[REVIEW]: An open learning resource on Reproducible Data Science with Open-Source Python Tools and Real-World Data

Question

[REVIEW]: An open learning resource on Reproducible Data Science with Open-Source Python Tools and Real-World Data

Closed this issue 2 years ago · 77 comments

Submitting author: @valdanchev (Valentin Danchev)
Repository: https://github.com/valdanchev/reproducible-data-science-python
Version: v2.1.2
Editor: @ShanEllis
Reviewer: @TomDonoghue, @lechten
Archive: 10.5281/zenodo.6895578

⚠️ 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/3e1de7c74161a5b2c4ce74e536ef6898"><img src="https://jose.theoj.org/papers/3e1de7c74161a5b2c4ce74e536ef6898/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/3e1de7c74161a5b2c4ce74e536ef6898/status.svg)](https://jose.theoj.org/papers/3e1de7c74161a5b2c4ce74e536ef6898)

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

@TomDonoghue & @lechten, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @ShanEllis 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 @TomDonoghue

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: v2.1.2
Authorship: Has the submitting author (@valdanchev) 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 @lechten

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: v2.1.2
Authorship: Has the submitting author (@valdanchev) 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)?

Answer 1 · 2022-01-12T14:38:06.000Z

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

Set yourself as 'Not watching' https://github.com/openjournals/jose-reviews:

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

Answer 2 · 2022-01-12T14:38:26.000Z

Wordcount for paper.md is 1603

Answer 3 · 2022-01-12T14:38:34.000Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.30 s (88.3 files/s, 108947.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            22           1735            128          37365
SVG                              6              0             13           9323
JavaScript                      16           2342           2391           8757
Jupyter Notebook                32              0          71448           2037
Python                          13           1433            546           1963
CSS                             14            237             96           1321
Markdown                         7             82              0            251
TeX                              2             23              0            238
YAML                             2             16             16             52
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           115           5868          74638          61308
-------------------------------------------------------------------------------


Statistical information for the repository '75c25ff7f7e841b795a1a850' was
gathered on 2022/01/12.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
valdanchev                       5         17466             34          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
Valentin Danchev          17432          100.0          0.0               16.85

Answer 4 · 2022-01-12T14:38:38.000Z

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

Answer 5 · 2022-01-12T14:39:27.000Z

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

OK DOIs

- 10.1162/99608f92.cb0fa8d2 is OK
- 10.17226/25104 is OK
- 10.1145/3408877.3432586 is OK
- 10.1371/journal.pcbi.1008770 is OK
- 10.1080/09332480.2019.1579578 is OK
- 10.21105/joss.03021 is OK
- 10.18148/srm/2020.v14i2.7746 is OK
- 10.1371/journal.pcbi.1007007 is OK

MISSING DOIs

- 10.1038/d41586-018-07196-1 may be a valid DOI for title: Why Jupyter is data scientists’ computational notebook of choice
- 10.25080/majora-92bf1922-00a may be a valid DOI for title: Data Structures for Statistical Computing in Python
- 10.25080/majora-92bf1922-011 may be a valid DOI for title: statsmodels: Econometric and statistical modeling with python

INVALID DOIs

- None

Answer 6 · 2022-01-25T00:25:36.000Z

I've worked through my review, including exploring through the content, and checking I can run some examples through Binder etc. As a note I did skim the notebooks, and read sections, but I did do a full read of the content. I've checked off most things above, with the remainer being left open for small potential updates detailed here.

I have some practical suggestions, that I have described in detail on the resource repository, including:

Other notes:

In terms of requirements, I think there is an implicit dependency whereby some notebooks only work on Collab (not Binder), because they load the google module. This is captured in this pre-existing issue. I don't think this is a huge issue, per se, but I think some notes in the notebooks about this kind of extra dependency (what works where and/or what would need to be installed) could be added somewhere.
There is not a version identifier that I found, though I admit I'm not entirely sure how versions are supposed to work for this kind of resource
Though it's perhaps implicit, for Community Guidelines, an explicit note in the README, and/or textbook landing page about what to do to make a suggestion / report a problem (open an issue, presumably) might be useful, especially for students who might not be clear on standard Github practices.

