[PRE REVIEW]: MapReader: v1.1.0

[editorialbot]

Submitting author: !--author-handle-->@kmcdono2<!--end-author-handle-- (Katherine McDonough) Repository: https://github.com/Living-with-machines/MapReader Branch with paper.md (empty if default branch): Version: v1.1.0 Editor: !--editor-->@emdupre<!--end-editor-- Reviewers: @geekysquirrel, @PipGrylls, @jordibc Managing EiC: Arfon Smith

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Author instructions

Thanks for submitting your paper to JOSS @kmcdono2. Currently, there isn't a JOSS editor assigned to your paper.

@kmcdono2 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]

Software report:

github.com/AlDanial/cloc v 1.88  T=2.47 s (45.4 files/s, 16533.8 lines/s)
-----------------------------------------------------------------------------------
Language                         files          blank        comment           code
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Python                              37           2577           5206           8683
Jupyter Notebook                    10              0          18199           1261
reStructuredText                    24           1176            755           1237
Markdown                            12            167              0            441
YAML                                19             79            125            431
JSON                                 4              0              0            281
TeX                                  1              9              0            103
DOS Batch                            1              8              1             26
TOML                                 1              1              2             17
Sass                                 1              3              3             12
make                                 1              4              7              9
Windows Resource File                1              0              0              4
-----------------------------------------------------------------------------------
SUM:                               112           4024          24298          12505
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1146

[editorialbot]

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

OK DOIs

- 10.1145/3557919.3565812 is OK
- 10.5281/ZENODO.7147906 is OK
- 10.1093/jvcult/vcab009 is OK
- 10.1016/j.regsciurbeco.2021.103711 is OK
- 10.48550/ARXIV.2101.12478 is OK
- 10.21105/joss.01800 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

AtlasReader: A Python package to generate coordinate tables, region labels, and informative figures from statistical MRI images Submitting author: @miykael Handling editor: @cMadan (Active) Reviewers: @andrewheusser Similarity score: 0.8078

Mapelia and friends: create 3D models from maps Submitting author: @jordibc Handling editor: @arfon (Active) Reviewers: @hugoledoux, @ThomasA Similarity score: 0.8053

cartoee: Publication quality maps using Earth Engine Submitting author: @kmarkert Handling editor: @lheagy (Retired) Reviewers: @Fil Similarity score: 0.8046

3dfier: automatic reconstruction of 3D city models Submitting author: @hugoledoux Handling editor: @arfon (Active) Reviewers: @GANys, @chenkianwee Similarity score: 0.8023

BigX: A geographical dataset visualisation tool Submitting author: @geekysquirrel Handling editor: @hugoledoux (Active) Reviewers: @liberostelios, @jvdkwast Similarity score: 0.7998

⚠️ 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.

[kmcdono2]

Suggested reviewer: Rebecca Sutton Koeser

[kthyng]

Hi @kmcdono2 and thanks for your submission. Sorry for the delay — we've decided to change which track it is in which is book-keeping on the editor side. My next step is to find an editor for this, though we have a waitlist of submissions I will add this too. Thanks for your patience.

In the meantime, please take a look at our reviewer database listed above and list 5 github handles for suggested reviewers who aren't conflicted with you (but please don't include a "@" since that will preemptively ping them). Reviewers can instead be from your extended network too.

[kthyng]

@kmcdono2 Also usually our submissions have more of a descriptive title and the version is added in a separate step at the end of the review. Could you take a look at other JOSS submission names/titles and see if you might want to add a descriptor after "MapReader"?

[kmcdono2]

@kthyng - thanks! We'll come up with an alternative subtitle this week and also make some more editor suggestions asap.

[kmcdono2]

Editor suggestions:

• rlskoeser
• SamHames
• ArcticSnow
• mikemahoney218
• PipGrylls

[kthyng]

Hi Adam! Might you edit this submission or is it too far afield for your first submission?

[kthyng]

@editorialbot invite @adamltyson as editor

[editorialbot]

Invitation to edit this submission sent!

[adamltyson]

Hi @kthyng,

This might be a bit outside my expertise, but I'm away for the next two weeks either way, sorry!

[kthyng]

@emdupre might this overlap with your neuroimaging background such that you can edit it?

[kthyng]

@editorialbot invite @emdupre as editor

[editorialbot]

Invitation to edit this submission sent!

[emdupre]

👋 Hi @kthyng, and thanks for the invitation !

This is indeed a bit outside of my expertise, but I think I should still be able to edit it. I'll go ahead and get this started !

[emdupre]

@editorialbot assign @emdupre as editor

[editorialbot]

Assigned! @emdupre is now the editor

[emdupre]

👋 Hi @kmcdono2, and thanks for your submission to JOSS !

I see that you have suggested Rebecca Sutton Koeser as a reviewer. If you have suggestions for additional potential reviewers, please let me know by listing their names or GitHub handles (without the @, so they don't receive a notification) here. This would be particularly helpful as I don't have directly overlapping expertise with this project, so it's useful to know who you would consider to be a good reviewer for the work !

You can suggest reviewers from any relevant project, though we often recommend starting with this database of people who have already agreed to review for JOSS.

I'll put together a list of folks to reach out to as reviewers based on these suggestions and my own recommendations. I'll update this thread with that outreach.

[kmcdono2]

Hi @emdupre - Thanks for being our editor! Sorry for the mixup, I meant those as suggestions for reviewers, not editors. Now that you're the editor, this list below still applies for reviewers!

rlskoeser SamHames ArcticSnow mikemahoney218 PipGrylls

[kmcdono2]

PS - we are still working on a new subtitle

[kthyng]

thanks @emdupre! And I'll note that mikemahoney218 is actually a new editor to JOSS so not a great choice for reviewer as he's got other things going on with JOSS now.

[emdupre]

👋 Hi @SamHames, @geekysquirrel, @Anaphory,

Would you be willing to review MapReader: A computer vision pipeline for exploring and analyzing images at scale for JOSS (the Journal of Open Source Software)?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here.

The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-papers/blob/joss.06168/joss.06168/10.21105.joss.06168.pdf

If you're available to review this work within the next month—or six weeks, at most—please let me know and I'll add you as a reviewer.

Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you for considering !

[emdupre]

👋 Hi @kmcdono2 ! While we're waiting to hear back from potential reviewers, I wanted to quickly check in re: a few details on the software paper.

1. Have you decided on a new subtitle for this submission ? I noticed a subtitle in the documentation, which I've included in the invitation to reviewers. This isn't in the paper draft, though, so I wanted to explicitly check with you.
2. In the listed author affiliations, please explicitly write out all acronyms; e.g., "UK" should be "United Kingdom." Please also include the city for each affiliation such that all affiliations follow "Department, Institute/Univ., City, Country" as closely as possible.
3. Your references are not currently rendering in the compiled PDF. Looking at the raw markdown file, I believe this is because you've enclosed them in backticks. If you remove these, I expect the references should compile correctly ! Please see the example JOSS submission for more examples on how these should be included.

If you have any questions, of course, please don't hesitate to ask !

[geekysquirrel]

Hm I'm not a computer vision expert but experienced in geospatial software and would be happy to review.

[emdupre]

Thank you, @geekysquirrel ! We don't expect reviewers to be experts in all areas of the submission, but you have very relevant expertise that I know would be appreciated in this review of MapReader.

I'll add you as a reviewer on this issue now. Once we have a sufficient number of reviewers, I'll open a dedicated review issue 🚀

[emdupre]

@editorialbot add @geekysquirrel as reviewer

[editorialbot]

@geekysquirrel added to the reviewers list!

[kmcdono2]

hi! Could I request that we prioritize asking rlskoeser to review? Thanks! Working on your other queries this Thursday.

[emdupre]

Hi @kmcdono2, thanks for your reply ! rlskoeser is actually already reviewing a JOSS submission, so we prioritize reviewers who are not actively managing other reviews.

I will, though, be sending out additional review invitations shortly ; we may ask rlskoeser to take on this additional review if no other suitable reviewers are available.

[Anaphory]

Hi @emdupre, as much as I like JOSS and would like to help out I'm unfortunately not able to review in the forseeable future.

[emdupre]

Thank you for letting us know, @Anaphory ! If you'd like me to remove you from the JOSS reviewer database, please let me know. Otherwise, feel free to mute this issue so you don't receive any additional pings !

[emdupre]

👋 Hi @PipGrylls, @KMarkert,

Would you be willing to review MapReader: Open software for the visual analysis of maps for JOSS (the Journal of Open Source Software)?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here.

