From 7eecf4a79610f1c133a78088a36c47d4050e0464 Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Sun, 11 Jun 2017 15:47:23 +0200 Subject: [PATCH 01/10] Add 32 bits tests Use a custom version of the ci-helper that installs 32 bits miniconda. --- .travis.yml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 18fcfc5a74e..fa12761e16f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -37,6 +37,7 @@ env: - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable + - ARCHITECTURE_32BIT=False @@ -86,8 +87,14 @@ matrix: CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} EVENT_TYPE='cron' + - os : linux + env: NAME='32bits' + PYTHON_VERSION=2.7 + ARCHITECTURE_32BIT=True + install: - - git clone git://github.com/astropy/ci-helpers.git + #- git clone git://github.com/astropy/ci-helpers.git + - git clone -b 32bits git://github.com/jbarnoud/ci-helpers.git - source ci-helpers/travis/setup_conda.sh # additional external tools (Issue #898) -- HOLE - | From a40c0e540cf37ee3012a404f0fe594485101a2d5 Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Sun, 11 Jun 2017 16:06:09 +0200 Subject: [PATCH 02/10] Add some apt packages for 32 bits --- .travis.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.travis.yml b/.travis.yml index fa12761e16f..c26b0ade692 100644 --- a/.travis.yml +++ b/.travis.yml @@ -91,6 +91,11 @@ matrix: env: NAME='32bits' PYTHON_VERSION=2.7 ARCHITECTURE_32BIT=True + addons: + apt: + packages: + - libstdc++6:i386 + - gcc-multilib install: #- git clone git://github.com/astropy/ci-helpers.git From 0656560c875962aa812b43b91ecc871aa3252325 Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Sun, 11 Jun 2017 16:52:02 +0200 Subject: [PATCH 03/10] Add compile flag for 32 bits --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index c26b0ade692..d394ed5429e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -38,6 +38,7 @@ env: - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable - ARCHITECTURE_32BIT=False + - ADD_CFLAGS="" @@ -91,6 +92,7 @@ matrix: env: NAME='32bits' PYTHON_VERSION=2.7 ARCHITECTURE_32BIT=True + ADD_CFLAGS='-m32' addons: apt: packages: From 23781fe909b02dde7d0f005fc9ccb386396177da Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Sun, 11 Jun 2017 16:52:43 +0200 Subject: [PATCH 04/10] Move mmtf source from conda to pip Conda-forge ony provides 64 bits packages, this prevent installing mmtf-python on the 32 bits build. Here I try to install it from pypi instead. --- .travis.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index d394ed5429e..400f6359a3e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -29,11 +29,10 @@ env: - NOSE_COVERAGE2="coverage2" - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS}" - SETUP_CMD="" - - BUILD_CMD="pip install -v package/ && pip install testsuite/" - - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer" + - BUILD_CMD="CFLAGS=${ADD_CFLAGS} pip install -v package/ && pip install testsuite/" - 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" # Install griddataformats from PIP so that scipy is only installed in the full build (#1147) - - PIP_DEPENDENCIES='griddataformats' + - PIP_DEPENDENCIES='griddataformats mmtf-python' - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable From f40ce7cb240044ac67b3e42ece73b75a83ebc6b5 Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Sun, 11 Jun 2017 17:43:12 +0200 Subject: [PATCH 05/10] Try differently --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 400f6359a3e..0b162f3094e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -29,7 +29,7 @@ env: - NOSE_COVERAGE2="coverage2" - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS}" - SETUP_CMD="" - - BUILD_CMD="CFLAGS=${ADD_CFLAGS} pip install -v package/ && pip install testsuite/" + - BUILD_CMD="OPT=${ADD_CFLAGS} pip install -v package/ && pip install testsuite/" - 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" # Install griddataformats from PIP so that scipy is only installed in the full build (#1147) - PIP_DEPENDENCIES='griddataformats mmtf-python' From 5c2fdbeeaaf220b7e8dc086789c5f5494318661d Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Sun, 11 Jun 2017 18:20:58 +0200 Subject: [PATCH 06/10] CONDA_FORCE_32BIT --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 0b162f3094e..0494e29109b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -92,6 +92,7 @@ matrix: PYTHON_VERSION=2.7 ARCHITECTURE_32BIT=True ADD_CFLAGS='-m32' + CONDA_FORCE_32BIT=1 addons: apt: packages: From 297247ebf772407f93f25953bd1e76ab631a75f6 Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Sun, 18 Jun 2017 15:14:25 +0200 Subject: [PATCH 07/10] Revert "CONDA_FORCE_32BIT" This reverts commit 8d5b3dea593f6383af0bc8241d491cfcb3a75cba. --- .travis.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 0494e29109b..0b162f3094e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -92,7 +92,6 @@ matrix: PYTHON_VERSION=2.7 ARCHITECTURE_32BIT=True ADD_CFLAGS='-m32' - CONDA_FORCE_32BIT=1 addons: apt: packages: From e77373ad858f84e96163b25a70a1da80e79da774 Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Sun, 18 Jun 2017 16:05:38 +0200 Subject: [PATCH 08/10] debug 32bits --- .travis.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 0b162f3094e..449965dad8d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -29,7 +29,7 @@ env: - NOSE_COVERAGE2="coverage2" - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS}" - SETUP_CMD="" - - BUILD_CMD="OPT=${ADD_CFLAGS} pip install -v package/ && pip install testsuite/" + - BUILD_CMD="pip install -v package/ && pip install testsuite/" - 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" # Install griddataformats from PIP so that scipy is only installed in the full build (#1147) - PIP_DEPENDENCIES='griddataformats mmtf-python' @@ -37,7 +37,6 @@ env: - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable - ARCHITECTURE_32BIT=False - - ADD_CFLAGS="" @@ -91,7 +90,7 @@ matrix: env: NAME='32bits' PYTHON_VERSION=2.7 ARCHITECTURE_32BIT=True - ADD_CFLAGS='-m32' + CFLAGS='-m32' addons: apt: packages: @@ -112,6 +111,7 @@ install: - eval $BUILD_CMD script: + - echo ${LD_LIBRARY_PATH} - cd ${TRAVIS_BUILD_DIR} - if [[ $TRAVIS_OS_NAME == 'osx' ]]; then ulimit -S -n 2048; fi - echo $MAIN_CMD $SETUP_CMD From e61e5057b395a4d52fb405ae4a80132137a436ba Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Tue, 20 Jun 2017 13:39:51 +0200 Subject: [PATCH 09/10] Hopefully fixed the mess of the rebase --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 449965dad8d..0154437f51d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -30,7 +30,7 @@ env: - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS}" - SETUP_CMD="" - BUILD_CMD="pip install -v package/ && pip install testsuite/" - - 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="nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 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 mmtf-python' - CONDA_CHANNELS='biobuilds conda-forge' From e052b12eaa0f291b0a6be5f5c86570c05a2e6368 Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Tue, 20 Jun 2017 13:50:34 +0200 Subject: [PATCH 10/10] Restore a lost line --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 0154437f51d..b173740d054 100644 --- a/.travis.yml +++ b/.travis.yml @@ -30,6 +30,7 @@ env: - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS}" - SETUP_CMD="" - BUILD_CMD="pip install -v package/ && pip install testsuite/" + - CONDA_DEPENDENCIES="nose=1.3.7 mock six biopython networkx cython joblib nose-timer" - CONDA_ALL_DEPENDENCIES="nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 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 mmtf-python'