From ec56567c577facc39cc0684573f898a705d3c112 Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Thu, 22 Sep 2016 22:58:29 +0000 Subject: [PATCH 01/12] induce failures in travis for testing --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index eb2b9291c3..37727ad505 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,6 +10,7 @@ env: - INSTALL_DEB_DEPENDECIES=false - INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes before_install: +- bleh - wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh -O /home/travis/.cache/miniconda.sh - bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda From 79e274303b624396c831d3ede04e67da0f78e0f9 Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Fri, 23 Sep 2016 00:08:29 +0000 Subject: [PATCH 02/12] add travis_retry --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 37727ad505..9be3235153 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,7 +9,7 @@ env: - INSTALL_DEB_DEPENDECIES=true - INSTALL_DEB_DEPENDECIES=false - INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes -before_install: +before_install: travis_retry - bleh - wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh -O /home/travis/.cache/miniconda.sh From 3fd2372657fd3b7aa8c102d3a2e3780701795df0 Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Fri, 23 Sep 2016 02:45:36 +0000 Subject: [PATCH 03/12] add travis_retry --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 9be3235153..41f951e212 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,8 +9,8 @@ env: - INSTALL_DEB_DEPENDECIES=true - INSTALL_DEB_DEPENDECIES=false - INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes -before_install: travis_retry -- bleh +before_install: +- travis_retry bleh - wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh -O /home/travis/.cache/miniconda.sh - bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda From 46866e72257aecd79d46713030d9f84f136d1442 Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Fri, 23 Sep 2016 03:07:29 +0000 Subject: [PATCH 04/12] travis_retry custom function --- .travis.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 41f951e212..6d7bd4f6ab 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,7 +10,8 @@ env: - INSTALL_DEB_DEPENDECIES=false - INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes before_install: -- travis_retry bleh +- function download {bleh} +- travis_retry download - wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh -O /home/travis/.cache/miniconda.sh - bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda From c597b0c8caad964340c4e35d9990bd236a49f826 Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Fri, 23 Sep 2016 03:22:58 +0000 Subject: [PATCH 05/12] bash syntax --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 6d7bd4f6ab..cf7aede72c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,7 +10,7 @@ env: - INSTALL_DEB_DEPENDECIES=false - INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes before_install: -- function download {bleh} +- function download { bleh; } - travis_retry download - wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh -O /home/travis/.cache/miniconda.sh From 75af34893b3193bc012229cd7de3743d6fda4ea1 Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Fri, 23 Sep 2016 03:27:35 +0000 Subject: [PATCH 06/12] try wget --- .travis.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index cf7aede72c..40254e6f7a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,10 +10,11 @@ env: - INSTALL_DEB_DEPENDECIES=false - INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes before_install: -- function download { bleh; } +- function download { + wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh + -O /home/travis/.cache/miniconda.sh; + bleh; } - travis_retry download -- wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh - -O /home/travis/.cache/miniconda.sh - bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda - export PATH=/home/travis/miniconda/bin:$PATH - if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi From 527620f8c0f6c6b70ca3bd30e8117945fd674930 Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Fri, 23 Sep 2016 03:38:02 +0000 Subject: [PATCH 07/12] put it all in a function --- .travis.yml | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/.travis.yml b/.travis.yml index 40254e6f7a..aa1e629efb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,24 +10,24 @@ env: - INSTALL_DEB_DEPENDECIES=false - INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes before_install: -- function download { +- function download_bi { wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh -O /home/travis/.cache/miniconda.sh; - bleh; } -- travis_retry download -- bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda -- export PATH=/home/travis/miniconda/bin:$PATH -- if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi -- if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi -- bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) -- sudo apt-get -y update -- sudo apt-get -y install xvfb fusefat -- if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -y -qq + bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda; + export PATH=/home/travis/miniconda/bin:$PATH; + if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi + if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi + bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh); + sudo apt-get -y update; + sudo apt-get -y install xvfb fusefat; + if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -y -qq fsl afni elastix fsl-atlases; fi -- if $INSTALL_DEB_DEPENDECIES; then - source /etc/fsl/fsl.sh; - source /etc/afni/afni.sh; fi -- export FSLOUTPUTTYPE=NIFTI_GZ + if $INSTALL_DEB_DEPENDECIES; then + source /etc/fsl/fsl.sh; + source /etc/afni/afni.sh; fi + export FSLOUTPUTTYPE=NIFTI_GZ; + bleh; } +- travis_retry download_bi install: - conda config --add channels conda-forge - conda update --yes conda From b388fd6aebef5127a3e12292e1ffcbc4e9755178 Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Fri, 23 Sep 2016 04:09:08 +0000 Subject: [PATCH 08/12] bash quirk --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index aa1e629efb..2042b620a8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -14,7 +14,7 @@ before_install: wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh -O /home/travis/.cache/miniconda.sh; bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda; - export PATH=/home/travis/miniconda/bin:$PATH; + export PATH=/home/travis/miniconda/bin:$PATH ; if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh); From 37221304eaffa07645277f9a662440e480aa187a Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Fri, 23 Sep 2016 05:14:41 +0000 Subject: [PATCH 09/12] semicolons? --- .travis.