Merge pull request #58 from ksunden/jupyterlite

WIP: enable jupyterlite pixi tasks

Author: danielballan

.github/workflows/cd.yml

@@ -29,9 +29,12 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da  # v0.8.8
 
-      - name: Build executed notebooks and HTML
+      - name: Build HTML
         run: pixi run build
 
+      - name: Build jupyterlite
+        run: pixi run build_wasm
+
       - name: Upload executed notebooks as GitHub artifact (for debugging)
         uses: actions/upload-artifact@v4
         with:

.github/workflows/ci.yml

@@ -100,3 +100,15 @@ jobs:
 
     - name: Build static site
       run: pixi run build
+
+  pixi_build_wasm:
+    name: Build jupyterlite site with pixi
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup pixi
+      uses: prefix-dev/setup-pixi@v0.8.1
+
+    - name: Build jupyterlite site
+      run: pixi run build_wasm

.gitignore

@@ -5,6 +5,9 @@ _build/*
 # No .ipynb files should be stored in this repository.
 *.ipynb
 
+# Jupyterlite Database
+.jupyterlite.doit.db
+
 # We treat this repository as a library, not an application, and thus we do not
 # include the lockfile in source control. For a specific event, like a
 # workshop, we suggest committing the lockfile on a branch dedicated to the

activate.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+set -eux
+
+mkdir -p ${CONDA_PREFIX}/share/jupyter/lab/settings
+cp ${PIXI_PROJECT_ROOT}/.binder/overrides.json ${CONDA_PREFIX}/share/jupyter/lab/settings/overrides.json

convert_all_jupyterlite.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+
+# This is a script which copies the contents of the tutorials
+# directory into a build directory (_build/ipynbs).
+# The notebook markdown files are converted to ipynbs with other
+# files (non-executable md files, static images, etc) are copied
+# directly.
+# This is intended for jupyterlite to build pointing to the build
+# directory since the markdown files do not currently work in 
+# jupyterlite.
+
+# Find Markdown files convert.
+files_to_process=$(find tutorials -type f)
+
+OUTDIR="_build/ipynbs"
+
+# Identify Markdown files that are Jupytext and convert them all.
+for file in ${files_to_process}; do
+    # Ensure result directory exists
+    echo "Making directory: $OUTDIR/$(dirname $file)"
+    mkdir -p $OUTDIR/$(dirname $file)
+
+    echo loop in $file
+    # Extract the kernel information from the Jupytext Markdown file.
+    kernel_info=$(grep -A 10 '^---$' "$file" | grep -E 'kernelspec')
+    # Copy directly if not a notebook file
+    if [ -z "$kernel_info" ]; then
+      cp $file $OUTDIR/$file
+      continue
+    fi
+    # Convert to ipynb format, to be consumed by pytest nbval plugin.
+    notebook_file="${file%.md}.ipynb"
+    jupytext --to ipynb "$file" --output $OUTDIR/${notebook_file}
+done

pixi.toml

@@ -5,13 +5,16 @@ authors = [
     "Ross Barnowski <rossbar@caltech.edu>",
     "Kyle Sunden <git@ksunden.space>",
 ]
-channels = ["conda-forge"]
+channels = ["https://repo.mamba.pm/emscripten-forge", "conda-forge"]
 description = "Add a short description here"
 name = "executable-tutorials"
-platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
+platforms = ["linux-64", "osx-64", "osx-arm64", "win-64", "emscripten-wasm32"]
 version = "0.1.0"
 
-[tasks]
+[feature.base]
+platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
+
+[feature.base.tasks]
 build = { cmd = [
     "sphinx-build",
     ".",  # source directory
@@ -25,22 +28,23 @@ clean = "rm -rf _build/*"
 start = "jupyter lab  --FileContentsManager.preferred_dir tutorials"
 test = "bash ./test.sh"
 
-[activation]
+[feature.base.activation]
 # Workaround overrides JupyterLab configuration (at the environment level) to
 # make double-clicking on a Jupytext Markdown file open that file as a
 # notebook. This is important for the development workflow for contributors.
-scripts = ["bash .binder/postBuild"]
+scripts = ["activate.sh"]
 
-[dependencies]
+[feature.base.dependencies]
 python = ">=3.11"
 matplotlib-base = ">=3.9"
-ipympl = ">=0.9"
 jupyterlab = ">=4.2"
 jupyterlab-myst = ">=2.4"
 pytest = ">=8.3.5,<9"
 nbval = ">=0.11.0,<0.12"
+jupytext = ">=1.17.1,<2"
+ipympl = ">=0.9"
 
-[pypi-dependencies]
+[feature.base.pypi-dependencies]
 sphinx = ">=8.0.2"
 myst-nb = ">=1.1"
 jupytext = ">=1.16"
@@ -49,19 +53,59 @@ sphinx-copybutton = ">=0.5"
 sphinx-design = "*"
 pytest-custom_exit_code = "*"
 
+[feature.py312]
+platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
+
 [feature.py312.dependencies]
 python = "3.12.*"
 
+[feature.py313]
+platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
+
 [feature.py313.dependencies]
 python = "3.13.*"
 
-[feature.jupyterlite.dependencies]
+[feature.jupyterlite-runtime]
+channels = ["https://repo.mamba.pm/emscripten-forge", "conda-forge"]
+platforms = ["emscripten-wasm32"]
+
+[feature.jupyterlite-runtime.dependencies]
+xeus-python = "*"
+python = ">=3.11"
+matplotlib = ">=3.9"
+ipympl = ">=0.9"
+jupytext = ">=1.16"
+
+[feature.jupyterlite-host]
+channels = ["conda-forge"]
+platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
+
+[feature.jupyterlite-host.dependencies]
 jupyterlab = "~=4.2.4"
 jupyterlite-core = "==0.4.0"
-jupyterlite-pyodide-kernel = "==0.4.1"
+jupyterlite-xeus = "*"
 notebook = "~=7.2.1"
+jupyterlab-myst = ">=2.4"
+jupytext = ">=1.16"
+ipympl = ">=0.9"
+
+[feature.jupyterlite-host.tasks]
+setup_wasm = {cmd = "pixi install -e jupyterlite-runtime", inputs = ["pixi.lock"]}
+convert_ipynbs = {cmd = "bash convert_all_jupyterlite.sh", inputs = ["tutorials/"], outputs = ["_build/ipynbs"]}
+
+[feature.jupyterlite-host.tasks.build_wasm]
+cmd = "jupyter lite build --XeusAddon.prefix=.pixi/envs/jupyterlite-runtime --contents _build/ipynbs/tutorials --output-dir _build/html/jupyterlite --settings-overrides=.binder/overrides.json --log-level DEBUG"
+depends-on = ["setup_wasm", "convert_ipynbs"]
+outputs = ["_build/html/jupyterlite/"]
+inputs = ["pixi.lock", "tutorials/"]
+
+[feature.jupyterlite-host.tasks.start_wasm]
+cmd = "python -m http.server 8000 -d _build/html/jupyterlite/"
+depends-on = ["build_wasm"]
 
 [environments]
-py312 = ["py312"]
-py313 = ["py313"]
-jupyterlite = ["jupyterlite"]
+default = ["base"]
+py312 = ["base", "py312"]
+py313 = ["base", "py313"]
+jupyterlite-runtime = ["jupyterlite-runtime"]
+jupyterlite-host = ["jupyterlite-host"]