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[PRE REVIEW]: ratesb_python: Rate Law Analysis for SBML and Antimony #7268

Open editorialbot opened 2 months ago

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@longxf21<!--end-author-handle-- (Longxuan Fan) Repository: https://github.com/sys-bio/ratesb_python Branch with paper.md (empty if default branch): Version: v0.2.6 Editor: !--editor-->@RMeli<!--end-editor-- Reviewers: Pending Managing EiC: Kevin M. Moerman

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Thanks for submitting your paper to JOSS @longxf21. Currently, there isn't a JOSS editor assigned to your paper.

@longxf21 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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editorialbot commented 2 months ago

Hello human, 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
editorialbot commented 2 months ago

:warning: An error happened when generating the pdf.

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (2478.1 files/s, 113993.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11            351            500           1669
XML                             62              8             10            686
reStructuredText                 8            122             98            278
JSON                             8              1              0            274
Markdown                         2             79              0            220
TeX                              1              3              0             50
YAML                             2              7              0             44
DOS Batch                        1              8              1             26
TOML                             1              0              0             21
Dockerfile                       1              5              7             20
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            98            588            623           3297
-------------------------------------------------------------------------------

Commit count by author:

    44  Aldrich Fan
     2  longxf
     1  Joseph Hellerstein
editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 863

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

Kevin-Mattheus-Moerman commented 2 months ago

@longxf21 Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. The paper compilation error above seems to relate to the fact that the paper lacks the required YAML content. Please update the paper as per our guidelines and include the required YAML content.

Kevin-Mattheus-Moerman commented 2 months ago

@longxf21 :wave:

longxf21 commented 2 months ago

Hi Kevin,

Thanks! I will revise it soon.

Longxuan

On Thu, Sep 26, 2024 at 08:54 Kevin Mattheus Moerman < @.***> wrote:

@longxf21 https://github.com/longxf21 👋

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7268#issuecomment-2377353843, or unsubscribe https://github.com/notifications/unsubscribe-auth/AY2M7DBQUEKU3533XZ4HCFTZYQU33AVCNFSM6AAAAABOWF7MB6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZXGM2TGOBUGM . You are receiving this because you were mentioned.Message ID: @.***>

Kevin-Mattheus-Moerman commented 1 month ago

@longxf21 have you updated the paper yet?

longxf21 commented 1 month ago

Hi Kevin,

I apologize that I didn't get back to you. I took some time to review the submission guidelines and followed the Docker one. I compiled it with Docker and it works fine now.

Thanks Longxuan

On Mon, Oct 14, 2024 at 03:18 Kevin Mattheus Moerman < @.***> wrote:

@longxf21 https://github.com/longxf21 have you updated the paper yet?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7268#issuecomment-2410712228, or unsubscribe https://github.com/notifications/unsubscribe-auth/AY2M7DEV6VLRFSFKCQJ64WLZ3OK6LAVCNFSM6AAAAABOWF7MB6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJQG4YTEMRSHA . You are receiving this because you were mentioned.Message ID: @.***>

Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

dfba: Software for efficient simulation of dynamic flux-balance analysis models in Python Submitting author: @davidtourigny Handling editor: @marcosvital (Active) Reviewers: @jdbrunner, @pstjohn, @synchon Similarity score: 0.7309

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape Submitting author: @ayush9pandey Handling editor: @csoneson (Active) Reviewers: @Farnazmdi, @Robaina Similarity score: 0.7212

BASICO: A simplified Python interface to COPASI Submitting author: @fbergmann Handling editor: @marcosvital (Active) Reviewers: @ayush9pandey, @jguhlin, @darogan Similarity score: 0.7139

ChemPy: A package useful for chemistry written in Python Submitting author: @bjodah Handling editor: @kyleniemeyer (Active) Reviewers: @bryanwweber Similarity score: 0.7053

Heta compiler: a software tool for the development of large-scale QSP models and compilation into simulation formats Submitting author: @metelkin Handling editor: @fboehm (Active) Reviewers: @martinmodrak, @elimillera Similarity score: 0.7014

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Kevin-Mattheus-Moerman commented 1 month ago

@longxf21 thanks for updating the paper. That compiled now and I had a quick look, and have some comments below:

Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot invite @ppxasjsm as editor

editorialbot commented 1 month ago

Invitation to edit this submission sent!

ppxasjsm commented 1 month ago

I don't think I can do this one I am afraid. My next few weeks are very busy with teaching.

