add debug trace to failing operation, update dockerimages

Author: oesteban

docker/nipype_test/Dockerfile_base

@@ -95,6 +95,23 @@ ENV MATLABCMD "/opt/mcr/v85/toolbox/matlab" \
     SPMMCRCMD "/opt/spm12/run_spm12.sh /opt/mcr/v85/ script" \
     FORCE_SPMMCR 1
 
+WORKDIR /root
+# Install miniconda
+RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    /bin/bash Miniconda3-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
+    rm Miniconda3-latest-Linux-x86_64.sh
+
+ENV PATH /usr/local/miniconda/bin:$PATH
+
+# http://bugs.python.org/issue19846
+# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
+ENV LANG C.UTF-8 \
+    LC_ALL C.UTF-8
+
+# Add conda-forge channel in conda
+RUN conda config --add channels conda-forge && \
+    conda install -y lockfile nipype matplotlib sphinx boto boto3 coverage mock pbr nitime dipy && \
+    pip install nose-cov doctest-ignore-unicode configparser
 
 CMD ["/bin/bash"]
 

docker/nipype_test/Dockerfile_py27

@@ -26,28 +26,12 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-FROM nipype/nipype_test:base
+FROM nipype/nipype_test:base-0.0.2
 MAINTAINER The nipype developers https://github.com/nipy/nipype
-# Preparations
-RUN ln -snf /bin/bash /bin/sh
-WORKDIR /root
 
-# Install miniconda
-RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh && \
-    /bin/bash Miniconda-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
-    rm Miniconda-latest-Linux-x86_64.sh
-
-ENV PATH /usr/local/miniconda/bin:$PATH
-
-# http://bugs.python.org/issue19846
-# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
-ENV LANG C.UTF-8
-ENV LC_ALL C.UTF-8
-
-# Add conda-forge channel in conda
-RUN conda config --add channels conda-forge && \
-    conda install -y lockfile nipype matplotlib sphinx boto boto3 coverage mock pbr nitime dipy && \
-    pip install nose-cov doctest-ignore-unicode configparser
+# Downgrade python to 2.7
+RUN conda update -y conda && \
+    conda update --all -y python=2.7
 
 COPY docker/circleci/run_* /usr/bin/
 RUN chmod +x /usr/bin/run_*

docker/nipype_test/Dockerfile_py34

@@ -26,35 +26,17 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-FROM nipype/nipype_test:base
+FROM nipype/nipype_test:base-0.0.2
 MAINTAINER The nipype developers https://github.com/nipy/nipype
-# Preparations
-RUN ln -snf /bin/bash /bin/sh
-WORKDIR /root
 
-# Install miniconda
-RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    /bin/bash Miniconda3-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
-    rm Miniconda3-latest-Linux-x86_64.sh
+# Downgrade python to 3.4
+RUN conda update -y conda && \
+    conda update --all -y python=3.4
 
-ENV PATH /usr/local/miniconda/bin:$PATH
-
-# http://bugs.python.org/issue19846
-# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
-ENV LANG C.UTF-8
-ENV LC_ALL C.UTF-8
-
-# Add conda-forge channel in conda
-RUN conda config --add channels conda-forge && \
-    conda update -y conda && \
-    conda update --all -y python=3.4 && \
-    conda install -y lockfile nipype matplotlib sphinx boto boto3 coverage mock pbr nitime dipy && \
-    pip install nose-cov doctest-ignore-unicode configparser
-   
 COPY docker/circleci/run_* /usr/bin/
 RUN chmod +x /usr/bin/run_*
 
-# Replace imglob with Python3 compatible version
+# Replace imglob with a Python3 compatible version
 COPY nipype/external/fsl_imglob.py /usr/bin/fsl_imglob.py
 RUN rm -r ${FSLDIR}/bin/imglob && \
     chmod +x /usr/bin/fsl_imglob.py && \

docker/nipype_test/Dockerfile_py35

@@ -26,33 +26,15 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-FROM nipype/nipype_test:base
+FROM nipype/nipype_test:base-0.0.2
 MAINTAINER The nipype developers https://github.com/nipy/nipype
-# Preparations
-RUN ln -snf /bin/bash /bin/sh
-WORKDIR /root
-
-# Install miniconda
-RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    /bin/bash Miniconda3-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
-    rm Miniconda3-latest-Linux-x86_64.sh
-
-ENV PATH /usr/local/miniconda/bin:$PATH
 
-# http://bugs.python.org/issue19846
-# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
-ENV LANG C.UTF-8
-ENV LC_ALL C.UTF-8
-
-# Add conda-forge channel in conda
-RUN conda config --add channels conda-forge && \
-    conda install -y lockfile nipype matplotlib sphinx boto boto3 coverage mock pbr nitime dipy && \
-    pip install nose-cov doctest-ignore-unicode configparser
+WORKDIR /root
 
 COPY docker/circleci/run_* /usr/bin/
 RUN chmod +x /usr/bin/run_*
 
-# Replace imglob with Python3 compatible version
+# Replace imglob with a Python3 compatible version
 COPY nipype/external/fsl_imglob.py /usr/bin/fsl_imglob.py
 RUN rm -r ${FSLDIR}/bin/imglob && \
     chmod +x /usr/bin/fsl_imglob.py && \

nipype/utils/filemanip.py

@@ -466,6 +466,7 @@ def loadcrash(infile, *args):
 def loadpkl(infile):
     """Load a zipped or plain cPickled file
     """
+    fmlogger.debug('Loading pkl: %s', infile)
     if infile.endswith('pklz'):
         pkl_file = gzip.open(infile, 'rb')
     else: