pyOpenSci/software-submission

FElupe Submission

adtzlr opened this issue · 24 comments

adtzlr commented

Submitting Author: Andreas Dutzler (@adtzlr)
All current maintainers: (@adtzlr)
Package Name: FElupe
One-Line Description of Package: Finite element analysis for continuum mechanics of solid bodies.
Repository Link: https://github.com/adtzlr/felupe
Version submitted: v9.0.0 v9.1.0 (updated on 2024-11-23)
EiC: @cmarmo
Editor: @tkoyama010
Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD
JOSS DOI: TBD
Version accepted: TBD
Date accepted (month/day/year): TBD

Code of Conduct & Commitment to Maintain Package

Description

  • Include a brief paragraph describing what your package does:

FElupe is a Python finite element analysis package focusing on the formulation and numerical solution of nonlinear problems in continuum mechanics of solid bodies. Easy-to-learn classes are provided to simulate the nonlinear deformation of hyperelastic solid bodies, see Getting Started. The constitutive material formulation of a hyperelastic solid body may be defined by its strain energy density function only (gradient and hessian are carried out by optional automatic differentiation). Strain energy functions for selected hyperelastic models are included. FElupe has only few dependencies, is a pure Python package but is also efficient enough for rubber-like structures. Several extension packages exist, e.g. to use a different automatic differentation backend or an interactive plot window.

grafik

Scope

  • Please indicate which category or categories.
    Check out our package scope page to learn more about our
    scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry):

    • Data retrieval
    • Data extraction
    • Data processing/munging
    • Data deposition
    • Data validation and testing
    • Data visualization1
    • Workflow automation
    • Citation management and bibliometrics
    • Scientific software wrappers
    • Database interoperability

Domain Specific

  • Geospatial
  • Education

Community Partnerships

If your package is associated with an
existing community please check below:

  • For all submissions, explain how and why the package falls under the categories you indicated above. In your explanation, please address the following points (briefly, 1-2 sentences for each):

    • Who is the target audience and what are scientific applications of this package?

FElupe is great for teaching, scientific research as well as for mid-sized industry-problems related to the deformation of solid bodies. It has already been used in scientific articles which are listed in the README.

  • Are there other Python packages that accomplish the same thing? If so, how does yours differ?

Yes, there is scikit-fem, FEniCS, GetFEM and probably some others. While scikit-fem is definitely lightweight and easy-to-install, I found out that it is typically too slow for running hyperelastic simulations, e.g. the deformation of a rubber-like solid (see also my initial questions / posts in kinnala/scikit-fem#616). FEniCS on the other hand has a great community but the install-entry-barrier is much higher compared to a pure PyPI Python package. The same also applies for GetFEM, because both projects provide Python packages for their compiled code. I was looking for a more lightweight Python package but also efficient enough for simulating typical rubber-like structures. Hence, I started working on FElupe in 2021.

Instead of assembling general weak forms like scikit-fem and FEniCS, FElupe follows a more Abaqus-like UMAT (user material) approach for constitutive material formulations of solid bodies, see e.g. ConstitutiveMaterial or Hyperelastic.

  • If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted:

#211

Technical checks

For details about the pyOpenSci packaging requirements, see our packaging guide. Confirm each of the following by checking the box. This package:

  • does not violate the Terms of Service of any service it interacts with.
  • uses an OSI approved license.
  • contains a README with instructions for installing the development version.
  • includes documentation with examples for all functions.
  • contains a tutorial with examples of its essential functions and uses.
  • has a test suite.
  • has continuous integration setup, such as GitHub Actions CircleCI, and/or others.

Publication Options

JOSS Checks
  • The package has an obvious research application according to JOSS's definition in their submission requirements. Be aware that completing the pyOpenSci review process does not guarantee acceptance to JOSS. Be sure to read their submission requirements (linked above) if you are interested in submitting to JOSS.
  • The package is not a "minor utility" as defined by JOSS's submission requirements: "Minor ‘utility’ packages, including ‘thin’ API clients, are not acceptable." pyOpenSci welcomes these packages under "Data Retrieval", but JOSS has slightly different criteria.
  • The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
    Note: Will be added soon - not present in the submitted v9.0.0. Edit: Added in v9.1.0 at paper/paper.md, a compiled PDF version of the draft is available here.
  • The package is deposited in a long-term repository with the DOI: https://zenodo.org/doi/10.5281/zenodo.4817406

Note: JOSS accepts our review as theirs. You will NOT need to go through another full review. JOSS will only review your paper.md file. Be sure to link to this pyOpenSci issue when a JOSS issue is opened for your package. Also be sure to tell the JOSS editor that this is a pyOpenSci reviewed package once you reach this step.

Are you OK with Reviewers Submitting Issues and/or pull requests to your Repo Directly?

This option will allow reviewers to open smaller issues that can then be linked to PR's rather than submitting a more dense text based review. It will also allow you to demonstrate addressing the issue via PR links.

  • Yes I am OK with reviewers submitting requested changes as issues to my repo. Reviewers will then link to the issues in their submitted review.

Confirm each of the following by checking the box.

  • I have read the author guide.
  • I expect to maintain this package for at least 2 years and can help find a replacement for the maintainer (team) if needed.

Please fill out our survey

P.S. Have feedback/comments about our review process? Leave a comment here

Editor and Review Templates

The editor template can be found here.

The review template can be found here.

Footnotes

  1. Please fill out a pre-submission inquiry before submitting a data visualization package. ↩

cmarmo commented

Editor in Chief checks

Hi @adtzlr! Thank you for submitting your package for pyOpenSci review.
Sorry to have kept you waiting!

Below are the basic checks that your package needs to pass to begin our review.
If some of these are missing, we will ask you to work on them before the review process begins.

Please check our Python packaging guide for more information on the elements below.

  • Installation The package can be installed from a community repository such as PyPI (preferred), and/or a community channel on conda (e.g. conda-forge, bioconda).
    • The package imports properly into a standard Python environment import package.
  • Fit The package meets criteria for fit and overlap.
  • Documentation The package has sufficient online documentation to allow us to evaluate package function and scope without installing the package. This includes:
    • User-facing documentation that overviews how to install and start using the package.
    • Short tutorials that help a user understand how to use the package and what it can do for them.
    • API documentation (documentation for your code's functions, classes, methods and attributes): this includes clearly written docstrings with variables defined using a standard docstring format.
  • Core GitHub repository Files
    • README The package has a README.md file with clear explanation of what the package does, instructions on how to install it, and a link to development instructions.
    • Contributing File The package has a CONTRIBUTING.md file that details how to install and contribute to the package.
    • Code of Conduct The package has a CODE_OF_CONDUCT.md file.
    • License The package has an OSI approved license.
      NOTE: We prefer that you have development instructions in your documentation too.
  • Issue Submission Documentation All of the information is filled out in the YAML header of the issue (located at the top of the issue template).
  • Automated tests Package has a testing suite and is tested via a Continuous Integration service.
  • Repository The repository link resolves correctly.
  • Package overlap The package doesn't entirely overlap with the functionality of other packages that have already been submitted to pyOpenSci.
  • Archive (JOSS only, may be post-review): The repository DOI resolves correctly.
  • Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?
  • Initial onboarding survey was filled out
    We appreciate each maintainer of the package filling out this survey individually. 🙌
    Thank you authors in advance for setting aside five to ten minutes to do this. It truly helps our organization. 🙌

Editor comments

Your package is already in great shape! Congratulation!
While my background is quite far from continuum mechanics of solid bodies, I particularly enjoyed the documentation and the graphical examples.

Here some clarifications about the unchecked boxes:

  • your README.md is very detailed but it is missing a link to the development instructions: in fact there are no development instructions in the documentation. Do you mind adding some? This will also allows you to link them in the CONTRIBUTING.md file.
  • Issue templates are not available in the .github repository: as your CONTRIBUTING.md clearly defines different kind of contributions, then issues, creating the templates will direct the contributor to the right type of feedback.
  • It looks like the majority of the links in the CONTRIBUTING.md gives a 404 not found error. Do you mind checking them?

Once those items are fixed we probably already have an editor for your submission... 🚀

adtzlr commented

Thank you very much @cmarmo for the basic checks and your detailed comments on what is missing. I'll enhance the mentioned files and add the missing issue templates.

Thank you also for your kind words on the docs ✍🏻! The graphical examples are implemented by PyVista for Sphinx and Sphinx-Gallery - its plot-directive is a really great feature.

... ⌛⌛⌛ ...

Note: All items are fixed! 🎉🎉🎉

  • The development install instructions are added to the docs and a link to it is added in README.md and CONTRIBUTING.md.
  • Issue templates are now available for bug reports and enhancement suggestions; questions are left unchanged as discussions (I'd like to keep them separated, this is now mentioned in CONTRIBUTING.md).
  • Links are fixed in CONTRIBUTING.md.
cmarmo commented

Thank you @adtzlr for your prompt reaction!
I am happy to announce that @tkoyama010 will serve as editor for your submission.
I am letting him introduce himself here and wishing a kind review process to everyone!

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adtzlr commented

Thank you @tkoyama010 for taking your time to serve as an editor for this review, that's great 🥳 🚀. If you have any initial questions, please let me know!

  • 👍1
tkoyama010 commented

@cmarmo I have completed the review by taking over your checklist. Please tell us the flow from here.

cmarmo commented

Thank you @tkoyama010 for following-up! Now the hard part will start... We need to look for reviewers for the package.
I have added you to the editor's Slack channel, so feel free to chat there: we can check in our pool of reviewers if some of them fit this package.

adtzlr commented

Hey @cmarmo and @tkoyama010!

In the meantime we prepared a draft paper 📝 for JOSS (meanwhile located in a private repo 🔒). Do you think it is okay to already include it in the FElupe-repo or better wait until the PyOpenSci review is finished?

Why do you require that the paper must be ...in the package root or in inst/? There are a lot of published papers which have their paper located at subfolders, like paper/paper.md (I checked a few of the latest published papers).

🙏🏻 Thank you! 🙏🏻

cmarmo commented

In the meantime we prepared a draft paper 📝 for JOSS (meanwhile located in a private repo 🔒). Do you think it is okay to already include it in the FElupe-repo or better wait until the PyOpenSci review is finished?

Please, add the paper to the repo, so our reviewers can have a look at it, this will speed up things for the JOSS submission.

Why do you require that the paper must be ...in the package root or in inst/? There are a lot of published papers which have their paper located at subfolders, like paper/paper.md (I checked a few of the latest published papers).

euh .... 🤔 I cannot find an explanation for that... I suggest you to follow JOSS requirements, while we clarify this.

Thank you!

adtzlr commented

Hi @tkoyama010, @cmarmo!

The draft for the FElupe JOSS-paper is ready and it is included in the repo paper/paper.md 📃 . Meanwhile, a compiled PDF is available here. A new version of FElupe is available since the initial submission, I've updated the submitted version from 9.0.0 to 9.1.0 - I hope this is fine. Feel free to switch back if needed!

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