feat: readme info

Author: dmyersturnbull

.github/settings.yml

@@ -5,14 +5,22 @@ repository:
 
   name: "science-notebook-template"
 
-  description: "A sciencey project"
+  description: "🧪 A simple, elegant template for repositories with Jupyter notebooks supporting publications."
 
-  homepage: "https://github.com/dmyersturnbull/always-initialized"
+  homepage: "https://github.com/dmyersturnbull/science-notebook-template"
 
-  topics: [""]
+  topics:
+    [
+      "template",
+      "cookiecutter",
+      "jupyter",
+      "jupyterlab",
+      "science",
+      "notebooks",
+    ]
 
   has_issues: true
-  has_projects: true
+  has_projects: false
   has_wiki: false
   has_downloads: true
 
@@ -28,45 +36,15 @@ labels:
   - name: "a notice ♢"
     description: "Bulletin; notice me!"
     color: "#ffffff"
-  - name: "breaking ⚙"
-    description: "Requires a breaking change"
-    color: "#000000"
-  - name: "difficulty: easy"
-    description: "< 30 min"
-    color: "#bbddbb"
-  - name: "difficulty: hard"
-    description: "difficulty: hard"
-    color: "#009900"
-  - name: "difficulty: milestone ⚑"
-    description: "⚑ A milestone referencing other issues"
-    color: "#00ff00"
-  - name: "difficulty: severe"
-    description: "difficulty: severe"
-    color: "#006600"
-  - name: "difficulty: typical"
-    description: "30 min – 4 hours"
-    color: "#66bb66"
   - name: "kind: bug"
     description: "Something isn’t working"
     color: "#ee5500"
-  - name: "kind: cleanup"
-    description: "Simplify or improve code"
-    color: "#84b6eb"
   - name: "kind: documentation"
     description: "A feature needs better documentation"
     color: "#006b75"
-  - name: "kind: enhancement"
-    description: "Improve functionality"
-    color: "#2060cc"
-  - name: "kind: infrastructure"
-    description: "Modify dependencies, installation, tools, etc."
-    color: "#333788"
   - name: "kind: new feature"
     description: "Create something new"
     color: "#0000ff"
-  - name: "kind: performance"
-    description: "Improve speed or resource usage"
-    color: "#bbbbdd"
   - name: "kind: question"
     description: "Further information is requested"
     color: "#66317c"
@@ -76,33 +54,18 @@ labels:
   - name: "kind: tests"
     description: "Write or improve tests"
     color: "#d08000"
-  - name: "priority: critical ⚠"
-    description: "⚠ Must be done NOW"
-    color: "#ff0000"
   - name: "priority: important"
     description: "Should be done soon"
     color: "#cc0000"
   - name: "priority: minor"
     description: "Should do, but not important"
     color: "#ddaa99"
-  - name: "priority: pickmeup"
-    description: "Too minor to bother"
-    color: "#f0e9e9"
   - name: "priority: wontfix"
     description: "Should not be fixed"
     color: "#fff9f9"
-  - name: "status: decision"
-    description: "Whether to fix / how to fix"
-    color: "#33aaaa"
   - name: "status: duplicate"
     description: "This issue or pull request already exists"
     color: "#cfd3d7"
-  - name: "status: fixed ✓"
-    description: "100% done"
-    color: "#ddffee"
-  - name: "status: help needed ◉"
-    description: "◉  More contributors need to be assigned"
-    color: "#55cccc"
   - name: 'status: in progress \U0001F846'
     description: "Assigned and in progress"
     color: "#aacfbb"
@@ -112,27 +75,17 @@ labels:
   - name: "status: invalid"
     description: "Not a real issue"
     color: "#e6e6e6"
-  - name: "status: unresolvable"
-    description: "Can’t be fixed: The required info doesn’t exist."
-    color: "#111111"
-  - name: "status: in upstream"
-    description: "Can’t fix until a dependency is fixed"
-    color: "#fefeee"
   - name: "sticky note ☆"
     description: "☆ Important for reference even after it’s closed"
     color: "#ffee00"
 
 branches:
   - name: "main"
     protection:
-      required_pull_request_reviews:
-        required_approving_review_count: 1
-        dismiss_stale_reviews: true
-        require_code_owner_reviews: true
       required_status_checks:
         strict: true
         contexts:
-          - "markdown-link-check"
-      enforce_admins: true
+          - "Check Markdown links"
+      enforce_admins: false
       required_linear_history: true
       restrictions: null

