From 102342538901e90f25399118e4301c45056b8ef4 Mon Sep 17 00:00:00 2001
From: vferat <victor.ferat@live.fr>
Date: Sun, 15 Dec 2024 11:31:29 +0100
Subject: [PATCH] Update test_commands.py

---
 mne/commands/tests/test_commands.py | 82 ++++++++++++++++++-----------
 1 file changed, 51 insertions(+), 31 deletions(-)

diff --git a/mne/commands/tests/test_commands.py b/mne/commands/tests/test_commands.py
index ae885d3c21d..82d0f7f3a11 100644
--- a/mne/commands/tests/test_commands.py
+++ b/mne/commands/tests/test_commands.py
@@ -167,55 +167,75 @@ def test_kit2fiff():
     check_usage(mne_kit2fiff, force_help=True)
 
 
-@pytest.mark.slowtest
 @pytest.mark.ultraslowtest
 @testing.requires_testing_data
+@requires_freesurfer("mkheadsurf")
 def test_make_scalp_surfaces(tmp_path, monkeypatch):
     """Test mne make_scalp_surfaces."""
     pytest.importorskip("nibabel")
     pytest.importorskip("pyvista")
     check_usage(mne_make_scalp_surfaces)
-    has = "SUBJECTS_DIR" in os.environ
-    # Copy necessary files to avoid FreeSurfer call
+
     tempdir = str(tmp_path)
-    surf_path = op.join(subjects_dir, "sample", "surf")
-    surf_path_new = op.join(tempdir, "sample", "surf")
-    os.mkdir(op.join(tempdir, "sample"))
-    os.mkdir(surf_path_new)
-    subj_dir = op.join(tempdir, "sample", "bem")
-    os.mkdir(subj_dir)
+    t1_path = op.join(subjects_dir, "sample", "mri", "T1.mgz")
+    t1_path_new = op.join(tempdir, "sample", "mri", "T1.mgz")
 
-    cmd = ("-s", "sample", "--subjects-dir", tempdir)
-    monkeypatch.setattr(
-        mne.bem,
-        "decimate_surface",
-        lambda points, triangles, n_triangles: (points, triangles),
-    )
-    dense_fname = op.join(subj_dir, "sample-head-dense.fif")
-    medium_fname = op.join(subj_dir, "sample-head-medium.fif")
+    headseg_path = op.join(tempdir, "sample", "mri", "seghead.mgz")
+    surf_path = op.join(tempdir, "sample", "surf", "lh.seghead")
+    dense_fname = op.join(tempdir, "sample", "bem", "sample-head-dense.fif")
+    medium_fname = op.join(tempdir, "sample", "bem", "sample-head-medium.fif")
+    sparse_fname = op.join(tempdir, "sample", "bem", "sample-head-sparse.fif")
+
+    os.makedirs(op.join(tempdir, "sample", "mri"), exist_ok=True) 
+    os.makedirs(op.join(tempdir, "sample", "surf"), exist_ok=True) 
+
+    shutil.copy(op.join(t1_path, t1_path_new))
+    cmd = ("-s", "sample", "--subjects-dir", tempdir, "--no-decimate")
     with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
         monkeypatch.delenv("FREESURFER_HOME", raising=False)
         with pytest.raises(RuntimeError, match="The FreeSurfer environ"):
             mne_make_scalp_surfaces.run()
-        shutil.copy(op.join(surf_path, "lh.seghead"), surf_path_new)
-        monkeypatch.setenv("FREESURFER_HOME", tempdir)
+
+        shutil.copy(op.join(t1_path, t1_path_new))
         mne_make_scalp_surfaces.run()
+
+        assert op.isfile(headseg_path)
+        assert op.isfile(surf_path)
         assert op.isfile(dense_fname)
-        assert op.isfile(medium_fname)
-        with pytest.raises(OSError, match="overwrite"):
+        assert not op.isfile(medium_fname)
+        assert not op.isfile(sparse_fname)
+
+    cmd = ("-s", "sample", "--subjects-dir", tempdir)
+    with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
+        with pytest.raises(RuntimeError, match="use --overwrite to overwrite it"):
             mne_make_scalp_surfaces.run()
-    # actually check the outputs
-    head_py = read_bem_surfaces(dense_fname)
-    assert_equal(len(head_py), 1)
-    head_py = head_py[0]
-    head_c = read_bem_surfaces(
-        op.join(subjects_dir, "sample", "bem", "sample-head-dense.fif")
-    )[0]
-    assert_allclose(head_py["rr"], head_c["rr"])
-    if not has:
-        assert "SUBJECTS_DIR" not in os.environ
 
+    cmd = ("-s", "sample", "--subjects-dir", tempdir, "--overwrite")
+    with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
+        mne_make_scalp_surfaces.run()
+        assert op.isfile(headseg_path)
+        assert op.isfile(surf_path)
+        assert op.isfile(dense_fname)
+        assert op.isfile(medium_fname)
+        assert op.isfile(sparse_fname)
 
+    cmd = ("-s", "sample", "--subjects-dir", tempdir, "--no-decimate", "--overwrite")
+    with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
+        mne_make_scalp_surfaces.run()
+        assert op.isfile(headseg_path)
+        assert op.isfile(surf_path)
+        assert op.isfile(dense_fname)
+        assert not op.isfile(medium_fname)
+        assert not op.isfile(sparse_fname)
+    
+    os.remove(headseg_path)
+    os.remove(surf_path)
+    os.remove(dense_fname)
+    cmd = ("-s", "sample", "--subjects-dir", tempdir, "--no-decimate")
+    with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
+        with pytest.raises(RuntimeError, match="Trying to generate new scalp surfaces"):
+            mne_make_scalp_surfaces.run()
+    
 @pytest.mark.slowtest
 @testing.requires_testing_data
 def test_report(tmp_path):