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science-notebook-template

🧪 A simple, elegant template for repositories with Jupyter notebooks supporting publications.

https://github.com/dmyersturnbull/science-notebook-template

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.6%) to scientific vocabulary

Keywords

cookiecutter-template jupyter jupyterlab notebooks science template
Last synced: 6 months ago · JSON representation ·

Repository

🧪 A simple, elegant template for repositories with Jupyter notebooks supporting publications.

Basic Info
Statistics
  • Stars: 12
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
cookiecutter-template jupyter jupyterlab notebooks science template
Created about 5 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog Contributing License Citation Codeowners Security

README.md

Science notebook template

Binder DOI License template science_notebook

🧪 A simple, elegant template for repositories supporting publications. Scientific companion to the much more sophisticated code template Tyrannosaurus 🦖 No cookiecutter. Just click Use this Template above.

👋 Citing

Just tell people how to cite your work.

Please reference the manuscript with this BibTeX:

@misc{sciencenotebooktemplate, doi = {10.5281/zenodo.4495745}, url = {https://zenodo.org/record/4485186}, author = {Myers-Turnbull, Douglas}, title = {dmyersturnbull/science-notebook-template: v0.1.0}, publisher = {Zenodo}, year = {2021}, copyright = {Open Access} }

Or APA format:

Myers-Turnbull, D. (2021). dmyersturnbull/science-notebook-template (v0.1.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.4495745

🎁 About this repository

What’s in this repo?

  • Automatic linting of Python, Markdown, config files, etc. using pre-commit
  • Nice default GitHub settings (just install the Probot settings app to your repo
  • IDE hints via EditorConfig with good defaults for most languages CITATION.cff
  • Nice gitignore, dockerignore, changelog, and other misc files
  • Example/stub Conda environment file, Vagrantfile, and shields

📜 Steps to reproduce

How to download needed data, run the code, etc.

  1. Fork this repository as a template.
  2. Clone and run pip install pre-commit and pre-commit install.
  3. Install the Probot settings app.
  4. Fix .github/CODEOWNERS. Replace with your username or org name.
  5. Fix .github/settings.yml. (NOTE: Make sure to change private and name.)
  6. If you want to use Commitizen, uncomment the lines in .pre-commit.yaml. Otherwise, delete .cz.toml.
  7. Add to Binder and Get a DOI for your repo.
  8. Make a local clone of your repo. Modify the readme, changelog, etc. Add your code/notebooks. Feel free to remove or replace SPDX headers.
  9. Commit and push to main. (If a linter fails on commit, just re-run. It just meant the linter modified a file.)
  10. Configure branch rules Settings.

🌳 Layout

Describe the layout of this repo.

bash ├── src/ ⟵ project source code ├── data │ ├── temp-output/ ⟵ files generated per-run │ │ ├── figures/ ⟵ raw charts and graphs │ │ └── ...misc. files │ ├── living/ ⟵ files we are actively curating │ │ ├── figures/ │ │ ├── manuscript/ │ │ └── ...misc. files │ └── frozen/ ⟵ non-modifiable files │ ├── raw/ ⟵ experimental or downloaded data │ └── ref/ ⟵ frozen analyses and figures └── README.md

See research projects guide for more info.

🔌 External resources

Describe any external resources needed (e.g., API keys).

🍁 Contributing

Tell people how to report problems and ask questions.

The source code in this repository is licensed under the terms of the Apache License 2.0. Contributions and questions are welcome via issues. For reference, refer to the contributing guide and security policy.

Note: The source code headers (i.e., SPDX) are to protect you, the user. I don’t expect you to retain them. Remove them or replace them with your own when you modify them.

Owner

  • Name: Douglas Myers-Turnbull
  • Login: dmyersturnbull
  • Kind: user
  • Location: Stanford, CA
  • Company: Stanford University

Citation (CITATION.cff) 

cff-version: 1.2.0
message: Software reference
title: science-notebook-template
version: 0.1.0
abstract: Simple template for science notebooks
authors:
  -
    family-names: Myers-Turnbull
    given-names: Douglas
    orcid: 0000-0003-3610-4808
keywords: ["open-science", "notebooks", "jupyter", "template", "cookiecutter"]
date-released: 2021-02-01

GitHub Events

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Last synced: over 1 year ago

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  • Average time to close pull requests: about 2 months
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  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.5
  • Merged pull requests: 2
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  • Bot pull requests: 2
Past Year
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  • Pull requests: 0
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Dependencies

.github/workflows/checks.yaml actions
  • actions/checkout master composite
  • actions/checkout v3 composite
  • gaurav-nelson/github-action-markdown-link-check v1 composite
  • github/codeql-action/analyze v2 composite
  • github/codeql-action/autobuild v2 composite
  • github/codeql-action/init v2 composite
environment.yaml pypi