[REVIEW]: Salabim: discrete event simulation and animation in Python

whedon commented 6 years ago

Submitting author: @salabim (Ruud van der Ham) Repository: https://github.com/salabim/salabim Version: 2.2.23 Editor: @danielskatz Reviewer: @gonsie, @pspringer Archive: 10.6084/m9.figshare.6791129

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

@gonsie & @pspringer, 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/joss-reviews/invitations

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

Review checklist for @gonsie

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 (2.2.23)?
[x] Authorship: Has the submitting author (@salabim) 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.
[x] 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)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] 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

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @pspringer

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 (2.2.23)?
[x] Authorship: Has the submitting author (@salabim) 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.
[x] 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)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] 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

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 6 years ago

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @gonsie, 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:

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

watching

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

notifications

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

@whedon commands

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

danielskatz commented 6 years ago

👋 @arfon - I screwed up and added @pspringer twice as a reviewer. I'm going to manually edit the first comment in the issue to fix this, but if there's something in the @whedon database that also needs to be fixed, please do so.

danielskatz commented 6 years ago

👋 @gonsie, @pspringer - thanks for volunteering to review. Instructions and the review checklists are in the first comment in this issue. Please go ahead and start your reviews when you are ready.

If you have any questions, please feel free to ask me.

pspringer commented 6 years ago

Hi Dan, this is Paul. I've not done this sort of collaboration before, so I am completely lost. I don't even know if you will get this if I don't put that @ sign in front of your name. I'm not even sure what button to click at the bottom to send this. At any rate, if you could point me to a guide for how to do this, it would help. Thanks

danielskatz commented 6 years ago

@pspringer - We're using GitHub's notification feature within issues, so if you put @danielskatz, I will be notified.

And these are typical GitHub issues - fully public for anyone who cares to look, and continually added to as more comments are added (by the green comment button under the empty box at the end of a current list of comments on an issue)

It might be useful for us to talk offline on some of the details of how this reviewing process works within GitHub, and not bother others who may be following this issue. I'll followup by email.

pspringer commented 6 years ago

@salabim, the documentation section on Reading items from a file is pretty slim. I would recommend either adding some detail to it, or inserting a note that the Reference section has more detail.

salabim commented 6 years ago

@pspringer I have updated the section on reading files and the requirement section (re Pillow).

@pspringer I would like to say something about the unique features of salabim, but where?

pspringer commented 6 years ago

@salabim I would recommend mentioning the unique features in the README file, but let's see if @danielskatz concurs.

danielskatz commented 6 years ago

one or both of the following would be appropriate: the readme, the documentation in addition to in the paper.

salabim commented 6 years ago

I have added the requested information to paper.md and READ.me.

Ruud van der Ham rt.van.der.ham@gmail.com rt.van.der.ham@gmail.com

On 15 June 2018 at 08:30, Daniel S. Katz notifications@github.com wrote:

one or both of the following would be appropriate: the readme, the documentation in addition to in the paper.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/767#issuecomment-397526754, or mute the thread https://github.com/notifications/unsubscribe-auth/Ac9rCym9PVEaaQW2EBpjHSL6BAGypS-0ks5t81SagaJpZM4UdQqy .

danielskatz commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

danielskatz commented 6 years ago

@salabim - Just looking at the paper, I think it's still too short, and also it doesn't have any references. See http://joss.theoj.org/about#author_guidelines, and perhaps take a look at some of the accepted submissions in http://joss.theoj.org

For example, I'm not sure the paper clearly state what problems the software is designed to solve and who the target audience is? Also, the paper could briefly explain what DES is.

salabim commented 6 years ago

Updated.

Ruud van der Ham rt.van.der.ham@gmail.com rt.van.der.ham@gmail.com

On 15 June 2018 at 13:29, Daniel S. Katz notifications@github.com wrote:

@salabim https://github.com/salabim - Just looking at the paper, I think it's still too short, and also it doesn't have any references. See http://joss.theoj.org/about#author_guidelines, and perhaps take a look at some of the accepted submissions in http://joss.theoj.org

For example, I'm not sure the paper clearly state what problems the software is designed to solve and who the target audience is? Also, the paper could briefly explain what DES is.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/767#issuecomment-397593038, or mute the thread https://github.com/notifications/unsubscribe-auth/Ac9rCyz8y0SOEX8W0SLRY0EttbbNLFlwks5t85qzgaJpZM4UdQqy .

danielskatz commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

danielskatz commented 6 years ago

@salabim - References should be to specific articles or web sites. See some of the accepted submissions in http://joss.theoj.org Otherwise, I will leave it to @pspringer and @gonsie to provide more feedback on the content.

gonsie commented 6 years ago

@salabim - Please respond to the issues in the salabim/salabim repo (here)

danielskatz commented 6 years ago

@pspringer and @gonsie - I don't see any open issues in the salabim repo currently, so I think this review is back to you both. Can you please update us on anything you are waiting for, or how this stands to you otherwise?

danielskatz commented 6 years ago

Also @salabim - the paper still needs to have specific references added, and cited in the body of the paper.

salabim commented 6 years ago

What kind of references are we talking about. I know that there some users who are going to publish an article, but nothing concrete yet. Is that a problem? Otherwise, can I just cite some sample projects?

Ruud van der Ham rt.van.der.ham@gmail.com rt.van.der.ham@gmail.com

On 21 June 2018 at 17:07, Daniel S. Katz notifications@github.com wrote:

Also @salabim https://github.com/salabim - the paper still needs to have specific references added, and cited in the body of the paper.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/767#issuecomment-399137269, or mute the thread https://github.com/notifications/unsubscribe-auth/Ac9rC-ihFrs0i9e-5bruvIuedIeRQ1enks5t-7augaJpZM4UdQqy .

danielskatz commented 6 years ago

RIght now, the references says "Several wikipedia articles on DES and simulation languages."

What are these articles? You need to list them. Are there academic papers about DES and the simulations languages? If so, you should list them as well.

To pick a recent example, see https://github.com/openjournals/joss-papers/blob/joss.00773/joss.00773/10.21105.joss.00773.pdf which has a lot of reference (likely more than you need). The paper includes citations to the references, which are listed in the bibliography file.

This is what I'm looking for.

pspringer commented 6 years ago

@danielskatz and @salabim I'm going through the six functional blocks I've identified to make sure all are as documented. I should be able to finish that this week.

salabim commented 6 years ago

I have updated the paper.bib file to contain a couple of relevant references. Does this meets the requirements. now?

On Thu, Jun 21, 2018 at 6:34pm, Daniel S. Katz < notifications@github.com [notifications@github.com] > wrote:RIght now, the references says "Several wikipedia articles on DES and simulation languages."

What are these articles? You need to list them. Are there academic papers about DES and the simulations languages? If so, you should list them as well.

To pick a recent example, see https://github.com/openjournals/joss-papers/blob/joss.00773/joss.00773/10.21105.joss.00773.pdf [https://github.com/openjournals/joss-papers/blob/joss.00773/joss.00773/10.21105.joss.00773.pdf] which has a lot of reference (likely more than you need). The paper [https://github.com/SMTG-UCL/galore/blob/master/paper.md] includes citations to the references, which are listed in the bibliography file [https://github.com/SMTG-UCL/galore/blob/master/paper.bib]

This is what I'm looking for

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub [https://github.com/openjournals/joss-reviews/issues/767#issuecomment-399166220] , or mute the thread [https://github.com/notifications/unsubscribe-auth/Ac9rC83wjAPRjfoAlK85244OrlIXatUIks5t-8sDgaJpZM4UdQqy] .

danielskatz commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

danielskatz commented 6 years ago

Add the papers to .bib file is good, but now you have to update the .md file to cite them. Only references that are cited are built into the pdf.

salabim commented 6 years ago

I have updated the paper.md and paper.bib files. Sorry for my stupid questions ...

On Tue, Jun 26, 2018 at 20:35, Daniel S. Katz notifications@github.com wrote: Add the papers to .bib file is good, but now you have to update the .md file to cite them. Only references that are cited are built into the pdf.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub [https://github.com/openjournals/joss-reviews/issues/767#issuecomment-400418903] , or mute the thread [https://github.com/notifications/unsubscribe-auth/Ac9rC4XV8z2xQE6g5X2TH55ocy2Op5BNks5uAn7hgaJpZM4UdQqy] .

danielskatz commented 6 years ago

Thanks - I think you can also regenerate the PDF to check it (this is not just something I can do).

Though I will do it again this time.

danielskatz commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

danielskatz commented 6 years ago

Those bibtex entries didn't quite work right...

danielskatz commented 6 years ago

I've created 2 pull requests for the bib and the md of the paper - let's see if these fix the problems

salabim commented 6 years ago

Daniel,

I have updated the paper.bib document and double checked it manually. I still don't know how to check or generate the pdf myself. Could you be so kind as to do that for me?

Ruud van der Ham

rt.van.der.ham@gmail.com rt.van.der.ham@gmail.com

On Thu, 28 Jun 2018 at 14:49, Daniel S. Katz notifications@github.com wrote:

I've created 2 pull requests for the bib and the md of the paper - let's see if these fix the problems

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/767#issuecomment-401022786, or mute the thread https://github.com/notifications/unsubscribe-auth/Ac9rC7v4w2sU3-k3UkEQ05YnI6vVA6TZks5uBNDCgaJpZM4UdQqy .

danielskatz commented 6 years ago

@whedon generate pdf

@salabim - I think you should also be able to give this command as a comment in this GitHub issue

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

PDF failed to compile for issue #767 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 11 0 11 0 0 134 0 --:--:-- --:--:-- --:--:-- 135 Error reading bibliography ./paper.bib (line 12, column 32): unexpected "{" expecting space or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

danielskatz commented 6 years ago

I'm a little confused why you didn't merge my pull requests: https://github.com/salabim/salabim/pull/10 and https://github.com/salabim/salabim/pull/11

danielskatz commented 6 years ago

These pull requests should fix the problems.

salabim commented 6 years ago

Sorry, but I am very confused and far from an expert in GitHub.

I have now merged the pull requests (no idea what that means) and uploaded a corrected vetsion of paper.bib.

And now?

Ruud, just a simple open source software developer ...

From: Daniel S. Katz notifications@github.com Sent: Wednesday, July 4, 2018 7:40:25 PM To: openjournals/joss-reviews Cc: salabim; Mention Subject: Re: [openjournals/joss-reviews] [REVIEW]: Salabim: discrete event simulation and animation in Python (#767)

These pull requests should fix the problems.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/767#issuecomment-402532808, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Ac9rC3wE-ROIb1Ps5YFPjuVloX5KrUDDks5uDP4JgaJpZM4UdQqy.

danielskatz commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

danielskatz commented 6 years ago

@salabim - you might want to read through some of the GitHub Guides, in particular the one on Git

openjournals / joss-reviews