In terms of the literal content - I don't have as much to say. Based on skimming it all, I think all the content (ideas and concepts) look good to me. It's a bit tricky for me to know exactly how an unfamiliar student would feel about the progression through things. My sense is perhaps that there is a lot introduced quite quickly, and one might need a bit of a sense of basic coding to really be able to jump in - but under the idea of it as a "crash course", I think it broadly works, and is a useful resource to have available.

My one more practical content note is that I think the end_to_end_data_science_project, which in particular feels like jumping in the deep end, could be more explicit that it skims through topics as an introduction (it effectively overviews the course), and that these topics are dealt with in more detail in future notebooks, and that it might make sense for students "jump ahead" to practice these topics there first (at first I even thought maybe this notebook was supposed to come at the end?).

Overall, I think this looks like an interesting resource, with it's strengths being that it:

introduces a lot of topics in data science, with a focus on practical elements (working with data, reproducibility, ethics, etc)
has a lot of links to other resources to map out other places to learn things
uses some real data to demonstrate these things in practice, and is re-runnable by students
is focused at a particular area / group of students (social science / sociology) for whom there be fewer dedicated materials

Conclusion: I think if the relatively minor notes I've mentioned can be fixed up a bit, my overall impression is that this is a useful resource, responsive to JOSE's aims and requirements, and after the review edits I'd be happy to sign off on it as a reviewer.

Answer 7 · 2022-01-26T14:38:17.000Z

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

Answer 8 · 2022-01-27T16:59:46.000Z

Thank you so much for these very helpful comments @TomDonoghue. Will go through all of your notes and issues and will write back when I have a revised version that addresses them.

Answer 9 · 2022-02-14T15:54:32.000Z

I agree with all points raised by @TomDonoghue above. In summary, this is a valuable and ambitious course/resource.

I’d like to emphasize that I also believe the first notebook to need more descriptions: How might this be presented to students? What is expected of them? What should they be able to do?

For other comments, I opened issues in the source repository.

Answer 10 · 2022-02-25T08:27:51.000Z

Thanks so much, @lechten for your very helpful comments and suggestions for improvements. The pointer to nbqa is extremely useful. My teaching-heavy term will be over in a few weeks, and I am looking forward to then revising the resource based on your and @TomDonoghue comments.

Answer 11 · 2022-03-24T16:58:09.000Z

Thanks to both reviewers!

@valdanchev Just checking in on your current expected timeline? (I totally understand the chaos that is the end of teaching-heavy terms...so not rushing just wanted to get a possible timeline established.)

Answer 12 · 2022-03-28T09:49:17.000Z

Totally understand @ShanEllis, I'll plan to finalise all the revisions by the end of April if that sounds good.

Answer 13 · 2022-05-18T17:10:58.000Z

@ShanEllis thank you for organising the review process, @TomDonoghue and @lechten thank you for your very helpful and constructive feedback and suggestions. The review process was very valuable for improving the resource, repository, and paper. Sorry for my delayed revisions.

I have now made the revisions and addressed all the feedback and comments above as well as the issues #5, #6, #7, #8, #9, #10. Specifically,

In relation to code quality #8 and code formating #5:
- The code now conforms to PEP 8 by running automated code formatters Black and flake8 on Jupyter through nbQA, following very helpful recommendations in #8.
- Added a section entitled Readability of your Python code in which PEP 8 style guide for Python code is introduced and key relevant recommendations for writing a readable Python code are outlined, including (i) naming conventions, (ii) maximum line length, (iii) indentation, (iv) tabs or spaces?, (v) whitespace in expressions and statements.
- Added also a new section on code reusability named Code reuse: creating your own functions, related to #8.
In relation to content #5, added the following sections in the notebook Python for Data Analysis on the Cloud:
Regarding the structure of the resource GitHub repository, following the very helpful suggestions #6, the files are now reorganised and ordered in a more structured and intuitive manner:
- different types of content are now assigned to sub-folders notebooks/, images/, data/, paper/;
- notebooks are sorted in ascending order;
- unused/unnecessary files are deleted.
To address issues #9 and #6, the role of the resource website, GitHub, MyBinder, and Colab are now clarified and differentiated in:
- the JOSE paper
- the learning resource website, section How to get the most of the open learning resource?
- the README in the resource repository
- Also, links to notebooks on GitHub, MyBidner, and Colab are provided in a table on the resource website and in the README.
Added a release version identifier.
Added notes in the resource and the repository README file addressing dependencies issues, as noted in comment above and in a pre-existing issue.
Regarding Community Guidelines, the README includes now a note about how to contribute to the resource, create an issue etc.
The first notebook End-to-End Data Science Project includes a note describing the purpose of the notebook and what is expected by the learners, as suggested by @TomDonoghue here and by @lechten here.

