From aefa33aec6355dae9fd2144c2875d37b80db531f Mon Sep 17 00:00:00 2001 From: Max Linke Date: Thu, 15 Jun 2017 19:38:58 +0200 Subject: [PATCH 1/6] debug travis builds --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 18fcfc5a74e..97cda6d33fa 100644 --- a/.travis.yml +++ b/.travis.yml @@ -37,6 +37,7 @@ env: - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable + - DEBUG=True From 824eea296c30c247dc8f18e981fad46356be00ed Mon Sep 17 00:00:00 2001 From: Max Linke Date: Sat, 17 Jun 2017 11:03:01 +0200 Subject: [PATCH 2/6] use netcdf4 from pypa there seems to be a version conflict in conda-forge and the defaults channel right now. This might be a band-aid fix. --- .travis.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 97cda6d33fa..3ffe4b7d63c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -31,13 +31,12 @@ env: - SETUP_CMD="" - BUILD_CMD="pip install -v package/ && pip install testsuite/" - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer" - - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy seaborn coveralls clustalw=2.1" + - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scikit-learn scipy seaborn coveralls clustalw=2.1" # Install griddataformats from PIP so that scipy is only installed in the full build (#1147) - PIP_DEPENDENCIES='griddataformats' - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable - - DEBUG=True @@ -57,6 +56,7 @@ matrix: BUILD_DOCS=true BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace" CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} + PIP_DEPENDENCIES="griddataformats netcdf4" - os: linux env: NAME="Lint" @@ -70,21 +70,25 @@ matrix: COVERAGE='--with-coverage --cover-package MDAnalysis' MAIN_CMD='export COVERAGE_FILE=$NOSE_COVERAGE1; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS} ${COVERAGE}; export COVERAGE_FILE=$NOSE_COVERAGE2; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS} ${COVERAGE}' CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} + PIP_DEPENDENCIES="griddataformats netcdf4" COVERALLS='true' - os: osx env: NAME='osx' CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} + PIP_DEPENDENCIES="griddataformats netcdf4" - os: linux env: NAME='old numpy' NUMPY_VERSION=1.10.4 CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} + PIP_DEPENDENCIES="griddataformats netcdf4" - os: linux env: NAME='numpy dev' NUMPY_VERSION=dev CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} + PIP_DEPENDENCIES="griddataformats netcdf4" EVENT_TYPE='cron' install: From ee6a2163dab8be7eea3050504689fc9379172ebe Mon Sep 17 00:00:00 2001 From: Max Linke Date: Sat, 17 Jun 2017 14:11:46 +0200 Subject: [PATCH 3/6] add debug flag --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 3ffe4b7d63c..7d3ecd80009 100644 --- a/.travis.yml +++ b/.travis.yml @@ -37,6 +37,7 @@ env: - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable + - DEBUG=True From 4e697a98f54eeb45c31fd3fb9dc52178b1f87983 Mon Sep 17 00:00:00 2001 From: Max Linke Date: Sun, 18 Jun 2017 17:06:10 +0200 Subject: [PATCH 4/6] remove debug flag --- .travis.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 7d3ecd80009..3ffe4b7d63c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -37,7 +37,6 @@ env: - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable - - DEBUG=True From 95a00125f32fd58c38074e14adefd42c70481851 Mon Sep 17 00:00:00 2001 From: Max Linke Date: Mon, 19 Jun 2017 14:18:42 +0200 Subject: [PATCH 5/6] time installation of dependencies --- .travis.yml | 151 +++++++++++++++++++++++----------------------------- 1 file changed, 66 insertions(+), 85 deletions(-) diff --git a/.travis.yml b/.travis.yml index 3ffe4b7d63c..aa931c370ad 100644 --- a/.travis.yml +++ b/.travis.yml @@ -11,29 +11,14 @@ os: env: global: - - secure: "f8EMSWeYC38elhpB4B/ddxlklEvQoycaxnt90Xw2tH/+ThdP1qteQ2vdgNFy1KL7Am/xnbrRhavI5K+ayfxJ93NoE2adaJ9f9aljXK+Oeu+buv5MVo2E2HhN9mX9opSSxiqGmnHIVYcdLP+1soIsDD78SGL7hB/u5nQ1aTzkbaM=" - - GH_DOC_BRANCH=develop - - GH_REPOSITORY=github.com/MDAnalysis/mdanalysis.git - - GIT_CI_USER=TravisCI - - GIT_CI_EMAIL=TravisCI@mdanalysis.org - - MDA_DOCDIR=${TRAVIS_BUILD_DIR}/package/doc/html/html - - MDA_OPTPACKAGES=opt/packages # Set default python version to avoid repetition later - BUILD_DOCS=false - PYTHON_VERSION=2.7 - - COVERALLS=false - - NOSE_FLAGS="--processes=2 --process-timeout=400 --no-open-files --with-timer --timer-top-n 50" - - NOSE_TEST_LIST1="analysis auxiliary coordinates core formats topology utils" - - NOSE_TEST_LIST2="lib" - - NOSE_COVERAGE1="coverage1" - - NOSE_COVERAGE2="coverage2" - - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS}" + - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests --processes=2 --process-timeout=400 --no-open-files --with-timer --timer-top-n 50" - SETUP_CMD="" + - COVERALLS=false - BUILD_CMD="pip install -v package/ && pip install