From 7a823f6b8736ffc567f123a208a7a07141862f34 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 14 May 2018 11:18:15 -0400 Subject: [PATCH 1/5] CI: Test against minimum versions --- .travis.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 7735d7ebb4..e30c1fd1fb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,6 +12,7 @@ python: env: - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1 - INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1 +- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" MIN_DEP=1 CI_SKIP_TEST=1 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh" CI_SKIP_TEST=1 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1 @@ -49,7 +50,12 @@ before_install: - travis_retry conda update -q conda - conda config --add channels conda-forge - travis_retry conda install -y python=${TRAVIS_PYTHON_VERSION} icu -- travis_retry pip install -r requirements.txt +- if [ "$MIN_DEP" = "1" ]; then + sed -e 's/>=/==/' < requirements.txt > requirements_min.txt; + travis_retry pip install -r requirements_min.txt; + else + travis_retry pip install -r requirements.txt; + fi; - travis_retry git clone https://github.com/INCF/pybids.git ${HOME}/pybids && pip install -e ${HOME}/pybids - travis_retry pip install codecov From 0d64df6b7c44e5af85a7fdfd6a15eb5971abc0c8 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 14 May 2018 13:58:19 -0400 Subject: [PATCH 2/5] FIX: Minimum scipy wheels for 3.5, 3.6 --- .travis.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.travis.yml b/.travis.yml index e30c1fd1fb..e4bfebb66d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -52,6 +52,11 @@ before_install: - travis_retry conda install -y python=${TRAVIS_PYTHON_VERSION} icu - if [ "$MIN_DEP" = "1" ]; then sed -e 's/>=/==/' < requirements.txt > requirements_min.txt; + if [ "$TRAVIS_PYTHON_VERSION" = "3.5" ]; then + sed -i -e "s/scipy==.*/scipy==0.16.0/" requirements_min.txt; + elif [ "$TRAVIS_PYTHON_VERSION" = "3.6" ]; then + sed -i -e "s/scipy==.*/scipy==0.18.1/" requirements_min.txt; + fi; travis_retry pip install -r requirements_min.txt; else travis_retry pip install -r requirements.txt; From c6381f00f2ff2aa8838a3728a1d6eb5dbf9eb90e Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 14 May 2018 14:41:16 -0400 Subject: [PATCH 3/5] FIX: Find traceback data if result missing --- nipype/pipeline/plugins/base.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index ff84937bc6..20f545b4fe 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -224,7 +224,11 @@ def _clean_queue(self, jobid, graph, result=None): self._status_callback(self.procs[jobid], 'exception') if str2bool(self._config['execution']['stop_on_first_crash']): - raise RuntimeError("".join(result['traceback'])) + if result is None: + tb = '\n'.join(format_exception(*sys.exc_info())) + else: + tb = result['traceback'] + raise RuntimeError("".join(tb)) crashfile = self._report_crash(self.procs[jobid], result=result) if jobid in self.mapnodesubids: # remove current jobid From 143e18f90b41359ef48506c65ac2166d41815eb4 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 14 May 2018 15:35:32 -0400 Subject: [PATCH 4/5] DEP: Try scipy>=0.19 --- .travis.yml | 5 ----- requirements.txt | 4 ++-- 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index e4bfebb66d..e30c1fd1fb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -52,11 +52,6 @@ before_install: - travis_retry conda install -y python=${TRAVIS_PYTHON_VERSION} icu - if [ "$MIN_DEP" = "1" ]; then sed -e 's/>=/==/' < requirements.txt > requirements_min.txt; - if [ "$TRAVIS_PYTHON_VERSION" = "3.5" ]; then - sed -i -e "s/scipy==.*/scipy==0.16.0/" requirements_min.txt; - elif [ "$TRAVIS_PYTHON_VERSION" = "3.6" ]; then - sed -i -e "s/scipy==.*/scipy==0.18.1/" requirements_min.txt; - fi; travis_retry pip install -r requirements_min.txt; else travis_retry pip install -r requirements.txt; diff --git a/requirements.txt b/requirements.txt index 5ef00ec98b..b827adb384 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ -numpy>=1.9.0 -scipy>=0.14 +numpy>=1.9.3 +scipy>=0.19.1 networkx>=1.9 traits>=4.6 python-dateutil>=2.2 From 62e1734ea2523acc786f04175275117b4fd7e636 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 14 May 2018 16:02:17 -0400 Subject: [PATCH 5/5] CI: No "fmri" extra --- .travis.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.travis.yml b/.travis.yml index e30c1fd1fb..f458cf7a0b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,11 +10,11 @@ python: - 3.6 env: -- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1 -- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1 -- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" MIN_DEP=1 CI_SKIP_TEST=1 -- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh" CI_SKIP_TEST=1 -- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1 +- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,profiler" CI_SKIP_TEST=1 +- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,profiler" CI_SKIP_TEST=1 +- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,profiler" MIN_DEP=1 CI_SKIP_TEST=1 +- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,profiler,duecredit,ssh" CI_SKIP_TEST=1 +- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1 addons: apt: