From 8680de1db1e00666e7865740b4b0206badd1a550 Mon Sep 17 00:00:00 2001 From: Kris Thielemans Date: Sat, 6 Jun 2020 23:28:07 +0100 Subject: [PATCH 1/2] [TRAVIS] fix coverage lines coverage was broken in a few ways: - .coverage was in a different place than we thought - OSX sed doesn't support -r but needs -E - we were not necessarily using the correct python fixes #709 --- .travis.yml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/.travis.yml b/.travis.yml index e99347b4b..060977538 100644 --- a/.travis.yml +++ b/.travis.yml @@ -223,7 +223,8 @@ before_install: - popd # no point re-downloading SIRF - just use local version # N.B.: don't put into build matrix to allow caching. -- BUILD_FLAGS="$BUILD_FLAGS -DPYVER=$PYMVER -DSIRF_SOURCE_DIR:PATH=$PWD -DDISABLE_GIT_CHECKOUT_SIRF=ON" +- SIRF_SOURCE_DIR=$PWD +- BUILD_FLAGS="$BUILD_FLAGS -DPYVER=$PYMVER -DSIRF_SOURCE_DIR:PATH=$SIRF_SOURCE_DIR -DDISABLE_GIT_CHECKOUT_SIRF=ON" # get SuperBuild - cd .. - git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b master @@ -259,8 +260,10 @@ script: fi after_success: -- pushd ../SIRF -- sed -r 's/SIRF-SuperBuild\/INSTALL\/python\/sirf\/(\w*)\.py/SIRF\/src\/x\1\/p\1\/\1.py/g' ../SIRF-SuperBuild/sources/SIRF/.coverage > .coverage -- codecov -- coveralls +- pushd $SIRF_SOURCE_DIR +# replace name of installed .py files in .coverage (as OSX sed is tricky with sed -i, first write to tmp file, then move to .coverage) +- sed -E 's/SIRF-SuperBuild\/INSTALL\/python\/sirf\/(\w*)\.py/SIRF\/src\/x\1\/p\1\/\1.py/g' $SIRF_SOURCE_DIR/.coverage > .coverage.tmp +- mv .coverage.tmp .coverage +- $PY_EXE -m codecov +- $PY_EXE -m coveralls - popd From a3465a917ff6d8d40cac7af67fcd21a58122a903 Mon Sep 17 00:00:00 2001 From: Kris Thielemans Date: Sat, 6 Jun 2020 23:33:15 +0100 Subject: [PATCH 2/2] fix badges in README to use SyneRBI --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 22b26df55..1701589c3 100644 --- a/README.md +++ b/README.md @@ -9,9 +9,9 @@ Platform for Synergistic Reconstruction for Biomedical Imaging (formerly CCP PET Please start with our latest [User's Guide](doc/UserGuide.md). See [our Wiki page for installation instructions](https://github.com/CCPPETMR/SIRF/wiki/Installation-instructions). -[coveralls-badge]: https://coveralls.io/repos/github/CCPPETMR/SIRF/badge.svg?branch=master -[coveralls]: https://coveralls.io/github/CCPPETMR/SIRF?branch=master -[codecov-badge]: https://codecov.io/gh/CCPPETMR/SIRF/branch/master/graph/badge.svg -[codecov]: https://codecov.io/gh/CCPPETMR/SIRF -[travis-badge]: https://travis-ci.org/CCPPETMR/SIRF.svg?branch=master -[travis]: https://travis-ci.org/CCPPETMR/SIRF +[coveralls-badge]: https://coveralls.io/repos/github/SyneRBI/SIRF/badge.svg?branch=master +[coveralls]: https://coveralls.io/github/SyneRBI/SIRF?branch=master +[codecov-badge]: https://codecov.io/gh/SyneRBI/SIRF/branch/master/graph/badge.svg +[codecov]: https://codecov.io/gh/SyneRBI/SIRF +[travis-badge]: https://travis-ci.org/SyneRBI/SIRF.svg?branch=master +[travis]: https://travis-ci.org/SyneRBI/SIRF