[build] intermediate updates

Author: terhorst

.travis.yml

@@ -6,11 +6,6 @@ os:
   - linux
   - osx
 
-env:
-  matrix:
-    - CONDA_PY=3.5
-    - CONDA_PY=3.6
-
 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
@@ -20,13 +15,13 @@ install:
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
   - conda info -a
-  - conda install conda-build anaconda-client constructor git python=$CONDA_PY
-  - conda build --debug -c terhorst -c conda-forge -c bioconda conda --python=$CONDA_PY
-  - conda create -n smcpp_install --use-local -c terhorst -c bioconda -c conda-forge python=$CONDA_PY smcpp
+  - 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/template.py conda/construct.tpl $VERSION > conda/construct.yaml 
+  - conda/template.py conda/construct.tpl $VERSION > conda/construct.yaml
   - source deactivate
 
 deploy:
@@ -40,7 +35,6 @@ deploy:
     on:
       repo: popgenmethods/smcpp
       tags: true
-      condition: "$CONDA_PY = 3.6"
     api_key:
       secure: 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
     file_glob: true

conda/conda_build_config.yaml

@@ -0,0 +1,8 @@
+python:
+    - 3.5
+    - 3.6
+openblas:
+    - 0.2.19
+
+pin_run_as_build:
+    openblas: {}

conda/construct.tpl

@@ -6,6 +6,7 @@ channels:
   - http://conda.anaconda.org/terhorst
   - http://conda.anaconda.org/conda-forge
 specs:
+  - python 3.6
   - smcpp
   - conda 4.3.21
 post_install: post_install.sh

conda/meta.yaml

@@ -7,39 +7,26 @@ source:
 
 requirements:
   build:
-    - python
+    - python {{ python }}
     - nomkl
     - gcc >=4.8.5
-    - libgcc
-    - openblas 0.2.19
+    - libgcc 
+    - openblas {{ openblas }}
     - git >=2.9.3
     - 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
-    - matplotlib >=2.0
-    - pandas >=0.19
-    - python-dateutil >=2.6
-    - scipy >=0.18
-    - six >=1.10
-    - appdirs >=1.4
-    - tqdm >=4.10
-    - wrapt >=1.10
-    - ad >=1.3.2
-    - readline >=6.2
-    - attrs >=17.2.0
   run:
     - python
     - nomkl
     - gcc >=4.8.5
     - libgcc
-    - openblas 0.2.19
+    - openblas
     - git >=2.9.3
     - cython >=0.25
     - setuptools >=33.1
@@ -64,11 +51,19 @@ requirements:
     - attrs >=17.2.0
 
 about:
-  home: https://github.com/popgenmethods/smcpp
-  license: BSD
-  license_file: LICENSE
+    home: https://github.com/popgenmethods/smcpp
+    license: BSD
+    license_file: LICENSE
 
 test:
-  imports:
-    - smcpp
-    - smcpp._smcpp
+    imports:
+        - 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++