.github/workflows/checks.yml

@@ -4,7 +4,11 @@
 name: Static checks
 on:
   push:
+    branches:
+      - main
   pull_request:
+    branches:
+      - main
   schedule:
     - cron: 0 7 * * 6
 jobs:

README.md

@@ -1,13 +1,72 @@
 # Science notebook template
 
-[![DOI:10.1007/978-3-319-76207-4_15](https://zenodo.org/badge/DOI/10.1007/978-3-319-76207-4_15.svg)](https://doi.org/10.1007/978-3-319-76207-4_15)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dmyersturnbull/science-notebook-template/HEAD)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4485186.svg)](https://doi.org/10.5281/zenodo.4485186)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![template science_notebook](https://img.shields.io/badge/template-science_notebook-990099.svg)](https://github.com/dmyersturnbull/science-notebook-template)
 
-🧪 A simple, elegant template for repositories with Jupyter notebooks supporting publications.
-No cookiecutter. Just click _Use as Template_ above.
+🧪 A simple, elegant template for repositories supporting publications.
 Companion to the more sophisticated [Tyrannosaurus](https://github.com/dmyersturnbull/tyrannosaurus), which is for code projects.
+No cookiecutter. Just click _Use this Template_ above.
 
-Licensed under the terms of the [Apache License 2.0](https://spdx.org/licenses/Apache-2.0.html).
-[Contributions and questions](https://github.com/dmyersturnbull/science-notebook-template/issues) are welcome.
-Please refer to the [contributing guide](https://github.com/dmyersturnbull/science-notebook-template/blob/main/CONTRIBUTING.md)
+### Citing
+
+**Just tell people how to cite your work.**
+
+Please reference the manuscript with this BibTeX:
+
+```
+@misc{https://doi.org/10.5281/zenodo.4485186,
+  doi = {10.5281/ZENODO.4485186},
+  url = {https://zenodo.org/record/4485186},
+  author = {Myers-Turnbull, Douglas},
+  title = {dmyersturnbull/tyrannosaurus: v0.9.1},
+  publisher = {Zenodo},
+  year = {2021},
+  copyright = {Open Access}
+}
+```
+
+Or APA format:
+
+> Myers-Turnbull, D. (2021). dmyersturnbull/tyrannosaurus: v0.9.1 (v0.9.1) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.4485186
+
+### About this repository
+
+**What’s in this repo?**
+
+- Automatic linting of Python, Markdown, config files, etc. using [pre-commit](https://pre-commit.com/)
+- Nice default GitHub settings (just install the [Probot settings app](https://github.com/apps/settings) to your repo
+- IDE hints via [EditorConfig](https://editorconfig.org/) with good defaults for most languages
+- [CodeMeta](https://codemeta.github.io/user-guide/) and [CITATION.cff](https://citation-file-format.github.io/)
+- Nice gitignore, dockerignore, changelog, and other misc files
+- Example Conda environment file and Vagrantfile
+
+### Steps to reproduce
+
+**How to download needed data, run the code, etc.**
+
+1. Clone this repository as a template and run `pre-commit install`. (`pip install pre-commit`).
+2. Install the [Probot settings app](https://github.com/apps/settings).
+3. Add to [Binder](https://mybinder.org/) and [Get a DOI](https://guides.github.com/activities/citable-code/) for your repo.
+4. Make a local clone of your repo. Modify the readme, changelog, etc. Add your code/notebooks.
+5. Commit and push to *main*. (If a linter fails on commit, just re-run. It just meant the linter modified a file.)
+
+### Branch protection rules
+
+This template includes
+[branch protection](https://docs.github.com/en/github-ae@latest/github/administering-a-repository/managing-a-branch-protection-rule)
+rules for the _main_ branch that disable force-commits, forbid direct pushes,
+require status checks to pass, and require a linear history.
+You can configure these rules under *Settings → Branches → main*.
+The typical workflow is: push changes to a new branch, make a pull request against *main*, and squash–merge or rebase into *main* after the status checks pass.
+An *admin*-role user *can* push directly to *main*, but non-*admin* users (with write access) must make pull requests.
+
+### 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](https://spdx.org/licenses/Apache-2.0.html).
+Contributions and questions are welcome via issues.
+For reference, refer to the [contributing guide](https://github.com/dmyersturnbull/science-notebook-template/blob/main/CONTRIBUTING.md)
 and [security policy](https://github.com/dmyersturnbull/science-notebook-template/blob/main/SECURITY.md).

environment.yml

@@ -1,4 +1,4 @@
-name: tyrannosaurus
+name: sciencenotebooktemplate
 channels:
   - conda-forge
 dependencies: