[build] fix missing dependency for constructor

Author: terhorst

.gitignore

@@ -26,5 +26,3 @@ smcpp/version.py
 smcpp/_estimation_tools.c
 <<<<<<< HEAD
 src/.release_time
-=======
->>>>>>> 7bb56d8... [core] refactor estimation_tools to a different cython module. prevent loading _smcpp/openmp until necessary. add --cores open to control core usage. reduce memory consumption by eliminating unnecessary copies of the observations matrix. reduce thread overhead. fixes #46

.travis.yml

@@ -4,24 +4,22 @@ sudo: false
 
 os:
   - linux
-  - osx
+  # - osx
 
 install:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export OS=MacOSX; else export OS=Linux; fi
-  - wget https://repo.continuum.io/miniconda/Miniconda3-4.3.21-$OS-x86_64.sh -O miniconda.sh
+  - wget https://repo.continuum.io/miniconda/Miniconda3-4.3.30-$OS-x86_64.sh -O miniconda.sh
   - bash miniconda.sh -b -p $HOME/miniconda
   - export OLDPATH=$PATH PATH="$HOME/miniconda/bin:$PATH" VERSION=$(git describe --tags) MACOSX_DEPLOYMENT_TARGET=10.9
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
+  - conda update -y conda python
   - conda info -a
   - conda install conda-build anaconda-client constructor git
-  - conda build -c terhorst -c conda-forge -c bioconda conda
-  - conda build -c terhorst -c conda-forge -c bioconda conda --output | tee .packages
+  - conda build -c terhorst -c bioconda conda
+  - conda build -c terhorst -c bioconda conda --output | tee .packages
   - conda/template.py conda/construct.tpl $VERSION > conda/construct.yaml
 
-before_deploy:
-  - constructor conda
 deploy:
   - provider: script
     script: conda/deploy.sh

conda/build.sh

@@ -1,3 +1,8 @@
 #!/bin/bash -ex
-export CFLAGS="-mtune=generic" CXXFLAGS="-mtune=generic"
+CFLAGS="-I$PREFIX/include -Wno-int-in-bool-context -mtune=generic $CFLAGS"
+CXXFLAGS="-Wno-int-in-bool-context -I$PREFIX/include -mtune=generic $CXXFLAGS"
+LDFLAGS="-L$PREFIX/lib $LDFLAGS"
+PATH="$PREFIX/bin:$PATH"
+LDSHARED=$(python -c "import sys;from distutils import sysconfig;lds = sysconfig.get_config_var('LDSHARED').split(' ');print(' '.join(['$GCC'] + lds[1:]))")
+export CFLAGS CXXFLAGS LDFLAGS PATH LDSHARED
 $PYTHON setup.py install --single-version-externally-managed --record=/dev/null

conda/conda_build_config.yaml

@@ -1,10 +1,3 @@
 python:
     - 3.5
     - 3.6
-openblas:
-    - 0.2.19
-libgcc:
-    - 4.8.5
-pin_run_as_build:
-    openblas: {}
-    libgcc: {}

conda/construct.tpl

@@ -1,13 +1,12 @@
 name: smcpp
 version: {version}
 channels:
+  - http://repo.continuum.io/pkgs/main/
   - http://repo.continuum.io/pkgs/free/
   - http://conda.anaconda.org/bioconda
   - http://conda.anaconda.org/terhorst
-  - http://conda.anaconda.org/conda-forge
 specs:
-  - smcpp
+  - smcpp {version}
   - python 3.6.*
-  - conda 4.3.21
 post_install: post_install.sh
 license_file: ../LICENSE

conda/construct.yaml

@@ -0,0 +1,13 @@
+name: smcpp
+version: 1.11.0dev
+channels:
+  - http://repo.continuum.io/pkgs/main/
+  - http://repo.continuum.io/pkgs/free/
+  - http://conda.anaconda.org/bioconda
+  - http://conda.anaconda.org/terhorst
+specs:
+  - smcpp 1.11.0dev
+  - python 3.6.*
+post_install: post_install.sh
+license_file: ../LICENSE
+

conda/deploy.sh

@@ -4,5 +4,5 @@ export PATH="$HOME/miniconda/bin:$PATH"
 PKGS=$(cat .packages)
 anaconda -t $ANACONDA_TOKEN upload --force $PKGS
 
-# Next, pull uploaded pkg and create a binary installed
-constructor conda
+# Next, pull uploaded pkg and create a binary
+constructor conda -v

conda/meta.yaml

@@ -8,33 +8,25 @@ source:
 requirements:
   build:
     - python {{ python }}
-    - nomkl
-    - gcc >=4.8.5
-    - libgcc 
-    - openblas {{ openblas }}
+    - {{ compiler('cxx') }}
     - git >=2.9.3
     - cython >=0.25
     - setuptools >=33.1
     - numpy >=1.10
     - gmp >=6.1.0
     - gsl >=2.2.1
-    - mpc >=1.0.3
     - mpfr >=3.1.5
     - setuptools_scm >=1.15
   run:
     - python
-    - nomkl
-    - libgcc
-    - openblas
-    - isl
-    - git >=2.9.3
+    - {{ pin_compatible('libgcc-ng') }}
+    - {{ pin_compatible('libstdcxx-ng') }}
     - cython >=0.25
     - setuptools >=33.1
     - numpy >=1.10
     - gnuplot >=4.6.0
     - gmp >=6.1.0
     - gsl >=2.2.1
-    - mpc >=1.0.3
     - mpfr >=3.1.5
     - setuptools_scm >=1.15
     - pysam >=0.11

setup.py

@@ -44,7 +44,7 @@
 setup(name='smcpp',
         description='SMC++',
         author='Jonathan Terhorst, Jack Kamm, Yun S. Song',
-        author_email='[email protected].edu',
+        author_email='jonth@umich.edu',
         url='https://github.com/popgenmethods/smc++',
         ext_modules=cythonize(extensions),
         packages=find_packages(),

smcpp/_smcpp.pxd

@@ -5,7 +5,7 @@ from libcpp cimport bool
 from libcpp.memory cimport unique_ptr
 from libcpp.string cimport string
 
-cdef extern from "gsl/gsl_sf_gamma.h":
+cdef extern from "<gsl/gsl_sf_gamma.h>":
     double gsl_sf_lnbeta(double, double) nogil
 
 cdef extern from "common.h":