I've shortened the title of the resource to "Reproducible Data Science with Python" and would like to also shorten the title of the paper to "Reproducible Data Science with Python: An open learning resource".

Thank you again for the very constructive and transparent review process and feedback.

Answer 14 · 2022-05-19T14:32:15.000Z

@whedon generate pdf

Answer 15 · 2022-05-19T14:32:28.000Z

PDF failed to compile for issue #156 with the following error:

 pandoc: paper.bib: openBinaryFile: does not exist (No such file or directory)
Looks like we failed to compile the PDF

Answer 16 · 2022-05-19T14:57:09.000Z

@whedon commands

Answer 17 · 2022-05-19T14:57:13.000Z

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

Answer 18 · 2022-05-19T15:05:33.000Z

@whedon generate pdf

Answer 19 · 2022-05-19T15:05:44.000Z

PDF failed to compile for issue #156 with the following error:

 /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse': (da632d62dda40da88c8646e4/paper/paper.md): mapping values are not allowed in this context at line 2 column 45 (Psych::SyntaxError)
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse_stream'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:390:in `parse'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:277:in `load'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:578:in `block in load_file'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `open'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `load_file'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:127:in `load_yaml'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:87:in `initialize'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:66:in `prepare'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

Answer 20 · 2022-05-19T16:31:24.000Z

@whedon generate pdf

Answer 21 · 2022-05-20T06:47:25.000Z

@whedon generate pdf

Answer 22 · 2022-05-20T06:52:05.000Z

@ShanEllis Whedon does not seem to work any more. Are you able to generate a new PDF?

Answer 23 · 2022-05-23T15:30:25.000Z

I have checked through the updates to the resource and everything looks good to me! I have checked of my remaining review items, and as far as I'm concerned, this is good to go!

Quick note: as things get wrapped up, I think the version number that is listed in this issue (1.0.0) needs to be updated to reflect the version number listed in the most recent release (I think there is a whedon command to do this).

Answer 24 · 2022-05-23T18:42:33.000Z

@whedon set v2.0.0 as version

Answer 25 · 2022-05-23T18:42:36.000Z

I'm sorry @valdanchev, I'm afraid I can't do that. That's something only editors are allowed to do.

Answer 26 · 2022-05-23T19:00:16.000Z

Many thanks, @TomDonoghue. On the version number, it seems that only editors can do the update. @ShanEllis will know best how to update the version number.

Answer 27 · 2022-06-01T06:36:12.000Z

@whedon generate pdf

Answer 28 · 2022-06-21T16:28:49.000Z

Sorry y'all! Recently had a baby and am just super behind on things. Just wanted to reply here to say that I'm looking into what's going on re: PDF generation (after which I can update the version).

Will update/tag others as there's progress!

Answer 29 · 2022-06-21T16:38:19.000Z

@valdanchev I'm not 100% sure, but I believe the PDF won't compile due to YAML formatting issues at the top of paper.md. Specifically, for each bullet point entry, it looks to me like a space is missing before each dash ( -).

Sharing a link to a random accepted paper whose YAML formatting looks right to me in case helpful: https://raw.githubusercontent.com/americocunhajr/EPIDEMIC/master/paper/paper.md

Mind making these edits and trying to recompile PDF? (If this isn't the issue I'll dig deeper.)

Answer 30 · 2022-06-21T16:50:08.000Z

@whedon generate pdf

Answer 31 · 2022-06-21T16:50:19.000Z

PDF failed to compile for issue #156 with the following error:

 /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse': (4d4bd54800247dd4827f3cec/paper/paper.md): did not find expected '-' indicator while parsing a block collection at line 15 column 2 (Psych::SyntaxError)
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse_stream'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:390:in `parse'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:277:in `load'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:578:in `block in load_file'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `open'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `load_file'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:127:in `load_yaml'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:87:in `initialize'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:66:in `prepare'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

Answer 32 · 2022-06-21T17:05:05.000Z

@whedon generate pdf

Answer 33 · 2022-06-21T18:28:55.000Z

I see that it's still not generating....but also not throwing an error. Pinging people who know the system better than I to see what's going on/how to fix.

Answer 34 · 2022-06-22T23:29:10.000Z

@whedon generate pdf

Answer 35 · 2022-06-23T09:20:14.000Z

@openjournals/dev – S.O.S. We're stumped with a paper compilation error here. Can you help?

Answer 36 · 2022-06-23T12:00:28.000Z

This is probably because you have three paper.md files in your repo, and @whedon will just pick the first by default:

1. tmp/156/_build/html/_sources/JOSE_paper/paper.md
2. tmp/156/_build/html/_sources/paper/paper.md
3. tmp/156/paper/paper.md

The third one (at tmp/156/paper/paper.md) seems to compile fine. I would suggest either removing or renaming the first two (to not be called paper.md).

Answer 37 · 2022-06-23T12:13:17.000Z

@whedon generate pdf

Answer 38 · 2022-06-23T12:13:35.000Z

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

Answer 39 · 2022-06-23T12:20:12.000Z

Thanks a million, @arfon. That was the problem indeed; removed the unnecessary files and the file compiles now.

Answer 40 · 2022-06-23T12:34:03.000Z

@whedon generate pdf

Answer 41 · 2022-06-23T12:34:21.000Z

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

Answer 42 · 2022-06-23T13:23:13.000Z

Given the new PDF, I just closed my final issue at the source repository. I vote to accept this paper.

Answer 43 · 2022-07-07T19:33:16.000Z

@whedon set v2.0.0 as version

Answer 44 · 2022-07-07T19:33:20.000Z

OK. v2.0.0 is the version.

Answer 45 · 2022-07-07T19:36:14.000Z

Just did a final read-through of the manuscript and a review of all the issues that have been resolved. Would like to thank @TomDonoghue and @lechten for their careful review of this manuscript and @valdanchev for being so responsive to their feedback.

(And, thanks for hanging in there with me as I've been a tad slower getting back to things here than I typically would be.)

Answer 46 · 2022-07-07T19:36:21.000Z

@whendon recommend-accept

Answer 47 · 2022-07-07T20:11:00.000Z

Thank you @ShanEllis, @TomDonoghue, and @lechten for the very constructive and helpful review process!

Answer 48 · 2022-07-20T15:03:31.000Z

@whedon recommend-accept

Answer 49 · 2022-07-20T15:03:35.000Z

No archive DOI set. Exiting...

Answer 50 · 2022-07-21T15:59:49.000Z

@valdanchev — As this review is finalized, please make an archive of the target repository on Zenodo, and report the archive DOI here. We request that authors edit the metadata of the Zenodo deposit so title and author list match the JOSE paper.

Answer 51 · 2022-07-24T18:20:19.000Z

@labarba and @ShanEllis — I've archived the resource repository on Zenodo. The archived version is v2.1.1.

Here are:
DOI: 10.5281/zenodo.6895578
URL: https://doi.org/10.5281/zenodo.6895578
DOI badge

I edited the metadata of the Zenodo repository to match the JOSE paper (I revised/shortened the paper title during the revision and the Zenodo metadata matches the revised title).

Answer 52 · 2022-07-24T22:50:13.000Z

@whedon set 10.5281/zenodo.6895578 as archive

Answer 53 · 2022-07-24T22:50:16.000Z

OK. 10.5281/zenodo.6895578 is the archive.

Answer 54 · 2022-07-24T22:50:40.000Z

@whedon recommend-accept

Answer 55 · 2022-07-24T22:50:43.000Z

Attempting dry run of processing paper acceptance...

Answer 56 · 2022-08-10T13:44:47.000Z

@whedon generate pdf

Answer 57 · 2022-08-10T13:58:54.000Z

@whedon generate pdf

Answer 58 · 2022-08-10T13:59:14.000Z

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

Answer 59 · 2022-08-22T17:25:33.000Z

@labarba & @ShanEllis — I think all should work now. There was a problem similar to the one Arfon identified before — a redundant paper.md file was generated after an update just before archiving the repository on Zenodo, — which is now corrected. The pdf can be generated again and hopefully, the other commands would work too.

