding points on @KiCh84's reviewer checklist. Fortunately, most of the items are finished; the unresolved ones seem to revolve around the paper itself. I should have some time tomorrow to go through them and then, providing everything checks out, we can start the publication process.

I sincerely apologize for how long it's taken. Let's see if we can't get this wrapped by the weekend.

openjournals / jose-reviews