search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
720 stars 38 forks source link

[PRE REVIEW]: hstrat: a Python Package for phylogenetic inference on distributed digital evolution populations #4860

Closed editorialbot closed 2 years ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@mmore500<!--end-author-handle-- (Matthew Andres Moreno) Repository: https://github.com/mmore500/hstrat Branch with paper.md (empty if default branch): Version: v1.0.3 Editor: !--editor-->@osorensen<!--end-editor-- Reviewers: @GeekLogan, @JJ, @kgd-al Managing EiC: Daniel S. Katz

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9bfd6debc03eb724b58be1864c0d5901"><img src="https://joss.theoj.org/papers/9bfd6debc03eb724b58be1864c0d5901/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9bfd6debc03eb724b58be1864c0d5901/status.svg)](https://joss.theoj.org/papers/9bfd6debc03eb724b58be1864c0d5901)

Author instructions

Thanks for submitting your paper to JOSS @mmore500. Currently, there isn't a JOSS editor assigned to your paper.

@mmore500 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
editorialbot commented 2 years 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 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.72 s (701.3 files/s, 68917.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         442           4849           4010          37425
SVG                              2              0              0            905
Markdown                         8            189              0            517
TeX                              1              0              0            481
Bourne Shell                    31            123            102            416
reStructuredText                14             94             68            201
YAML                             2              9              4            113
make                             2             31              7             93
INI                              2             10              3             50
CSS                              1              4              3             11
TOML                             1              1              0              7
-------------------------------------------------------------------------------
SUM:                           506           5310           4197          40219
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 1413

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-3-662-44874-8 is OK
- 10.1007/s10710-021-09406-8 is OK
- 10.17605/osf.io/tcjfy is OK
- 10.17605/osf.io/53vgh is OK
- 10.1162/isal_a_00550 is OK
- 10.5281/zenodo.4141943 is OK

MISSING DOIs

- 10.1109/sasow.2011.18 may be a valid DOI for title: Homeostatic architectures for robust spatial computing
- 10.7551/978-0-262-32621-6-ch098 may be a valid DOI for title: Indefinitely scalable computing= artificial life engineering
- 10.1007/11795490_30 may be a valid DOI for title: On the power of anonymous one-way communication
- 10.1007/978-3-540-89707-1_5 may be a valid DOI for title: An introduction to population protocols
- 10.1016/s0167-739x(02)00171-1 may be a valid DOI for title: Automated scientific software scripting with SWIG
- 10.7551/ecal_a_016 may be a valid DOI for title: MABE (Modular Agent Based Evolver): A framework for digital evolution research
- 10.1109/cec.2003.1299834 may be a valid DOI for title: Is increased diversity in genetic programming beneficial? an analysis of lineage selection
- 10.1162/artl_a_00285 may be a valid DOI for title: Maximum individual complexity is indefinitely scalable in Geb
- 10.1098/rspb.2010.1557 may be a valid DOI for title: Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory
- 10.1111/ecog.05427 may be a valid DOI for title: Diversity and phylogenetic community structure across elevation during climate change in a family of hyperdiverse neotropical beetles (Staphylinidae)
- 10.1186/1741-7007-12-29 may be a valid DOI for title: Models in biology:‘accurate descriptions of our pathetic thinking’
- 10.1109/hpcs.2007.17 may be a valid DOI for title: Fast genetic programming and artificial developmental systems on GPUs
- 10.1007/978-981-16-8113-4_4 may be a valid DOI for title: What can phylogenetic metrics tell us about useful diversity in evolutionary algorithms?
- 10.1145/3520304.3534079 may be a valid DOI for title: Phylogenetic diversity predicts future success in evolutionary computation
- 10.1586/14737159.4.3.339 may be a valid DOI for title: Phylogenetic analyses: a brief introduction to methods and their application
- 10.1145/3205455.3205523 may be a valid DOI for title: Evolving event-driven programs with SignalGP
- 10.1162/isal_a_00191.xml may be a valid DOI for title: Continuous long-term evolution of genetic programming
- 10.1109/mm.2021.3112025 may be a valid DOI for title: The Path to Successful Wafer-Scale Integration: The Cerebras Story
- 10.4024/40701.jbpc.07.04 may be a valid DOI for title: Principles of modularity, regularity, and hierarchy for scalable systems
- 10.1109/mc.2008.17 may be a valid DOI for title: Harnessing digital evolution
- 10.7551/mitpress/8775.003.0005 may be a valid DOI for title: The miscellaneous transitions in evolution
- 10.1016/j.devcel.2006.08.004 may be a valid DOI for title: Quantitative modeling in cell biology: what is it good for?
- 10.7287/peerj.preprints.27275v2 may be a valid DOI for title: Toward open-ended fraternal transitions in individuality
- 10.3389/fevo.2022.750837 may be a valid DOI for title: Exploring Evolved Multicellular Life Histories in a Open-Ended Digital Evolution System
- 10.1007/978-3-540-78671-9_13 may be a valid DOI for title: A simple powerful constraint for genetic programming
- 10.1080/09528130601116113 may be a valid DOI for title: Models, simulations, instantiations, and evidence: the case of digital evolution
- 10.4081/eb.2013.br1 may be a valid DOI for title: What is life?: How chemistry becomes biology
- 10.1007/s12064-010-0110-z may be a valid DOI for title: Mathematical modeling of evolution. Solved and open problems
- 10.1145/3520304.3534028 may be a valid DOI for title: Untangling phylogenetic diversity’s role in evolutionary computation using a suite of diagnostic fitness landscapes
- 10.2307/1576602 may be a valid DOI for title: Life as we know it and/or life as it could be: Epistemology and the ontology/ontogeny of artificial life
- 10.7551/mitpress/1428.003.0007 may be a valid DOI for title: Evolving 3D morphology and behavior by competition
- 10.1109/12.811115 may be a valid DOI for title: Branch prediction, instruction-window size, and cache size: Performance trade-offs and simulation techniques

