Closed whedon closed 2 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dirmeier, @StefanOlin it looks like you're currently assigned to review this paper :tada:.
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PDF failed to compile for issue #3631 with the following error:
Can't find any papers to compile :-(
Software report (experimental):
github.com/AlDanial/cloc v 1.88 T=0.23 s (964.1 files/s, 234167.1 lines/s)
--------------------------------------------------------------------------------
Language files blank comment code
--------------------------------------------------------------------------------
C/C++ Header 58 4273 4851 17680
C++ 83 1283 1608 7174
SVG 12 0 0 7161
TOML 34 763 535 2750
Markdown 11 565 0 1745
TeX 1 94 0 1074
CMake 8 205 231 864
XML 1 1 0 537
YAML 5 25 58 452
Rmd 1 25 29 173
R 4 34 51 158
Bourne Again Shell 2 28 18 76
JSON 1 0 0 44
Bourne Shell 2 9 5 22
make 1 5 10 9
Python 1 3 18 6
--------------------------------------------------------------------------------
SUM: 225 7313 7414 39925
--------------------------------------------------------------------------------
Statistical information for the repository '6aebd874519ee052772ef905' was
gathered on 2021/08/18.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Unknown 1 0 2 0.00
Wolfgang Pappa 131 7195 2472 7.55
Wolfgang Traylor 519 59152 37701 75.65
wolfgangp 32 16225 5273 16.79
Below are the number of rows from each author that have survived and are still
intact in the current revision:
Author Rows Stability Age % in comments
Wolfgang Pappa 1434 19.9 41.6 46.03
Wolfgang Traylor 34079 57.6 22.3 15.78
wolfgangp 1383 8.5 43.4 31.60
Failed to discover a valid open source license.
@whedon generate pdf from branch joss-paper
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Failed to discover a valid open source license.
See https://github.com/openjournals/joss-reviews/issues/3450#issuecomment-874160752
:wave: @dirmeier, please update us on how your review is going (this is an automated reminder).
:wave: @StefanOlin, please update us on how your review is going (this is an automated reminder).
I currently don't have access to a computer where I can compile and run the code, not sure when I'm allowed back in the office, but it won't be this month (September).
Den ons 1 sep. 2021 kl 17:28 skrev whedon @.***>:
👋 @StefanOlin, please update us on how your review is going (this is an automated reminder).
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.
-- Stefan Olin Researcher Department of Physical Geography and Ecosystem Science Lund University
@. @.
I currently don't have access to a computer where I can compile and run the code, not sure when I'm allowed back in the office, but it won't be this month (September). Den ons 1 sep. 2021 kl 17:28 skrev whedon @.>: … 👋 @StefanOlin, please update us on how your review is going (this is an automated reminder). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. -- Stefan Olin Researcher Department of Physical Geography and Ecosystem Science Lund University @. @.***
@StefanOlin Thanks for the update.
Hello, sorry for the delay. I'll finish the review this weekend.
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Ciao @diehlpk, you can find my reviews here: https://github.com/wtraylor/modular_megafauna_model/issues/51, https://github.com/wtraylor/modular_megafauna_model/issues/52
Cheers, S
@wtraylor please have a look at these comments. Please ping the reviewer once you are done.
@dirmeier Thank you very much for the review. I will get to read and respond to the comments by the end of October, when I am back from vacation.
I currently don't have access to a computer where I can compile and run the code, not sure when I'm allowed back in the office, but it won't be this month (September). Den ons 1 sep. 2021 kl 17:28 skrev whedon @.**>: … wave @StefanOlin, please update us on how your review is going (this is an automated reminder). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. -- Stefan Olin Researcher Department of Physical Geography and Ecosystem Science Lund University @.** @.***
@StefanOlin Thanks for the update.
@StefanOlin Any news from your side?
:wave: @dirmeier, please update us on how your review is going (this is an automated reminder).
@dirmeier Thank you very much for the review. I will get to read and respond to the comments by the end of October, when I am back from vacation.
@wtraylor Please let us know once you finished the review.
@StefanOlin How is your review going?
@wtraylor How is the editing going?
@wtraylor Could you might recommend some additional reviewers?
How is the editing going?
@diehlpk Thanks for checking in. I have adopted the (minor) changes suggested by @dirmeier.
Could you might recommend some additional reviewers?
I think I have tapped most of my network already, but I will try to come up with other suggestions.
