cleaning changes

.travis.yml

@@ -8,22 +8,14 @@ before_install:
   - export PATH=/home/travis/miniconda3/bin:$PATH
   # Update conda itself
   - conda update --yes conda
-  - export TMPDIR=/tmp/deblur-testing
-  - mkdir $TMPDIR
 install:
-  - conda create --yes -n deblur python=$PYTHON_VERSION pip nose flake8 h5py libgcc
+  - conda create --yes -n deblur python=$PYTHON_VERSION pip nose flake8 h5py
   - source activate deblur
-  - conda install --yes -c bioconda "VSEARCH=2.7.0" 
-  - conda install --yes -c bioconda MAFFT=7.310
-  - conda install --yes -c bioconda SortMeRNA=2.0
+  - conda install --yes -c bioconda "VSEARCH=2.7.0" MAFFT=7.310 SortMeRNA=2.0
   - pip install -U pip coveralls
   - pip install --process-dependency-links .
 script:
-  #- nosetests --with-doctest --with-coverage --cover-package=deblur
-    # flake8 --max-line-length=200 deblur scripts/deblur setup.py
-  - vsearch --version
-  - ldd $(which vsearch)
-  - bash replicate.sh
-  - dmesg | tail -n 100
+  - nosetests --with-doctest --with-coverage --cover-package=deblur
+  - flake8 --max-line-length=200 deblur scripts/deblur setup.py
 after_success:
   - coveralls

deblur/workflow.py

@@ -962,8 +962,4 @@ def _system_call(cmd, stdoutfilename=None):
     stdout, stderr = proc.communicate()
     return_value = proc.returncode
 
-    print(cmd)
-    print(stdout)
-    print(stderr)
-    print(return_value)
     return stdout, stderr, return_value