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[PRE REVIEW]: Tesseract Core: Autodiff-native, self-documenting software components for Simulation Intelligence #8201

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editorialbot opened this issue May 14, 2025 · 23 comments
Open

[PRE REVIEW]: Tesseract Core: Autodiff-native, self-documenting software components for Simulation Intelligence #8201

editorialbot opened this issue May 14, 2025 · 23 comments
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pre-review Python Shell TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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Submitting author: @BoltzmannBrain (Alexander Lavin)
Repository: https://github.com/pasteurlabs/tesseract-core
Branch with paper.md (empty if default branch): joss
Version: v0.9.0
Editor: Pending
Reviewers: Pending
Managing EiC: Daniel S. Katz

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/26dba0e3ce422ffca5e6e78042ff44d9"><img src="https://joss.theoj.org/papers/26dba0e3ce422ffca5e6e78042ff44d9/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/26dba0e3ce422ffca5e6e78042ff44d9/status.svg)](https://joss.theoj.org/papers/26dba0e3ce422ffca5e6e78042ff44d9)

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

@BoltzmannBrain 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 editorialbot added pre-review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels May 14, 2025
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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

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Software report:

github.com/AlDanial/cloc v 1.98  T=0.13 s (1411.5 files/s, 156745.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          63           2806           1927          10665
Markdown                        28            588             41           1618
JSON                            35              0              0           1042
YAML                            32            164             93            850
TOML                             5             25             44            188
Bourne Shell                     5             54             16            159
Text                            13              8              0            105
TeX                              1             10              0             80
Dockerfile                       1             17             15             70
DOS Batch                        1              8              1             26
CSS                              1              3              0             12
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           186           3687           2144          14824
-------------------------------------------------------------------------------

Commit count by author:

    44	Dion Häfner
    16	github-actions[bot]
    12	Alessandro Angioi
     9	dependabot[bot]
     7	Jonathan Brodrick
     5	Niklas Heim
     3	Angela Ko
     2	Andrei Paleyes
     2	Matteo Salvador
     1	Alexander Lavin
     1	Andrin Rehmann
     1	Heiko Zimmermann
     1	Jacan Chaplais

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: Simulation intelligence: Towards a new generation ...
- No DOI given, and none found for title: Pydantic
- No DOI given, and none found for title: Neural general circulation models for weather and ...
- No DOI given, and none found for title: Solver-in-the-loop: Learning from differentiable p...
- No DOI given, and none found for title: End-to-end differentiable physics for learning and...
- No DOI given, and none found for title: Solver-in-the-loop approach to turbulence closure
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...

❌ MISSING DOIs

- 10.1103/physrevfluids.10.024605 may be a valid DOI for title: Differentiable turbulence: Closure as a partial di...
- 10.1109/hpec49654.2021.9622796 may be a valid DOI for title: A comparison of automatic differentiation and cont...
- 10.1145/3571236 may be a valid DOI for title: You only linearize once: Tangents transpose to gra...

❌ INVALID DOIs

- None

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Paper file info:

⚠️ Wordcount for paper.md is 1205

✅ The paper includes a Statement of need section

@editorialbot
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License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

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

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Five most similar historical JOSS papers:

TensorFlow.jl: An Idiomatic Julia Front End for TensorFlow
Submitting author: @malmaud
Handling editor: @arokem (Retired)
Reviewers: @jekbradbury
Similarity score: 0.6873

CoSApp: a Python library to create, simulate and design complex systems.
Submitting author: @elac-safran
Handling editor: @HaoZeke (Active)
Reviewers: @jbussemaker, @chenxinye
Similarity score: 0.6631

TLViz: Visualising and analysing tensor decomposition models with Python
Submitting author: @marieroald
Handling editor: @faroit (Active)
Reviewers: @sara-02, @yiitozer
Similarity score: 0.6623

giotto-deep: A Python Package for Topological Deep Learning
Submitting author: @matteocao
Handling editor: @osorensen (Active)
Reviewers: @EduPH, @leotrs, @ismailguzel
Similarity score: 0.6548

flowTorch - a Python library for analysis and reduced-order modeling of fluid flows
Submitting author: @AndreWeiner
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @akaptano, @JaroslavHron, @salrm8, @hkjeldsberg
Similarity score: 0.6535

⚠️ 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.

@danielskatz
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danielskatz commented May 14, 2025 •
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👋 @BoltzmannBrain - thanks for your submission.

However, I don't think I really understand what the software here is, what it is used for, or who would use it. Is there something in the documentation or repo that walks through some type of a simple research use case? The paper currently is a little too abstract for me, and adding something more specific pointing to the documentation would be helpful. I suggest this because the paper is already too long, and adding more would not be a good fit for JOSS. In fact, if there's anything in the paper that can be removed in favor of pointing to the documentation or the repo, please do that as well.

Additionally, and as a minor point in comparison, please see the JOSS example paper for how references that are directly addressed should be mentioned in the .md file.

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.

@BoltzmannBrain
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Hi @danielskatz, thank you for the speedy follow-up and helpful comments!

Yes we have tons of research use-cases:

We will address your other comments and push the updates ASAP this week.

@dionhaefner

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

@editorialbot
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Five most similar historical JOSS papers:

TensorFlow.jl: An Idiomatic Julia Front End for TensorFlow
Submitting author: @malmaud
Handling editor: @arokem (Retired)
Reviewers: @jekbradbury
Similarity score: 0.6908

CoSApp: a Python library to create, simulate and design complex systems.
Submitting author: @elac-safran
Handling editor: @HaoZeke (Active)
Reviewers: @jbussemaker, @chenxinye
Similarity score: 0.6624

Φ-ML: Intuitive Scientific Computing with Dimension Types for Jax, PyTorch, TensorFlow & NumPy
Submitting author: @holl-
Handling editor: @mstimberg (Active)
Reviewers: @wandeln, @chaoming0625, @gauravbokil8
Similarity score: 0.6577

TLViz: Visualising and analysing tensor decomposition models with Python
Submitting author: @marieroald
Handling editor: @faroit (Active)
Reviewers: @sara-02, @yiitozer
Similarity score: 0.6552

flowTorch - a Python library for analysis and reduced-order modeling of fluid flows
Submitting author: @AndreWeiner
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @akaptano, @JaroslavHron, @salrm8, @hkjeldsberg
Similarity score: 0.6487

⚠️ 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.

@dionhaefner

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Hello @dionhaefner, 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

@dionhaefner
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@editorialbot generate pdf

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

@editorialbot
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Five most similar historical JOSS papers:

TensorFlow.jl: An Idiomatic Julia Front End for TensorFlow
Submitting author: @malmaud
Handling editor: @arokem (Retired)
Reviewers: @jekbradbury
Similarity score: 0.6973

CoSApp: a Python library to create, simulate and design complex systems.
Submitting author: @elac-safran
Handling editor: @HaoZeke (Active)
Reviewers: @jbussemaker, @chenxinye
Similarity score: 0.6627

JAXbind: Bind any function to JAX
Submitting author: @roth-jakob
Handling editor: @danielskatz (Active)
Reviewers: @dfm, @hawkinsp, @wsmoses
Similarity score: 0.6505

Φ-ML: Intuitive Scientific Computing with Dimension Types for Jax, PyTorch, TensorFlow & NumPy
Submitting author: @holl-
Handling editor: @mstimberg (Active)
Reviewers: @wandeln, @chaoming0625, @gauravbokil8
Similarity score: 0.6502

SICOPOLIS-AD v2: tangent linear and adjoint modeling framework for ice sheet modeling enabled by automatic differentiation tool Tapenade
Submitting author: @Shreyas911
Handling editor: @crvernon (Active)
Reviewers: @svchb, @ifthompson
Similarity score: 0.6458

⚠️ 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.

@dionhaefner
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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.98  T=0.13 s (1413.2 files/s, 156995.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          63           2806           1927          10665
Markdown                        28            589             41           1625
JSON                            35              0              0           1042
YAML                            32            164             93            850
TOML                             5             25             44            188
Bourne Shell                     5             54             16            159
Text                            13              8              0            105
TeX                              1             10              0             80
Dockerfile                       1             17             15             70
DOS Batch                        1              8              1             26
CSS                              1              3              0             12
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           186           3688           2144          14831
-------------------------------------------------------------------------------

Commit count by author:

    46	Dion Häfner
    16	github-actions[bot]
    12	Alessandro Angioi
     9	dependabot[bot]
     7	Jonathan Brodrick
     5	Niklas Heim
     3	Angela Ko
     2	Andrei Paleyes
     2	Matteo Salvador
     1	Alexander Lavin
     1	Andrin Rehmann
     1	Heiko Zimmermann
     1	Jacan Chaplais

@editorialbot
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Paper file info:

⚠️ Wordcount for paper.md is 1227

✅ The paper includes a Statement of need section

@editorialbot
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License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

@dionhaefner
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@danielskatz Thanks for the feedback! I went ahead and added a section with more concrete example use cases to the "Statement of need", and deleted some other sections to make up for it – at least the paper didn't get even longer this way.

Let us know in case you need anything else to elucidate potential use cases or make this a better fit for JOSS.

@danielskatz
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Hi @danielskatz, thank you for the speedy follow-up and helpful comments!

Yes we have tons of research use-cases:

This is useful. Could the paper text point to this?

I'm sorry, but when I look at that page, I don't see anything about scientific machine learning or differentiable physics. Machine learning is mentioned at the very top as a motivation, but there's nothing that makes this clear. And "physics" doesn't appear in that page at all. I think this is a case where the documentation makes a lot of assumptions about the reader and their knowledge.

  • and of course more getting added to the main repo and community forum every week.

We will address your other comments and push the updates ASAP this week.

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