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FIX: Nipype 1.7 compatibility #176

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Merged
merged 3 commits into from
Apr 4, 2022
Merged

FIX: Nipype 1.7 compatibility #176

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831c597
FIX: Be more forgiving of the exception type
effigies Oct 18, 2021
4846005
ENH: Update to more recent PyBIDS
effigies Oct 18, 2021
0ca3dd8
MNT: Update Python to 3.8
effigies Apr 4, 2022
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6 changes: 3 additions & 3 deletions generate.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,10 @@ generate_docker() {
--user=neuro \
--workdir /home/neuro \
--miniconda \
conda_install="python=3.7 pytest jupyter jupyterlab jupyter_contrib_nbextensions
conda_install="python=3.8 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 \
Expand Down Expand Up @@ -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 \
Expand Down
4 changes: 2 additions & 2 deletions notebooks/basic_data_input_bids.ipynb
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Expand Up @@ -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'])"
]
},
{
Expand All @@ -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')"
]
},
{
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12 changes: 8 additions & 4 deletions notebooks/basic_function_interface.ipynb
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Expand Up @@ -247,8 +247,8 @@
"# Run node\n",
"try:\n",
" rndArray.run()\n",
"except(NameError) as err:\n",
" print(\"NameError:\", err)\n",
"except Exception as err:\n",
" print(err)\n",
"else:\n",
" raise"
]
Expand All @@ -259,8 +259,12 @@
"source": [
"As you can see, if we don't import `random` inside the scope of the function, we receive the following error:\n",
"\n",
" NameError: global name 'random' is not defined\n",
" Interface Function failed to run. "
" Exception raised while executing Node rndArray_node.\n",
"\n",
" Traceback (most recent call last):\n",
" [...]\n",
" File \"<string>\", line 3, in get_random_array\n",
" NameError: name 'random' is not defined"
]
}
],
Expand Down