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[PRE REVIEW]: DVMDOSTEM: a terrestrial ecosystem model designed to represent arctic, boreal and permafrost ecosystem dynamics #7136

Open editorialbot opened 3 weeks ago

editorialbot commented 3 weeks ago

Submitting author: !--author-handle-->@tobeycarman<!--end-author-handle-- (Tobey Carman) Repository: https://github.com/uaf-arctic-eco-modeling/dvm-dos-tem Branch with paper.md (empty if default branch): joss-paper-2 Version: v0.8.0 Editor: Pending Reviewers: Pending Managing EiC: Kristen Thyng

Status

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HTML: <a href="https://joss.theoj.org/papers/de6adf41412b7028d7be0a2064ea78cf"><img src="https://joss.theoj.org/papers/de6adf41412b7028d7be0a2064ea78cf/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/de6adf41412b7028d7be0a2064ea78cf/status.svg)](https://joss.theoj.org/papers/de6adf41412b7028d7be0a2064ea78cf)

Author instructions

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

@tobeycarman 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.

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:

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editorialbot commented 3 weeks 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 3 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.28 s (945.7 files/s, 329801.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             45           4659           4328          19754
Python                          61           5869           7099          12768
C/C++ Header                    57           1302            685           3499
reStructuredText                26           1412           1736           2882
Markdown                        13            506              0           1623
Jupyter Notebook                12              0          18877           1047
Bourne Shell                    32            387            556            845
TeX                              1              0              0            326
Julia                            2             51            139            234
CSV                              2              0              0            228
Dockerfile                       1             40            137            182
JavaScript                       2              8             40            181
YAML                             4             60            152            141
make                             2             22             15            130
diff                             1              2              6             44
JSON                             1              0              0             27
DOS Batch                        1              8              1             26
CSS                              1              3              3             24
-------------------------------------------------------------------------------
SUM:                           264          14329          33774          43961
-------------------------------------------------------------------------------

Commit count by author:

  2213  Tobey Carman
   545  Ruth Rutter
    83  Tobey B. Carman
    58  Heather Greaves
    54  Elchin
    40  Colin Tucker
    31  Helene Genet
    18  dependabot[bot]
    17  tobey
    15  Aiza Kabeer
    12  El
    11  benjamin-maglio
     9  Jana Canary
     9  vbriones
     7  Elchin Jafarov
     6  Hannah Mevenkamp
     6  amullen01
     5  Fengming Yuan
     5  bmaglio
     4  rarutter
     3  Heather E Greaves
     2  Alec Bennett
     2  Dogukan Teber
     2  Shawn P. Serbin
     2  colin tucker
     1  Christina Schaedel
     1  Doğukan Teber
     1  Joshua Rady
     1  Mark Lara
     1  Tobey
     1  Yuan
editorialbot commented 3 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1088/1748-9326/ad50ed is OK
- 10.1002/eap.2499 is OK
- 10.1890/08-0806.1 is OK
- 10.1111/gcb.12392 is OK
- 10.1002/eap.1641 is OK
- 10.1088/1748-9326/8/4/045016 is OK
- 10.5194/bg-11-6573-2014 is OK
- 10.5194/bg-11-6573-2014 is OK
- 10.1088/1748-9326/8/3/035030 is OK
- 10.1111/j.1365-2486.2009.02051.x is OK
- 10.1073/pnas.1103910108 is OK
- 10.52381/ICOP2024.190.1 is OK
- 10.1029/92GB00219 is OK
- 10.1002/eap.1768 is OK
- 10.2307/1941899 is OK
- 10.1038/s43247-022-00498-3 is OK
- 10.1109/38.56302 is OK
- 10.1038/s41558-023-01909-9 is OK
- 10.1146/annurev-environ-012220-011847 is OK
- 10.1038/nature14338 is OK
- 10.1146/annurev-environ-012220-011847 is OK
- 10.1038/nature14338 is OK
- 10.1038/s43017-021-00240-1 is OK
- 10.1029/2010JG001302 is OK
- 10.1029/2008JG000841 is OK
- 10.1029/2001jd001244 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: NetCDF Climate and Forecast (CF) Metadata Conventi...
- No DOI given, and none found for title: Estimation of above- and below-ground ecosystem pa...
- No DOI given, and none found for title: Docker: lightweight Linux containers for consisten...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
editorialbot commented 3 weeks ago

