Merge branch 'devel'

Author: terhorst

.gitignore

@@ -23,3 +23,6 @@ dist/
 smcpp.egg-info
 .cache
 smcpp/version.py
+smcpp/_estimation_tools.c
+<<<<<<< HEAD
+src/.release_time

.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 > .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

@@ -1,8 +1,3 @@
 python:
     - 3.5
     - 3.6
-openblas:
-    - 0.2.19
-
-pin_run_as_build:
-    openblas: {}

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
-    - gcc >=4.8.5
-    - libgcc
-    - openblas
-    - 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

conda/run_test.sh

@@ -4,7 +4,7 @@ set -e
 $SMC vcf2smc -v example/example.vcf.gz /tmp/example.1.smc.gz 1 msp1:msp_0,msp_1,msp_2
 $SMC vcf2smc -d msp_0 msp_0 example/example.vcf.gz /tmp/example.2.smc.gz 1 msp2:msp_0,msp_3,msp_4
 $SMC vcf2smc -d msp_1 msp_1 example/example.vcf.gz /tmp/example.12.smc.gz 1 msp1:msp_1,msp_2 msp2:msp_3,msp_4,msp_0
-$SMC estimate -o /tmp/out/1 --unfold --knots 5 --multi --em-iterations 1 1.25e-8 /tmp/example.1.smc.gz
+$SMC estimate -o /tmp/out/1 --unfold --knots 5 --no-multi --em-iterations 1 1.25e-8 /tmp/example.1.smc.gz
 $SMC estimate -p 0.01 -r 1e-8 -o /tmp/out/2 --knots 5 --em-iterations 1 1.25e-8 /tmp/example.2.smc.gz
 $SMC split -o /tmp/out/split --em-iterations 1 \
     /tmp/out/1/model.final.json \

include/bin_key.h

@@ -53,12 +53,24 @@ std::set<block_key> bin_key<1>::run(
     else
     {
         ret.emplace(key);
+        if (true) // or undistinguish)
+            for (int aa = 0; aa <= na(0); ++aa)
+            {
+                int bb = key(1) - aa;
+                tmp(0) = aa;
+                if ((aa + bb == key(0) + key(1)) and
+                        (0 <= bb) and
+                        (bb <= key(2)))
+                    ret.emplace(tmp);
+            }
+        /*
         if (nb > 0 and ((double)b / (double)nb > cutoff))
             for (int bb = (int)(cutoff * nb); bb <= nb; ++bb)
             {
                 tmp(1) = bb;
                 ret.emplace(tmp);
             }
+        */
     }
     return ret;
 }