Merge pull request miykael#45 from djarecka/1.0.1

djarecka · web-flow · commit 316d37d271de · 2018-02-27T13:50:58.000-05:00
testing nipype 1.0.1 before release

I'm merging this to have the new version of neurodocker command (so it's not failing due to miniconda bugs). 

Will improve CircleCI in a separate PR
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -11,10 +11,12 @@ jobs:
           name: docker build
           no_output_timeout: 60m
           command: |
-            docker build -t djarecka/nipype_tutorial:$CIRCLE_BRANCH .
+            for i in {1..5}; do
+              docker build -t djarecka/nipype_tutorial:$CIRCLE_BRANCH . && break || sleep 15
+            done 
       - run:
           name: docker run
-          no_output_timeout: 60m
+          no_output_timeout: 90m
           command: |
             docker run -it --rm djarecka/nipype_tutorial:$CIRCLE_BRANCH pytest -v -s /home/neuro/nipype_tutorial/test_notebooks.py
          
diff --git a/Dockerfile b/Dockerfile
@@ -1,11 +1,11 @@
-# Generated by Neurodocker v0.3.2.
+# Generated by Neurodocker v0.3.2-7-g4b0f32d.
 #
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
 # pull request on our GitHub repository:
 #     https://github.com/kaczmarj/neurodocker
 #
-# Timestamp: 2017-12-28 23:39:47
+# Timestamp: 2018-02-26 18:15:43
 
 FROM neurodebian:stretch-non-free
 
@@ -90,7 +90,7 @@ ENV CONDA_DIR=/opt/conda \
     PATH=/opt/conda/bin:$PATH
 RUN echo "Downloading Miniconda installer ..." \
     && miniconda_installer=/tmp/miniconda.sh \
-    && curl -sSL --retry 5 -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && curl -sSL --retry 5 -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-4.3.31-Linux-x86_64.sh \
     && /bin/bash $miniconda_installer -b -p $CONDA_DIR \
     && rm -f $miniconda_installer \
     && conda config --system --prepend channels conda-forge \
@@ -210,6 +210,7 @@ RUN echo '{ \
     \n    [ \
     \n      "miniconda", \
     \n      { \
+    \n        "miniconda_version": "4.3.31", \
     \n        "conda_install": "python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions traits pandas matplotlib scikit-learn seaborn nbformat", \
     \n        "pip_install": "https://github.com/nipy/nipype/tarball/master https://github.com/INCF/pybids/tarball/master nilearn datalad[full] nipy duecredit", \
     \n        "env_name": "neuro", \
@@ -278,6 +279,6 @@ RUN echo '{ \
     \n      ] \
     \n    ] \
     \n  ], \
-    \n  "generation_timestamp": "2017-12-28 23:39:47", \
-    \n  "neurodocker_version": "0.3.2" \
+    \n  "generation_timestamp": "2018-02-26 18:15:43", \
+    \n  "neurodocker_version": "0.3.2-7-g4b0f32d" \
     \n}' > /neurodocker/neurodocker_specs.json
diff --git a/create_dockerfile.sh b/create_dockerfile.sh
@@ -7,7 +7,7 @@ docker run --rm kaczmarj/neurodocker:master generate -b neurodebian:stretch-non-
 --add-to-entrypoint "source /etc/fsl/fsl.sh" \
 --spm version=12 matlab_version=R2017a \
 --user=neuro \
---miniconda \
+--miniconda miniconda_version="4.3.31" \
   conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions 
                  traits pandas matplotlib scikit-learn seaborn nbformat" \
   pip_install="https://github.com/nipy/nipype/tarball/master 
diff --git a/test_notebooks.py b/test_notebooks.py
@@ -6,6 +6,12 @@
 from nbconvert.preprocessors import ExecutePreprocessor
 from nbconvert.preprocessors.execute import CellExecutionError
 
+
+def test_version():
+    import nipype
+    print("nipype version: ", nipype.__version__)
+
+
 def _notebook_run(path):
     """
     Execute a notebook via nbconvert and collect output.
