Merge pull request miykael#176 from effigies/mnt/ci_check

djarecka · web-flow · commit 650ff4550c4e · 2022-04-04T18:42:10.000-04:00
FIX: Nipype 1.7 compatibility
diff --git a/generate.sh b/generate.sh
@@ -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 \
@@ -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 \
diff --git a/notebooks/basic_data_input_bids.ipynb b/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')"
    ]
   },
   {
diff --git a/notebooks/basic_function_interface.ipynb b/notebooks/basic_function_interface.ipynb
@@ -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"
    ]
@@ -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"
    ]
   }
  ],

Original file line number	Diff line number	Diff line change
`@@ -140,7 +140,7 @@`
`140`	`140`	`"metadata": {},`
`141`	`141`	`"outputs": [],`
`142`	`142`	`"source": [`
`143`		`- "layout.get(subject='01', suffix='bold', extensions=['nii', 'nii.gz'])"`
	`143`	`+ "layout.get(subject='01', suffix='bold', extension=['.nii', '.nii.gz'])"`
`144`	`144`	`]`
`145`	`145`	`},`
`146`	`146`	`{`
`@@ -156,7 +156,7 @@`
`156`	`156`	`"metadata": {},`
`157`	`157`	`"outputs": [],`
`158`	`158`	`"source": [`
`159`		`- "layout.get(subject='01', suffix='bold', extensions=['nii', 'nii.gz'], return_type='file')"`
	`159`	`+ "layout.get(subject='01', suffix='bold', extension=['.nii', '.nii.gz'], return_type='file')"`
`160`	`160`	`]`
`161`	`161`	`},`
`162`	`162`	`{`