MAINT: Dependencies, CI (ruff pin, macOS, release tests) and dead code

.github/workflows/docs.yml

@@ -6,10 +6,11 @@ on:
   pull_request:
     branches: [main]
 
-# Allow only one concurrent deployment
+# One run per branch at a time. Superseded pull request builds are
+# cancelled, but a running deploy from main is never cut off.
 concurrency:
   group: pages-${{ github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
 
 jobs:
   build:

.github/workflows/release.yml

@@ -10,7 +10,24 @@ on:
   workflow_dispatch:
 
 jobs:
+  test:
+    # Never publish a build whose tests fail
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+      - name: Install package and test dependencies
+        run: |
+          pip install -e ".[test]"
+      - name: Run test suite
+        run: |
+          pytest
+
   build:
+    needs: test
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

.github/workflows/tests.yml

@@ -19,13 +19,14 @@ jobs:
         with:
           python-version: "3.12"
       - name: Ruff
+        # Same version as in .pre-commit-config.yaml
         run: |
-          pip install ruff
+          pip install ruff==0.17.1
           ruff check .
           ruff format --check .
 
   test:
-    # Oldest and newest supported Python on Linux, plus Windows
+    # Oldest and newest supported Python on Linux, plus Windows and macOS
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -37,6 +38,8 @@ jobs:
             python-version: "3.13"
           - os: windows-latest
             python-version: "3.13"
+          - os: macos-latest
+            python-version: "3.13"
     steps:
       - uses: actions/checkout@v4
 
@@ -78,7 +81,7 @@ jobs:
 
       - name: Install package with minimum dependency versions
         run: |
-          pip install -e ".[test]" "mne==1.13.0" "mne-bids==0.18.0" "pyprep==0.8.0" "mne-icalabel==0.8.0" "jamica[jax]==0.3.0"
+          pip install -e ".[test]" "mne==1.13.0" "mne-bids==0.18.0" "pyprep==0.8.0" "mne-icalabel==0.8.0" "jamica[jax]==0.3.0" "mne-denoise==0.0.3"
 
       - name: Run test suite
         run: |

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.2
+    rev: v0.17.1  # keep in sync with the ruff pin in tests.yml
     hooks:
       - id: ruff
         name: ruff check --fix

pybemobil/io/utils.py

@@ -13,14 +13,14 @@
 
 
 class NumpyEncoder(json.JSONEncoder):
-    """Help encoding numpy arrays in JSON."""
+    """Help encoding numpy arrays and scalars in JSON."""
 
     def default(self, obj):
-        """Convert numpy arrays and floats to lists and native floats."""
+        """Convert numpy arrays and scalars to lists and native Python types."""
         if isinstance(obj, np.ndarray):
             return obj.tolist()
-        if isinstance(obj, np.float32):
-            return float(obj)
+        if isinstance(obj, np.generic):  # np.int64, np.float32, np.bool_, ...
+            return obj.item()
         return super().default(obj)
 
 

pybemobil/preproc/__init__.py

@@ -15,8 +15,6 @@
 )
 from pybemobil.preproc.utils import (
     StepTimer,
-    _annotate_break_iter,
-    _handle_trans,
     append_desc,
     auto_coreg_fsaverage,
     build_sys_info,
@@ -67,8 +65,6 @@
     # Utilities
     "format_duration",
     "build_sys_info",
-    "_annotate_break_iter",
-    "_handle_trans",
     # Epoching
     "get_stimulus_rename_map",
 ]

pybemobil/preproc/make_report.py

@@ -11,6 +11,7 @@
 import logging
 import os
 import re
+import sys
 import tempfile
 import warnings
 from pathlib import Path
@@ -20,14 +21,17 @@
 import numpy as np
 
 from pybemobil.preproc.utils import format_duration
+from pybemobil.viz.plotting import glue_imgs
 
 # %% Settings & Constants
 
 LOGGER = logging.getLogger(__name__)
 
