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Commit17c5be2

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Merge pull requestmiykael#162 from djarecka/fix/fixing_tests
[CI] fixing tests
2 parents3633d35 +e0c7152 commit17c5be2

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4 files changed

+32
-21
lines changed

4 files changed

+32
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‎.github/workflows/testing.yml

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@ jobs:
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# In this step, this action saves a list of existing images,
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# the cache is created without them in the post run.
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# It also restores the cache if it exists.
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-uses:satackey/action-docker-layer-caching@v0.0.5
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-uses:satackey/action-docker-layer-caching@v0.0.7
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-name:build the image
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run:docker build . --file Dockerfile -t nipype_tutorial:latest
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@@ -27,7 +27,7 @@ jobs:
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runs-on:ubuntu-latest
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steps:
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-uses:actions/checkout@v2
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-uses:satackey/action-docker-layer-caching@v0.0.5
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-uses:satackey/action-docker-layer-caching@v0.0.7
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-name:run test 1
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run:docker run --rm nipype_tutorial:latest python /home/neuro/nipype_tutorial/test_notebooks.py 1
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@@ -36,7 +36,7 @@ jobs:
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runs-on:ubuntu-latest
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steps:
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-uses:actions/checkout@v2
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-uses:satackey/action-docker-layer-caching@v0.0.5
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-uses:satackey/action-docker-layer-caching@v0.0.7
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-name:runtest 2
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run:docker run --rm nipype_tutorial:latest python /home/neuro/nipype_tutorial/test_notebooks.py 2
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@@ -45,6 +45,6 @@ jobs:
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runs-on:ubuntu-latest
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steps:
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-uses:actions/checkout@v2
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-uses:satackey/action-docker-layer-caching@v0.0.5
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-uses:satackey/action-docker-layer-caching@v0.0.7
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-name:runtest 3
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run:docker run --rm nipype_tutorial:latest python /home/neuro/nipype_tutorial/test_notebooks.py 3

‎notebooks/advanced_create_interfaces.ipynb

Lines changed: 14 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1214,7 +1214,7 @@
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"from scipy.io import savemat\n",
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"\n",
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"# 1. save the image in matlab format as tmp_image.mat\n",
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"tmp_image = 'tmp_image'\n",
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"tmp_image = 'tmp_image.mat'\n",
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"data = nb.load(in_file).get_data()\n",
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"savemat(tmp_image, {b'data': data}, do_compression=False)"
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]
@@ -1298,7 +1298,7 @@
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"\n",
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" def _run_interface(self, runtime):\n",
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" # Save the image in matlab format as tmp_image.mat\n",
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" tmp_image = 'tmp_image'\n",
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" tmp_image = 'tmp_image.mat'\n",
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" data = nb.load(self.inputs.in_file).get_data()\n",
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" savemat(tmp_image, {b'data': data}, do_compression=False)\n",
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"\n",
@@ -1374,7 +1374,7 @@
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"cell_type":"code",
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"execution_count":null,
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"metadata": {
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"solution2":"hidden",
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"solution2":"shown",
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"solution2_first":true
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},
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"outputs": [],
@@ -1386,7 +1386,7 @@
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"cell_type":"code",
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"execution_count":null,
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"metadata": {
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"solution2":"hidden"
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"solution2":"shown"
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},
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"outputs": [],
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"source": [
@@ -1411,7 +1411,7 @@
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"\n",
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" def _run_interface(self, runtime):\n",
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" # Save the image in matlab format as tmp_image.mat\n",
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" tmp_image = 'tmp_image'\n",
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" tmp_image = 'tmp_image.mat'\n",
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" data = nb.load(self.inputs.in_file).get_data()\n",
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" savemat(tmp_image, {b'data': data}, do_compression=False)\n",
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"\n",
@@ -1495,11 +1495,18 @@
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"source": [
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"!cat volume.txt"
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]
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},
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{
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"cell_type":"code",
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"execution_count":null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name":"Python[default]",
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"display_name":"Python3",
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"language":"python",
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"name":"python3"
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},
@@ -1513,7 +1520,7 @@
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"name":"python",
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"nbconvert_exporter":"python",
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"pygments_lexer":"ipython3",
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"version":"3.6.5"
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"version":"3.7.8"
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}
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},
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"nbformat":4,

‎notebooks/handson_analysis.ipynb

Lines changed: 10 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -998,8 +998,11 @@
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"outputs": [],
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"source": [
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"plot_glass_brain('/output/datasink_handson/normalized/sub-07/wess_0008.nii',\n",
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" output_file=\"/output/datasink_handson/normalized/sub-07/f-contr_activation.png\",\n",
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" colorbar=True, display_mode='lyrz', black_bg=True, threshold=25,\n",
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" title='subject 7 - F-contrast: Activation');"
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" title='subject 7 - F-contrast: Activation');\n",
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"\n",
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"Image(filename='/output/datasink_handson/normalized/sub-07/f-contr_activation.png')"
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]
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},
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{
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"outputs": [],
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"source": [
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"plot_glass_brain('/output/datasink_handson/normalized/sub-07/wess_0009.nii',\n",
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" output_file=\"/output/datasink_handson/normalized/sub-07/f-contr_differences.png\",\n",
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" colorbar=True, display_mode='lyrz', black_bg=True, threshold=25,\n",
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" title='subject 7 - F-contrast: Differences');"
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" title='subject 7 - F-contrast: Differences');\n",
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"\n",
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"Image(filename='/output/datasink_handson/normalized/sub-07/f-contr_differences.png')"
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]
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},
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{
@@ -1648,7 +1654,7 @@
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name":"Python[default]",
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"display_name":"Python3",
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"language":"python",
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"name":"python3"
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},
@@ -1662,7 +1668,7 @@
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"name":"python",
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"nbconvert_exporter":"python",
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"pygments_lexer":"ipython3",
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"version":"3.6.5"
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"version":"3.7.8"
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}
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},
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"nbformat":4,

‎test_notebooks.py

Lines changed: 4 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,6 @@
1-
importos
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importsys
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importtime
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fromglobimportglob
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importpytest
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deftest_version():
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importnipype
@@ -90,7 +89,6 @@ def reduce_notebook_load(path):
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print('Reducing: %s'%n)
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notebooks.append(reduce_notebook_load(n))
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93-
fortestinnotebooks:
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pytest_cmd='pytest --nbval-lax --nbval-cell-timeout 7200 -v -s %s'%test
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print(pytest_cmd)
96-
os.system(pytest_cmd)
92+
# testing all tests from the notebooks list
93+
pytest_exit_code=pytest.main(["--nbval-lax","--nbval-cell-timeout","7200","-vs"]+notebooks)
94+
sys.exit(pytest_exit_code)

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