Answer 60 · 2022-08-23T01:15:34.000Z

@whedon recommend-accept

Answer 61 · 2022-08-23T01:15:37.000Z

Attempting dry run of processing paper acceptance...

Answer 62 · 2022-08-23T01:16:03.000Z

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

Check final proof 👉 openjournals/jose-papers#101

If the paper PDF and Crossref deposit XML look good in openjournals/jose-papers#101, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

Answer 63 · 2022-08-23T01:16:05.000Z

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

OK DOIs

- 10.1162/99608f92.cb0fa8d2 is OK
- 10.17226/25104 is OK
- 10.1145/3408877.3432586 is OK
- 10.5281/zenodo.3233853 is OK
- 10.1371/journal.pcbi.1008770 is OK
- 10.3233/978-1-61499-649-1-87 is OK
- 10.1038/d41586-018-07196-1 is OK
- 10.1080/09332480.2019.1579578 is OK
- 10.48550/arXiv.1201.0490 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.21105/joss.03021 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.18148/srm/2020.v14i2.7746 is OK
- 10.48550/arXiv.2004.04145 is OK
- 10.1093/comjnl/27.2.97 is OK
- 10.1371/journal.pcbi.1007007 is OK
- 10.25080/Majora-4af1f417-011 is OK
- 10.1201/9781003080978 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Answer 64 · 2022-10-23T12:46:47.000Z

hi @valdanchev — it looks like this one slipped through the cracks, sorry (I have total email overload). On a quick browse, I noticed that the repo has as latest tag v2.1.1, while the version here is noted as v2.0.0. Meanwhile, you have a lot of newer commits. (Unfortunately, you do not have meaningful commit messages, as all are titled "Updates"—I do urge you to revisit this practice!!)

Can you make a tagged release with all the latest changes, corresponding to the reviewed and revised JOSE submission? Then report the version number here and we will update it.

Answer 65 · 2022-10-24T10:34:35.000Z

@labarba - many thanks, this is very helpful! I have now made a new tagged release corresponding to the JOSE publication (with added informative commit messages) and updated the Zenodo archive, details are below. Let me know if any additional changes are needed. Thank you again.

Latest repo version: v2.1.2
Zenodo DOI: 10.5281/zenodo.7244097

Answer 66 · 2022-10-24T10:34:59.000Z

@whedon generate pdf

Answer 67 · 2022-10-24T10:35:29.000Z

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

Answer 68 · 2022-10-24T10:39:09.000Z

@whedon set v2.1.2 as version

Answer 69 · 2022-10-24T10:39:15.000Z

OK. v2.1.2 is the version.

Answer 70 · 2022-10-24T20:05:32.000Z

hi @valdanchev — One last thing: We request that authors edit the metadata of the Zenodo deposit so title and author list match the JOSE paper. It's just cleaner that way as readers see these as part of the "same scholarly object." Could you do that?

Answer 71 · 2022-10-24T20:35:01.000Z

hi @labarba — thank you, more than happy to do that, just updated the metadata of the deposit.

Answer 72 · 2022-10-24T21:20:14.000Z

@whedon accept deposit=true

Answer 73 · 2022-10-24T21:20:18.000Z

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

Answer 74 · 2022-10-24T21:20:52.000Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 openjournals/jose-papers#107
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jose.00156
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Answer 75 · 2022-10-24T21:26:43.000Z

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

Huge thanks to our editor: @ShanEllis and the reviewers: @TomDonoghue, @lechten — your contribution makes this adventure possible 🙏

Answer 76 · 2022-10-24T21:30:20.000Z

🎉🎉🎉 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.00156/status.svg)](https://doi.org/10.21105/jose.00156)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00156">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00156/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00156/status.svg
   :target: https://doi.org/10.21105/jose.00156

This is how it will look in your documentation:

We need your help!

Journal of Open Source Education is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://jose.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.org/donate-to-jose

Answer 77 · 2022-10-24T22:31:32.000Z

Great!! Thank you so much @labarba, @ShanEllis, @TomDonoghue, and @lechten for all of your work — the review process has really improved the learning resource!