Kevin-Mattheus-Moerman commented 3 weeks ago

@longxf21 please see my comments above :point_up:

longxf21 commented 3 weeks ago

Hi Kevin,

Thanks for your comments, but I thought having a commit after the first review would be better. Next time I would let you know first!

Thanks! Longxuan

On Fri, Nov 1, 2024 at 08:24 Kevin Mattheus Moerman < @.***> wrote:

@longxf21 https://github.com/longxf21 please see my comments above ☝️

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7268#issuecomment-2452064170, or unsubscribe https://github.com/notifications/unsubscribe-auth/AY2M7DDBL2WGPW3TCSBDMC3Z6OMK5AVCNFSM6AAAAABOWF7MB6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJSGA3DIMJXGA . You are receiving this because you were mentioned.Message ID: @.***>

longxf21 commented 3 weeks ago

If you would like me to make a commit before further review, please let me know, I would be happy to do that!

Longxuan

On Fri, Nov 1, 2024 at 09:19 sparrow 123 @.***> wrote:

Hi Kevin,

Thanks for your comments, but I thought having a commit after the first review would be better. Next time I would let you know first!

Thanks! Longxuan

On Fri, Nov 1, 2024 at 08:24 Kevin Mattheus Moerman < @.***> wrote:

@longxf21 https://github.com/longxf21 please see my comments above ☝️

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7268#issuecomment-2452064170, or unsubscribe https://github.com/notifications/unsubscribe-auth/AY2M7DDBL2WGPW3TCSBDMC3Z6OMK5AVCNFSM6AAAAABOWF7MB6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJSGA3DIMJXGA . You are receiving this because you were mentioned.Message ID: @.***>

Kevin-Mattheus-Moerman commented 1 week ago

@longxf21 yes please do commit and update as requested on a rolling bases.

Kevin-Mattheus-Moerman commented 1 week ago

@longxf21 apologies for the delays encountered so far. Many editors have been preoccupied handling other submissions. I hope to be able to invite one today so hopefully that will work out and we'll be able to move on from there.

Kevin-Mattheus-Moerman commented 1 week ago

@editorialbot invite @RMeli as editor

editorialbot commented 1 week ago

Invitation to edit this submission sent!

RMeli commented 1 week ago

@Kevin-Mattheus-Moerman I think this one is a bit too far from my area of expertise, I would probably struggle to find suitable reviewers. But if you can't find anyone more suitable, I'll take it.

Kevin-Mattheus-Moerman commented 2 days ago

@longxf21 did you see my comments above? Please implement the required changes. Thanks.

longxf21 commented 1 day ago

@editorialbot generate pdf

editorialbot commented 1 day ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 1 day ago

Five most similar historical JOSS papers:

dfba: Software for efficient simulation of dynamic flux-balance analysis models in Python Submitting author: @davidtourigny Handling editor: @marcosvital (Active) Reviewers: @jdbrunner, @pstjohn, @synchon Similarity score: 0.7250

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape Submitting author: @ayush9pandey Handling editor: @csoneson (Active) Reviewers: @Farnazmdi, @Robaina Similarity score: 0.7193

BASICO: A simplified Python interface to COPASI Submitting author: @fbergmann Handling editor: @marcosvital (Active) Reviewers: @ayush9pandey, @jguhlin, @darogan Similarity score: 0.7097

ChemPy: A package useful for chemistry written in Python Submitting author: @bjodah Handling editor: @kyleniemeyer (Active) Reviewers: @bryanwweber Similarity score: 0.7054

Heta compiler: a software tool for the development of large-scale QSP models and compilation into simulation formats Submitting author: @metelkin Handling editor: @fboehm (Active) Reviewers: @martinmodrak, @elimillera Similarity score: 0.7008

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

longxf21 commented 1 day ago

@Kevin-Mattheus-Moerman Apologies for the delay, I've checked the compiled paper pdf and the problems are fixed! Thanks!

Kevin-Mattheus-Moerman commented 1 day ago

@editorialbot assign @RMeli as editor

editorialbot commented 1 day ago

Assigned! @RMeli is now the editor

Kevin-Mattheus-Moerman commented 1 day ago

@RMeli thanks for still agreeing to be editor. I'll tag @lucydot @rkurchin @HaoZeke @mbarzegary to see if they can help suggest reviewers too in case you are stuck. Let me know if I can help too.

Kevin-Mattheus-Moerman commented 1 day ago

@longxf21 we've now assigned an editor @RMeli who will be the point of contact from now on. They will be looking for a set of reviewers now. If at this point you'd like to suggest any reviewers, please feel free to mention their GitHub handles here. But please do leave out the @ symbol so they are not tagged. Thanks!