MAINT: Update BIDS Validator infrastructure (#1303)

* try remove error

* remove env vars, simplify install

* updates to bids-validator infrastructure

.github/workflows/unit_tests.yml

@@ -208,29 +208,26 @@ jobs:
       if: matrix.bids-validator-version == 'validator-stable'
       run: |
         npm install -g bids-validator
-        echo "BIDS_VALIDATOR_BRANCH=stable" >> $GITHUB_ENV
 
     - name: Download BIDS validator (main)
       if: matrix.bids-validator-version == 'validator-main'
       run: |
         pushd ..
         git clone --depth 1 https://github.com/bids-standard/bids-validator
         popd
-        echo "BIDS_VALIDATOR_BRANCH=main" >> $GITHUB_ENV
 
     - name: Install BIDS validator (main)
       if: matrix.bids-validator-version == 'validator-main'
       run: |
-        pushd ..
-        cd bids-validator
+        pushd ../bids-validator
         # Generate the full development node_modules
         npm install
         # Build & bundle the bids-validator CLI package
         npm -w bids-validator run build
         # Generate a package to install globally
         npm -w bids-validator pack
         # Install the package globally
-        bash -c "npm install -g bids-validator-*.tgz"
+        npm install -g bids-validator-*.tgz
         popd
 
     - name: Display versions and environment information

CONTRIBUTING.md

@@ -153,13 +153,6 @@ you can then simply use the following command from the root of the `mne-bids` re
 make test
 ```
 
-If you have installed the `bids-validator` on a per-user basis (that is, *not* globally),
-set the environment variable `VALIDATOR_EXECUTABLE` to point to the path of the `bids-validator` before invoking `pytest`:
-
-```Shell
-VALIDATOR_EXECUTABLE=../bids-validator/bids-validator/bin/bids-validator pytest
-```
-
 ## Building the documentation
 
 The documentation can be built using [Sphinx](https://www.sphinx-doc.org).

mne_bids/tests/conftest.py

@@ -3,36 +3,24 @@
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause
 
-import os
 import platform
 
 import pytest
 from mne.utils import run_subprocess
 
 
-# WINDOWS issues:
-# the bids-validator development version does not work properly on Windows as
-# of 2019-06-25 --> https://github.com/bids-standard/bids-validator/issues/790
-# As a workaround, we try to get the path to the executable from an environment
-# variable VALIDATOR_EXECUTABLE ... if this is not possible we assume to be
-# using the stable bids-validator and make a direct call of bids-validator
-# also: for windows, shell = True is needed to call npm, bids-validator etc.
-# see: https://stackoverflow.com/q/28891053/5201771
 @pytest.fixture(scope="session")
 def _bids_validate():
     """Fixture to run BIDS validator."""
-    vadlidator_args = ["--config.error=41"]
-    exe = os.getenv("VALIDATOR_EXECUTABLE", "bids-validator")
-
+    # See: https://stackoverflow.com/q/28891053/5201771
+    # On Windows, shell must be True
     if platform.system() == "Windows":
         shell = True
     else:
         shell = False
 
-    bids_validator_exe = [exe, *vadlidator_args]
-
     def _validate(bids_root):
-        cmd = [*bids_validator_exe, bids_root]
+        cmd = ["bids-validator", bids_root]
         run_subprocess(cmd, shell=shell)
 
     return _validate

mne_bids/tests/test_report.py

@@ -45,7 +45,8 @@ def test_report(tmp_path):
 
     report = make_report(bids_root)
 
-    expected_report = f"""This dataset was created by [Unspecified] and conforms to BIDS version {BIDS_VERSION}.
+    expected_report = f""" The [Unspecified] dataset was created by [Unspecified1], and [Unspecified2] and
+conforms to BIDS version {BIDS_VERSION}.
 This report was generated with MNE-BIDS (https://doi.org/10.21105/joss.01896).
 The dataset consists of 1 participants (sex were all unknown; handedness were
 all unknown; ages all unknown) and 1 recording sessions: 01. Data was recorded
@@ -79,7 +80,8 @@ def test_report_no_participant_information(tmp_path):
 
     report = make_report(bids_root)
 
-    expected_report = f"""This dataset was created by [Unspecified] and conforms to BIDS version {BIDS_VERSION}.
+    expected_report = f""" The [Unspecified] dataset was created by [Unspecified1], and [Unspecified2] and
+conforms to BIDS version {BIDS_VERSION}.
 This report was generated with MNE-BIDS (https://doi.org/10.21105/joss.01896).
 The dataset consists of 1 participants (sex were all unknown; handedness were
 all unknown; ages all unknown) and 1 recording sessions: 01. Data was recorded

mne_bids/tests/test_write.py

@@ -350,7 +350,10 @@ def test_make_dataset_description(tmp_path, monkeypatch):
 
     with open(op.join(tmp_path, "dataset_description.json"), encoding="utf-8") as fid:
         dataset_description_json = json.load(fid)
-        assert dataset_description_json["Authors"] == ["[Unspecified]"]
+        assert dataset_description_json["Authors"] == [
+            "[Unspecified1]",
+            "[Unspecified2]",
+        ]
 
     make_dataset_description(
         path=tmp_path,
@@ -365,7 +368,10 @@ def test_make_dataset_description(tmp_path, monkeypatch):
 
     with open(op.join(tmp_path, "dataset_description.json"), encoding="utf-8") as fid:
         dataset_description_json = json.load(fid)
-        assert dataset_description_json["Authors"] == ["[Unspecified]"]
+        assert dataset_description_json["Authors"] == [
+            "[Unspecified1]",
+            "[Unspecified2]",
+        ]
 
     make_dataset_description(
         path=tmp_path,

mne_bids/write.py

@@ -1386,7 +1386,7 @@ def make_dataset_description(
     # if the user passed an author don't overwrite,
     # if there was an author there, only overwrite if `overwrite=True`
     if authors is None and (description["Authors"] is None or overwrite):
-        description["Authors"] = ["[Unspecified]"]
+        description["Authors"] = ["[Unspecified1]", "[Unspecified2]"]
 
     # Only write data that is not None
     pop_keys = [key for key, val in description.items() if val is None]
@@ -2055,7 +2055,7 @@ def write_raw_bids(
     # already exist. Always set overwrite to False here. If users
     # want to edit their dataset_description, they can directly call
     # this function.
-    make_dataset_description(path=bids_path.root, name=" ", overwrite=False)
+    make_dataset_description(path=bids_path.root, name="[Unspecified]", overwrite=False)
 
     _sidecar_json(
         raw,