Paper file info:

📄 Wordcount for paper.md is 2444

✅ The paper includes a Statement of need section

editorialbot commented 3 weeks ago

License info:

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

editorialbot commented 3 weeks ago

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

editorialbot commented 3 weeks ago

Five most similar historical JOSS papers:

growR: R Implementation of the Vegetation Model ModVege Submitting author: @kuadrat Handling editor: @mikemahoney218 (Active) Reviewers: @shubhamjain15, @RobLBaker Similarity score: 0.6375

Enhanced software and platform for the Town Energy Balance (TEB) model Submitting author: @dmey Handling editor: @mjsottile (Retired) Reviewers: @ethan-nelson, @jayten Similarity score: 0.6159

WDPM: the Wetland DEM Ponding Model Submitting author: @KevinShook Handling editor: @kbarnhart (Retired) Reviewers: @r-barnes, @awickert, @KCallaghan Similarity score: 0.6130

MetSim: A Python package for estimation and disaggregation of meteorological data Submitting author: @arbennett Handling editor: @sjpfenninger (Retired) Reviewers: @Chilipp, @dsryberg Similarity score: 0.6122

pyDeltaRCM: a flexible numerical delta model Submitting author: @amoodie Handling editor: @kbarnhart (Retired) Reviewers: @zsylvester, @jhnienhuis, @salterg Similarity score: 0.6067

⚠️ 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.

kthyng commented 3 weeks ago

Hi @tobeycarman and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

tobeycarman commented 3 weeks ago

@kthyng Thanks! re: the above issues:

One note - I just discovered an issue with Git LFS which we have been using to manage testing data. I will try to address this ASAP, but if you or any other editors run into issues with cloning or pulling from the repo, please let me know.

tobeycarman commented 2 weeks ago

@kthyng, see below for list of 5 possible reviewers, selected from the database:

kthyng commented 2 weeks ago

@tobeycarman Some questions/comments:

tobeycarman commented 2 weeks ago

@kthyng,

editorialbot commented 2 weeks ago

My name is now @editorialbot

editorialbot commented 2 weeks ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

tobeycarman commented 2 weeks ago

@editorialbot commands

editorialbot commented 2 weeks ago

Hello @tobeycarman, 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

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

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

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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

# 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
tobeycarman commented 2 weeks ago

@editorialbot generate pdf

editorialbot commented 2 weeks ago

:warning: An error happened when generating the pdf.

tobeycarman commented 3 days ago

@editorialbot generate pdf

editorialbot commented 3 days ago

:warning: An error happened when generating the pdf.

kthyng commented 2 days ago

@tobeycarman

Docker, we don't actively maintain install instructions without Docker. We found that using Docker images and containers to standardize the development environments dramatically improved the development process.

I won't block this from review based on this but this may come up again.

Empty sections in the comments, I am not sure what you are referring to?

I see I wrote comment but I meant your docs. As an example, lots of this page says "write this".

Word count, I will look into reducing it. We would gladly accept feedback on which sections reviewers find to be less relevant.

Please, follow this: https://joss.readthedocs.io/en/latest/paper.html#what-should-my-paper-contain. Information that is not in the paper can be in your docs. You probably want sections Summary, Statement of Need, maybe one more section, and Acknowledgments, maybe a figure or two. The goal is to explain the software at a high level to a general audience initially, then give just enough information at the next level for someone to know if they want more information, comparing with the relevant other packages.