Merge pull request #41 from cggh/upgrades_20170126

Upgrades 20170126

.travis.yml

@@ -0,0 +1,30 @@
+language: python
+python:
+  - "3.5"
+install:
+  - sudo apt-get update
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda config --add channels r
+  - conda config --add channels bioconda
+  - conda config --add channels conda-forge
+  - conda info -a
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION
+  - source activate test-environment
+  - conda clean --lock
+  - conda install -q --yes gcc
+  - conda install -q --yes --file=conda_package_list.txt
+  - pip install --no-cache-dir -r pypi_package_list.txt
+
+script:
+  # run scikit-allel test suite to verify dependencies are good
+  - export PYTHONHASHSEED=42
+  - nosetests allel --exclude=from_gff3

base/Dockerfile

@@ -63,8 +63,8 @@ ENV PATH /anaconda/bin:$PATH
 
 RUN conda update -y conda
 
-# conda with python 3.5.1
-RUN conda create --name science --yes python=3.5.1
+# conda with python 3.5.2
+RUN conda create --name science --yes python=3.5.2
 
 RUN conda config --add channels r
 RUN conda config --add channels bioconda

conda_package_list.txt

@@ -1,44 +1,51 @@
 basemap=1.0.7
-bcolz=1.0.0
 biopython=1.68
-bokeh=0.11.1
-cartopy=0.14.2
-cython=0.24.1
-dask=0.11.0
-gdal=2.1.1
+bokeh=0.12.4
+cartopy=0.14.3
+cython=0.25.2
+dask=0.11.1
+ete3=3.0.0b35
+fastcluster=1.1.21
+gdal=2.1.2
 hapbin=1.0.0
 humanize=0.5.1 
 h5py=2.6.0
-icu=56.1
-joblib=0.10.2
+intervaltree=2.1.0
+joblib=0.10.3
 jupyter=1.0.0
-line_profiler=1.0
-matplotlib=1.5.3
-matplotlib-venn=0.11.1
+line_profiler=2.0
+matplotlib=2.0.0
+matplotlib-venn=0.11.4
 memory_profiler=0.41 
-msprime=0.3.2
+msprime=0.4.0
 nose=1.3.7
-numba=0.28.1
-numpy=1.11.2
-numexpr=2.6.1
-pandas=0.19.0
+numba=0.30.1
+numpy=1.11.3
+numexpr=2.6.2
+openpyxl=2.4.1
+pandas=0.19.2
+petl=1.1.1
 petlx=1.0.3
-pillow=3.4.1
-psutil=4.3.1
+pillow=4.0.0
+psutil=5.0.1
 psycopg2=2.6.2
 pyfasta=0.5.2
+pyfastaq=3.14.0
+pymysql=0.7.9
 pysam=0.8.4
-pysamstats=0.24.2 
+pysamstats=0.24.3 
 pytables=3.3.0
 pyvcf=0.6.8
-rpy2=2.7.6 
-scikit-allel=0.21.2
-scikit-learn=0.18
+rpy2=2.8.5
+scikit-allel=1.0.3
+scikit-learn=0.18.1
+scipy=0.18.1
 seaborn=0.7.1
 sh=1.11
-sqlalchemy=1.0.13
+sqlalchemy=1.1.5
 statsmodels=0.6.1
-toolz=0.8.0
+toolz=0.8.2
+cytoolz=0.8.2
 whoosh=2.7.4
 xlrd=1.0.0
-zarr=2.1.3
+zarr=2.1.4

pypi_package_list.txt

@@ -1,12 +1,9 @@
 anhima == 0.11.2 
-ete3 == 3.0.0b29 
-fastcluster == 1.1.20 
-IntervalTree == 2.1.0 
-openpyxl == 2.3.3 
-petl == 1.1.0 
-prettypandas == 0.0.2 
-py-cpuinfo == 0.1.8 
-pymysql == 0.7.1 
+prettypandas == 0.0.3 
+py-cpuinfo == 0.2.3
 scikits.bootstrap == 0.3.2 
-vcfnp == 2.2.0 
+vcfnp == 2.3.0 
 xlwt-future == 0.8.0 
+bcolz == 1.1.0
+hmmlearn == 0.2.0
+