Skip to content

Commit b87d8e5

Browse files
mgxdmgxd
authored
Merge pull request #1 from nipy/master
merge with upstream
2 parents 67b9d73 + d68b929 commit b87d8e5

File tree

104 files changed

+3195
-1225
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

104 files changed

+3195
-1225
lines changed

‎.circle/tests.sh

Lines changed: 43 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,43 @@
1+
#!/bin/bash
2+
#
3+
# Balance nipype testing workflows across CircleCI build nodes
4+
#
5+
6+
# Setting # $ help set
7+
set -e # Exit immediately if a command exits with a non-zero status.
8+
set -u # Treat unset variables as an error when substituting.
9+
set -x # Print command traces before executing command.
10+
11+
if [ "${CIRCLE_NODE_TOTAL:-}" != "4" ]; then
12+
echo "These tests were designed to be run at 4x parallelism."
13+
exit 1
14+
fi
15+
16+
# These tests are manually balanced based on previous build timings.
17+
# They may need to be rebalanced in the future.
18+
case ${CIRCLE_NODE_INDEX} in
19+
0)
20+
docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_pytests.sh && \
21+
docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_pytests.sh && \
22+
docker run --rm=false -it -v $WORKDIR:/work -w /src/nipype/doc nipype/nipype:py35 /usr/bin/run_builddocs.sh && \
23+
docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d && \
24+
docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
25+
;;
26+
1)
27+
docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ level1 && \
28+
docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ l2pipeline
29+
;;
30+
2)
31+
docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
32+
docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
33+
;;
34+
3)
35+
docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
36+
docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline && \
37+
docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
38+
;;
39+
esac
40+
41+
cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
42+
codecov -f "coverage*.xml" -s "${WORKDIR}/tests/" -R "${HOME}/nipype/" -F unittests -e CIRCLE_NODE_INDEX
43+
codecov -f "smoketest*.xml" -s "${WORKDIR}/tests/" -R "${HOME}/nipype/" -F smoketests -e CIRCLE_NODE_INDEX

‎.coveragerc

Lines changed: 0 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,2 @@
11
[run]
22
branch = True
3-
source = nipype
4-
include = */nipype/*
5-
omit =
6-
*/nipype/external/*
7-
*/nipype/fixes/*
8-
*/setup.py

‎.dockerignore

Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
# python cache
2-
__pycache__/**/*
32
__pycache__
3+
**/__pycache__
4+
**/*.pyc
45
*.pyc
56

67
# python distribution
@@ -23,12 +24,14 @@ src/
2324
# other
2425
docs/**/*
2526
docs/
26-
.coverage
27-
.coveragerc
28-
codecov.yml
29-
rtd_requirements.txt
27+
.cache/
28+
.circle/**/*
29+
.circle/
3030
circle.yml
31+
rtd_requirements.txt
3132
Vagrantfile
3233
.travis.yml
33-
.noserc
34+
.mailmap
3435

36+
# Previous coverage results
37+
.coverage

‎.gitignore

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -24,5 +24,6 @@ crash*.pklz
2424
htmlcov/
2525
__pycache__/
2626
*~
27+
.*.swp
2728
.ipynb_checkpoints/
2829
.ruby-version

‎.noserc

Lines changed: 0 additions & 11 deletions
This file was deleted.

‎.travis.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,7 @@ before_install:
4242
install:
4343
- travis_retry pip install -e .[$NIPYPE_EXTRAS]
4444
script:
45-
- py.test --doctest-modules nipype
45+
- py.test -v --doctest-modules nipype
4646
deploy:
4747
provider: pypi
4848
user: satra

0 commit comments

Comments
 (0)