From 7a4a2414900be7d3a705de5df4b67f2053743305 Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Fri, 11 Jan 2019 11:55:31 -0500 Subject: [PATCH 1/6] Conda/Jenkins: Always build with a fresh index cache --- Jenkinsfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Jenkinsfile b/Jenkinsfile index e8a7da4c5..7545d0d2e 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -21,6 +21,7 @@ pipeline { CONDA_ENV = "${env.WORKSPACE}/test/${env.STAGE_NAME}" } steps { + sh 'conda clean --index-cache' sh 'conda env create -q -f environment.yml -p $CONDA_ENV' sh '''#!/bin/bash -ex source $CONDA_ENV/bin/activate $CONDA_ENV From db101abb6ce6310379e72bc955873b8fc49a65b6 Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Wed, 30 Jan 2019 16:08:16 -0500 Subject: [PATCH 2/6] Caiman: Tweak C++ build flags for better OSX compatibility --- setup.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index dc7985260..7d97b9ae8 100755 --- a/setup.py +++ b/setup.py @@ -47,7 +47,8 @@ ext_modules = [Extension("caiman.source_extraction.cnmf.oasis", sources=["caiman/source_extraction/cnmf/oasis.pyx"], include_dirs=[np.get_include()], - language="c++")] + language="c++", + extra_compile_args = ["CFLAGS='-libstd=libc++'"])] setup( name='caiman', From 8ef06aa6e892daf2d67748ae755cb47b433cc774 Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Wed, 30 Jan 2019 16:41:35 -0500 Subject: [PATCH 3/6] Fix argument to C++ compiler --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 7d97b9ae8..b0edbbe7c 100755 --- a/setup.py +++ b/setup.py @@ -48,7 +48,7 @@ sources=["caiman/source_extraction/cnmf/oasis.pyx"], include_dirs=[np.get_include()], language="c++", - extra_compile_args = ["CFLAGS='-libstd=libc++'"])] + extra_compile_args = ['-libstd=libc++'])] setup( name='caiman', From f2c63fed8ef8961a7e2c73601d301c5dc1c3c4d3 Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Wed, 30 Jan 2019 17:06:35 -0500 Subject: [PATCH 4/6] On OSX only, add C++ args to clang needed for Mojave --- setup.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index b0edbbe7c..a889ac7d5 100755 --- a/setup.py +++ b/setup.py @@ -44,11 +44,16 @@ # compile with: python setup.py build_ext -i # clean up with: python setup.py clean --all +if sys.platform == 'darwin': + extra_compiler_args = ['stdlib=libc++'] +else: + extra_compiler_args = [] + ext_modules = [Extension("caiman.source_extraction.cnmf.oasis", sources=["caiman/source_extraction/cnmf/oasis.pyx"], include_dirs=[np.get_include()], language="c++", - extra_compile_args = ['-libstd=libc++'])] + extra_compile_args = extra_compiler_args)] setup( name='caiman', From 1d3e8a98bc419c86bb7560cc64c4a507e1fc4ff0 Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Wed, 30 Jan 2019 17:13:38 -0500 Subject: [PATCH 5/6] Forgot a dash --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index a889ac7d5..a4d3e11b8 100755 --- a/setup.py +++ b/setup.py @@ -45,7 +45,7 @@ # compile with: python setup.py build_ext -i # clean up with: python setup.py clean --all if sys.platform == 'darwin': - extra_compiler_args = ['stdlib=libc++'] + extra_compiler_args = ['-stdlib=libc++'] else: extra_compiler_args = [] From 05795a20070ed3d757e88846ede9ee79df70afb0 Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Wed, 30 Jan 2019 17:34:58 -0500 Subject: [PATCH 6/6] Forgot an import --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index a4d3e11b8..39608ef05 100755 --- a/setup.py +++ b/setup.py @@ -3,6 +3,7 @@ from setuptools import setup, find_packages import os from os import path +import sys import numpy as np from Cython.Build import cythonize from setuptools.extension import Extension