[REVIEW]: Virtual training on virtual environments: an online open-source introduction to conda

[whedon]

Submitting author: @marisalim (Marisa Lim)
Repository: https://github.com/nih-cfde/training-and-engagement
Version: v2021.12
Editor: @allisonhorst
Reviewer: @colbrydi, @shanamatthews
Archive: 10.5281/zenodo.5773212

⚠️ JOSE reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/17eef7276bb7ca1229556b8c0f44014e"><img src="https://jose.theoj.org/papers/17eef7276bb7ca1229556b8c0f44014e/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/17eef7276bb7ca1229556b8c0f44014e/status.svg)](https://jose.theoj.org/papers/17eef7276bb7ca1229556b8c0f44014e)

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

@colbrydi & @shanamatthews, 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 @allisonhorst 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 @colbrydi

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSE 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: v2021.12
• Authorship: Has the submitting author (@marisalim) 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 @shanamatthews

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSE 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: v2021.12
• Authorship: Has the submitting author (@marisalim) 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @colbrydi, @shanamatthews 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:

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

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

PDF failed to compile for issue #130 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.16 s (1088.4 files/s, 154107.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                       143           4853              0           9750
CSS                              4            854             71           6424
JavaScript                       4             31             52           1141
HTML                             5              1             14            375
YAML                            11             35             69            199
R                                2             72             51            157
Python                           1             13              5             30
reStructuredText                 1              5              7              3
-------------------------------------------------------------------------------
SUM:                           171           5864            269          18079
-------------------------------------------------------------------------------


Statistical information for the repository '1a8708eead20849fea4b9530' was
gathered on 2021/09/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Amanda Charbonneau              10         20107          20108           96.85
Jeremy Walter                   12             8              8            0.04
Marisa Lim                       2            49              1            0.12
Saranya Canchi                   4          1234              0            2.97
abhijna                          1             5              4            0.02

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
Marisa Lim                   48           98.0          9.8               10.42
Saranya Canchi             1224           99.2          8.4                4.25

[marisalim]

@whedon generate pdf from branch JOSE-conda-paper

[whedon]

Attempting PDF compilation from custom branch JOSE-conda-paper. Reticulating splines etc...

[whedon]

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

[marisalim]

@whedon check repository from branch JOSE-conda-paper

[whedon]

Wordcount for paper.md is 1307

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.14 s (1197.0 files/s, 168507.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                       144           4883              0           9816
CSS                              4            854             71           6424
JavaScript                       4             31             52           1141
HTML                             5              1             14            375
YAML                            11             35             69            199
R                                2             72             51            157
TeX                              1              3              0             44
Python                           1             13              5             30
reStructuredText                 1              5              7              3
-------------------------------------------------------------------------------
SUM:                           173           5897            269          18189
-------------------------------------------------------------------------------


Statistical information for the repository '266909db739cae38f109d8c1' was
gathered on 2021/09/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Amanda Charbonneau              10         20107          20108           96.85
Jeremy Walter                   12             8              8            0.04
Marisa Lim                       2            49              1            0.12
Saranya Canchi                   4          1234              0            2.97
abhijna                          1             5              4            0.02

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
Marisa Lim                   48           98.0          9.8               10.42
Saranya Canchi             1224           99.2          8.4                4.25

[allisonhorst]

Hi @colbrydi and @shanamatthews, thank you again for contributing to this review! The PRE-REVIEW issue is now closed, so this is where we'll be working from here on. The reviewer instructions are up above, as are your individual review checklists. I'm here to help & advise, please reach out any time if you have questions!

[shanamatthews]

Hey @allisonhorst - it looks like there are some broken links in the instructions:

• JOSE conflict of interest policy
• The code of conduct link on this page: https://jose.theoj.org/about#code_of_conduct (https://github.com/openjournals/jose/blob/main/CODE_OF_CONDUCT.md)

Possibly these files need to be copied over from the joss repository?

[allisonhorst]

Thanks for the heads up @shanamatthews!

@labarba can you update these links for JOSE reviewer COI and CoC (or let me know who at JOSE I should reach out to)? Thanks!

[labarba]

Yikes! It is the same as the JOSS COI policy. We will investigate that bug in our issue generator (JOSE is a fork of JOSS and we recently reorganized the repositories).

[shanamatthews]

Hello! I was able to spend some time reviewing this morning and found that the materials met most requirements and overall seemed high quality - great work!

I've pasted in the parts of the review checklist where I saw gaps. I was not able to find documentation in the repo or in the paper to help other users adopt or adapt the module, although there is plenty of information about how the original group of authors have used it. @marisalim Perhaps a short section on "teaching with this module" would be appropriate in both the repo and the paper?

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

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)?

