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[REVIEW]: EPICpy: A Python Interface for EPIC Computational Cognitive Modeling
Submitting author: @travisseymour (Travis Seymour) Repository: https://github.com/travisseymour/EPICpy Branch with paper.md (empty if default branch): JOSSArticle Version: v2022.3.5 Editor: @prashjha Reviewers: @Athene-ai, @jakdot Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/fb8bccc1dc65ca3afd6ad380f36a2957"><img src="https://joss.theoj.org/papers/fb8bccc1dc65ca3afd6ad380f36a2957/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/fb8bccc1dc65ca3afd6ad380f36a2957)
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
@Athene-ai & @jakdot, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:
@editorialbot generate my checklist
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @prashjha 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 ✨
Checklists
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Software report:
github.com/AlDanial/cloc v 1.88 T=0.35 s (1044.3 files/s, 213548.0 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
C++ 143 6394 9649 24457
C/C++ Header 154 3506 4498 11528
Python 53 1806 1338 8283
Qt 14 2 0 3750
Markdown 4 86 0 188
TeX 1 18 0 158
TOML 1 0 0 2
-------------------------------------------------------------------------------
SUM: 370 11812 15485 48366
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1037/0033-295X.104.1.3 is OK
- 10.1037//0033-295X.104.4.749 is OK
- 10.1207/s15327051hci1204_4 is OK
- 10.1007/s10462-018-9646-y is OK
- 10.1111/tops.12406 is OK
- 10.21105/joss.01026 is OK
- 10.3758/CABN.9.1.71 is OK
- 10.1145/2556288.2557351 is OK
- 10.1080/09541440042000250 is OK
- 10.1109/PyHPC.2016.008 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Dear @Athene-ai and @jakdot, please read the first couple of comments in this thread and create your review checklist. You can read the reviewer guidelines here. Also, you can browse the closed "REVIEW" issues on the "joss-reviews" repository to get some ideas on how to complete the reviews. Good luck!
Hi @Athene-ai and @jakdot, I am wondering if you have started the review and if there is any update. Thanks!
Review checklist for @Athene-ai
Conflict of interest
- [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.
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 https://github.com/travisseymour/EPICpy?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [x] Contribution and authorship: Has the submitting author (@travisseymour) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- [ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
- [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
Review checklist for @jakdot
Conflict of interest
- [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.
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 https://github.com/travisseymour/EPICpy?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [x] Contribution and authorship: Has the submitting author (@travisseymour) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
- [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
Hi @prashjha , done with my review. There was one issue with functionality, see here:
https://github.com/travisseymour/EPICpy/issues/1#issue-1338771489
Since the author provides a workaround in the thread on the issue, I see this as solved (I did not close the issue just yet in case the author wants to debug it further).
As far as I am concerned, the paper is accepted. Let me know if you need more from me.
Hi @prashjha https://github.com/prashjha , it looks like both reviews are in and I am wondering if there is anything I can or need to do to move things along. I have a promotion coming up and it would help to know whether or not this submission has been successful. Thanks Travis Seymour
On Mon, Aug 1, 2022 at 1:36 PM Prashant K. Jha @.***> wrote:
Hi @Athene-ai https://github.com/Athene-ai and @jakdot https://github.com/jakdot, I am wondering if you have started the review and if there is any update. Thanks!
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4533#issuecomment-1201694584, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJGI3XAZHLWLLWTHMCPFIDVXAYODANCNFSM52M745XA . You are receiving this because you were mentioned.Message ID: @.***>
--
Travis Seymour, PhD Associate Professor Psychology Department University of California Santa Cruz http://cogmodlab.ucsc.edu/
Hi @travisseymour, I will have a look at your draft today, and if there are any suggestions I will share them. Once you incorporate those suggestions and do a tagged release+archive release on zenodo, I will hand your paper to EiC for the final decision. It looks like both reviewers are positive so I will recommend accepting to EiCs.
Dear @Athene-ai and @jakdot, many thanks for your time and effort in reviewing this submission. I sincerely appreciate it. I am guessing @Athene-ai is also recommending acceptance.
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1037/0033-295X.104.1.3 is OK
- 10.1037//0033-295X.104.4.749 is OK
- 10.1207/s15327051hci1204_4 is OK
- 10.1007/s10462-018-9646-y is OK
- 10.1111/tops.12406 is OK
- 10.21105/joss.01026 is OK
- 10.3758/CABN.9.1.71 is OK
- 10.1145/2556288.2557351 is OK
- 10.1080/09541440042000250 is OK
- 10.1109/PyHPC.2016.008 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi Prashant, I'm new to all of this and I want to make sure I know what you mean. Are you suggesting I do a tagged release using git like this (if so, is there anything special you want in the message), or is this part also on zenodo?
git tag -a v1.0.0 -m "Releasing version v1.0.0"
As for the other stuff you suggested, I've never used zenodo, but I assume you are referring to this part of the setting-the-software-archive https://joss.readthedocs.io/en/latest/editorial_bot.html?highlight=zenodo#setting-the-software-archive page:
When a submission is accepted, we ask that the authors to create an archive (on Zenodo https://zenodo.org/, figshare https://figshare.com/, or other) and post the archive DOI in the REVIEW issue.
Correct? thanks, Travis
On Wed, Aug 24, 2022 at 8:51 AM Prashant K. Jha @.***> wrote:
Hi @travisseymour https://github.com/travisseymour, I will have a look at your draft today, and if there are any suggestions I will share them. Once you incorporate those suggestions and do a tagged release+archive release on zenodo, I will hand your paper to EiC for the final decision. It looks like both reviewers are positive so I will recommend accepting to EiCs.
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4533#issuecomment-1225911359, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJGI3SW4NUF2OKZX5PNJALV2ZAJBANCNFSM52M745XA . You are receiving this because you were mentioned.Message ID: @.***>
--
Travis Seymour, PhD Associate Professor Psychology Department University of California Santa Cruz http://cogmodlab.ucsc.edu/
Prashant, After reviewing the PDF you created, I realized that there were a couple of typo fixes and OS version clarifications needed. I made the required changes and pushed the updates to github. Please generate a new pdf. Thanks Travis
On Wed, Aug 24, 2022 at 8:57 AM The Open Journals editorial robot < @.***> wrote:
👉📄 Download article proof https://raw.githubusercontent.com/openjournals/joss-papers/joss.04533/joss.04533/10.21105.joss.04533.pdf 📄 View article proof on GitHub https://github.com/openjournals/joss-papers/blob/joss.04533/joss.04533/10.21105.joss.04533.pdf 📄 👈
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4533#issuecomment-1225918895, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJGI3XSYDSSTFVHL3UFYRDV2ZA73ANCNFSM52M745XA . You are receiving this because you were mentioned.Message ID: @.***>
--
Travis Seymour, PhD Associate Professor Psychology Department University of California Santa Cruz http://cogmodlab.ucsc.edu/
Sorry Prashant, I think I know what you're asking me to do. So please ignore my previous message about explaining the archival release.
On Wed, Aug 24, 2022 at 10:37 AM Travis Seymour @.***> wrote:
Hi Prashant, I'm new to all of this and I want to make sure I know what you mean. Are you suggesting I do a tagged release using git like this (if so, is there anything special you want in the message), or is this part also on zenodo?
git tag -a v1.0.0 -m "Releasing version v1.0.0"
As for the other stuff you suggested, I've never used zenodo, but I assume you are referring to this part of the setting-the-software-archive https://joss.readthedocs.io/en/latest/editorial_bot.html?highlight=zenodo#setting-the-software-archive page:
When a submission is accepted, we ask that the authors to create an archive (on Zenodo https://zenodo.org/, figshare https://figshare.com/, or other) and post the archive DOI in the REVIEW issue.
Correct? thanks, Travis
On Wed, Aug 24, 2022 at 8:51 AM Prashant K. Jha @.***> wrote:
Hi @travisseymour https://github.com/travisseymour, I will have a look at your draft today, and if there are any suggestions I will share them. Once you incorporate those suggestions and do a tagged release+archive release on zenodo, I will hand your paper to EiC for the final decision. It looks like both reviewers are positive so I will recommend accepting to EiCs.
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4533#issuecomment-1225911359, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJGI3SW4NUF2OKZX5PNJALV2ZAJBANCNFSM52M745XA . You are receiving this because you were mentioned.Message ID: @.***>
--
Travis Seymour, PhD Associate Professor Psychology Department University of California Santa Cruz http://cogmodlab.ucsc.edu/
--
Travis Seymour, PhD Associate Professor Psychology Department University of California Santa Cruz http://cogmodlab.ucsc.edu/
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Ok, I have the tagged release/archive on zenodo, this is the resulting DOI: 10.5281/zenodo.7020282
Hi @travisseymour, thanks for your response. The draft is well written. Here are a few suggestions on the draft (see if they make sense):
- Remove the extra
Figure 1from the Figure 1 caption. Same with Figure 2 caption. Also, you may highlight the change in Figure 2 (i.e., python) compared to Figure 1 in the caption of Figure 2. - I will suggest referring to Figure 1 in line 47:
of the following components (see Figure 1): - Line 67:
application:? - Line 69:
... with which the author showed ...?
Thanks for archiving the library. Let me know when you have made the changes (or prefer not to make changes), and I will hand the paper to EiC.
Hi @travisseymour, could you update the title of your zenodo archive to match the title of your JOSS article?
Thanks @prashjha, I've done the following:
- Changed the title of the zenodo archive as requested.
- Made the changes you suggested to the draft.