Joss-reviews: [REVIEW]: Dataviz: A package of domain specific visualizations and languages for the Pharo live coding environment

[whedon]

Submitting author: @offray (Offray Vladimir Luna Cárdenas)
Repository: https://mutabit.com/repos.fossil/dataviz/
Version: 2.2.3
Editor: @arfon
Reviewer: @seandenigris
Archive: Pending

Status

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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) 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

@seandenigris, 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/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @acabunoc know.

Review checklist for @seandenigris

Conflict of interest

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

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (2.2.3)?
• [x] Authorship: Has the submitting author (@offray) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [ ] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [ ] Authors: Does the paper.md file include a list of authors with their affiliations?
• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @seandenigris it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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

1. 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

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #720 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in block in find': No such file or directory (Errno::ENOENT) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/lib/whedon/processor.rb:52:infind_paper_paths'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/bin/whedon:32:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/bin/whedon:99:in from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

[arfon]

@whedon generate pdf

[arfon]

@whedon can't automatically compile this PDF so here is a manually generated one: 10.21105.joss.00238.pdf

[arfon]

@seandenigris - how are you getting along with your review?

[arfon]

@acabunoc - this review seems to be stuck?

[offray]

I'm waiting any comment from reviewers, I have already asked issued in the source code repository of the project, but after that the review is not advancing any more. How can I help?

[seandenigris]

Sorry @arfon and @offray, here is an issue with several hiccups in the installation process: http://mutabit.com/repos.fossil/grafoscopio/tktview/034355733a92437ab8a25a936bc8a003127f944a

[offray]

Thanks Sean. I will be dealing with this installation issues on this weekend. Now I'm finishing a writing with a close deadline.

[offray]

@seandenigris I have addressed your observations (including the creation of a new repository to avoid confusions between Grafoscopio and Dataviz packages and improved documentation). See the ticket in the new repository, at [1] (info from other issue/repository was migrated there also).

[1] https://mutabit.com/repos.fossil/dataviz/info/964c4bd0e0b2a112

@arfon I have changed the repository address of the submission I originally made to the JOSS. What I need to do to reflect that?

[arfon]

@offray - I've updated the repository address at the top of the issue.

[offray]

@arfon That link would work, but if you just put https://mutabit.com/repos.fossil/dataviz/ the repository will take care of any internal rerouting, including pointing to the readme file. Could you please change it to https://mutabit.com/repos.fossil/dataviz/ . Thanks.

[arfon]

@whedon assign @arfon as editor

[arfon]

I've followed up with @seandenigris by email.

[offray]

In my University, they have asked about a formal letter that says that this article is under review.

While review is finished, how can I get this formal letter from the JOSS?

[arfon]

Feel free to email me directly about this @offray ([email protected])

[arfon]

@offray - I think we might need to find a new reviewer for this submission. @yochannah - do you have any suggestions for potential reviewers?

[yochannah]

hmmm, I think @hendekagon is a Pharo aficionado - @hendekagon, might you be interested in reviewing this, and/or do you know anyone else who might be able to help?

[offray]

Let's wait to @Hendekagon's answer for a while, and then I could ask again in the broader Pharo community in case we need another reviewer.

Thanks

[yochannah]

I will also try pinging him by email in case his github notifications aren't set up to notify him

[seandenigris]

Sorry, recently became a dad. If you can find another reviewer great. Otherwise, I'll do what I can. Also, as I follow the readme, obvious problems pop up almost immediately. It is very slow for me to find and report these and would be more efficient if a project team member went through the process themselves to catch the obvious bugs and then I can verify in a fraction of the time.

The project now installs, but the first usage example in the readme failed. I created an issue: https://mutabit.com/repos.fossil/dataviz/tktview/966385f0fca0a889773bbfe8add9d850f6cb1c80

There is also an installation cleanup suggestion here: https://mutabit.com/repos.fossil/dataviz/tktview/26e5a577fe8e0eb5546104d7aa2bca22added06e

[yochannah]

Quick follow up - @arfon I don't think I'm going to be able to suggest any reviewers for a Pharo package in the end I'm afraid.

[offray]

@seandenigris Congrats on your fatherhood and glad to have you back. I will check the issues this week and report the corrections back to this thread and in the also the Fossil repository, which has a RSS subscription, in case you want to subscribe to automatic notifications.

[arfon]

Sorry, recently became a dad. If you can find another reviewer great. Otherwise, I'll do what I can.

@seandenigris - congratulations. We'd be very grateful if you could stick with us - finding reviewers for
Pharo submissions has proven very challenging.

Also, as I follow the readme, obvious problems pop up almost immediately. It is very slow for me to find and report these and would be more efficient if a project team member went through the process themselves to catch the obvious bugs and then I can verify in a fraction of the time.

@offray - to @seandenigris' point - please verify your own usage examples in your documentation. Reviewers shouldn't be responsible for catching obvious issues.

[Hendekagon]

hi - I'm sorry but I'm so busy this year I don't think I'm going to have time, but I'll help however I can

[Hendekagon]

BTW will this package install in Pharo 7 ?

[labarba]

👋 @offray — It looks like we're waiting for and your team to make improvements in the submission before continuing the review. Can you report on your status?

[offray]

@labarba This is my report:

• On 26e5a577fe
  
  
  
  • [x] I have been working on a better decoupling Dataviz and Grafoscopio, making the last a prerrequisite of the former.
  
  
  • [x] I'm improving the documentation for a more modern approach to installation using Metacello instead of Gopher (tested and working).
  
  
• I'm porting Grafoscopio and Dataviz to Pharo 7. It is not a requirement from the reviewer, @seandenigris, but since my first commit of the Dataviz paper, almost a year ago until today we have a new Pharo version and makes sense to have the package usable there (@Hendekagon asked for it and will be in common demand soon). This will imply to updating documentation and screenshots for Grafoscopio and will be the more demanding part.

I hope to have another update in the beginning of next week, but after that I will be pausing until first week of March, to prepare and make my final PhD dissertation.

[labarba]

Hi @offray — I hope your PhD dissertation has gone well. You mentioned the first week of March ... are you ready to re-engage with this submission? Please let us know.

[offray]

Hi @labarba the dissertation went pretty well. Thanks for asking.

I didn't take into account the time for paperwork after dissertation (I'm still on it), but hopefully it will be done this week so next one I will be re-engaging in the submission.

I have been porting Grafoscopio to Pharo 7 and I have it running now, but still more code migration needs to be done. On next week I will be having good news on the porting of Grafoscopio and Dataviz to Pharo 7 on showing the stoppers/delayers I have found (hopefully not many).

[offray]

@seandenigris 26e5a577fe has been closed

• [x] fixed installation and dependency issues, first example is running. All tested on Pharo 7.x.
• [ ] Examples in the first example are opening, but Offshore leaks needs to be updated to work with recent versions of UDBC using native Sqlite on Pharo 7.x. That would be the only remaining issue and my next work.

[seandenigris]

@offray great. Should I have another go or wait for 966385f0fc?

[offray]

@seandenigris Let's way for 966385f0fc. It should be done for this week. I will make here the proper announcement.

Thanks

[danielskatz]

👋 @offray - how is this change coming along?

[offray]

Hi Daniel,

Sorry, but I have still busy with paperwork for the PhD degree (yes
bureaucracy can be slowly painful in many places of the Global South).

I have been stabilizing important Grafoscopio functionality in the back
end with recent commits (as shown in Grafoscopio-OffrayLuna.360)
recently, but still I need to port SQLite DB functionality to have a
proper migration of Dataviz package to Pharo 7.0.x and dealing with all
the reported concerns of the reviewer in current Pharo stable release.

On 20/05/19 3:19 p. m., Daniel S. Katz wrote:
>

👋 @offray https://github.com/offray - how is this change coming along?

