Format docs with deno fmt (#176)

Author: manzt

.devcontainer/devcontainer.json

@@ -1,6 +1,6 @@
 {
-	"name": "Python 3.11",
-	"image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye",
-	"postCreateCommand": "pipx install hatch",
-	"postStartCommand": "hatch shell"
+  "name": "Python 3.11",
+  "image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye",
+  "postCreateCommand": "pipx install hatch",
+  "postStartCommand": "hatch shell"
 }

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,6 +9,7 @@ Fixes #___
 ## Checklist
 
 - [ ] **Clear PR title** (used for generating release notes).
-   - Prefer using prefixes like `fix:` or `feat:` to help organize auto-generated notes.
+  - Prefer using prefixes like `fix:` or `feat:` to help organize auto-generated
+    notes.
 - [ ] **Unit tests** added or updated.
 - [ ] **Documentation** added or updated.

.github/dependabot.yml

@@ -1,6 +1,5 @@
 version: 2
 updates:
-
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:

.github/workflows/ci.yml

@@ -39,8 +39,8 @@ jobs:
     runs-on: ubuntu-latest
     if: startsWith(github.ref, 'refs/tags')
     permissions:
-       id-token: write
-       contents: read
+      id-token: write
+      contents: read
     steps:
       - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v5

.github/workflows/docs.yml

@@ -37,7 +37,7 @@ jobs:
       - uses: actions/configure-pages@v4
       - uses: actions/upload-pages-artifact@v3
         with:
-          path: './docs/_build/html'
+          path: "./docs/_build/html"
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v4

README.md

@@ -1,9 +1,8 @@
 # higlass-python 🔎
 
 A fresh Python library for [`higlass`](https://github.com/higlass/higlass) built
-on top of:
-* [`higlass-schema`](https://github.com/higlass/higlass-schema): Pydantic models for HiGlass.
-* [`higlass-widget`](https://github.com/higlass/higlass-widget): A cross-platform [AnyWidget](https://github.com/manzt/anywidget) for Jupyter environments.
+on top of [`higlass-schema`](https://github.com/higlass/higlass-schema) and
+[anyiwdget](https://github.com/manzt/anywidget).
 
 [![License](https://img.shields.io/pypi/l/higlass-python.svg?color=green)](https://github.com/higlass/higlass-python/raw/main/LICENSE)
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/higlass/higlass-python/blob/main/examples/Examples.ipynb)
@@ -51,10 +50,11 @@ To learn more about the new API, check out the
 
 ## Upgrade Guide
 
-**higlass-python** v1.0 is a total rewrite of our prior
-implementation, aimed to offer a more ergonomic and flexible API. While this
-might present challenges when upgrading existing code, we've prepared
-[documentation](http://docs-python.higlass.io/) to guide you through the new API usage.
+**higlass-python** v1.0 is a total rewrite of our prior implementation, aimed to
+offer a more ergonomic and flexible API. While this might present challenges
+when upgrading existing code, we've prepared
+[documentation](http://docs-python.higlass.io/) to guide you through the new API
+usage.
 
 If you find a missing feature, please open an issue – we're committed to
 supporting your use cases with the new API.
@@ -76,13 +76,13 @@ and understanding are greatly appreciated.
 
 All commands are run from the root of the project, from a terminal:
 
-| Command | Action |
-|---------|--------|
-| `uv run ruff check --fix && uv run ruff format` | Lint and apply formatting |
-| `uv run check` | Check linting rules |
-| `uv run ruff format --check` | Check formatting |
-| `uv run pytest` | Run unit tests |
-| `uv run docs/build.py` | Build the documentation in `docs/_build/html` |
+| Command                                         | Action                                        |
+| ----------------------------------------------- | --------------------------------------------- |
+| `uv run ruff check --fix && uv run ruff format` | Lint and apply formatting                     |
+| `uv run check`                                  | Check linting rules                           |
+| `uv run ruff format --check`                    | Check formatting                              |
+| `uv run pytest`                                 | Run unit tests                                |
+| `uv run docs/build.py`                          | Build the documentation in `docs/_build/html` |
 
 This table now includes only the UV-related commands, with each command in the
 left column and its corresponding action in the right column. The formatting is
@@ -92,7 +92,8 @@ Our CI enforces formatting, linting, and tests.
 
 ## Changelog
 
-Check the [GitHub Releases](https://github.com/higlass/higlass-python/releases) for a detailed changelog.
+Check the [GitHub Releases](https://github.com/higlass/higlass-python/releases)
+for a detailed changelog.
 
 ## Release
 
@@ -101,8 +102,11 @@ Releases are managed via the GitHub UI.
 [Draft a new release](https://github.com/higlass/higlass-python/releases/new):
 
 1. **Create a tag**
-   - Click _"Choose a tag"_, then **type a new tag** in the format `v[major].[minor].[patch]` to create it.
-   - _Note_: The UI is not obvious about this. You can create a tag here, not just select one. Tag creation triggers a [workflow](.github/workflows/ci.yml) to publish to PyPI.
+   - Click _"Choose a tag"_, then **type a new tag** in the format
+     `v[major].[minor].[patch]` to create it.
+   - _Note_: The UI is not obvious about this. You can create a tag here, not
+     just select one. Tag creation triggers a
+     [workflow](.github/workflows/ci.yml) to publish to PyPI.
 
 2. **Generate release notes**
    - Click _"Generate Release Notes"_ to auto-summarize changes from merged PRs.

deno.json

@@ -8,5 +8,8 @@
     "rules": {
       "exclude": ["prefer-const"]
     }
+  },
+  "fmt": {
+    "exclude": ["examples"]
   }
 }

docs/README.md

@@ -1,8 +1,10 @@
 # HiGlass Docs
 
-Documentation for all HiGlass software ([viewer][hgv], [app][hga], [server][hgs], [docker][hgd])
+Documentation for all HiGlass software ([viewer][hgv], [app][hga],
+[server][hgs], [docker][hgd])
 
-Simple edits can be made in GitHub. For anything more extensive, build and preview it locally:
+Simple edits can be made in GitHub. For anything more extensive, build and
+preview it locally:
 
 ```
 uv run build.py
@@ -11,7 +13,8 @@ uv run python -m http.server 8000 --directory _build/html
 
 Then open your browser to `http://localhost:8000`.
 
-Docs are built and deployed via GitHub Actions via a [workflow](.github/workflows/docs.yml).
+Docs are built and deployed via GitHub Actions via a
+[workflow](.github/workflows/docs.yml).
 
 [hga]: https://github.com/higlass/higlass-app
 [hgd]: https://github.com/higlass/higlass-docker