update to jupyter-book 2.0

.github/workflows/build_site.yml

@@ -6,7 +6,6 @@ on:
     paths:
     - 'code/**/*.ipynb'
     - 'website/**'
-    - 'xqtl_flowchart.html'
 
 jobs:
   build_website:
@@ -21,28 +20,20 @@ jobs:
           token: ${{ secrets.CI_TOKEN }}
           fetch-depth: 0
 
-      - name: Set up Python
-        uses: actions/setup-python@v7
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0.10.2
         with:
-          python-version: '3.12'
-
-      - name: Install dependencies
-        run: |
-          pip install jupyter-book==1.0.4 ghp-import nbconvert
+          run-install: false
 
       - name: Build website and manuscript
+        shell: pixi exec --spec jupyter-book ghp-import nbconvert -- bash -e {0}
         run: |
-          # Build website from a temporary flat source tree. The source notebooks
-          # stay under code/SoS, while public pages are emitted as <notebook>.html.
           rm -f pipeline/*.ipynb
-          BOOK_SRC="$(mktemp -d)"
-          python website/build_flat_book.py --output "$BOOK_SRC"
-          jupyter-book build "$BOOK_SRC" --path-output . --config "$BOOK_SRC/website/_config.yml" --toc "$BOOK_SRC/website/_toc.yml"
-          python website/build_flat_book.py --redirects _build/html
-          rsync -auzP code/images/* _build/html/_images/
-          cp xqtl_flowchart.html _build/html/
+          python website/build_support.py --stage-widget
+          BASE_URL=/xqtl-protocol jupyter-book build --html
+          python website/build_support.py --widget _build/html --redirects _build/html
+          cp website/xqtl_flowchart.html _build/html/
           ghp-import -n -p -f _build/html
-
           # Link notebooks
           find code/SoS -name '*.ipynb' -not -path '*/.ipynb_checkpoints/*' -print0 | while IFS= read -r -d '' notebook; do
             ln -s "../${notebook}" "pipeline/$(basename "$notebook")"

.github/workflows/dispatch_build_site.yml

@@ -16,28 +16,20 @@ jobs:
           token: ${{ secrets.CI_TOKEN }}
           fetch-depth: 0
 
-      - name: Set up Python
-        uses: actions/setup-python@v7
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0.10.2
         with:
-          python-version: '3.12'
-
-      - name: Install dependencies
-        run: |
-          pip install jupyter-book==1.0.4 ghp-import nbconvert
+          run-install: false
 
       - name: Build website and manuscript
+        shell: pixi exec --spec jupyter-book ghp-import nbconvert -- bash -e {0}
         run: |
-          # Build website from a temporary flat source tree. The source notebooks
-          # stay under code/SoS, while public pages are emitted as <notebook>.html.
           rm -f pipeline/*.ipynb
-          BOOK_SRC="$(mktemp -d)"
-          python website/build_flat_book.py --output "$BOOK_SRC"
-          jupyter-book build "$BOOK_SRC" --path-output . --config "$BOOK_SRC/website/_config.yml" --toc "$BOOK_SRC/website/_toc.yml"
-          python website/build_flat_book.py --redirects _build/html
-          rsync -auzP code/images/* _build/html/_images/
-          cp xqtl_flowchart.html _build/html/
+          python website/build_support.py --stage-widget
+          BASE_URL=/xqtl-protocol jupyter-book build --html
+          python website/build_support.py --widget _build/html --redirects _build/html
+          cp website/xqtl_flowchart.html _build/html/
           ghp-import -n -p -f _build/html
-
           # Link notebooks
           find code/SoS -name '*.ipynb' -not -path '*/.ipynb_checkpoints/*' -print0 | while IFS= read -r -d '' notebook; do
             ln -s "../${notebook}" "pipeline/$(basename "$notebook")"

.gitignore

@@ -69,3 +69,4 @@ pixi.lock
 output_*/
 input/
 *.log
+website/_generated

CONTRIBUTORS.md

@@ -54,4 +54,4 @@ maintain it.
 
 ---
 
-New to the protocol? See [Environment Setup](https://statfungen.github.io/xqtl-protocol/xqtl_protocol_demo.html) to get running, or the [xQTL Analysis Workflow Builder](https://statfungen.github.io/xqtl-protocol/xqtl_protocol_workflow_builder.html) to find the pipelines for your study.
+New to the protocol? See [Environment Setup](https://statfungen.github.io/xqtl-protocol/xqtl-protocol-demo) to get running, or the [xQTL Analysis Workflow Builder](https://statfungen.github.io/xqtl-protocol/xqtl_protocol_workflow_builder.html) to find the pipelines for your study.

README.md

@@ -25,7 +25,7 @@ that route with the commands to run them.
 
 | I want to... | Go to |
 |---|---|
-| **Set up my computing environment** | [Environment Setup](https://statfungen.github.io/xqtl-protocol/xqtl_protocol_demo.html) |
+| **Set up my computing environment** | [Environment Setup](https://statfungen.github.io/xqtl-protocol/xqtl-protocol-demo) |
 | **Work out which pipelines I need** | [xQTL Analysis Workflow Builder](https://statfungen.github.io/xqtl-protocol/xqtl_protocol_workflow_builder.html) |
 
 ## Overview of the protocol

code/SoS/association_scan/TensorQTL/TensorQTL.ipynb

@@ -2,6 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
+   "id": "c57f2ed4",
    "metadata": {
     "kernel": "SoS"
    },
@@ -13,6 +14,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "f9a4a145",
    "metadata": {
     "kernel": "SoS"
    },
@@ -32,6 +34,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "280fd7c1",
    "metadata": {
     "kernel": "SoS"
    },
@@ -75,6 +78,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "ef210a58",
    "metadata": {
     "kernel": "SoS"
    },
@@ -85,6 +89,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
+   "id": "17baa000",
    "metadata": {
     "kernel": "R"
    },
@@ -211,6 +216,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "48374a8e",
    "metadata": {
     "kernel": "SoS"
    },
@@ -221,6 +227,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
+   "id": "72ddf454",
    "metadata": {
     "kernel": "R"
    },
@@ -375,6 +382,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "431b57e2",
    "metadata": {
     "kernel": "SoS"
    },
@@ -385,6 +393,7 @@
   {
    "cell_type": "code",
    "execution_count": 9,
+   "id": "b92a2458",
    "metadata": {
     "kernel": "R"
    },
@@ -578,6 +587,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "f5c7902c",
    "metadata": {
     "kernel": "SoS"
    },
@@ -588,6 +598,7 @@
   {
    "cell_type": "code",
    "execution_count": 10,
+   "id": "fbca14a5",
    "metadata": {
     "kernel": "R"
    },
@@ -665,6 +676,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "a11f0598",
    "metadata": {
     "kernel": "SoS"
    },
@@ -675,6 +687,7 @@
   {
    "cell_type": "code",
    "execution_count": 11,
+   "id": "203e2fb0",
    "metadata": {
     "kernel": "R"
    },
@@ -703,6 +716,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "2dd2644e",
    "metadata": {
     "kernel": "SoS"
    },
@@ -765,6 +779,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "c76f813b",
    "metadata": {
     "kernel": "SoS"
    },
@@ -867,6 +882,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "4c25577a",
    "metadata": {
     "kernel": "SoS"
    },
@@ -878,6 +894,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "613fc631",
    "metadata": {
     "kernel": "SoS"
    },
@@ -889,6 +906,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "6abf80d7",
    "metadata": {
     "kernel": "SoS"
    },
@@ -899,6 +917,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "57eb46a4",
    "metadata": {
     "kernel": "Bash"
    },
@@ -913,6 +932,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "8d378186",
    "metadata": {
     "kernel": "SoS"
    },
@@ -924,6 +944,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "c3b5fb81",
    "metadata": {
     "kernel": "SoS"
    },
@@ -934,6 +955,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "f40a4504",
    "metadata": {
     "kernel": "Bash"
    },
@@ -949,6 +971,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "22ce6ae7",
    "metadata": {
     "kernel": "SoS"
    },
@@ -959,6 +982,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "e75feaee",
    "metadata": {
     "kernel": "Bash"
    },
@@ -969,6 +993,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "a9807227",
    "metadata": {
     "kernel": "SoS"
    },
@@ -1079,6 +1104,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "8df2d07f",
    "metadata": {
     "kernel": "SoS"
    },
@@ -1091,6 +1117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "d079ab12",
    "metadata": {
     "kernel": "SoS"
    },
@@ -1244,6 +1271,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "5e19da07",
    "metadata": {
     "kernel": "SoS"
    },
@@ -1303,6 +1331,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "cdf89360",
    "metadata": {
     "kernel": "SoS"
    },
@@ -1324,6 +1353,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "861aefc3",
    "metadata": {
     "kernel": "SoS"
    },
@@ -1413,5 +1443,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 4
-}
+ "nbformat_minor": 5
+}