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 2042b620a8..ea3eb33cca 100644 --- a/.travis.yml +++ b/.travis.yml @@ -15,16 +15,16 @@ before_install: -O /home/travis/.cache/miniconda.sh; bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda; export PATH=/home/travis/miniconda/bin:$PATH ; - if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi - if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi + if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi; + if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi; bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh); sudo apt-get -y update; sudo apt-get -y install xvfb fusefat; if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -y -qq - fsl afni elastix fsl-atlases; fi + fsl afni elastix fsl-atlases; fi; if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; - source /etc/afni/afni.sh; fi + source /etc/afni/afni.sh; fi; export FSLOUTPUTTYPE=NIFTI_GZ; bleh; } - travis_retry download_bi From 5baa168c7fe686ca864a39c45f40d63beec38cad Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Fri, 23 Sep 2016 05:23:19 +0000 Subject: [PATCH 10/12] functionalize install step --- .travis.yml | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/.travis.yml b/.travis.yml index ea3eb33cca..cd24a7683e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,7 +10,7 @@ env: - INSTALL_DEB_DEPENDECIES=false - INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes before_install: -- function download_bi { +- function bef_inst { wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh -O /home/travis/.cache/miniconda.sh; bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda; @@ -25,24 +25,24 @@ before_install: if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; source /etc/afni/afni.sh; fi; - export FSLOUTPUTTYPE=NIFTI_GZ; - bleh; } -- travis_retry download_bi + export FSLOUTPUTTYPE=NIFTI_GZ; } +- travis_retry bef_inst install: -- conda config --add channels conda-forge -- conda update --yes conda -- conda update --all -y python=$TRAVIS_PYTHON_VERSION -# - if [[ "${INSTALL_DEB_DEPENDECIES}" == "true" && ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]]; then -# conda install -y vtk mayavi; fi -- conda install -y nipype matplotlib nitime -- pip install python-coveralls coverage doctest-ignore-unicode -- if [ ! -z "$DUECREDIT_ENABLE"]; then pip install duecredit; fi -- rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* -- pip install -r requirements.txt -- pip install -e . -- export COVERAGE_PROCESS_START=$(pwd)/.coveragerc -- export COVERAGE_DATA_FILE=$(pwd)/.coverage -- echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START} +- function inst { + conda config --add channels conda-forge ; + conda update --yes conda ; + conda update --all -y python=$TRAVIS_PYTHON_VERSION ; + conda install -y nipype matplotlib nitime ; + pip install python-coveralls coverage doctest-ignore-unicode ; + if [ ! -z "$DUECREDIT_ENABLE"]; then pip install duecredit; fi ; + rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* ; + pip install -r requirements.txt ; + pip install -e . ; + export COVERAGE_PROCESS_START=$(pwd)/.coveragerc ; + export COVERAGE_DATA_FILE=$(pwd)/.coverage ; + echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START} ; + bleh ; } +- travis_retry inst script: - python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-doctest-ignore-unicode --with-cov --cover-package nipype --logging-level=DEBUG --verbosity=3 after_success: From ad17e5299b6ac5de970a8645fd14c12dc0e8105d Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Fri, 23 Sep 2016 05:37:02 +0000 Subject: [PATCH 11/12] test w/o induced failures --- .travis.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index cd24a7683e..0a8f09c721 100644 --- a/.travis.yml +++ b/.travis.yml @@ -40,8 +40,7 @@ install: pip install -e . ; export COVERAGE_PROCESS_START=$(pwd)/.coveragerc ; export COVERAGE_DATA_FILE=$(pwd)/.coverage ; - echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START} ; - bleh ; } + echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START} ; } - travis_retry inst script: - python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-doctest-ignore-unicode --with-cov --cover-package nipype --logging-level=DEBUG --verbosity=3 From 96745847e9becb6c4e294b925ed8741f89f6be07 Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Fri, 23 Sep 2016 20:53:17 +0000 Subject: [PATCH 12/12] change ; to && --- .travis.yml | 44 ++++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/.travis.yml b/.travis.yml index 0a8f09c721..cdfe9d7173 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,35 +12,35 @@ env: before_install: - function bef_inst { wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh - -O /home/travis/.cache/miniconda.sh; - bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda; - export PATH=/home/travis/miniconda/bin:$PATH ; - if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi; - if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi; - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh); - sudo apt-get -y update; - sudo apt-get -y install xvfb fusefat; + -O /home/travis/.cache/miniconda.sh && + bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda && + export PATH=/home/travis/miniconda/bin:$PATH && + if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi && + if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi && + bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) && + sudo apt-get -y update && + sudo apt-get -y install xvfb fusefat && if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -y -qq - fsl afni elastix fsl-atlases; fi; + fsl afni elastix fsl-atlases; fi && if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; - source /etc/afni/afni.sh; fi; + source /etc/afni/afni.sh; fi && export FSLOUTPUTTYPE=NIFTI_GZ; } - travis_retry bef_inst install: - function inst { - conda config --add channels conda-forge ; - conda update --yes conda ; - conda update --all -y python=$TRAVIS_PYTHON_VERSION ; - conda install -y nipype matplotlib nitime ; - pip install python-coveralls coverage doctest-ignore-unicode ; - if [ ! -z "$DUECREDIT_ENABLE"]; then pip install duecredit; fi ; - rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* ; - pip install -r requirements.txt ; - pip install -e . ; - export COVERAGE_PROCESS_START=$(pwd)/.coveragerc ; - export COVERAGE_DATA_FILE=$(pwd)/.coverage ; - echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START} ; } + conda config --add channels conda-forge && + conda update --yes conda && + conda update --all -y python=$TRAVIS_PYTHON_VERSION && + conda install -y nipype matplotlib nitime && + pip install python-coveralls coverage doctest-ignore-unicode && + if [ ! -z "$DUECREDIT_ENABLE"]; then pip install duecredit; fi && + rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* && + pip install -r requirements.txt && + pip install -e . && + export COVERAGE_PROCESS_START=$(pwd)/.coveragerc && + export COVERAGE_DATA_FILE=$(pwd)/.coverage && + echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START}; } - travis_retry inst script: - python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-doctest-ignore-unicode --with-cov --cover-package nipype --logging-level=DEBUG --verbosity=3