Merge pull request #35 from jhlegarreta/RunNotebooksInTox

MAINT: Add additional environment to ``tox`` to run notebooks

Author: oesteban

.github/workflows/test.yml

@@ -70,6 +70,10 @@ jobs:
         with:
           path: /home/runner/nifreeze-tests/
           key: data-v0
+      - name: Install TeX Live
+        run: |
+          sudo apt-get update
+          sudo apt install texlive texlive-latex-extra texlive-fonts-recommended cm-super dvipng
       - name: Install tox
         run: |
           python -m pip install --upgrade pip

docs/notebooks/bold_realignment.ipynb

@@ -34,7 +34,7 @@
     "WORKDIR = Path.home() / \"tmp\" / \"nifreezedev\" / \"ismrm25\"\n",
     "WORKDIR.mkdir(parents=True, exist_ok=True)\n",
     "\n",
-    "OUTPUT_DIR = Path(\"/data/derivatives\") / \"nifreeze-ismrm25-exp2\"\n",
+    "OUTPUT_DIR = Path.home() / \"tmp\" / \"nifreezedev\" / \"ismrm25\" / \"nifreeze-ismrm25-exp2\"\n",
     "OUTPUT_DIR.mkdir(exist_ok=True, parents=True)"
    ]
   },

pyproject.toml

@@ -76,6 +76,14 @@ test = [
     "pytest-xdist >= 1.28"
 ]
 
+notebooks = [
+    "jupyter",
+    "nbclient",
+    "nbmake",
+    "mriqc_learn",
+    "nipreps-synthstrip",
+]
+
 antsopt = [
     "ConfigSpace",
     "nipreps",

tools/run_notebooks.py

@@ -0,0 +1,33 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+
+import glob
+import subprocess
+import sys
+
+notebooks = glob.glob("docs/notebooks/*.ipynb")
+# Make bold_realignment.ipynb Jupyter notebook an exception as it involves running a realignment
+# process for several DataLad datasets, which requires long running times.
+notebooks.remove("docs/notebooks/bold_realignment.ipynb")
+
+sys.exit(subprocess.call(["pytest", "--nbmake"] + notebooks))

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
@@ -39,6 +39,35 @@ 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 =
+   # pytest --nbmake docs/notebooks/*.ipynb
+   # not working due to https://github.com/tox-dev/tox/issues/1571
+   python {toxinidir}/tools/run_notebooks.py
+
 [testenv:docs]
 description = Build documentation site
 labels = docs