add another notebook

Author: Remi-Gau

.github/workflows/test_with_tox.yml

@@ -8,6 +8,9 @@ on:
     pull_request:
         branches:
         -   '*'
+    schedule:
+    -   cron: 0 8 1 * *
+    workflow_dispatch:
 
 concurrency:
     group: ${{ github.workflow }}-${{ github.ref }}
@@ -27,7 +30,7 @@ jobs:
         strategy:
             fail-fast: true
             matrix:
-                py: ['3.13', '3.12', '3.11']
+                py: ['3.13', '3.12', '3.11', '3.10', '3.9']
                 os: [ubuntu-latest]
         steps:
         -   uses: actions/checkout@v4
@@ -43,11 +46,4 @@ jobs:
             run: tox c
         -   name: Run test suite
             run: |
-                tox run --list-dependencies -e test -- poia/poia.py
-
-        -   name: Upload coverage to CodeCov
-            uses: codecov/codecov-action@v5
-            with:
-                flags: ${{ matrix.os }}_${{ matrix.py }}
-                token: ${{ secrets.CODECOV_TOKEN }}
-            if: success()
+                tox run --list-dependencies -e test

.pre-commit-config.yaml

@@ -46,11 +46,9 @@ repos:
     hooks:
     # Run the linter.
     -   id: ruff
-        # args: [--statistics]
         args: [--fix, --show-fixes]
     # Run the formatter.
     -   id: ruff-format
-        # args: [--diff]
 
 -   repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.15.0

notebooks/nilearn_notebooks_stable.py

@@ -0,0 +1,178 @@
+# /// script
+# requires-python = ">=3.9"
+# dependencies = [
+#     "marimo",
+#     "matplotlib",
+#     "nilearn==0.11.1",
+#     "numpy==2.2.4",
+# ]
+# ///
+
+import marimo
+
+__generated_with = "0.12.0"
+app = marimo.App(width="medium", app_title="nilearn stable")
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(
+        r"""
+        # Using nilearn in a marimo notebook
+
+        This notebook is mostly for nilearn developpers
+        to make sure nilearn functionalities run well
+        in a marimo notebook.
+
+        But this can serve as an starting point
+        for anyone to start using nilearn
+        in a marimo notebook.
+        """
+    )
+    return
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""## Volume plotting""")
+    return
+
+
+@app.cell
+def _(mo):
+    from nilearn.datasets import load_mni152_template
+    from nilearn.plotting import plot_img, show
+
+    template = load_mni152_template()
+    img_fig = plot_img(template)
+    show()
+
+    mo.md("Basic plotting of template.")
+    return img_fig, load_mni152_template, plot_img, show, template
+
+
+@app.cell
+def _(mo, show):
+    from nilearn.datasets import load_sample_motor_activation_image
+    from nilearn.plotting import plot_stat_map
+
+    motor_activation_image = load_sample_motor_activation_image()
+    stat_map_fig = plot_stat_map(motor_activation_image)
+    show()
+
+    mo.md("Basic plotting of statistical map.")
+    return (
+        load_sample_motor_activation_image,
+        motor_activation_image,
+        plot_stat_map,
+        stat_map_fig,
+    )
+
+
+@app.cell
+def _(mo, motor_activation_image, show):
+    from nilearn.plotting import plot_glass_brain
+
+    plot_glass_brain(motor_activation_image, threshold=3)
+    show()
+
+    mo.md("Basic plotting of a glass brain.")
+    return (plot_glass_brain,)
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""Interactive image ⬇️""")
+    return
+
+
+@app.cell
+def _(motor_activation_image):
+    from nilearn.plotting import view_img
+    html_fig = view_img(motor_activation_image)
+    html_fig
+    return html_fig, view_img
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""## Surface plotting""")
+    return
+
+
+@app.cell
+def _(mo, motor_activation_image, show):
+    from nilearn.datasets import load_fsaverage
+    from nilearn.surface import SurfaceImage
+    import numpy as np
+    from nilearn.plotting import plot_surf_stat_map
+    from nilearn.datasets import load_fsaverage_data
+
+    fsaverage_meshes = load_fsaverage()
+
+    surface_image = SurfaceImage.from_volume(
+        mesh=fsaverage_meshes["pial"],
+        volume_img=motor_activation_image,
+    )
+
+    curv_sign = load_fsaverage_data(data_type="curvature")
+
+    fig = plot_surf_stat_map(
+        stat_map=surface_image,
+        surf_mesh=fsaverage_meshes["inflated"],
+        title="Surface with matplotlib",
+        threshold=1.0,
+        bg_map=curv_sign,
+    )
+    show()
+
+    mo.md("Basic surface plotting.")
+    return (
+        SurfaceImage,
+        curv_sign,
+        fig,
+        fsaverage_meshes,
+        load_fsaverage,
+        load_fsaverage_data,
+        np,
+        plot_surf_stat_map,
+        surface_image,
+    )
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""Interactive surface viewing""")
+    return
+
+
+@app.cell
+def _(curv_sign, fsaverage_meshes, surface_image):
+    from nilearn.plotting import view_surf
+
+    view_surf(
+        surf_mesh=fsaverage_meshes["inflated"],
+        surf_map=surface_image,
+        threshold="90%",
+        bg_map=curv_sign,
+        title="3D visualization in a web browser",
+    )
+    return (view_surf,)
+
+
+@app.cell
+def _(motor_activation_image):
+    from nilearn.plotting import view_img_on_surf
+
+    view_img_on_surf(motor_activation_image, threshold="90%")
+    return (view_img_on_surf,)
+
+
+@app.cell
+def _():
+    import marimo as mo
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()

