CI: Move codecov into CI step

Author: effigies

.circleci/config.yml

@@ -95,6 +95,12 @@ _get_codecov: &_get_codecov
   command: |
     pip install --no-cache-dir codecov
 
+_run_codecov: &_run_codecov
+  name: Run codecov
+  command: |
+    codecov --file "$WORKDIR/tests/coverage*.xml" --root "$HOME/nipype" --flags unittests -e "$CIRCLE_JOB"
+    codecov --file "$WORKDIR/tests/smoketest*.xml" --root "$HOME/nipype" --flags smoketests -e "$CIRCLE_JOB"
+
 
 version: 2
 jobs:
@@ -164,6 +170,7 @@ jobs:
           no_output_timeout: 30m
           environment: *test_environment
           command: bash /home/circleci/nipype/.circleci/test_py3_docs.sh
+      - run: *_run_codecov
       - store_artifacts: *store_artifacts_kwds
 
   test_py3_fmri_fsl_spm:
@@ -201,6 +208,7 @@ jobs:
           no_output_timeout: 40m
           environment: *test_environment
           command: bash /home/circleci/nipype/.circleci/test_py3_fmri_spm_linear_4d.sh
+      - run: *_run_codecov
       - store_artifacts: *store_artifacts_kwds
 
   test_py3_fmri_spm_dartel_multiproc:
@@ -228,6 +236,7 @@ jobs:
           no_output_timeout: 30m
           environment: *test_environment
           command: bash /home/circleci/nipype/.circleci/test_py3_fmri_spm_dartel_multiproc_l2.sh
+      - run: *_run_codecov
       - store_artifacts: *store_artifacts_kwds
 
   test_fmri_spm_nested_multiproc:
@@ -256,6 +265,7 @@ jobs:
           no_output_timeout: 30m
           environment: *test_environment
           command: bash /home/circleci/nipype/.circleci/test_py2_fmri_spm_nested_multiproc_l2.sh
+      - run: *_run_codecov
       - store_artifacts: *store_artifacts_kwds
       - run:
           name: Save Docker images to workspace

.circleci/test_complete.sh

@@ -5,6 +5,3 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $DIR/test_init.sh
 
 docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py27" /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
-exitcode=$?
-
-. $DIR/test_complete.sh

.circleci/test_py2_fmri_spm_nested_multiproc_l2.sh

@@ -5,6 +5,3 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $DIR/test_init.sh
 
 docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" "${DOCKER_IMAGE}:py27" /usr/bin/run_pytests.sh
-exitcode=$?
-
-. $DIR/test_complete.sh

.circleci/test_py2_pytest.sh

@@ -5,6 +5,3 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $DIR/test_init.sh
 
 docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /src/nipype/doc "${DOCKER_IMAGE}:py36" /usr/bin/run_builddocs.sh
-exitcode=$?
-
-. $DIR/test_complete.sh

.circleci/test_py3_docs.sh

@@ -5,6 +5,3 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $DIR/test_init.sh
 
 docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline
-exitcode=$?
-
-. $DIR/test_complete.sh

.circleci/test_py3_fmri_fsl_feeds_linear_l1.sh

@@ -5,6 +5,3 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $DIR/test_init.sh
 
 docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
-exitcode=$?
-
-. $DIR/test_complete.sh

.circleci/test_py3_fmri_fsl_reuse_linear_l1.sh

@@ -5,6 +5,3 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $DIR/test_init.sh
 
 docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_dartel MultiProc /data/examples/ level1
-exitcode=$?
-
-. $DIR/test_complete.sh

.circleci/test_py3_fmri_spm_dartel_multiproc_l1.sh

@@ -5,6 +5,3 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $DIR/test_init.sh
 
 docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_dartel MultiProc /data/examples/ l2pipeline
-exitcode=$?
-
-. $DIR/test_complete.sh

.circleci/test_py3_fmri_spm_dartel_multiproc_l2.sh

@@ -5,6 +5,3 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $DIR/test_init.sh
 
 docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d
-exitcode=$?
-
-. $DIR/test_complete.sh

.circleci/test_py3_fmri_spm_linear_3d.sh

@@ -5,6 +5,3 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $DIR/test_init.sh
 
 docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
-exitcode=$?
-
-. $DIR/test_complete.sh

.circleci/test_py3_fmri_spm_linear_4d.sh

@@ -5,6 +5,3 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $DIR/test_init.sh
 
 docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e NIPYPE_NUMBER_OF_CPUS=4 "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1
-exitcode=$?
-
-. $DIR/test_complete.sh

.circleci/test_py3_fmri_spm_nested_multiproc_l1.sh

@@ -5,6 +5,3 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $DIR/test_init.sh
 
 docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data"  "${DOCKER_IMAGE}:py36" /usr/bin/run_pytests.sh
-exitcode=$?
-
-. $DIR/test_complete.sh