testsuite/" - - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer" - - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scikit-learn scipy seaborn coveralls clustalw=2.1" # Install griddataformats from PIP so that scipy is only installed in the full build (#1147) - - PIP_DEPENDENCIES='griddataformats' - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable @@ -43,80 +28,76 @@ env: matrix: fast_finish: true include: - - os : linux - env: NAME='minimal' - PYTHON_VERSION=2.7 - MEMLEAK='--with-memleak' - MAIN_CMD='python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS} ${MEMLEAK}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS} ${MEMLEAK}' - - - os: linux - env: NAME="Doc" - MAIN_CMD="cd package && python setup.py" - SETUP_CMD="build_sphinx" - BUILD_DOCS=true - BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace" - CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} - PIP_DEPENDENCIES="griddataformats netcdf4" - - - os: linux - env: NAME="Lint" - MAIN_CMD="pylint --rcfile=package/.pylintrc package/MDAnalysis && pylint --rcfile=package/.pylintrc testsuite/MDAnalysisTests" - BUILD_CMD="" - CONDA_DEPENDENCIES="pylint backports.functools_lru_cache" - PIP_DEPENDENCIES="" - - - os: linux - env: NAME='full' - COVERAGE='--with-coverage --cover-package MDAnalysis' - MAIN_CMD='export COVERAGE_FILE=$NOSE_COVERAGE1; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS} ${COVERAGE}; export COVERAGE_FILE=$NOSE_COVERAGE2; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS} ${COVERAGE}' - CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} - PIP_DEPENDENCIES="griddataformats netcdf4" - COVERALLS='true' - - - os: osx - env: NAME='osx' - CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} - PIP_DEPENDENCIES="griddataformats netcdf4" - - - os: linux - env: NAME='old numpy' - NUMPY_VERSION=1.10.4 - CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} - PIP_DEPENDENCIES="griddataformats netcdf4" - - - os: linux - env: NAME='numpy dev' - NUMPY_VERSION=dev - CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} - PIP_DEPENDENCIES="griddataformats netcdf4" - EVENT_TYPE='cron' + - env: CONDA_DEPENDENCIES="mmtf-python" + os: linux + - env: CONDA_DEPENDENCIES="nose=1.3.7" + os: linux + - env: CONDA_DEPENDENCIES="mock" + os: linux + - env: CONDA_DEPENDENCIES="six" + os: linux + - env: CONDA_DEPENDENCIES="biopython" + os: linux + - env: CONDA_DEPENDENCIES="networkx" + os: linux + - env: CONDA_DEPENDENCIES="cython" + os: linux + - env: CONDA_DEPENDENCIES="joblib" + os: linux + - env: CONDA_DEPENDENCIES="nose-timer" + os: linux + - env: CONDA_DEPENDENCIES="matplotlib" + os: linux + - env: CONDA_DEPENDENCIES="scikit-learn" + os: linux + - env: CONDA_DEPENDENCIES="scipy" + os: linux + - env: CONDA_DEPENDENCIES="seaborn" + os: linux + - env: CONDA_DEPENDENCIES="coveralls" + os: linux + - env: CONDA_DEPENDENCIES="clustalw=2.1" + os: linux + - env: CONDA_DEPENDENCIES="griddataformats" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scikit-learn" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scikit-learn scipy" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scikit-learn scipy seaborn" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scikit-learn scipy seaborn coveralls" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scikit-learn scipy seaborn coveralls clustalw=2.1" + os: linux + - env: CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scikit-learn scipy seaborn coveralls clustalw=2.1 griddataformats" + os: linux install: - git clone git://github.com/astropy/ci-helpers.git - source ci-helpers/travis/setup_conda.sh - # additional external tools (Issue #898) -- HOLE - - | - if [[ $NAME == 'full' ]]; then \ - bash ./maintainer/install_hole.sh $TRAVIS_OS_NAME "${HOME}/${MDA_OPTPACKAGES}"; \ - HOLE_BINDIR="${HOME}/${MDA_OPTPACKAGES}/hole2/exe"; \ - export PATH=${PATH}:${HOLE_BINDIR}; \ - fi - - eval $BUILD_CMD script: - cd ${TRAVIS_BUILD_DIR} - if [[ $TRAVIS_OS_NAME == 'osx' ]]; then ulimit -S -n 2048; fi - echo $MAIN_CMD $SETUP_CMD - - eval $MAIN_CMD $SETUP_CMD - - -after_success: - - | - if [[ $COVERALLS == 'true' ]]; then \ - coverage combine $NOSE_COVERAGE1 $NOSE_COVERAGE2; \ - coveralls; \ - fi - # can't use test here since this leads to travis fails even though the build passes - - if [[ ${TRAVIS_PULL_REQUEST} == "false" ]] && [[ ${BUILD_DOCS} == "true" ]] && [[ ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} ]]; then - bash ${TRAVIS_BUILD_DIR}/maintainer/deploy_docs.sh; - fi From e39189aa0b95dce0536ce3d4ab8e85e66b71729b Mon Sep 17 00:00:00 2001 From: Max Linke Date: Tue, 20 Jun 2017 15:59:11 +0200 Subject: [PATCH 6/6] use trusty image --- .travis.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.travis.yml b/.travis.yml index aa931c370ad..63d157781e5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,5 +1,8 @@ language: generic +sudo: false +dist: trusty + # Only build for develop and master (and PRs) branches: only: