Revert #1889

Author: oesteban

.circle/codecov.sh

@@ -10,11 +10,5 @@ set -u         # Treat unset variables as an error when substituting.
 set -x         # Print command traces before executing command.
 
 # Send coverage data to codecov.io
-curl -so codecov.io https://codecov.io/bash
-chmod 755 codecov.io
-
-find "${WORKDIR}/tests/" -name 'coverage*.xml' -maxdepth 1 -print0 | \
-  xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F unittests
-find "${WORKDIR}/tests/" -name 'smoketest*.xml' -maxdepth 1 -print0 | \
-  xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F smoketests
-
+${HOME}/bin/codecov -f "coverage*.xml" -s "${WORKDIR}/tests/" -R "${HOME}/nipype/" -F unittests -v -K
+${HOME}/bin/codecov -f "smoketest*.xml" -s "${WORKDIR}/tests/" -R "${HOME}/nipype/" -F smoketests -v -K

Dockerfile

@@ -71,6 +71,16 @@ RUN conda config --add channels conda-forge; sync && \
 RUN sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages/matplotlib/mpl-data/matplotlibrc && \
     python -c "from matplotlib import font_manager"
 
+# Install CI scripts
+COPY docker/files/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
+
+# Replace imglob with a Python3 compatible version
+COPY nipype/external/fsl_imglob.py /usr/bin/fsl_imglob.py
+RUN rm -rf ${FSLDIR}/bin/imglob && \
+    chmod +x /usr/bin/fsl_imglob.py && \
+    ln -s /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
+
 # Installing dev requirements (packages that are not in pypi)
 WORKDIR /src/
 COPY requirements.txt requirements.txt
@@ -83,16 +93,6 @@ RUN cd /src/nipype && \
     pip install -e .[all] && \
     rm -rf ~/.cache/pip
 
-# Install CI scripts
-COPY docker/files/run_* /usr/bin/
-RUN chmod +x /usr/bin/run_*
-
-# Replace imglob with a Python3 compatible version
-COPY nipype/external/fsl_imglob.py /usr/bin/fsl_imglob.py
-RUN rm -rf ${FSLDIR}/bin/imglob && \
-    chmod +x /usr/bin/fsl_imglob.py && \
-    ln -s /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
-
 WORKDIR /work/
 
 ARG BUILD_DATE

circle.yml

@@ -17,16 +17,18 @@ dependencies:
     - "~/docker"
     - "~/examples"
     - "~/.apt-cache"
+    - "~/bin"
 
   pre:
     # Let CircleCI cache the apt archive
     - mkdir -p ~/.apt-cache/partial && sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives
     - sudo apt-get -y update && sudo apt-get install -y wget bzip2
     # Create work folder and force group permissions
     - mkdir -p $WORKDIR && sudo setfacl -d -m group:ubuntu:rwx $WORKDIR && sudo setfacl -m group:ubuntu:rwx $WORKDIR
-    - mkdir -p $HOME/docker $HOME/examples $WORKDIR/pytest $WORKDIR/logs
+    - mkdir -p $HOME/docker $HOME/examples $HOME/bin $WORKDIR/tests $WORKDIR/logs $WORKDIR/crashfiles ${CIRCLE_TEST_REPORTS}/tests/
   override:
-    - if [[ -e $HOME/docker/cache.tar ]]; then docker load --input $HOME/docker/cache.tar; fi :
+    - if [[ -e "$HOME/bin/codecov.io" ]]; then curl -so $HOME/bin/codecov https://codecov.io/bash && chmod 755 $HOME/bin/codecov; fi
+    - if [[ -e "$HOME/docker/cache.tar" ]]; then docker load --input $HOME/docker/cache.tar; fi :
         timeout: 6000
     - docker images
     - docker pull nipype/base:latest
@@ -50,7 +52,7 @@ test:
         parallel: true
   post:
     # Place reports in the appropriate folder
-    - mkdir -p ${CIRCLE_TEST_REPORTS}/tests/ && cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
+    - cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
     # Send coverage data to codecov.io
     - bash .circle/codecov.sh
 

docker/files/run_pytests.sh

@@ -37,8 +37,7 @@ if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     exit_code=$(( $exit_code + $? ))
 fi
 
-find /work -name "crash-*" -maxdepth 1 -exec mv {} ${WORKDIR}/crashfiles/ \;
+# Collect crashfiles
+find ${WORKDIR} -name "crash-*" -maxdepth 1 -exec mv {} ${WORKDIR}/crashfiles/ \;
 
-# Just in case output xml files are misplaced,
-# then circle would not tell the tests failed otherwise
 exit ${exit_code}