[marisalim]

Hi @shanamatthews - thank you for reviewing our submission! Do you think additional information on this wiki page for instructors would work? We were trying to stay within the word limit for the paper, but are happy to add more information for using the module in the wiki!

[shanamatthews]

Hi @shanamatthews - thank you for reviewing our submission! Do you think additional information on this wiki page for instructors would work? We were trying to stay within the word limit for the paper, but are happy to add more information for using the module in the wiki!

That seems appropriate!

[whedon]

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

[whedon]

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

[colbrydi]

Hello I completed my review today. I happen to also be working on a tutorial for using conda environments in Python using jupyter notebooks and this could not have come at a better time for me. I learned a lot from your submission and look forward to being able to use and reference it in my own work. I submitted a couple of issue but they are just recommendations and I feel this is ready for publication. -- Thank you!

[shanamatthews]

I also think this submission is ready for publication. I've signed off on all the review criteria, but would love to see more explicit info on how external folks can adapt the training in the wiki page, as mentioned.

[marisalim]

Thank you @shanamatthews and @colbrydi! We are discussing your feedback and suggestions and will update the materials shortly!

[allisonhorst]

Thank you so much for your prompt review and feedback @shanamatthews and @colbrydi!

@marisalim please let me know if you have any questions that I can help with as your update your materials.

[labarba]

Hi everybody! 👋

I see that this submission targets a short tutorial on virtual environments and conda that is a slice of a repository hosting lots of other teaching materials:
https://github.com/nih-cfde/training-and-engagement/tree/dev/docs/General-Tools/Introduction-to-Conda

In addition, the same group is submitting for review another slice of the collection of materials, targeting an introduction to AWS services:
#132

This poses a few questions: first, it kind of looks like salami-slicing an educational initiative into a bunch of thin papers. Second, the JOSE publication workflow assumes one repository per paper, which gets archived in Zenodo after review, linking the DOI of the archive with the DOI of the paper. In this case, the large repository contains a lot of material not associated with the paper, and/or several JOSE papers would link to the same GitHub repo and Zenodo archive.

To move forward, in my opinion, the authors would have to re-organize their materials into substantial chunks that justify a scholarly publication, each in a separate GitHub repository that can have its own Zenodo archive in the end.

I suggest this submission be withdrawn in order to address this. Feel free to comment here with your thoughts or other ideas.

[allisonhorst]

Thank you @marisalim and others.

I do not have further comments and feel that all reviewer comments have been addressed. @labarba I recommend accepting this submission.

[labarba]

Hi Allison! Do run @whedon recommend accept as a final step :–)

[allisonhorst]

@whedon recommend accept

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[allisonhorst]

@whedon recommend-accept

[whedon]

No archive DOI set. Exiting...

[allisonhorst]

@labarba can you advise? do I need to whedon set doi as archive first?

[labarba]

Ah, yes. The final steps pre-publication are:

• author should make a tagged release of their repository, and report the version number
• editor runs @whedon set <v##> as version
• author should make an archive deposit of their repository on Zenodo or similar service, and reports the archive DOI here
• editor runs @whedon set <doi> as archive

[marisalim]

Hi @allisonhorst!

• the GitHub tag is: https://github.com/nih-cfde/training-and-engagement/releases/tag/2021.12
• this version of the repo is archived on Zenodo here: https://zenodo.org/record/5773212#.YbPeOVmIbb0

[allisonhorst]

@whedon set v2021.12 as version

[whedon]

OK. v2021.12 is the version.

[allisonhorst]

@whedon set 10.5281/zenodo.5773212 as archive

[whedon]

OK. 10.5281/zenodo.5773212 is the archive.

[allisonhorst]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #130 with the following error:

 Can't find any papers to compile :-(

[labarba]

@whedon recommend-accept from branch JOSE-conda-paper

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/sdata.2016.18 is OK
-  10.25080/Majora-4af1f417-011  is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/jose-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/jose-papers#70

If the paper PDF and Crossref deposit XML look good in openjournals/jose-papers#70, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch JOSE-conda-paper 

[labarba]

@whedon accept deposit=true from branch JOSE-conda-paper

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSE! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jose.00130 jose-papers#71
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jose.00130
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[labarba]

Congratulations, @marisalim, your JOSE paper is accepted! 🚀

Huge thanks to our Editor: @allisonhorst, and the Reviewers: @colbrydi, @shanamatthews — we couldn't do this without you 🙏

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://jose.theoj.org/papers/10.21105/jose.00130/status.svg)](https://doi.org/10.21105/jose.00130)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00130">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00130/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00130/status.svg
   :target: https://doi.org/10.21105/jose.00130

This is how it will look in your documentation:

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[marisalim]

Thank you @allisonhorst, @shanamatthews, @colbrydi, and @labarba! 👏