The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-papers/blob/joss.06168/joss.06168/10.21105.joss.06168.pdf

If you're available to review this work within the next month—or six weeks, at most—please let me know and I'll add you as a reviewer.

Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you for considering !

[kmcdono2]

@emdupre - the issues with the subtitle, affiliations, and references have been fixed and updated.

[emdupre]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

BigX: A geographical dataset visualisation tool Submitting author: @geekysquirrel Handling editor: @hugoledoux (Active) Reviewers: @liberostelios, @jvdkwast Similarity score: 0.8229

WhaleMap: a tool to collate and display whale survey results in near real-time Submitting author: @hansenjohnson Handling editor: @KristinaRiemer (Retired) Reviewers: @pjbouchet, @mcsiple Similarity score: 0.8207

open_iA: A tool for processing and visual analysis of industrial computed tomography datasets Submitting author: @codeling Handling editor: @katyhuff (Retired) Reviewers: @trallard, @behollister Similarity score: 0.8196

Minerva: a light-weight, narrative image browser for multiplexed tissue images Submitting author: @thejohnhoffer Handling editor: @jni (Retired) Reviewers: @will-moore, @sofroniewn Similarity score: 0.8178

Mapelia and friends: create 3D models from maps Submitting author: @jordibc Handling editor: @arfon (Active) Reviewers: @hugoledoux, @ThomasA Similarity score: 0.8176

⚠️ 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.

[PipGrylls]

Hello, Very happy to review this. I am busy until March but I can try and block a day or two early/mid march to give it the time it deserves. Let me know if this is okay. Best, Pip

[emdupre]

Thank you, @PipGrylls ! If you can provide a review within 4 weeks, we'd greatly appreciate it ! And early March is well within that timeline 🙂

I'll add you as a reviewer on this issue now. Once we have a sufficient number of reviewers, I'll open a dedicated review issue 🚀

[emdupre]

@editorialbot add @PipGrylls as reviewer

[editorialbot]

@PipGrylls added to the reviewers list!

[emdupre]

👋 Hi @SamHames, @KMarkert, @jordibc,

Would you be willing to review MapReader: Open software for the visual analysis of maps for JOSS (the Journal of Open Source Software)?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here.

The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-papers/blob/joss.06168/joss.06168/10.21105.joss.06168.pdf

If you're available to review this work within the next month—or six weeks, at most—please let me know and I'll add you as a reviewer.

Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you for considering !

[geekysquirrel]

Hi all, not sure where the best place to say this is but I've had an initial play and I've run into some issues with the installation that required a bit of fiddling so I think the other reviewers might appreciate a heads up:

The README suggests to install using python 3.8, which works for the most part but when it gets to installing Cartopy, it fails because the latest version requires minimum 3.9. I know it's not a dependency but without it, some of the worked examples are not as useful, so I reckon it should be installed. I originally tried with 3.11 which didn't work but I could get things running with 3.9.

Also I think it'd be good to update the docs to say that some of the examples (and indeed the tool and its dependencies) require quite a bit of disk space and downloads, so in case your machine is a bit older and/or you're not on a fast connection I'd set some time aside to run the downloads - one of them took almost an hour for me.

[emdupre]

Thank you, @geekysquirrel !

I'm having a little bit of trouble identifying a third reviewer, and I know that this is holding up your and @PipGrylls 's reviews. I'll continue trying to find suitable, available reviewers this week, but I'll plan to open the official review issue on Friday regardless.

[emdupre]

👋 Hi @jordibc, @ajoer,

Would you be willing to review MapReader: Open software for the visual analysis of maps for JOSS (the Journal of Open Source Software)?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here.

The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-papers/blob/joss.06168/joss.06168/10.21105.joss.06168.pdf

If you're available to review this work within the next month—or six weeks, at most—please let me know and I'll add you as a reviewer.

Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you for considering !

[jordibc]

Hi @emdupre ! Sorry for the delay. Yes, I am available to review this work within the next month if you are still interested.

[emdupre]

Thank you, @jordibc ! I'll go ahead and add you as a reviewer on this submission now.

We'll then have a sufficient number of reviewers, so I'll open a dedicated review issue ! 🚀

Thank you for considering, @ajoer, @SamHames, @KMarkert !