[build] streamline the process and fix incompatibilies with conda-build 3.x

Author: terhorst

.travis.yml

@@ -17,12 +17,8 @@ install:
   - conda info -a
   - conda install conda-build anaconda-client constructor git
   - conda build -c terhorst -c conda-forge -c bioconda conda
-  - conda create -n smcpp_install --use-local -c terhorst -c bioconda -c conda-forge smcpp
-  - source activate smcpp_install
-  - smc++ version
-  - test/integration/test.sh `which smc++`
+  - conda build -c terhorst -c conda-forge -c bioconda conda --output > .packages
   - conda/template.py conda/construct.tpl $VERSION > conda/construct.yaml
-  - source deactivate
 
 deploy:
   - provider: script

conda/construct.tpl

@@ -6,8 +6,8 @@ channels:
   - http://conda.anaconda.org/terhorst
   - http://conda.anaconda.org/conda-forge
 specs:
-  - python 3.6
   - smcpp
+  - python 3.6.*
   - conda 4.3.21
 post_install: post_install.sh
 license_file: ../LICENSE

conda/deploy.sh

@@ -1,7 +1,9 @@
 #!/bin/bash -x
 set -e
 export PATH="$HOME/miniconda/bin:$PATH"
-anaconda -t $ANACONDA_TOKEN upload --force $(conda build --output conda)
+PKGS=$(conda build -c terhorst -c conda-forge -c bioconda conda --output)
+PKGS=$(cat .packages)
+anaconda -t $ANACONDA_TOKEN upload --force $PKGS
 
-# Next, build 
+# Next, pull uploaded pkg and create a binary installed
 constructor conda

conda/meta.yaml

@@ -60,10 +60,5 @@ test:
         - smcpp
         - smcpp._smcpp
     source_files:
-        - test/integration/test.sh
         - example/example.vcf.gz
         - example/example.vcf.gz.csi
-    commands:
-        - mkdir example
-        - mv example.* example
-        - ./test.sh smc++

test/integration/test.sh conda/run_test.shtest/integration/test.sh renamed to conda/run_test.sh

@@ -1,5 +1,5 @@
 #!/bin/bash -x
-SMC=$1
+SMC=$(which smc++)
 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