pyproject.toml

@@ -9,15 +9,9 @@ warn_unreachable = false
 
 [[tool.mypy.overrides]]
 ignore_missing_imports = true
-module = [
-    "plotly.*",
-    "matplotlib.*",
-    "marimo.*",
-    "nilearn.*"
-]
+module = ["plotly.*", "matplotlib.*", "marimo.*", "nilearn.*"]
 
 [tool.ruff]
-include = ["pyproject.toml", "poia"]
 indent-width = 4
 line-length = 100
 
@@ -30,7 +24,6 @@ quote-style = "double"
 skip-magic-trailing-comma = false
 
 [tool.ruff.lint]
-dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 fixable = ["ALL"]
 ignore = [
     "B018",
@@ -88,7 +81,7 @@ select = [
 unfixable = []
 
 [tool.ruff.lint.mccabe]
-max-complexity = 29
+max-complexity = 15
 
 [tool.ruff.lint.per-file-ignores]
 "notebooks/**/*.py" = ["E501", "E741"]
@@ -101,7 +94,7 @@ convention = "numpy"
 # https://docs.astral.sh/ruff/settings/#lint_pylint_max-args
 max-args = 15
 # https://docs.astral.sh/ruff/settings/#lint_pylint_max-branches
-max-branches = 33
+max-branches = 15
 # https://docs.astral.sh/ruff/settings/#lint_pylint_max-returns
 max-returns = 10
 # https://docs.astral.sh/ruff/settings/#lint_pylint_max-statements

scripts/build.py

@@ -91,7 +91,11 @@ def generate_index(all_notebooks: list[str], output_dir: str) -> None:
 
 def main() -> None:
     parser = argparse.ArgumentParser(description="Build marimo notebooks")
-    parser.add_argument("--output-dir", default="_site", help="Output directory for built files")
+    parser.add_argument(
+        "--output-dir",
+        default="_site",
+        help="Output directory for built files",
+    )
     args = parser.parse_args()
 
     all_notebooks: list[str] = []

tox.ini

@@ -39,3 +39,13 @@ deps =
 commands =
     python scripts/build.py
 
+[testenv:test]
+description = Run tests on latest version of all dependencies.
+passenv = {[global_var]passenv}
+deps =
+    marimo
+    nilearn[plotly]
+    pytest
+commands =
+    python notebooks/intro_to_marimo.py
+    python notebooks/nilearn_notebooks_stable.py