Merge branch 'master' of github.com:nipreps/nibabies into pr/278

Author: mgxd

.github/workflows/pytest.yml

@@ -45,7 +45,6 @@ jobs:
         source /tmp/venv/bin/activate
         pytest -sv --doctest-modules --cov nibabies --cov-report xml nibabies
     - name: Submit coverage
-      run: |
-        # Pin codecov version to reduce scope for malicious updates
-        python -m pip install "codecov==2.1.11"
-        python -m codecov --file coverage.xml
+      uses: codecov/codecov-action@v3
+      with:
+        files: coverage.xml

nibabies/interfaces/mcribs.py

@@ -183,6 +183,12 @@ def _setup_directory_structure(self, mcribs_dir: Path) -> None:
                 surfrec.parent.mkdir(**mkdir_kw)
                 if not surfrec.exists():
                     surfrec.symlink_to(f'../../../RawT2/{sid}.nii.gz')
+
+        if self.inputs.surfrecon:
+            # Create FreeSurfer layout to safeguard against cd-ing into missing directories
+            for d in ('surf', 'mri', 'label', 'scripts', 'stats'):
+                (root / 'freesurfer' / sid / d).mkdir(**mkdir_kw)
+
         # TODO?: T1w -> <subject_id>/RawT1RadiologicalIsotropic/<subjectid>.nii.gz
         return
 

pyproject.toml

@@ -65,7 +65,6 @@ maint = [
 ]
 test = [
     "coverage",
-    "codecov",
     "pytest",
     "pytest-cov",
     "pytest-env",