ENH: Update to more recent PyBIDS

Author: effigies

generate.sh

@@ -18,7 +18,7 @@ generate_docker() {
              conda_install="python=3.7 pytest jupyter jupyterlab jupyter_contrib_nbextensions
                             traits pandas matplotlib scikit-learn scikit-image seaborn nbformat nb_conda" \
              pip_install="https://github.com/nipy/nipype/tarball/master
-                          https://github.com/INCF/pybids/tarball/0.7.1
+                          pybids==0.13.1
                           nilearn datalad[full] nipy duecredit nbval niflow-nipype1-workflows" \
              create_env="neuro" \
              activate=True \
@@ -57,7 +57,7 @@ generate_singularity() {
              conda_install="python=3.7 pytest jupyter jupyterlab jupyter_contrib_nbextensions
                             traits pandas matplotlib scikit-learn scikit-image seaborn nbformat nb_conda" \
              pip_install="https://github.com/nipy/nipype/tarball/master
-                          https://github.com/INCF/pybids/tarball/0.7.1
+                          pybids==0.13.1
                           nilearn datalad[full] nipy duecredit nbval niflow-nipype1-workflows" \
              create_env="neuro" \
              activate=True \

notebooks/basic_data_input_bids.ipynb

@@ -140,7 +140,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "layout.get(subject='01', suffix='bold', extensions=['nii', 'nii.gz'])"
+    "layout.get(subject='01', suffix='bold', extension=['.nii', '.nii.gz'])"
    ]
   },
   {
@@ -156,7 +156,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "layout.get(subject='01', suffix='bold', extensions=['nii', 'nii.gz'], return_type='file')"
+    "layout.get(subject='01', suffix='bold', extension=['.nii', '.nii.gz'], return_type='file')"
    ]
   },
   {