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[REVIEW]: ASTE: An artificial solver testing environment for partitioned coupling with preCICE #7127

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editorialbot opened this issue Aug 22, 2024 · 73 comments
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accepted C++ CMake published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Aug 22, 2024

Submitting author: @davidscn (David Schneider)
Repository: https://github.com/precice/aste
Branch with paper.md (empty if default branch): paper
Version: v3.3.0
Editor: @diehlpk
Reviewers: @asalmgren, @hverhelst
Archive: 10.18419/darus-4562

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/461395f81bcedd77828c4b44f53b7179"><img src="https://joss.theoj.org/papers/461395f81bcedd77828c4b44f53b7179/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/461395f81bcedd77828c4b44f53b7179/status.svg)](https://joss.theoj.org/papers/461395f81bcedd77828c4b44f53b7179)

Reviewers and authors:

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.)

Reviewer instructions & questions

@asalmgren & @hverhelst, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diehlpk know.

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

Checklists

📝 Checklist for @hverhelst

📝 Checklist for @asalmgren

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Hello humans, 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

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

✅ OK DOIs

- 10.12688/openreseurope.14445.2 is OK
- 10.3390/a14060166 is OK
- 10.18419/darus-4167 is OK
- 10.23967/c.coupled.2023.016 is OK
- 10.18419/opus-12128 is OK
- 10.18419/opus-10581 is OK
- 10.1007/978-3-030-47956-5_10 is OK
- 10.1002/nme.2579 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Robust and Efficient Barycentric Cell-Interpolatio...
- No DOI given, and none found for title: The Visualization Toolkit (4th ed.)
- No DOI given, and none found for title: MeTis: Unstructured Graph Partitioning and Sparse ...
- No DOI given, and none found for title: JSON for Modern C++

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.11 s (961.0 files/s, 334750.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                     8           3248           4216          17733
Python                          14            421            163           2512
JSON                             8              1              0           2086
C++                             15            266            109           1608
XML                             28            157             36           1583
Markdown                         4            122              0            359
YAML                             8              6             13            324
CMake                            2             40             64            150
TeX                              1             11              0            123
Bourne Shell                    13             41             30            100
make                             1              3              0              6
-------------------------------------------------------------------------------
SUM:                           102           4316           4631          26584
-------------------------------------------------------------------------------

Commit count by author:

   126	David Schneider
   117	Frédéric Simonis
   109	Florian Lindner
    67	Kursat Yurt
    56	Kürşat Yurt
    18	--global
    18	Frederic Simonis
     8	David Sommer
     7	Gerasimos Chourdakis
     6	Kursat_Yurt
     6	S0mmerD
     5	Kyle Davis
     4	Benjamin Uekermann
     4	Kursat
     4	dependabot[bot]
     3	Boris Martin
     1	Guillaume De Nayer
     1	Klaudius Scheufele
     1	timo-schrader
     1	uekerman

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Paper file info:

📄 Wordcount for paper.md is 1133

✅ The paper includes a Statement of need section

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License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@diehlpk
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diehlpk commented Aug 30, 2024

Hi @asalmgren, @hverhelst how is your review going?

@asalmgren
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asalmgren commented Aug 30, 2024 via email

@hverhelst
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hverhelst commented Sep 3, 2024

Review checklist for @hverhelst

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/precice/aste?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@davidscn) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@hverhelst
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I had some questions and published an issue here

@asalmgren
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@editorialbot commands

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Hello @asalmgren, 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

@asalmgren
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asalmgren commented Sep 5, 2024

Review checklist for @asalmgren

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/precice/aste?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@davidscn) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@asalmgren
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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@diehlpk
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diehlpk commented Sep 13, 2024

Hi @asalmgren how is your review going?

@hverhelst
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Hi @diehlpk , my review is finished, I would accept the software for publication.

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diehlpk commented Oct 2, 2024

Hi @asalmgren how is your review going? When do you think you can finish it?

1 similar comment
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diehlpk commented Oct 16, 2024

Hi @asalmgren how is your review going? When do you think you can finish it?

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Regarding the community guidelines -- I do not see a CONTRIBUTING.md or similar file that gives guidance to anyone wanting to contribute to the software or report bugs. I do not see this information in the README file either.

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Regarding the installation instructions -- the dependencies are clearly identified. However, if I follow the "Building and Installation" instructions I get the following error message. I'm assuming that I need to have built precice before I can build aste but that should be clearly stated in the "Building and installation" sections of the instructions.

CMake Error at CMakeLists.txt:24 (find_package):
By not providing "Findprecice.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "precice", but
CMake did not find one.

Could not find a package configuration file provided by "precice"
(requested version 3.0) with any of the following names:

preciceConfig.cmake
precice-config.cmake

Add the installation prefix of "precice" to CMAKE_PREFIX_PATH or set
"precice_DIR" to a directory containing one of the above files. If
"precice" provides a separate development package or SDK, be sure it has
been installed.

