Fix handling of README files with extensions (#1318)

* we have a failing test!

* lint fixes

* check for existing README with all allowed extensions and use that one.

* updated whats new

* fix scope

* Update doc/whats_new.rst

Co-authored-by: Daniel McCloy <[email protected]>

* remove extra print command

Co-authored-by: Daniel McCloy <[email protected]>

* do not cast to str

* throw exception when more than one readme is encountered.

* added a test for multiple readmes

---------

Co-authored-by: Daniel McCloy <[email protected]>

doc/whats_new.rst

@@ -59,6 +59,7 @@ Detailed list of changes
 - Dealing with alphanumeric ``sub`` entity labels is now fixed for :func:`~mne_bids.write_raw_bids`, by `Aaron Earle-Richardson`_ (:gh:`1291`)
 - When processing subject_info data that MNE Python imports as numpy arrays with only one item, MNE-BIDS now unpacks these, resulting in a correct participants.tsv, by `Thomas Hartmann`_ (:gh:`1310`)
 - Fixed broken links in examples 7 and 8, by `William Turner`_ (:gh:`1316`)
+- All valid extensions for ``README`` files are now accepted. This prevents an extra ``README`` file being created, when one with a ``.txt``, ``.md``, or ``.rst`` extension is already present. By `Thomas Hartmann`_ (:gh:`1318`)
 
 ⚕️ Code health
 ^^^^^^^^^^^^^^

mne_bids/tests/test_update.py

@@ -5,6 +5,7 @@
 
 import json
 import os.path as op
+import shutil
 from pathlib import Path
 
 import mne
@@ -38,7 +39,7 @@
 )
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="function")
 def _get_bids_test_dir(tmp_path_factory):
     """Return path to a written test BIDS dir."""
     bids_root = str(tmp_path_factory.mktemp("mnebids_utils_test_bids_ds"))
@@ -76,7 +77,7 @@ def _get_bids_test_dir(tmp_path_factory):
     return bids_root
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="function")
 def _get_sidecar_json_update_file(_get_bids_test_dir):
     """Return path to a sidecar JSON updating file."""
     bids_root = _get_bids_test_dir
@@ -292,3 +293,57 @@ def test_update_anat_landmarks(tmp_path):
         assert np.allclose(
             mri_json["AnatomicalLandmarkCoordinates"][landmark], expected_coords
         )
+
+
+@testing.requires_testing_data
+@pytest.mark.parametrize("extension", [None, ".txt", ".rst", ".md"])
+def test_readme_conflicts(extension, _get_bids_test_dir):
+    """Test that exisiting README files are respected with any extension."""
+    bids_root = _get_bids_test_dir
+    assert Path(bids_root, "README").exists()
+    all_readmes = Path(bids_root).rglob("README*")
+    assert len(list(all_readmes)) == 1
+    if extension is not None:
+        shutil.move(Path(bids_root, "README"), Path(bids_root, f"README{extension}"))
+
+    bids_path = BIDSPath(
+        subject="02",
+        session=session_id,
+        run=1,
+        acquisition=acq,
+        task=task,
+        suffix="meg",
+        root=_get_bids_test_dir,
+    )
+
+    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw = mne.io.read_raw_fif(raw_fname)
+
+    write_raw_bids(raw, bids_path, overwrite=False)
+    all_readmes = Path(bids_root).rglob("README*")
+    assert len(list(all_readmes)) == 1
+    shutil.rmtree(bids_root)
+
+
+@testing.requires_testing_data
+def test_multiple_readmes_invalid(_get_bids_test_dir):
+    """Test that multiple README files are not allowed."""
+    bids_root = _get_bids_test_dir
+    assert Path(bids_root, "README").exists()
+    shutil.copy(Path(bids_root, "README"), Path(bids_root, "README.md"))
+    bids_path = BIDSPath(
+        subject="02",
+        session=session_id,
+        run=1,
+        acquisition=acq,
+        task=task,
+        suffix="meg",
+        root=_get_bids_test_dir,
+    )
+
+    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw = mne.io.read_raw_fif(raw_fname)
+
+    with pytest.raises(RuntimeError, match="Multiple README files found"):
+        write_raw_bids(raw, bids_path, overwrite=False)
+    shutil.rmtree(bids_root)

mne_bids/write.py

@@ -1955,7 +1955,18 @@ def write_raw_bids(
     )
 
     # For the remaining files, we can use BIDSPath to alter.
-    readme_fname = op.join(bids_path.root, "README")
+    readme_suffixes = ("", ".md", ".rst", ".txt")
+    found_readmes = sorted(
+        filter(lambda x: x.suffix in readme_suffixes, bids_path.root.glob("README*"))
+    )
+    if len(found_readmes) > 1:
+        raise RuntimeError(
+            "Multiple README files found in the BIDS root folder. "
+            "This violates the BIDS specifications. "
+            "Please ensure there is only one README file."
+        )
+    readme_fname = str((found_readmes or [bids_path.root / "README"])[0])
+
     participants_tsv_fname = op.join(bids_path.root, "participants.tsv")
     participants_json_fname = participants_tsv_fname.replace(".tsv", ".json")