bib.bib

## Place biblatex entries here.
@inproceedings{paszke2017automatic,
  title={Automatic differentiation in pytorch},
  author={Paszke, Adam and Gross, Sam and Chintala, Soumith and Chanan, Gregory and Yang, Edward and DeVito, Zachary and Lin, Zeming and Desmaison, Alban and Antiga, Luca and Lerer, Adam},
  year={2017},
  booktitle = {NIPS 2017 Autodiff Workshop},
}

@software{jax2018github,
  author = {James Bradbury and Roy Frostig and Peter Hawkins and Matthew James Johnson and Chris Leary and Dougal Maclaurin and George Necula and Adam Paszke and Jake Vander{P}las and Skye Wanderman-{M}ilne and Qiao Zhang},
  title = {{JAX}: composable transformations of {P}ython+{N}um{P}y programs},
  url = {http://github.com/jax-ml/jax},
  version = {0.5.0},
  year = {2025},
}

@article{hutson2018artificial,
  title={Artificial intelligence faces reproducibility crisis},
  author={Hutson, Matthew},
  year={2018},
  journal={Science},
  volume = {359},
  publisher={American Association for the Advancement of Science}
}

@article{hoyt2023improving,
  title={Improving reproducibility and reusability in the Journal of Cheminformatics},
  author={Hoyt, Charles Tapley and Zdrazil, Barbara and Guha, Rajarshi and Jeliazkova, Nina and Martinez-Mayorga, Karina and Nittinger, Eva},
  journal={Journal of Cheminformatics},
  volume={15},
  number={1},
  pages={62},
  year={2023},
  publisher={Springer}
}

@book{popper2013logik,
  title={Logik der forschung},
  author={Popper, Karl},
  year={2013},
  publisher={Akademie Verlag}
}
@book{popper2005logic,
  title={The logic of scientific discovery},
  author={Popper, Karl},
  year={2005},
  publisher={Routledge}
}

@misc{NeuripsCodeguide,
  title = {Tips for releasing research code in Machine Learning (with official NeurIPS 2020 recommendations)},
  author = {Robert Stojnic and Ross Taylor and Sarthak Pati and Fabian-Robert Stöter and
  Viktor Kerkez andShagun Sodhani and Hamel Husain and Amit Chaudhary and  Rishabh Jain},
  year = {2020},
  url = {https://github.com/paperswithcode/releasing-research-code},
  note = {Accessed: 2025-01-28}
}

@article{Yasset2016TenGit,
  author       = {Yasset P{\'{e}}rez{-}Riverol and
                  Laurent Gatto and
                  Rui Wang and
                  Timo Sachsenberg and
                  Julian Uszkoreit and
                  Felipe da Veiga Leprevost and
                  Christian Fufezan and
                  Tobias Ternent and
                  Stephen J. Eglen and
                  Daniel S. Katz and
                  Tom J. Pollard and
                  Alexander Konovalov and
                  Robert M. Flight and
                  Kai Blin and
                  Juan Antonio Vizca{\'{\i}}no},
  title        = {Ten Simple Rules for Taking Advantage of Git and GitHub},
  journal      = {PLoS Comput. Biol.},
  volume       = {12},
  number       = {7},
  year         = {2016},
  url          = {https://doi.org/10.1371/journal.pcbi.1004947},
  doi          = {10.1371/JOURNAL.PCBI.1004947},
  timestamp    = {Sun, 25 Jul 2021 11:37:06 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/Perez-RiverolGW16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}



@article{Andreas2012TenSoftware,
  author       = {Andreas Prlic and
                  James B. Procter},
  title        = {Ten Simple Rules for the Open Development of Scientific Software},
  journal      = {PLoS Comput. Biol.},
  volume       = {8},
  number       = {12},
  year         = {2012},
  url          = {https://doi.org/10.1371/journal.pcbi.1002802},
  doi          = {10.1371/JOURNAL.PCBI.1002802},
  timestamp    = {Thu, 10 Sep 2020 13:19:12 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/PrlicP12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}



@article{Kjetil2013TenReproducible,
  author       = {Geir Kjetil Sandve and
                  Anton Nekrutenko and
                  James Taylor and
                  Eivind Hovig},
  title        = {Ten Simple Rules for Reproducible Computational Research},
  journal      = {PLoS Comput. Biol.},
  volume       = {9},
  number       = {10},
  year         = {2013},
  url          = {https://doi.org/10.1371/journal.pcbi.1003285},
  doi          = {10.1371/JOURNAL.PCBI.1003285},
  timestamp    = {Thu, 10 Sep 2020 13:21:11 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/SandveNTH13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{Lost2017TenUsable,
  author       = {Markus List and
                  Peter Ebert and
                  Felipe Albrecht},
  title        = {Ten Simple Rules for Developing Usable Software in Computational Biology},
  journal      = {PLoS Comput. Biol.},
  volume       = {13},
  number       = {1},
  year         = {2017},
  url          = {https://doi.org/10.1371/journal.pcbi.1005265},
  doi          = {10.1371/JOURNAL.PCBI.1005265},
  timestamp    = {Tue, 06 Oct 2020 17:43:03 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/ListEA17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@misc{opensource2025guide,
  title = {The Legal Side of Open Source},
  author = {opensourceguide},
  year = {2025},
  url = {https://opensource.guide/legal/}
  }

