From 6beae42e238ff7ec20e73a6a23d8646f7e123705 Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 09:10:35 -0700
Subject: [PATCH 01/13] Use consistent sphinx-build flags in Makefile

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index d4bb2cb..5b2e2f9 100644
--- a/Makefile
+++ b/Makefile
@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
-SPHINXOPTS    ?=
+SPHINXOPTS    ?= -n -W -T --keep-going
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build

From 050ac9000f4350a207fc9b3950dcc1e1a421d69c Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 09:11:11 -0700
Subject: [PATCH 02/13] Trivial: rename file

---
 .github/workflows/{ci_tests_run_notebooks.yml => ci.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{ci_tests_run_notebooks.yml => ci.yml} (100%)

diff --git a/.github/workflows/ci_tests_run_notebooks.yml b/.github/workflows/ci.yml
similarity index 100%
rename from .github/workflows/ci_tests_run_notebooks.yml
rename to .github/workflows/ci.yml

From 4f0b73ee2bf3f2d2c63835fbee9029e60f6c8084 Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 09:12:46 -0700
Subject: [PATCH 03/13] Namespace tox jobs in prep for adding more.

---
 .github/workflows/ci.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 523c9df..87e9bf6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,7 +16,7 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  tests:
+  tox_test:
     name: ${{ matrix.os }} ${{ matrix.name }}
     runs-on: ${{ matrix.os }}
     strategy:
@@ -52,8 +52,7 @@ jobs:
     - name: Test with tox
       run: tox ${{ matrix.toxargs }} -e ${{ matrix.toxenv }} -- ${{ matrix.toxposargs }}
 
-
-  gha_buildhtml:
+  tox_build:
     name: Buildhtml testing
     runs-on: ubuntu-latest
     steps:

From 13b2b3d956c9f2af886f1d8b28c19cb657aac279 Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 09:26:03 -0700
Subject: [PATCH 04/13] WIP

---
 .github/workflows/ci.yml | 35 ++++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 87e9bf6..45e17df 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -22,7 +22,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # Run all supported OS for one Python version, then add a few extra scenarios
+        # Run all supported OS for one Python version.
+        # The test additional Python versions on Linux only.
         os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ['3.12']
         toxenv: [py312-test]
@@ -68,3 +69,35 @@ jobs:
 
       - name: Execute notebooks as testing
         run: tox -e py311-buildhtml
+
+  pixi_test:
+    name: ${{ matrix.os }} ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Run all supported OS for one Python version, then add a few extra scenarios
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.12']
+        toxenv: [py312-test]
+        name: ['with Python 3.12',]
+        include:
+          - python-version: '3.10'
+            toxenv: py310-test-oldestdeps
+            name: with Python 3.10 and oldest versioned dependencies
+            os: ubuntu-latest
+
+          - python-version: '3.13'
+            toxenv: py313-test-devdeps
+            name: with Python 3.13 and developer versioned dependencies
+            os: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+
+    - name: Setup pixi
+      uses: prefix-dev/setup-pixi@v0.8.1
+
+    - name: Test all files
+      run: pixi run ./test.sh --all

From 6fb0bd455c77f052508f2d1daaeeed502464a629 Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 10:10:51 -0700
Subject: [PATCH 05/13] Refactored test works on pixi

---
 pixi.toml  |  2 ++
 pytest.ini |  2 ++
 test.sh    | 36 ++++++++++++++++++++++++++++++++++++
 3 files changed, 40 insertions(+)
 create mode 100644 pytest.ini
 create mode 100755 test.sh

diff --git a/pixi.toml b/pixi.toml
index 2a2bde1..42c23ab 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -33,6 +33,8 @@ 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"
 
 [pypi-dependencies]
 sphinx = ">=8.0.2"
diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 0000000..041ccff
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,2 @@
+[pytest]
+norecursedirs = _build
diff --git a/test.sh b/test.sh
new file mode 100755
index 0000000..5ec7964
--- /dev/null
+++ b/test.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+# Collect converted ipynb files to clean up at the end.
+notebook_files=()
+
+# Find Markdown files convert.
+all_markdown_files=$(find tutorials -type f -name "*.md")
+if [ $# -gt 0 ]; then
+    files_to_process="$@"
+else
+    files_to_process=$all_markdown_files
+fi
+
+# Identify Markdown files that are Jupytext and convert them all.
+for file in ${files_to_process}; do
+    echo loop in $file
+    # Extract the kernel information from the Jupytext Markdown file.
+    kernel_info=$(grep -A 10 '^---$' "$file" | grep -E 'kernelspec')
+    # Skip if no kernel information was found.
+    if [ -z "$kernel_info" ]; then
+        continue
+    fi
+    # Convert to ipynb format, to be consumed by pytest nbval plugin.
+    jupytext --to ipynb "$file"
+    notebook_file="${file%.md}.ipynb"
+    # Stash file in array to be cleaned up at the end.
+    notebook_files+=("${notebook_file}")
+done
+
+pytest --nbval-lax
+
+# Clean up ipynb files that were converted.  Any stray ipynb files that were
+# _not_ the result of conversion from Markdown will be left alone.
+for file in "${notebook_files[@]}"; do
+    rm -v "$file"
+done

From 6217fecd94a884d272e71b5597d6e7e4af64b0f2 Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 10:16:43 -0700
Subject: [PATCH 06/13] Fix usage

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 45e17df..3421e23 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -42,6 +42,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
@@ -94,7 +95,6 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
 
     - name: Setup pixi
       uses: prefix-dev/setup-pixi@v0.8.1

From eadb82c2ba98ff5e70d33637e99382f73b81b0a4 Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 10:19:56 -0700
Subject: [PATCH 07/13] Add pixi 'test' task

---
 .github/workflows/ci.yml | 2 +-
 pixi.toml                | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3421e23..ae4267f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -100,4 +100,4 @@ jobs:
       uses: prefix-dev/setup-pixi@v0.8.1
 
     - name: Test all files
-      run: pixi run ./test.sh --all
+      run: pixi run test
diff --git a/pixi.toml b/pixi.toml
index 42c23ab..b784cec 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -23,6 +23,7 @@ build = { cmd = [
 ] }
 clean = "rm -rf _build/*"
 start = "jupyter lab"
+test = "./test.sh"
 
 [activation]
 scripts = ["setup_jupyterlab_config.sh"]

From 6ce89fdf76b23933f0dc5eacdf7183405a1186e1 Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 10:21:52 -0700
Subject: [PATCH 08/13] Tweak job title

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ae4267f..64ad1e1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,4 +1,4 @@
-name: Test notebooks
+name: Test
 
 on:
   push:

From 31922e6c464328336a68bf318c6b1d768e08e562 Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 10:26:24 -0700
Subject: [PATCH 09/13] Specify bash for Windows CI

---
 pixi.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pixi.toml b/pixi.toml
index b784cec..6bd7d4b 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -23,7 +23,7 @@ build = { cmd = [
 ] }
 clean = "rm -rf _build/*"
 start = "jupyter lab"
-test = "./test.sh"
+test = "bash ./test.sh"
 
 [activation]
 scripts = ["setup_jupyterlab_config.sh"]

From 96da664dfd06e37e5fa53a5ff123e49f17772b1d Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 10:50:22 -0700
Subject: [PATCH 10/13] Bump to Python 3.11

---
 .github/workflows/ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 64ad1e1..7e577a2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -30,9 +30,9 @@ jobs:
         name: ['with Python 3.12',]
 
         include:
-          - python-version: '3.10'
-            toxenv: py310-test-oldestdeps
-            name: with Python 3.10 and oldest versioned dependencies
+          - python-version: '3.11'
+            toxenv: py311-test-oldestdeps
+            name: with Python 3.11 and oldest versioned dependencies
             os: ubuntu-latest
 
           - python-version: '3.13'

From 0985329262f0f7d9eb900deb804a129420acd716 Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 10:50:30 -0700
Subject: [PATCH 11/13] Test over a matrix of pixi environments.

