Merge branch 'master' into master

Author: effigies

.circleci/config.yml

@@ -202,9 +202,8 @@ jobs:
           no_output_timeout: 2h
           command: |
             docker run -ti --rm=false \
-              --entrypoint="/usr/local/miniconda/bin/py.test" \
-              poldracklab/fmriprep:latest . \
-              --doctest-modules --ignore=docs --ignore=setup.py
+              --entrypoint="py.test" poldracklab/fmriprep:latest \
+              /root/src/fmriprep/ --doctest-modules --ignore=docs --ignore=setup.py
       - run:
           name: Test fmriprep-wrapper (Python 2)
           command: |
@@ -268,7 +267,7 @@ jobs:
             docker run -ti --rm=false -v $PWD:/_build_html \
               --entrypoint=sphinx-build poldracklab/fmriprep:latest \
               -T -E -b html -d _build/doctrees-readthedocs -W -D \
-              language=en docs/ /_build_html 2>&1 \
+              language=en /root/src/fmriprep/docs/ /_build_html 2>&1 \
               | tee $PWD/builddocs.log
             cat $PWD/builddocs.log
             grep -qv "ERROR" $PWD/builddocs.log

Dockerfile

@@ -160,9 +160,7 @@ RUN echo "${VERSION}" > /root/src/fmriprep/fmriprep/VERSION && \
     rm -rf ~/.cache/pip
 
 RUN ldconfig
-
 WORKDIR /tmp/
-
 ENTRYPOINT ["/usr/local/miniconda/bin/fmriprep"]
 
 ARG BUILD_DATE
@@ -171,8 +169,9 @@ ARG VERSION
 LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.name="FMRIPREP" \
       org.label-schema.description="FMRIPREP - robust fMRI preprocessing tool" \
-      org.label-schema.url="http://fmriprep.readthedocs.io" \
+      org.label-schema.url="http://fmriprep.org" \
       org.label-schema.vcs-ref=$VCS_REF \
       org.label-schema.vcs-url="https://github.com/poldracklab/fmriprep" \
       org.label-schema.version=$VERSION \
       org.label-schema.schema-version="1.0"
+

fmriprep/interfaces/fmap.py

@@ -518,8 +518,15 @@ def _delta_te(in_values, te1=None, te2=None):
         if isinstance(te2, list):
             te2 = te2[1]
 
-    if te1 is None or te2 is None:
+    # For convienience if both are missing we should give one error about them
+    if te1 is None and te2 is None:
+        raise RuntimeError('EchoTime1 and EchoTime2 metadata fields not found. '
+                           'Please consult the BIDS specification.')
+    if te1 is None:
         raise RuntimeError(
-            'No echo time information found')
+            'EchoTime1 metadata field not found. Please consult the BIDS specification.')
+    if te2 is None:
+        raise RuntimeError(
+            'EchoTime2 metadata field not found. Please consult the BIDS specification.')
 
     return abs(float(te2) - float(te1))