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Done! version is now v.3.3.0

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diehlpk commented Nov 12, 2024

@davidscn could you please update the title on darus to match the one of the paper?

Currently, the title is ASTE Version v3.3.0.

@davidscn
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Done! version is now v.3.3.0

The version set here has an additional dot after the v as opposed to the actual version v3.3.0

Currently, the title is ASTE Version v3.3.0.

Sorry, I solely focused on the authors and thought it would be ambiguous to use the same for the data. I contacted DaRUS and asked for fix. The fix is now published as a new (major) version of the data set. The DOI is

DOI: 10.18419/darus-4562

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diehlpk commented Nov 12, 2024

@editorialbot set v3.3.0 as version

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Done! version is now v3.3.0

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diehlpk commented Nov 12, 2024

@editorialbot set 10.18419/darus-4562 as archive

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Done! archive is now 10.18419/darus-4562

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diehlpk commented Nov 12, 2024

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

✅ OK DOIs

- 10.12688/openreseurope.14445.2 is OK
- 10.3390/a14060166 is OK
- 10.3390/mca27020031 is OK
- 10.18419/darus-4167 is OK
- 10.23967/c.coupled.2023.016 is OK
- 10.18419/opus-12128 is OK
- 10.18419/opus-10581 is OK
- 10.1007/978-3-030-47956-5_10 is OK
- 10.1002/nme.2579 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Robust and Efficient Barycentric Cell-Interpolatio...
- No DOI given, and none found for title: The Visualization Toolkit (4th ed.)
- No DOI given, and none found for title: MeTis: Unstructured Graph Partitioning and Sparse ...
- No DOI given, and none found for title: JSON for Modern C++

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6127, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Nov 12, 2024
@davidscn
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@diehlpk Thank you very much for your support and effort!

@danielskatz
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@davidscn - As track chair, I've suggested some changes in precice/aste#218 - please merge this or let me know what you disagree with, then we can proceed.

@danielskatz
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

✅ OK DOIs

- 10.12688/openreseurope.14445.2 is OK
- 10.3390/a14060166 is OK
- 10.3390/mca27020031 is OK
- 10.18419/darus-4167 is OK
- 10.23967/c.coupled.2023.016 is OK
- 10.18419/opus-12128 is OK
- 10.18419/opus-10581 is OK
- 10.1007/978-3-030-47956-5_10 is OK
- 10.1002/nme.2579 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Robust and Efficient Barycentric Cell-Interpolatio...
- No DOI given, and none found for title: The Visualization Toolkit (4th ed.)
- No DOI given, and none found for title: MeTis: Unstructured Graph Partitioning and Sparse ...
- No DOI given, and none found for title: JSON for Modern C++

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6139, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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@editorialbot accept

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Doing it live! Attempting automated processing of paper acceptance...

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Schneider
  given-names: David
  orcid: "https://orcid.org/0000-0002-3487-9688"
- family-names: Yurt
  given-names: Muhammed Kürşat
  orcid: "https://orcid.org/0000-0001-6497-3184"
- family-names: Simonis
  given-names: Frédéric
  orcid: "https://orcid.org/0000-0003-3390-157X"
- family-names: Uekermann
  given-names: Benjamin
  orcid: "https://orcid.org/0000-0002-1314-9969"
contact:
- family-names: Schneider
  given-names: David
  orcid: "https://orcid.org/0000-0002-3487-9688"
doi: 10.18419/darus-4562
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Schneider
    given-names: David
    orcid: "https://orcid.org/0000-0002-3487-9688"
  - family-names: Yurt
    given-names: Muhammed Kürşat
    orcid: "https://orcid.org/0000-0001-6497-3184"
  - family-names: Simonis
    given-names: Frédéric
    orcid: "https://orcid.org/0000-0003-3390-157X"
  - family-names: Uekermann
    given-names: Benjamin
    orcid: "https://orcid.org/0000-0002-1314-9969"
  date-published: 2024-11-14
  doi: 10.21105/joss.07127
  issn: 2475-9066
  issue: 103
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7127
  title: "ASTE: An artificial solver testing environment for partitioned
    coupling with preCICE"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07127"
  volume: 9
title: "ASTE: An artificial solver testing environment for partitioned
  coupling with preCICE"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07127 joss-papers#6141
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07127
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Nov 14, 2024
@danielskatz
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Congratulations to @davidscn (David Schneider) and co-authors on your publication!!

And thanks to @asalmgren and @hverhelst for reviewing, and to @diehlpk for editing!
JOSS depends on volunteers; we couldn't do this without you

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following

code snippets

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.07127/status.svg)](https://doi.org/10.21105/joss.07127)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.07127">
  <img src="https://joss.theoj.org/papers/10.21105/joss.07127/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07127/status.svg
   :target: https://doi.org/10.21105/joss.07127

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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Thanks again to everyone for your help and contributions!

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