Merge pull request #162 from djarecka/fix/fixing_tests

[CI] fixing tests

Author: djarecka

.github/workflows/testing.yml

@@ -18,7 +18,7 @@ jobs:
     # In this step, this action saves a list of existing images,
     # the cache is created without them in the post run.
     # It also restores the cache if it exists.
-    - uses: satackey/action-docker-layer-caching@v0.0.5
+    - uses: satackey/action-docker-layer-caching@v0.0.7
     - name: build the image
       run: docker build . --file Dockerfile -t nipype_tutorial:latest
 
@@ -27,7 +27,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - uses: satackey/action-docker-layer-caching@v0.0.5
+    - uses: satackey/action-docker-layer-caching@v0.0.7
     - name: run test 1
       run: docker run --rm nipype_tutorial:latest python /home/neuro/nipype_tutorial/test_notebooks.py 1
 
@@ -36,7 +36,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - uses: satackey/action-docker-layer-caching@v0.0.5
+    - uses: satackey/action-docker-layer-caching@v0.0.7
     - name: run	test 2
       run: docker run --rm nipype_tutorial:latest python /home/neuro/nipype_tutorial/test_notebooks.py 2
 
@@ -45,6 +45,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - uses: satackey/action-docker-layer-caching@v0.0.5
+    - uses: satackey/action-docker-layer-caching@v0.0.7
     - name: run	test 3
       run: docker run --rm nipype_tutorial:latest python /home/neuro/nipype_tutorial/test_notebooks.py 3

notebooks/advanced_create_interfaces.ipynb

@@ -1214,7 +1214,7 @@
     "from scipy.io import savemat\n",
     "\n",
     "# 1. save the image in matlab format as tmp_image.mat\n",
-    "tmp_image = 'tmp_image'\n",
+    "tmp_image = 'tmp_image.mat'\n",
     "data = nb.load(in_file).get_data()\n",
     "savemat(tmp_image, {b'data': data}, do_compression=False)"
    ]
@@ -1298,7 +1298,7 @@
     "\n",
     "    def _run_interface(self, runtime): \n",
     "        # Save the image in matlab format as tmp_image.mat\n",
-    "        tmp_image = 'tmp_image'\n",
+    "        tmp_image = 'tmp_image.mat'\n",
     "        data = nb.load(self.inputs.in_file).get_data()\n",
     "        savemat(tmp_image, {b'data': data}, do_compression=False)\n",
     "        \n",
@@ -1374,7 +1374,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "solution2": "hidden",
+    "solution2": "shown",
     "solution2_first": true
    },
    "outputs": [],
@@ -1386,7 +1386,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "solution2": "hidden"
+    "solution2": "shown"
    },
    "outputs": [],
    "source": [
@@ -1411,7 +1411,7 @@
     "\n",
     "    def _run_interface(self, runtime): \n",
     "        # Save the image in matlab format as tmp_image.mat\n",
-    "        tmp_image = 'tmp_image'\n",
+    "        tmp_image = 'tmp_image.mat'\n",
     "        data = nb.load(self.inputs.in_file).get_data()\n",
     "        savemat(tmp_image, {b'data': data}, do_compression=False)\n",
     "        \n",
@@ -1495,11 +1495,18 @@
    "source": [
     "!cat volume.txt"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python [default]",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -1513,7 +1520,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.7.8"
   }
  },
  "nbformat": 4,

notebooks/handson_analysis.ipynb

@@ -998,8 +998,11 @@
    "outputs": [],
    "source": [
     "plot_glass_brain('/output/datasink_handson/normalized/sub-07/wess_0008.nii',\n",
+    "                 output_file=\"/output/datasink_handson/normalized/sub-07/f-contr_activation.png\",\n",
     "                 colorbar=True, display_mode='lyrz', black_bg=True, threshold=25,\n",
-    "                 title='subject 7 - F-contrast: Activation');"
+    "                 title='subject 7 - F-contrast: Activation');\n",
+    "\n",
+    "Image(filename='/output/datasink_handson/normalized/sub-07/f-contr_activation.png')"
    ]
   },
   {
@@ -1009,8 +1012,11 @@
    "outputs": [],
    "source": [
     "plot_glass_brain('/output/datasink_handson/normalized/sub-07/wess_0009.nii',\n",
+    "                 output_file=\"/output/datasink_handson/normalized/sub-07/f-contr_differences.png\",\n",
     "                 colorbar=True, display_mode='lyrz', black_bg=True, threshold=25,\n",
-    "                 title='subject 7 - F-contrast: Differences');"
+    "                 title='subject 7 - F-contrast: Differences');\n",
+    "\n",
+    "Image(filename='/output/datasink_handson/normalized/sub-07/f-contr_differences.png')"
    ]
   },
   {
@@ -1648,7 +1654,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python [default]",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -1662,7 +1668,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.7.8"
   }
  },
  "nbformat": 4,

test_notebooks.py

@@ -1,7 +1,6 @@
-import os
 import sys
-import time
 from glob import glob
+import pytest
 
 def test_version():
     import nipype
@@ -90,7 +89,6 @@ def reduce_notebook_load(path):
             print('Reducing: %s' % n)
             notebooks.append(reduce_notebook_load(n))
 
-    for test in notebooks:
-        pytest_cmd = 'pytest --nbval-lax --nbval-cell-timeout 7200 -v -s %s' % test
-        print(pytest_cmd)
-        os.system(pytest_cmd)
+    # testing all tests from the notebooks list
+    pytest_exit_code = pytest.main(["--nbval-lax",  "--nbval-cell-timeout", "7200", "-vs"] + notebooks)
+    sys.exit(pytest_exit_code)