DX: workflows including MyST NB and precommit added

.github/workflows/deploy.yml

@@ -1,46 +1,34 @@
-# This file was created automatically with `myst init --gh-pages` 🪄 💚
-
 name: MyST GitHub Pages Deploy
 on:
+  pull_request:
+    branches: [main]
   push:
     # Runs on pushes targeting the default branch
     branches: [main]
-env:
-  # `BASE_URL` determines the website is served from, including CSS & JS assets
-  # You may need to change this to `BASE_URL: ''`
-  BASE_URL: /${{ github.event.repository.name }}
-
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
-permissions:
-  contents: read
-  pages: write
-  id-token: write
-# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
-# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
-concurrency:
-  group: "pages"
-  cancel-in-progress: false
 jobs:
-  deploy:
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
+  build:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - name: Setup Pages
-        uses: actions/configure-pages@v3
-      - uses: actions/setup-node@v4
+        uses: actions/configure-pages@v5
         with:
-          node-version: 18.x
-      - name: Install MyST Markdown
-        run: npm install -g mystmd
-      - name: Build HTML Assets
-        run: myst build --html
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+          enablement: "true"
+      - uses: prefix-dev/[email protected]
         with:
-          path: "./_build/html"
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v2
+          path: ./_build/html
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    if: >-
+      github.event_name == 'push' && github.ref == format('refs/heads/{0}', github.event.repository.default_branch)
+    needs: build
+    permissions:
+      pages: write
+      id-token: write
+    runs-on: ubuntu-latest
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -1,5 +1,4 @@
-# pixi environments
-.pixi
 *.egg-info
 .ipynb_checkpoints/
-
+.pixi
+node_modules/

.pre-commit-config.yaml

@@ -2,10 +2,10 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-      - id: check-yaml
       - id: check-added-large-files
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.7.1
@@ -16,3 +16,16 @@ repos:
     rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
+
+  - repo: https://github.com/redeboer/taplo-pre-commit
+    rev: v0.9.1rc1
+    hooks:
+      - id: taplo
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]

.taplo.toml

@@ -0,0 +1,12 @@
+[formatting]
+align_comments = false
+align_entries = false
+allowed_blank_lines = 1
+array_auto_collapse = false
+array_auto_expand = true
+array_trailing_comma = true
+column_width = 88
+compact_inline_tables = true
+indent_string = "    "
+reorder_arrays = true
+reorder_keys = true

docs/.gitignore

@@ -0,0 +1,2 @@
+.ipynb_checkpoints
+_build

docs/conf.py

@@ -0,0 +1,11 @@
+exclude_patterns = [
+    "**.ipynb_checkpoints",
+    ".DS_Store",
+    ".pixi",
+    "Thumbs.db",
+    "_build",
+]
+extensions = ["myst_nb"]
+master_doc = "index"
+nitpicky = True
+project = "GlueX N-Star"

Hello.ipynb → docs/hello.ipynb

@@ -1,27 +1,27 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# Starting document"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": 1,
-   "id": "086f6c1d-4e2d-4a97-85fb-c61cd55634d7",
+   "execution_count": null,
+   "id": "1",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Hello World!\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(\"Hello World!\")"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f32a577e-5098-4070-b58b-274d4314cb07",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": []

docs/index.md

@@ -0,0 +1,5 @@
+# MyST-NB Quickstart
+
+```{toctree}
+hello
+```

pixi.toml

@@ -1,20 +1,38 @@
 [project]
-name = "gluex-nstar"
-version = "0.1.0"
-description = "Add a short description here"
 authors = ["Vitor Shen <[email protected]>"]
 channels = ["conda-forge"]
+name = "gluex-nstar"
 platforms = ["linux-64"]
 
 [tasks]
+docnb = """
+sphinx-build \
+    -nW --keep-going \
+    -b html \
+    docs _build/html
+"""
+docnblive = """
+sphinx-autobuild \
+    --watch docs \
+    -nW --keep-going \
+    -b html \
+    docs _build/html
+"""
 
 [dependencies]
-jaxlib = ">=0.4.23,<0.5"
-sympy = ">=1.12,<2"
-python = ">=3.12.3,<3.13"
-jupyterlab = ">=4.2.0,<4.3"
-jax = ">=0.4.26,<0.5"
-numpy = ">=1.26.4,<1.27"
 black = ">=24.4.2,<24.5"
 isort = ">=5.13.2,<5.14"
+jax = ">=0.4.26,<0.5"
+jaxlib = ">=0.4.23,<0.5"
+jupyterlab = ">=4.2.0,<4.3"
 jupyterlab-git = ">=0.50.0,<0.51"
+jupyterlab-lsp = ">=5.1.0,<5.2"
+jupyterlab-myst = ">=2.4.2,<2.5"
+myst-nb = ">=1.1.0,<1.2"
+numpy = ">=1.26.4,<1.27"
+pre-commit = ">=3.7.1,<3.8"
+python = ">=3.12.3,<3.13"
+python-graphviz = ">=0.20.3,<0.21"
+scipy = ">=1.13.0,<1.14"
+sphinx-autobuild = ">=2024.4.16,<2024.5"
+sympy = ">=1.12,<2"