fix travis, keep coverage reports in artifacts

Author: oesteban

.circle/codecov.sh

@@ -13,13 +13,12 @@ set -x         # Print command traces before executing command.
 curl -so codecov.io https://codecov.io/bash
 chmod 755 codecov.io
 
-find "${WORKDIR}/" -name 'coverage*.xml' -maxdepth 1 -print0 | \
+find "${WORKDIR}/tests/" -name 'coverage*.xml' -maxdepth 1 -print0 | \
   xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F unittests
-find "${WORKDIR}/" -name 'smoketest*.xml' -maxdepth 1 -print0 | \
+find "${WORKDIR}/tests/" -name 'smoketest*.xml' -maxdepth 1 -print0 | \
   xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F smoketests
 
 # Place test and coverage in the tests folder
 mkdir -p ${CIRCLE_TEST_REPORTS}/tests/
-cp ${WORKDIR}/pytest*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
-cp ${WORKDIR}/coverage*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
-cp ${WORKDIR}/smoketest*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
+cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
+

.travis.yml

@@ -42,7 +42,7 @@ before_install:
 install:
 - travis_retry pip install -e .[$NIPYPE_EXTRAS]
 script:
-- py.test -v --doctest-modules .
+- py.test -v --doctest-modules nipype
 deploy:
   provider: pypi
   user: satra

circle.yml

@@ -56,6 +56,7 @@ general:
   artifacts:
     - "~/work/docs"
     - "~/work/logs"
+    - "~/work/tests"
 
 deployment:
   production:

docker/files/run_examples.sh

@@ -8,7 +8,7 @@ arr=$@
 tmp_var=$( IFS=$' '; echo "${arr[*]}" )
 example_id=${tmp_var//[^A-Za-z0-9_-]/_}
 
-mkdir -p ${HOME}/.nipype ${WORKDIR}/logs/example_${example_id}
+mkdir -p ${HOME}/.nipype ${WORKDIR}/logs/example_${example_id} ${WORKDIR}/tests
 echo "[logging]" > ${HOME}/.nipype/nipype.cfg
 echo "workflow_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
 echo "interface_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
@@ -17,7 +17,7 @@ echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg
 echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg
 
 # Set up coverage
-export COVERAGE_FILE=${WORKDIR}/.coverage_${example_id}
+export COVERAGE_FILE=${WORKDIR}/tests/.coverage_${example_id}
 #sed -i -E "s/(source = ).*'/\1\/src\/nipype\/nipype/" /src/nipype/.coveragerc
 
 if [ "$2" == "MultiProc" ]; then
@@ -27,6 +27,6 @@ fi
 coverage run /src/nipype/tools/run_examples.py $@
 exit_code=$?
 
-coverage xml -o ${WORKDIR}/smoketest_${example_id}.xml || true
-
+coverage xml -o ${WORKDIR}/tests/smoketest_${example_id}.xml
 exit $exit_code
+

docker/files/run_pytests.sh

@@ -9,7 +9,7 @@ WORKDIR=${WORK:-/work}
 PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
 
 # Create necessary directories
-mkdir -p ${WORKDIR}/crashfiles ${WORKDIR}/logs/py${PYTHON_VERSION}
+mkdir -p ${WORKDIR}/tests ${WORKDIR}/crashfiles ${WORKDIR}/logs/py${PYTHON_VERSION}
 
 # Create a nipype config file
 mkdir -p ${HOME}/.nipype
@@ -24,16 +24,16 @@ if [[ "${PYTHON_VERSION}" -lt "30" ]]; then
 fi
 
 # Run tests using pytest
-export COVERAGE_FILE=${WORKDIR}/.coverage_py${PYTHON_VERSION}
-py.test -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}.xml --cov nipype --cov-config /src/nipype/.coveragerc --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}.xml ${TESTPATH}
+export COVERAGE_FILE=${WORKDIR}/tests/.coverage_py${PYTHON_VERSION}
+py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}.xml --cov nipype --cov-config /src/nipype/.coveragerc --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}.xml ${TESTPATH}
 exit_code=$?
 
 # Workaround: run here the profiler tests in python 3
 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
     echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
-    export COVERAGE_FILE=${WORKDIR}/.coverage_py${PYTHON_VERSION}_extra
-    py.test -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
+    export COVERAGE_FILE=${WORKDIR}/tests/.coverage_py${PYTHON_VERSION}_extra
+    py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
     exit_code=$(( $exit_code + $? ))
 fi