scientificcomputing / scientificcomputing.github.io Goto Github PK

For journals that don't specify explicitly how to reference your code, it would be nice to have a recommendation on the github pages for how this should be done. Providing an example paper could be one way of showing this.

Describe new/missing feature

We would like people to create releases / tags but we haven't written about this yet.

Suggestion user interface

No response

Title

Using data from other workflows

Link

https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#using-data-from-the-triggering-workflow

Details

We should write about this.
Currently used in https://github.com/scientificcomputing/example-python-package/tree/dokken/upload_artifact_to_book
To add coverage reports to the jupyter-book

Instead of splitting the information over three repos: scientificcomputing.github.io, paper-with-code and reproducibility, we should merge then into a single repository.

We currently have a lot of nice templates but we should add a recipe for what do to once you have created a new repository with that template. For example

1. Click on the Use this template button - specify the name of the repo, add a description and decide whether to make it public or private. If you make it private you can make it public later
2. Remove these files...
3. Change these files
4. Enable github pages ...
5. Etc

Add these links to repositories
https://documentation.sigma2.no/files_storage/nird/access.html
https://dataverse.no

We should have a page where we explain a little bit what we are working on in ComPhy, SCAN and HPC. Having some figures from simulations and some figures of the people would also be good.

As this webpage is probably only going to contain standard markdown and not python files, I guess we should use the official actions:

• https://github.com/actions/upload-pages-artifact
• https://github.com/actions/deploy-pages
  What do you think @finsberg ?

Describe new/missing feature

We could add tox as an option

Suggestion user interface

No response

As we want to make this easy to contribute to we should add guidelines, and instructions on how to use Pre-commit hooks

Title

Medical image registration using optimal control of a linear hyperbolic transport equation with a DG discretization

Link

https://github.com/JohannesHaubner/mapMRI

Bibliography

@misc{zapf2023medical,
      title={Medical image registration using optimal control of a linear hyperbolic transport equation with a DG discretization}, 
      author={Bastian Zapf and Johannes Haubner and Lukas Baumgärtner and Stephan Schmidt},
      year={2023},
      eprint={2305.03020},
      archivePrefix={arXiv},
      primaryClass={math.NA}
}

Add link to: https://citation-file-format.github.io/cff-initializer-javascript/#/start

We should create research objects and connect each paper to https://www.openaire.eu

Title

HAZniCS - Software Components for Multiphysics Problems

Link

https://github.com/anabudisa/HAZniCS-examples

Bibliography

@misc{budisa2022,
  doi = {10.48550/ARXIV.2210.13274},  
  url = {https://arxiv.org/abs/2210.13274},
  author = {Budisa, Ana and Hu, Xiaozhe and Kuchta, Miroslav and Mardal, Kent-Andre and Zikatanov, Ludmil},
  keywords = {Numerical Analysis (math.NA), FOS: Mathematics, FOS: Mathematics, G.1.8; G.4, 65-04, 65N55, 65F08, 65H10},
  title = {{HAZniCS -- Software Components for Multiphysics Problems}},
  publisher = {arXiv},
  year = {2022},
  copyright = {arXiv.org perpetual, non-exclusive license}
}

Title

An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain

Link

https://github.com/CINPLA/edNEGmodel_analysis

Bibliography

@article{saetra2021,
    doi = {10.1371/journal.pcbi.1008143},
    author = {Sætra, Marte J. AND Einevoll, Gaute T. AND Halnes, Geir},
    journal = {PLOS Computational Biology},
    publisher = {Public Library of Science},
    title = {An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain},
    year = {2021},
    month = {07},
    volume = {17},
    pages = {1-45},
    number = {7}
}

Missing - in jupyterbook twice.

This software is related to the paper HAZniCS - Software Components for Multiphysics Problems and the demos in the paper are already linked in one of the "add-repo" issues here.

The software can be installed via script install_haznics.sh which is available here and there is a README file that should help with installation. Long story short, this creates a Python library haznics.py from the present code in the parent directory/repo (which is mostly in C/C++) and installs all dependencies for the demos.

To be able to do import haznics in any script, we link the library with running source setup.rc.

I wish this was simpler, but here we are. If you have any recommendations on easier installation/workflow for this software, I welcome all the help.

Title

Add instructions on how to use conda-build with pypi

Link

https://github.com/scientificcomputing/generate-python-package

Details

Would be optimal to have this in the cookie cutter.
Also have a description of how it works, similar to your presentation today.

We should find a way to categorise the different repositories. One way could be to use tags such as a heart, brain, blood, electrophysiology, mechanics, flow, but we could also use emojis to make it a bit more visual, e.g 🫀 , 🧠 , 🩸 , ⚡ , ⚙️ , 🌊 .

We could also make this into a table e.g