-_REPORT_N_JOBS = int(os.environ.get("BPN_REPORT_N_JOBS", "1"))
-DIPOLE_PLOT_N_JOBS = _REPORT_N_JOBS
-ICA_REPORT_N_JOBS = _REPORT_N_JOBS
+# Parallel jobs for the ICA section of the report (BPN_REPORT_N_JOBS is the
+# old name of the variable).
+ICA_REPORT_N_JOBS = int(
+    os.environ.get("PYBEMOBIL_REPORT_N_JOBS", os.environ.get("BPN_REPORT_N_JOBS", "1"))
+)
 
 try:
     import seaborn as _sns
@@ -57,12 +61,13 @@ def _add_temp_image(report, fig, *, title, caption="", section=None):
 def _gui_available() -> bool:
     """Return True when a display is available for 3-D rendering.
 
-    On Linux/macOS headless servers ``DISPLAY`` is unset; on Windows the check
-    is skipped (a display is always assumed to be available).
+    On Linux, headless servers have neither ``DISPLAY`` nor
+    ``WAYLAND_DISPLAY`` set. Windows and macOS do not use ``DISPLAY``, so a
+    display is assumed there.
     """
-    if os.name == "nt":
+    if sys.platform in ("win32", "darwin"):
         return True
-    return bool(os.environ.get("DISPLAY", ""))
+    return bool(os.environ.get("DISPLAY") or os.environ.get("WAYLAND_DISPLAY"))
 
 
 def _esc(value) -> str:
@@ -432,29 +437,6 @@ def _add_trans(report, trans, raw_clean, subjects_dir) -> None:
             raise
 
 
-def _glue_imgs(paths: list, out_path: str | Path) -> bool:
-    """Vertically concatenate images at *paths* and save to *out_path*.
-
-    Returns ``True`` on success, ``False`` when Pillow is not available.
-    """
-    try:
-        from PIL import Image
-    except ImportError:
-        warnings.warn("Pillow not available; skipping joint-plot combination.")
-        return False
-
-    imgs = [Image.open(str(p)) for p in paths]
-    w = max(img.width for img in imgs)
-    h = sum(img.height for img in imgs)
-    combined = Image.new("RGB", (w, h), (255, 255, 255))
-    y = 0
-    for img in imgs:
-        combined.paste(img, (0, y))
-        y += img.height
-    combined.save(str(out_path))
-    return True
-
-
 def _safe_label(label: str) -> str:
     """Return *label* reduced to characters that are valid in file names.
 
@@ -508,8 +490,7 @@ def _add_joint_plot(report, evokeds_dict_ave: dict, fname_out: Path | None) -> N
                 combined_path = figdir / "joint-COMBINED.png"
             else:
                 combined_path = Path(tmpdir) / "joint-COMBINED.png"
-            if not _glue_imgs(savenames, combined_path):
-                combined_path = savenames[0]
+            glue_imgs(savenames, combined_path, delete_fnames=False)
 
         report.add_image(str(combined_path), title="Butterfly, GFP, and Topoplots")
 

pybemobil/viz/plotting.py

@@ -60,8 +60,8 @@ def _parametric(data):
 def glue_imgs(fnames, fname, delete_fnames=True):
     """Glue images together.
 
-    Use Pillow to read standard image files from disk and concatenate them vertically.
-    Save the resulting image back to disk.
+    Use Pillow to read standard image files from disk and concatenate them vertically
+    (narrower images are padded with white). Save the resulting image back to disk.
 
     Parameters
     ----------
@@ -83,7 +83,7 @@ def glue_imgs(fnames, fname, delete_fnames=True):
         hx_total += hx
         images.append(img)
 
-    new_img = Image.new("RGB", (wx_max, hx_total))
+    new_img = Image.new("RGB", (wx_max, hx_total), (255, 255, 255))
     y_offset = 0
     for img in images:
         new_img.paste(img, (0, y_offset))

pyproject.toml

@@ -22,19 +22,20 @@ dependencies = [
   "matplotlib",
   "meegkit",
   "mne-bids>=0.18",
-  "mne-denoise",
+  "mne-denoise>=0.0.3",  # ZapLine n_select and adaptive mode (0.0.2 needs Python 3.12)
   "mne-faster",
   "mne-icalabel>=0.8",
   "mne>=1.13",
-  "nibabel",
+  "nibabel",  # not imported directly: MNE reads fsaverage MRIs with it (plots)
   "numpy",
   "onnxruntime",
-  "pandas",
-  "pybv",
+  "Pillow",
+  "pybv",  # not imported directly: MNE exports BrainVision (BIDS) with it
   "pyprep>=0.8",
   "python-picard",
   "pyxdf",
-  "scikit-learn",
+  "scikit-learn",  # not imported directly: MNE's ICA (fastica) and covariances
+  "scipy",
 ]
 description = "MoBI data loading, preprocessing, and visualization built on MNE-Python"
 dynamic = ["version"]
@@ -67,8 +68,11 @@ docs = [
 # (the default).  Optional: compute_ica falls back to picard with a warning
 # when this is not installed.
 jamica = ["jamica[jax]>=0.3"]
+# Nicer ICLabel probability plots in the HTML report (falls back to
+# matplotlib without it)
+report = ["seaborn"]
 # Dependencies for running the test infrastructure
-test = ["pybemobil[jamica]", "pytest", "pytest-cov", "pytest-sugar", "pytest-xdist"]
+test = ["pybemobil[jamica,report]", "pytest", "pytest-cov", "pytest-sugar", "pytest-xdist"]
 
 [project.urls]
 "Bug Tracker" = "https://github.com/BeMoBIL/pybemobil/issues/"
@@ -77,10 +81,13 @@ test = ["pybemobil[jamica]", "pytest", "pytest-cov", "pytest-sugar", "pytest-xdi
 
 [tool.hatch.build]
 exclude = [
-  "**/tests",
   "/.*",
 ]
 
+[tool.hatch.build.targets.sdist]
+# The sdist carries the tests so that downstream packagers can run them.
+include = ["/pybemobil", "/tests", "/doc", "/CITATION.cff", "/README.md", "/LICENSE"]
+
 [tool.hatch.build.targets.wheel]
 packages = ["pybemobil"]
 

tests/test_encoder_display.py

@@ -0,0 +1,48 @@
+"""NumpyEncoder handles numpy scalars; the report's display check per OS."""
+
+import importlib
+import json
+
+import numpy as np
+import pytest
+
+from pybemobil.io.utils import NumpyEncoder
+
+# pybemobil.preproc.make_report is shadowed by the function of that name
+mr = importlib.import_module("pybemobil.preproc.make_report")
+
+
+def test_numpy_encoder_scalars_and_arrays():
+    """Integers, floats, bools and arrays become native JSON values."""
+    data = {
+        "n": np.int64(3),
+        "x": np.float32(0.5),
+        "ok": np.bool_(True),
+        "a": np.arange(3),
+    }
+    assert json.loads(json.dumps(data, cls=NumpyEncoder)) == {
+        "n": 3,
+        "x": 0.5,
+        "ok": True,
+        "a": [0, 1, 2],
+    }
+
+
+@pytest.mark.parametrize(
+    "platform, env, expected",
+    [
+        ("darwin", {}, True),
+        ("win32", {}, True),
+        ("linux", {}, False),
+        ("linux", {"DISPLAY": ":0"}, True),
+        ("linux", {"WAYLAND_DISPLAY": "wayland-0"}, True),
+    ],
+)
+def test_gui_available(monkeypatch, platform, env, expected):
+    """Windows and macOS have a display without DISPLAY; Linux needs one set."""
+    monkeypatch.setattr(mr.sys, "platform", platform)
+    monkeypatch.delenv("DISPLAY", raising=False)
+    monkeypatch.delenv("WAYLAND_DISPLAY", raising=False)
+    for key, value in env.items():
+        monkeypatch.setenv(key, value)
+    assert mr._gui_available() is expected