@misc{tensorflow2015-whitepaper,
title={ {TensorFlow}: Large-Scale Machine Learning on Heterogeneous Systems},
url={https://www.tensorflow.org/},
note={Software available from tensorflow.org},
author={
    Mart\'{i}n~Abadi and
    Ashish~Agarwal and
    Paul~Barham and
    Eugene~Brevdo and
    Zhifeng~Chen and
    Craig~Citro and
    Greg~S.~Corrado and
    Andy~Davis and
    Jeffrey~Dean and
    Matthieu~Devin and
    Sanjay~Ghemawat and
    Ian~Goodfellow and
    Andrew~Harp and
    Geoffrey~Irving and
    Michael~Isard and
    Yangqing Jia and
    Rafal~Jozefowicz and
    Lukasz~Kaiser and
    Manjunath~Kudlur and
    Josh~Levenberg and
    Dandelion~Man\'{e} and
    Rajat~Monga and
    Sherry~Moore and
    Derek~Murray and
    Chris~Olah and
    Mike~Schuster and
    Jonathon~Shlens and
    Benoit~Steiner and
    Ilya~Sutskever and
    Kunal~Talwar and
    Paul~Tucker and
    Vincent~Vanhoucke and
    Vijay~Vasudevan and
    Fernanda~Vi\'{e}gas and
    Oriol~Vinyals and
    Pete~Warden and
    Martin~Wattenberg and
    Martin~Wicke and
    Yuan~Yu and
    Xiaoqiang~Zheng},
  year={2015},
}

@misc{emerson1841self,
  title={Self-Reliance},
  author={Emerson, Ralph Waldo},
  year={1841},
  url={https://www.emersoncentral.com/selfreliance.htm}
}

@misc{pep8,
  title={PEP 8 -- Style Guide for Python Code},
  author={van Rossum, Guido and Warsaw, Barry and Coghlan, Nick},
  year={2001},
  url={https://www.python.org/dev/peps/pep-0008/}
}

@misc{pip2025docs,
  title = {Requirements File Format - Pip documentation v25.0},
  author={Pip-developers},
  year={2025},
  url={https://pip.pypa.io/en/stable/reference/requirements-file-format/}
}

@misc{conda2025repo,
  title = {Conda documentation},
  author={Conda-developers},
  year={2025},
  url={https://github.com/conda/conda}
}

@misc{pytest2025docs,
  title = {Pytest documentation},
  author={Pytest-developers},
  year={2025},
  url={https://docs.pytest.org/en/stable/}
}

@misc{unittest2025pythondocs,
  title = {unittest - Unit testing framework},
  author={Python-developers},
  year={2025},
  url={https://docs.python.org/3/library/unittest.html}
}

@misc{packaging2025python,
  title={Packaging Python-Projects},
  author={Python-Packaging-Authority},
  year={2025},
  url={https://packaging.python.org/tutorials/packaging-projects/}
  }

@misc{setuptools2025docs,
  title={Setuptools documentation},
  author={Setuptools-Team},
  year={2025},
  url={https://setuptools.pypa.io/en/stable/}
}

@misc{nox2025docs,
  title={Nox documentation},
  author={Alethea Katherine Flowers and
          Chris Wilcox and
          Claudio Jolowicz and
          Danny Hermes and
          Diego Ramirez and
          Henry Schreiner and
          Luke Sneeringer and
          Santos Gallegos and
          Tom Fleet
 },
  year={2025},
  url={https://nox.thea.codes/en/stable/}
}

@misc{tox2025docs,
  title={tox - automation project},
  author={tox-devs},
  year = {2025},
  url={https://tox.wiki/en/latest/}
}

@misc{richardson2023soupdocs,
  title = {Beautiful Soup Documentation},
  author = {Leonard Richardson},
  year = {2023},
  url = {https://www.crummy.com/software/BeautifulSoup/bs4/doc/}
}

@misc{Hager2021pdfx,
  title = {PDFx},
  author = {Chris Hager},
  year = {2021},
  url = {https://github.com/metachris/pdfx}
}

@misc{Cannon2016pep518,
  title = {PEP 518 – Specifying Minimum Build System Requirements for Python Projects},
  author = {Brett Cannon, Nathaniel J. Smith, Donald Stufft },
  year = {2016},
  url = {https://peps.python.org/pep-0518/}
}

@misc{chex2025docs,
    title = {Chex documentation},
    author = {Jax-ecosystem-authors},
    year = {2025},
    URL = {https://chex.readthedocs.io/en/latest/}
}

@misc{PyTorch2024randomness,
    title = {Reproducibility},
    author = {PyTorch-Contributors},
    year = {2024},
    URL = {https://pytorch.org/docs/stable/notes/randomness.html}
}