—
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[offray]

@seandenigris I have finally closed [966385f0fc], so I think that that closes all your open issues on the paper and gives support of the package on Pharo 7. All dependencies are pulled correctly with a simplified and modern installation (using Metacello instead of Gopher), and the proper interactive notebooks loading has been checked. I have updated the readme documentation in the package documentation repository.

Thanks for your valuable feedback in helping me to improve Dataviz package.

Could you please take a look to see if all your issues/tickets have been properly addressed?

[arfon]

I have just emailed @seandenigris and asked him to take another look.

[seandenigris]

I did another pass and opened a new ticket:

I don't think any of them are necessarily blocking. I'm just not sure how to judge e.g. "functionality" and performance. What's the metric? Is it a judgement call? There is extensive documentation in various sources, so it seems impractical to verify everything

[offray]

Thanks @seandenigris for your detailed ticket. For organizational purposes, I will split it into smaller ones trying to separate Dataviz related ones from Grafoscopio GUI and other non-package issues. Despite of not being blocking concerns, I would like to review them and to tell you when they have been addressed to have the best package I can have after this process. I'll do it soon, to keep the review momentum.

[seandenigris]

Sounds good, @offray. Pending an answer to my previous question, I'm going to conditionally check off Functionality and Performance, as well as Documentation, statement of need, and Installation instructions.

For "Example usage", while there is plenty of information available in the docs, I'd like to see at least one easily findable and runnable example in the image. Maybe fixing point 3 or 5 in my ticket would help.

[arfon]

:wave: @offray - how are you getting along here?

[offray]

Hi @arfon and @seandenigris, I'm fighting some bugs, not directly addressed by the review before going fully into it, to improve user experience.

This week I'm attending ESUG, and next one on the eLife Sprint on reproducible research, so I hope to work on those bugs usability bugs and to address the ones in the review and update advances here in 2nd or 3rd week of September.

[arfon]

Got it. Thanks for the update @offray.

[arfon]

:wave: @offray - any updates on progress here?

[offray]

Hi @arfon

Unfortunately I am unable to made further advances, because I needed to deal with the bureaucracy and legalize of my University. So after having previous consent of my thesis advisor, proper written approval of the previous PhD director about publishing in JOSS as a way to cover one of my graduation requisites and started this long time ago with my two submitted papers to the JOSS in early 2018), the new PhD director decided that JOSS is not a valid journal to fulfill publishing requirements and told me that I need to find another place to submit my new articles and restart the process. This ended in a law suit that I lost, because in Colombia courts are not a guarantee for equal treatment between citizens and institutions, or making the last ones to keep their word to the firsts.

The law suit final decision came last Thursday and now I'm restarting the process of writing academic papers about my research and finding "proper" publications under "particular indexes" to fulfill a convoluted process, where new University administrator can reverse any written decision of the previous ones, and make PhD students to restart a totally new papers submission and publishing process, even after a public thesis dissertation.

It's really a shame that frontier ways of publishing, as JOSS, are not recognized as valid because they are not in particular indexes (that was the University's argument). I will try to finish this paper, but, after 7 months using regular conduits and even legal resources to validate these alternative circuits and publications and trying to make my university to keep its written words, I need to follow the final decision.

I'm really sorry about this and I understand if this process has taken too long for the review and JOSS decided to end it, but I could not focus on writing or normal academic activities, while the diplomatic and legal process where happening with all the uncertainty behind the decision. At least, this repository is a public record of the injustices we need to fight, particularly in the Global South about getting alternative publishing circuits recognized as equals.

Thanks for your patience and understanding.

[arfon]

❤️ sorry to hear about these struggles @offray. Can I just check what 'indexes' are you referring to here? Do the journals you publish in need to be indexed by e.g. Scopus or something else?

[offray]

@arfon yes, the journals do need to be in a particular index. Because my thesis deals with non-hegemonic subjects, artifacts and places of knowledge, like hackerspaces, where the Grafoscopio and Dataviz software packages were prototyped, developed and extended, trying to make visible other ways of publishing and places for that, seem like a perfect fit in my view, the one of my advisor and the previous PhD director. But under the new administration, seems that anything not listed in Scopus, Scimago or something like that, is not valid peer review, even despite the previous documented knowledge and written acceptance of JOSS and the (also written) acknowledgement about it not being in those indexes.

:-/

I will need to find a "traditional" journal in particular indexes and places. Once I get my new papers accepted in those magazines, I will come back to finish this paper. Because documenting the struggles that new magazines like JOSS have into being treated as equals in particular places, like my university, is part of the shared effort we as a academic community made to create alternative ways of publishing.

[kthyng]

Hi @offray. We are working on being indexed by Scopus, though I believe it hasn't come through yet. (@arfon would know best.) Would that change things for you? If so, we could keep this submission open for now.

[arfon]

@arfon would know best

Still no news on this but we've not received a 'no'.

[kthyng]

Perhaps we could do something like pause this submission if it would be fine once we are indexed on Scopus. @offray what do you think?

[offray]

Yes, being indexed in Scopus would change things for me. The issue is that it needs to have a particular rank on it. I think that pausing this submission is the best approach meanwhile, but I'm pretty interested in the Scopus indexing/ranking for JOSS. Let me know how it advances.

[kthyng]

@offray I have added the "paused" label for now. I will try to add a reminder to this issue to ping you in a month to check in about Scopus, but I'm not sure if it works on non-reviewers. I'm afraid I can't commit to keeping you up-to-date on the status myself.

[kthyng]

@whedon remind @offray in 4 weeks

[whedon]

Reminder set for @offray in 4 weeks

[offray]

Thanks @kthyng . Any news on the Scopus issue would be greatly appreciated. I'm now trying to find and write a new publication for my research related articles, but I really would like to use the ones already submitted in JOSS to fulfill my degree requirements.

JOSS is on equal foot as any journal on Scopus and pushing the boundaries about academic/research peer review process and artifacts.

[whedon]

:wave: @offray, please update us on how things are progressing here.

[offray]

@kthyng Hi. Is there any news on the Scopus front? Fo the moment I'm looking for a place to publish, included in such index (or similar ones). It may seems that Software X, will fit the requirement, with a more traditional publishing approach.

Hopefully soon JOSS will be included in the index that some universities consider the valid ones.

[ooo[bot]]

:wave: Hey @offray...

Letting you know, @kthyng is currently OOO until Thursday, January 23rd 2020. :heart:

[arfon]

@kthyng Hi. Is there any news on the Scopus front? Fo the moment I'm looking for a place to publish, included in such index (or similar ones). It may seems that Software X, will fit the requirement, with a more traditional publishing approach.

Unfortunately not. Our application is still being considered but we don't have any update other than that. I suspect it will be many more months rather than something that will be resolved imminently.

I'm not sure if Google Scholar is relevant to you but JOSS is now properly indexed there.

[ooo[bot]]

:wave: Hey @arfon...

Letting you know, @kthyng is currently OOO until Thursday, January 23rd 2020. :heart:

[danielskatz]

@offray & @kthyng - since we don't have any knowledge on when Scopus indexing will happen, I suggest that we mark this as withdrawn. It's now been almost 3 years since the original submission and holding this here isn't fair to anyone.

[kthyng]

@danielskatz Yes that makes sense.

@offray ok?

[arfon]

@offray & @kthyng - since we don't have any knowledge on when Scopus indexing will happen, I suggest that we mark this as withdrawn. It's now been almost 3 years since the original submission and holding this here isn't fair to anyone.

👍 I support this decision.

[offray]

I support this decision also.

It's a shame that my University decided to only value particular indexes as the only ones required for quality per review. Also the long and painful process for me, of having a written permission to apply here and seeing how the new PhD director took back decisions made by his predecessor.

Thanks for the work with my other approved paper and with this one and I hope to participate again with other publicacion once conditions change.

[danielskatz]

@whedon withdraw

[whedon]

Paper withdrawn.