Merge pull request #101 from joachimwolff/develop

Changed travis tests, fixed pandas warning

.planemo.sh

@@ -1,13 +1,16 @@
 #!/bin/bash
 
-blah=`mktemp -d`
-/home/travis/build/maxplanck-ie/HiCExplorer/foo/bin/planemo database_create galaxy
-/home/travis/build/maxplanck-ie/HiCExplorer/foo/bin/planemo conda_init --conda_prefix $blah/conda
-export PATH=$blah/conda/bin:$PATH
+tmp_dir=`mktemp -d`
+
+planemo_test_env/bin/planemo database_create galaxy
+planemo_test_env/bin/planemo conda_init --conda_prefix $tmp_dir/conda
+export PATH=$tmp_dir/conda/bin:$PATH
 conda create -y -c bioconda --name hicexplorer_galaxy samtools python=2.7.13 numpy scipy matplotlib=1.5.3 nose flake8 pytables biopython pysam pybigwig intervaltree
 source activate hicexplorer_galaxy
 
 pip install .
 
+
 # Galaxy wrapper testing
-/home/travis/build/maxplanck-ie/HiCExplorer/foo/bin/planemo test --skip_venv --install_galaxy --no_conda_auto_install --no_conda_auto_init --galaxy_branch release_17.01 --postgres galaxy/wrapper/
+planemo_test_env/bin/planemo test --skip_venv --install_galaxy --no_conda_auto_install --no_conda_auto_init --galaxy_branch release_17.01 --postgres galaxy/wrapper/
+# /home/travis/build/maxplanck-ie/HiCExplorer/foo/bin/planemo test --skip_venv --install_galaxy --no_conda_auto_install --no_conda_auto_init --galaxy_branch release_17.01 --postgres galaxy/wrapper/

.travis.yml

@@ -13,7 +13,7 @@ before_install:
   - export HIC_TEST_DATA_DIR="`pwd`/hicexplorer/test/test_data/"
   - echo $HIC_TEST_DATA_DIR
   - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then pip install virtualenv --user ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then virtualenv foo; source foo/bin/activate; pip install planemo ; deactivate ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then virtualenv planemo_test_env; source planemo_test_env/bin/activate; pip install six; pip install planemo ; deactivate ; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then curl https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -o miniconda.sh ; fi
   #- if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "3.5" ]]; then curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh ; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then curl https://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh -o miniconda.sh ; fi
@@ -29,17 +29,18 @@ before_install:
 
 # Install packages
 install:
-  - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib=1.5.3 nose flake8 pytables biopython pandas
+  - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib=2.0.0 nose flake8 pytables biopython pandas
   - conda install --yes -c bioconda pysam intervaltree
   - pip install pyBigWig
   - python setup.py install
 
 # command to run tests
 script:
-  - flake8 . --exclude=.venv,.build,foo,build --ignore=E501,F403,E402,F999,F405,E712
+  - flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F403,E402,F999,F405,E712
   - export owd=`pwd`
   - cd ~/ && nosetests --with-doctest -sv hicexplorer
   - cd ${owd}
   - echo ${owd}
   #- if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then /home/travis/build/maxplanck-ie/HiCExplorer/foo/bin/planemo lint galaxy/wrapper/ ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then bash /home/travis/build/maxplanck-ie/HiCExplorer/.planemo.sh ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then bash .planemo.sh ; fi
+  # - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then bash /home/travis/build/maxplanck-ie/HiCExplorer/.planemo.sh ; fi

galaxy/wrapper/hicPlotTADs.xml

@@ -8,7 +8,6 @@
     <command detect_errors="aggressive">
 <![CDATA[
         sed '/^$/d' '$tracks_config' &&
-
         @BINARY@
             --tracks '$tracks_config'
             #if $region and $region is not None:
@@ -59,7 +58,7 @@ color = $track.color
 #end if
 
 #if $track.border_color:
-color = $track.border_color
+border_color = $track.border_color
 #end if
 
 #if $track.depth:

hicexplorer/HiCMatrix.py

@@ -11,6 +11,9 @@
 
 import gzip
 
+import warnings
+warnings.simplefilter(action='ignore', category=FutureWarning)
+
 # try to import pandas if exists
 try:
     import pandas as pd