INVALID DOIs

- None
danielskatz commented 2 years ago

@mmore500 - thanks for your submission to JOSS. I'll be looking for an editor for this.

While I do so, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

Also, if you have references in your bib file that you are not actually citing in the paper, you could remove them, as our bot checks everything in the bib file, whether it is used in the paper or not.

danielskatz commented 2 years ago

👋 @osorensen - This might be a bit outside your area, but I wanted to check and see if you might be able to edit it

danielskatz commented 2 years ago

@editorialbot invite @osorensen as editor

editorialbot commented 2 years ago

Invitation to edit this submission sent!

osorensen commented 2 years ago

@danielskatz, I can do it

osorensen commented 2 years ago

@editorialbot assign @osorensen as editor

editorialbot commented 2 years ago

Assigned! @osorensen is now the editor

osorensen commented 2 years ago

👋 @jmcbroome @jsun @tkmamidi @GeekLogan would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

mmore500 commented 2 years ago

I will make a pass to fixup the dois. Looking forward to working with you all on this review process!

mmore500 commented 2 years ago

I am consulting with my coauthors to come up with some additional reviewers to suggest if necessary. I’ll follow up here shortly.

mmore500 commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/sasow.2011.18 is OK
- 10.1007/11795490_30 is OK
- 10.1007/978-3-540-89707-1_5 is OK
- 10.1145/3319619.3326825 is OK
- 10.1109/cec.2003.1299834 is OK
- 10.1162/artl_a_00285 is OK
- 10.1098/rspb.2010.1557 is OK
- 10.1145/2330784.2330799 is OK
- 10.1145/3205651.3205780 is OK
- 10.1007/978-3-662-44874-8 is OK
- 10.1109/jproc.2014.2304638 is OK
- 10.7312/crac92306-005 is OK
- 10.13140/rg.2.2.33781.93921 is OK
- 10.1109/hpcs.2007.17 is OK
- 10.1007/978-981-16-8113-4_4 is OK
- 10.1145/3520304.3534079 is OK
- 10.48550/arxiv.2204.13839 is OK
- 10.1586/14737159.4.3.339 is OK
- 10.1162/isal_a_00191 is OK
- 10.1109/mm.2021.3112025 is OK
- 10.4024/40701.jbpc.07.04 is OK
- 10.1109/mc.2008.17 is OK
- 10.7551/mitpress/9780262015240.003.0002 is OK
- 10.17605/osf.io/53vgh is OK
- 10.3389/fevo.2022.750837 is OK
- 10.1162/isal_a_00550 is OK
- 10.1371/journal.pbio.0000018 is OK
- 10.1162/106454604773563612 is OK
- 10.5281/zenodo.4141943 is OK
- 10.1080/09528130601116113 is OK
- 10.1145/3520304.3534028 is OK
- 10.1162/artl.1994.1.4.353 is OK

MISSING DOIs

- 10.1007/978-3-540-78671-9_13 may be a valid DOI for title: A Simple Powerful Constraint for Genetic Programming
- 10.4081/eb.2013.br1 may be a valid DOI for title: What is life?: How chemistry becomes biology

INVALID DOIs

- 10.1162/978-0-262-32621-6-ch098 is INVALID
- https://doi.org/10.1016/S0167-739X(02)00171-1 is INVALID because of 'https://doi.org/' prefix
- 10.1162/isal_a_016 is INVALID
- https://doi.org/10.1016/B978-0-12-815480-9.00015-3 is INVALID because of 'https://doi.org/' prefix
mmore500 commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/sasow.2011.18 is OK
- 10.1007/11795490_30 is OK
- 10.1007/978-3-540-89707-1_5 is OK
- 10.1016/s0167-739x(02)00171-1 is OK
- 10.1145/3319619.3326825 is OK
- 10.1109/cec.2003.1299834 is OK
- 10.1162/artl_a_00285 is OK
- 10.1098/rspb.2010.1557 is OK
- 10.1145/2330784.2330799 is OK
- 10.1145/3205651.3205780 is OK
- 10.1007/978-3-662-44874-8 is OK
- 10.1109/jproc.2014.2304638 is OK
- 10.7312/crac92306-005 is OK
- 10.13140/rg.2.2.33781.93921 is OK
- 10.1109/hpcs.2007.17 is OK
- 10.1007/978-981-16-8113-4_4 is OK
- 10.1145/3520304.3534079 is OK
- 10.48550/arxiv.2204.13839 is OK
- 10.1586/14737159.4.3.339 is OK
- 10.1162/isal_a_00191 is OK
- 10.1109/mm.2021.3112025 is OK
- 10.4024/40701.jbpc.07.04 is OK
- 10.1109/mc.2008.17 is OK
- 10.7551/mitpress/9780262015240.003.0002 is OK
- 10.1016/b978-0-12-815480-9.00015-3 is OK
- 10.17605/osf.io/53vgh is OK
- 10.3389/fevo.2022.750837 is OK
- 10.1162/isal_a_00550 is OK
- 10.1371/journal.pbio.0000018 is OK
- 10.1162/106454604773563612 is OK
- 10.5281/zenodo.4141943 is OK
- 10.1080/09528130601116113 is OK
- 10.1145/3520304.3534028 is OK
- 10.1162/artl.1994.1.4.353 is OK

MISSING DOIs

- 10.1007/978-3-540-78671-9_13 may be a valid DOI for title: A Simple Powerful Constraint for Genetic Programming
- 10.4081/eb.2013.br1 may be a valid DOI for title: What is life?: How chemistry becomes biology

INVALID DOIs

- 10.1162/978-0-262-32621-6-ch098 is INVALID
- 10.1162/isal_a_016 is INVALID
mmore500 commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/sasow.2011.18 is OK
- 10.1007/11795490_30 is OK
- 10.1007/978-3-540-89707-1_5 is OK
- 10.1016/s0167-739x(02)00171-1 is OK
- 10.1145/3319619.3326825 is OK
- 10.1109/cec.2003.1299834 is OK
- 10.1162/artl_a_00285 is OK
- 10.1098/rspb.2010.1557 is OK
- 10.1145/2330784.2330799 is OK
- 10.1145/3205651.3205780 is OK
- 10.1007/978-3-662-44874-8 is OK
- 10.1109/jproc.2014.2304638 is OK
- 10.7312/crac92306-005 is OK
- 10.13140/rg.2.2.33781.93921 is OK
- 10.1109/hpcs.2007.17 is OK
- 10.1007/978-981-16-8113-4_4 is OK
- 10.1145/3520304.3534079 is OK
- 10.48550/arxiv.2204.13839 is OK
- 10.1586/14737159.4.3.339 is OK
- 10.1162/isal_a_00191 is OK
- 10.1109/mm.2021.3112025 is OK
- 10.4024/40701.jbpc.07.04 is OK
- 10.1109/mc.2008.17 is OK
- 10.7551/mitpress/9780262015240.003.0002 is OK
- 10.1016/b978-0-12-815480-9.00015-3 is OK
- 10.17605/osf.io/53vgh is OK
- 10.3389/fevo.2022.750837 is OK
- 10.1162/isal_a_00550 is OK
- 10.1007/978-3-540-78671-9_13 is OK
- 10.1371/journal.pbio.0000018 is OK
- 10.1162/106454604773563612 is OK
- 10.5281/zenodo.4141943 is OK
- 10.1080/09528130601116113 is OK
- 10.1145/3520304.3534028 is OK
- 10.1162/artl.1994.1.4.353 is OK

MISSING DOIs

- 10.4081/eb.2013.br1 may be a valid DOI for title: What is life?: How chemistry becomes biology

INVALID DOIs

- 10.1162/978-0-262-32621-6-ch098 is INVALID
- 10.1162/isal_a_016 is INVALID
mmore500 commented 2 years ago

@editorialbot generate pdf

All good! The two invalid doi's are directly from publisher's website --- they appear to be dead, so I have submitted error reports to the doi folks. Suggested doi is for a book review, not the source itself.

editorialbot commented 2 years ago

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

mmore500 commented 2 years ago

Reviewers I could suggest (if this is still needed) would be @/jj (who is also listed on the joss registry!), @/kgd-al, @/tim-taylor, or David Parsons (https://www.parsons.eu/) who I can’t find listed on GitHub.

osorensen commented 2 years ago

Thanks @mmore500!

osorensen commented 2 years ago

👋 @jj, @kgd-al, @tim-taylor would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

GeekLogan commented 2 years ago

👋 @jmcbroome @jsun @tkmamidi @GeekLogan would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Hi 👋 @osorensen! I would be happy to review if you are still in need, however, I am not super experienced with this subject area so the suggested reviewers may be a better fit if they are available. Feel free to let me know

osorensen commented 2 years ago

Thanks @GeekLogan, your review will be much appreciated

osorensen commented 2 years ago

@editorialbot add @GeekLogan as reviewer

editorialbot commented 2 years ago

@GeekLogan added to the reviewers list!

JJ commented 2 years ago

wave @JJ, @kgd-al, @tim-taylor would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

I did the thumbs-up here, but I guess it's not enough...

osorensen commented 2 years ago

Ahh, sorry! Thanks for the thumbs up!

osorensen commented 2 years ago

@editorialbot add @JJ as reviewer

editorialbot commented 2 years ago

@JJ added to the reviewers list!

osorensen commented 2 years ago

wave @JJ, @kgd-al, @tim-taylor would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

I did the thumbs-up here, but I guess it's not enough...

Does the same apply to you @kgd-al?

JJ commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @JJ, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
JJ commented 2 years ago

@editorialbot generate my checklist

editorialbot commented 2 years ago

Checklists can only be created once the review has started in the review issue

kgd-al commented 2 years ago

wave @JJ, @kgd-al, @tim-taylor would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

I did the thumbs-up here, but I guess it's not enough...

Does the same apply to you @kgd-al?

Indeed. I would be happy to review although this is a first so I will probably have a few questions later on.

osorensen commented 2 years ago

Perfect @kgd-al ! You're welcome to reach out to me whenever you have questions

osorensen commented 2 years ago

@editorialbot add @kgd-al as reviewer

editorialbot commented 2 years ago

@kgd-al added to the reviewers list!

osorensen commented 2 years ago

@editorialbot start review

editorialbot commented 2 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4866.

tim-taylor commented 2 years ago

wave @JJ, @kgd-al, @tim-taylor would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

@osorensen I'm sorry but I don't have time to do this as I'm travelling a lot over the next few weeks. But it sounds like you are sorted for reviewers now anyway 👍

osorensen commented 2 years ago

Yes we're sorted @tim-taylor, but thanks for responding