@whedon generate pdf
PDF failed to compile for issue #3631 with the following error:
Can't find any papers to compile :-(
@whedon generate pdf from branch joss-paper
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Thanks for the updates to code and paper @wtraylor
Hi @amadeusine @no @sa501428 @luciorq @dilawar would you be interest to review this paper?
@diehlpk I am happy to review this work.
@whedon add @dilawar as reviewer
OK, @dilawar is now a reviewer
@whedon commands
Here are some things you can ask me to do:
# List all of Whedon's capabilities
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# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer
# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer
# Re-invite a reviewer (if they can't update checklists)
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@whedon remove @username as reviewer
# List of editor GitHub usernames
@whedon list editors
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@whedon list reviewers
# Change editorial assignment
@whedon assign @username as editor
# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive
# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version
# Open the review issue
@whedon start review
EDITORIAL TASKS
# All commands can be run on a non-default branch, to do this pass a custom
# branch name by following the command with `from branch custom-branch-name`.
# For example:
# Compile the paper
@whedon generate pdf
# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name
# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks
# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon recommend-accept
# Ask Whedon to check the references for missing DOIs
@whedon check references
# Ask Whedon to check repository statistics for the submitted software
@whedon check repository
EiC TASKS
# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor
# Reject a paper
@whedon reject
# Withdraw a paper
@whedon withdraw
# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true
@whedon remove @StefanOlin as reviewer
OK, @StefanOlin is no longer a reviewer
@StefanOlin I removed you as a reviewer, since I have not heard back from you in a while. If you are still interested, I will add you again.
@diehlpk I am happy to review this work.
@dilawar Thanks, I added you as the second reviewer.
How is the editing going?
@diehlpk Thanks for checking in. I have adopted the (minor) changes suggested by @dirmeier.
Could you might recommend some additional reviewers?
I think I have tapped most of my network already, but I will try to come up with other suggestions.
@wtraylor I found a new reviewer and we seem to be good again.
MMM is a very high-quality library with an excellent user and API documentation. The repository follows state-of-the-art DevOps. The library is a step towards a critical and hard problem of validating assumptions and discovering missing parameters while modeling a complex system. The library can also serve as a very useful pedagogical tool in Ecology class (I'd have certainly enjoyed seeing some simulations of important ideas).
The author has designed the library to be (C++) user-friendly by choosing a modern build system (CMake). I also appreciate in-source dependencies and choosing an easy-to-read TOML over often used but hardly human-readable XML for user-program interaction.
The CI/CD pipeline is comprehensive. It not only tests for the correctness, but also for memory leaks and lint errors. Tooling is provided for code-formatting.
Contribution guidelines are clear. The author has also set up a social channel (matrix) to engage with the users.
It is heartening to an academic software built with so much care. I wholeheartedly recommend publication of this library.
Following are a few more comments and a question.
Using first time: It was a breeze to build the library. All CMake options (i.e., -DBUILD_DOC
and -DBUILD_TESTING
) worked as expected. Demo also ran fine. After the run, I was asked to install R to see the plots. I installed R and required dependencies (including Pandoc) and managed to see the plots. Perhaps, the author would like to add expected results (plots) to the demo documentation.
[x] Following lines from the paper has confused me:
Here, MMM is coupled with LPJ-GUESS [refs], using daily grass growth (Boke-Olén et al., 2018). LPJ-GUESS is proprietary software and not publicly available.
Is LPJ-GUESS a hard dependency? I guess not because I could run megafauna_demo_simulator
without installing LPJ-GUESS. However, I am under the impression that it is an optional dependency and can be used along with HMM? If yes, then there is no indication of it in the documentation. Moreover, the educational version (binary) of LPJ-GUESS is only available for Windows. It is not clear how LPJ-GUESS and MMM will interact with each (if they do).
@dilawar Thanks for the quick review time.
@wtraylor Could you please have a look by Friday, so we can finalize the paper?
@whedon generate pdf from branch joss-paper
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
Submitting author: @wtraylor (Wolfgang Traylor) Repository: https://github.com/wtraylor/modular_megafauna_model Version: v1.1.3 Editor: @diehlpk Reviewers: @dirmeier, @dilawar Archive: 10.5281/zenodo.5779267
:warning: JOSS reduced service mode :warning:
Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.
Status
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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.)
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@dirmeier & @dilawar, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
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✨ 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 ✨
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Conflict of interest
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Software paper
Review checklist for @dilawar
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Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper