From be31b087b8c15840f63478da0b3af523eb3d0ff5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?=
 <jon.haitz.legarreta@gmail.com>
Date: Fri, 8 Nov 2024 18:16:15 -0500
Subject: [PATCH] ENH: Add additional environment to `tox` to run notebooks

Add an additional environment to `tox` to run notebooks.

Add a new table to `pyproject.toml` to host the `jupyter`, `nbconvert`
and `nbclient` dependencies so that the notebooks can be run.

Install `textlive` in the test CI so that LaTeX decoration in plots can
be employed.
---
 .github/workflows/test.yml |  4 ++++
 pyproject.toml             |  6 ++++++
 tox.ini                    | 31 +++++++++++++++++++++++++++++--
 3 files changed, 39 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 0293c50..480b2d2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -69,6 +69,10 @@ jobs:
         with:
           path: /home/runner/nifreeze-tests/
           key: data-v0
+      - name: Install TeX Live
+        run: |
+          sudo apt-get update
+          sudo apt install texlive
       - name: Install tox
         run: |
           python -m pip install --upgrade pip
diff --git a/pyproject.toml b/pyproject.toml
index 70ace46..9059ea7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -74,6 +74,12 @@ test = [
     "pytest-xdist >= 1.28"
 ]
 
+notebooks = [
+    "jupyter",
+    "nbconvert",
+    "nbclient",
+]
+
 antsopt = [
     "ConfigSpace",
     "nipreps",
diff --git a/tox.ini b/tox.ini
index 77371e1..1a1655b 100644
--- a/tox.ini
+++ b/tox.ini
@@ -2,13 +2,13 @@
 requires =
   tox>=4
 envlist =
-  py312
+  py312, notebooks
 skip_missing_interpreters = true
 
 # Configuration that allows us to split tests across GitHub runners effectively
 [gh-actions]
 python =
-  3.12: py312
+  3.12: py312, notebooks
 
 [testenv]
 description = Pytest with coverage
@@ -38,6 +38,33 @@ commands =
   pytest --doctest-modules --cov nifreeze -n auto --cov-report xml \
   --junitxml=test-results.xml -v src test {posargs}
 
+[testenv:notebooks]
+description = Run notebooks
+labels = notebooks
+pass_env =
+  # getpass.getuser() sources for Windows:
+  LOGNAME
+  USER
+  LNAME
+  USERNAME
+  # Pass user color preferences through
+  PY_COLORS
+  FORCE_COLOR
+  NO_COLOR
+  CLICOLOR
+  CLICOLOR_FORCE
+  CURBRANCH
+  GITHUB_ACTIONS
+  TEST_DATA_HOME
+  TEST_OUTPUT_DIR
+  TEST_WORK_DIR
+  PYTHONHASHSEED
+  ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
+  PATH
+extras = notebooks
+commands =
+  python -m nbconvert --to notebook --ExecutePreprocessor.kernel_name=python3 --execute docs/notebooks/*
+
 [testenv:docs]
 description = Build documentation site
 labels = docs