[PRE REVIEW]: DTCC Builder: A mesh generator for automatic, efficient, and robust mesh generation for large-scale city modeling and simulation

[editorialbot]

Submitting author: !--author-handle-->@alogg<!--end-author-handle-- (Anders Logg) Repository: https://gitlab.com/dtcc-platform/dtcc-builder.git Branch with paper.md (empty if default branch): joss-2022 Version: 1.0.0 Editor: !--editor-->@crvernon<!--end-editor-- Reviewers: @pralitp, @ifthompson Managing EiC: Daniel S. Katz

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

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[editorialbot]

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[editorialbot]

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[danielskatz]

@editorialbot set main as branch

[editorialbot]

Done! branch is now main

[danielskatz]

@editorialbot check repository

[danielskatz]

@editorialbot set paper-joss-2022 as branch

[danielskatz]

👋 @alogg - note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it. Please feel free to make changes to your .md file, then use the command @editorialbot generate pdf to make a new PDF. editorialbot commands need to be the first entry in a new comment.

Once that works, you should also use the command @editorialbot check references to check the references in the paper, then work on any problems that editorialbot suggests, noting that some may be incorrect. After you make changes to your .bib file, use the command @editorialbot check references to check again, and the command @editorialbot generate pdf after making changes to the .md file or when the references are right to make a new PDF.

[danielskatz]

@alogg - we also have a really weird bug that happens when the branch name (paper-joss-2022) is the same as the folder name the paper is in on the repo. (doc/paper-joss-2022) that prevents some of our automated checking from working. Can you change one of these to something different and let me know that you have done so? (We are also working on fixing this bug)

[alogg]

@danielskatz Weird... It worked fine before we submitted (using your Docker build script). Could it be related to the branch naming?

I have now renamed the branch paper-joss-2022 --> joss-2022.

[alogg]

@editorialbot set joss-2022 as branch

[editorialbot]

Done! branch is now joss-2022

[alogg]

@editorialbot check repository

[danielskatz]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[danielskatz]

@editorialbot set main as branch

[editorialbot]

Done! branch is now main

[danielskatz]

@editorialbot check repository

[danielskatz]

@alogg - the error in the paper includes

(tmp/6c4fc491ef3d472a9f9eb67cc731b1d1/doc/paper-joss-2022/paper.md): found a tab character that violate indentation while scanning a plain scalar at line 16 column 11

[danielskatz]

@editorialbot set joss-2022 as branch

[editorialbot]

Done! branch is now joss-2022

[alogg]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[danielskatz]

I now see

Problem with ORCID (FIXME) for Dag Wästberg. ORCID looks malformed (Theoj::Error)

[alogg]

@danielskatz There was a problem with some tabs in place of spaces in the paper.md. I also noticed the missing ORCID. Will add now (was sure I had fixed it before).

Why doesn't the Docker command we used to test before submission report the same errors?

[alogg]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[alogg]

Hmm... Missing ORCID added but don't understand new error message:

Metadata created for paper: DTCC Builder: A mesh generator for automatic, efficient, and robust mesh generation for large-scale city modeling and
simulation
Error: Unable to process file command 'output' successfully.
Error: Invalid format 'simulation'

Seems last word of title is line-wrapped but it's not wrapped in my editor.

[danielskatz]

👋 @xuanxu - can you take a look at this?

[arfon]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=2.20 s (89.9 files/s, 84250.2 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
JSON                             13              0              0         136731
C/C++ Header                     94           6098           5423          32299
C++                              15            276            434           1249
Bourne Again Shell               21            149             98            716
Python                            9            165            110            468
Markdown                          6            146              0            415
CMake                            24             53             84            242
Bourne Shell                      6             11              1             98
XML                               3              0              0             86
YAML                              4             12              8             83
TeX                               1             10              0             75
Dockerfile                        1             12             23             21
make                              1              0              0              2
--------------------------------------------------------------------------------
SUM:                            198           6932           6181         172485
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 730

[arfon]

Why doesn't the Docker command we used to test before submission report the same errors?

@tarleb – is the Docker command/GitHub Action less sensitive than the GitHub Action we're running here?

[xuanxu]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[tarleb]

It shouldn't. The main difference to running it in the docker container is metadata handling, so my guess is that this is the issue here.

[xuanxu]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[tarleb]

The YAML contains tab characters. @alogg, could you try to replace those with the appropriate amount of spaces?

Never mind, I was using the wrong branch. It is already fixed in joss-2022.

[xuanxu]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[xuanxu]

@editorialbot generate pdf

Cause of the error after some digging: title was too long for our parser, that was adding newlines after 128 characters. Should be fixed now.

[editorialbot]

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

[danielskatz]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.2148/benv.46.4.547 is OK
- 10.21105/joss.02866 is OK
- 10.1186/s40965-019-0064-0 is OK

MISSING DOIs

- 10.3389/fbuil.2022.899332 may be a valid DOI for title: Towards Automatic Reconstruction of 3D City Models Tailored for Urban Flow Simulations
- 10.1007/bfb0014497 may be a valid DOI for title: Triangle: Engineering a 2D Quality Mesh Generator and Delaunay Triangulator

INVALID DOIs

- None

[danielskatz]

👋 @alogg - While I look for an editor, 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.

[danielskatz]

Also, should the first reference have some URL associated?

[danielskatz]

👋 @crvernon - Do you think you could edit this submission? It might be a little outside your area, but I'm hopeful :)

[danielskatz]

@editorialbot invite @crvernon as editor

[editorialbot]

Invitation to edit this submission sent!

[crvernon]

@danielskatz happy to help! I'll kick things off after I handle a few things this morning.