---
 .github/workflows/ci.yml | 17 ++---------------
 pixi.toml                |  8 ++++++++
 2 files changed, 10 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7e577a2..dc26fc8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -72,27 +72,14 @@ jobs:
         run: tox -e py311-buildhtml
 
   pixi_test:
-    name: ${{ matrix.os }} ${{ matrix.name }}
+    name: ${{ matrix.os }} with ${{ matrix.environment}}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         # Run all supported OS for one Python version, then add a few extra scenarios
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.12']
-        toxenv: [py312-test]
-        name: ['with Python 3.12',]
-        include:
-          - python-version: '3.10'
-            toxenv: py310-test-oldestdeps
-            name: with Python 3.10 and oldest versioned dependencies
-            os: ubuntu-latest
-
-          - python-version: '3.13'
-            toxenv: py313-test-devdeps
-            name: with Python 3.13 and developer versioned dependencies
-            os: ubuntu-latest
-
+        environment: [py311, py312]
     steps:
     - uses: actions/checkout@v4
 
diff --git a/pixi.toml b/pixi.toml
index 6bd7d4b..c83a7bb 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -44,6 +44,12 @@ jupytext = ">=1.16"
 sphinx-book-theme = ">=1.1"
 sphinx-copybutton = ">=0.5"
 
+[feature.py312.dependencies]
+python = "3.12.*"
+
+[feature.py313.dependencies]
+python = "3.13.*"
+
 [feature.jupyterlite.dependencies]
 jupyterlab = "~=4.2.4"
 jupyterlite-core = "==0.4.0"
@@ -51,4 +57,6 @@ jupyterlite-pyodide-kernel = "==0.4.1"
 notebook = "~=7.2.1"
 
 [environments]
+py312 = ["py312"]
+py313 = ["py313"]
 jupyterlite = ["jupyterlite"]

From 65c7f015157e31babe80ead55675cf30210e3042 Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 10:58:40 -0700
Subject: [PATCH 12/13] Tweak names

---
 .github/workflows/ci.yml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index dc26fc8..87fb4f6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -17,7 +17,7 @@ concurrency:
 
 jobs:
   tox_test:
-    name: ${{ matrix.os }} ${{ matrix.name }}
+    name: tox on ${{ matrix.os }} with ${{ matrix.name }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -27,17 +27,17 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ['3.12']
         toxenv: [py312-test]
-        name: ['with Python 3.12',]
+        name: ['Python 3.12',]
 
         include:
           - python-version: '3.11'
             toxenv: py311-test-oldestdeps
-            name: with Python 3.11 and oldest versioned dependencies
+            name: Python 3.11 and oldest versioned dependencies
             os: ubuntu-latest
 
           - python-version: '3.13'
             toxenv: py313-test-devdeps
-            name: with Python 3.13 and developer versioned dependencies
+            name: Python 3.13 and developer versioned dependencies
             os: ubuntu-latest
 
     steps:
@@ -55,7 +55,7 @@ jobs:
       run: tox ${{ matrix.toxargs }} -e ${{ matrix.toxenv }} -- ${{ matrix.toxposargs }}
 
   tox_build:
-    name: Buildhtml testing
+    name: Build static site with tox
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -63,16 +63,16 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Install dependencies
         run: python -m pip install --upgrade tox
 
-      - name: Execute notebooks as testing
-        run: tox -e py311-buildhtml
+      - name: Build static site
+        run: tox -e py312-buildhtml
 
   pixi_test:
-    name: ${{ matrix.os }} with ${{ matrix.environment}}
+    name: pixi on ${{ matrix.os }} with ${{ matrix.environment}}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false

From 2fc5f2e605d28e44d834bbbf3c454cdd5e5ff164 Mon Sep 17 00:00:00 2001
From: Dan Allan <dallan@bnl.gov>
Date: Tue, 13 May 2025 10:58:44 -0700
Subject: [PATCH 13/13] Add pixi_build job.

---
 .github/workflows/ci.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 87fb4f6..8587102 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -88,3 +88,15 @@ jobs:
 
     - name: Test all files
       run: pixi run test
+
+  pixi_build:
+    name: Build static 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 static site
+      run: pixi run build