Merge pull request #291 from JakaKokosar/travis_integration

[ENH]Travis integration

Author: lanzagar

.travis.yml

@@ -1,24 +1,34 @@
 language: python
-
+dist: trusty
 sudo: false
 
-python:
-    - "3.4"
+matrix:
+    include:
+        - python: '3.6'
+          env: ORANGE_INSTALL=conda
+        - python: '3.6'
+          env: ORANGE_INSTALL=source
 
 cache:
     apt: true
     pip: true
+    ccache: true
 
-addons:
-    apt:
-        packages:
-            - libblas-dev
-            - liblapack-dev
-            - gfortran
+before_install:
+    - source $TRAVIS_BUILD_DIR/.travis/install_miniconda.sh
+    - echo $TRAVIS_PYTHON_VERSION
+    - conda env create -f conda_environment.yml python=$TRAVIS_PYTHON_VERSION
+    - source $TRAVIS_BUILD_DIR/.travis/install_orange.sh
+    - source activate orange3-single-cell
 
 install:
-    # Update pip to be able to install wheel dependencies
-    - pip install -U pip wheel
+    - pip install -U pip wheel coverage codecov
+    - source $TRAVIS_BUILD_DIR/.travis/install_orange.sh
     - pip install -e .
+    - pip freeze
+
+script:
+    - catchsegv xvfb-run -a -s "-screen 0 1280x1024x24" coverage run setup.py test
 
-script: python setup.py test
+after_success:
+    - codecov

.travis/install_miniconda.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# https://conda.io/docs/user-guide/tasks/use-conda-with-travis-ci.html#the-travis-yml-file
+
+# install miniconda
+wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+bash miniconda.sh -b -p $HOME/miniconda
+export PATH="$HOME/miniconda/bin:$PATH"
+hash -r
+# update miniconda
+conda config --set always_yes yes --set changeps1 no
+conda update -q conda
+conda info -a

.travis/install_orange.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+if [ $ORANGE_INSTALL == "source" ];
+then
+    echo "Orange install for source"
+    pip install https://github.com/biolab/orange3/archive/master.zip
+else
+    echo "Orange install for conda"
+    conda install orange3
+
+fi

MANIFEST.in

@@ -5,6 +5,9 @@ recursive-include orangecontrib/single_cell/tutorials *.ows *.tsv *.mtx *.tab.gz
 recursive-include orangecontrib/single_cell/launcher/icons *.svg *.png
 recursive-include orangecontrib/single_cell/widgets/icons *.svg
 
+# include test files
+recursive-include orangecontrib/single_cell/tests/ *
+
 # include meta data
 include requirements.txt
 include README.md

codecov.yml

@@ -0,0 +1,10 @@
+comment:
+  layout: header, diff, changes, sunburst, uncovered
+coverage:
+  status:
+    patch:
+      default:
+        target: '80'
+    project:
+      default:
+        target: auto

conda_environment.yml

@@ -0,0 +1,13 @@
+name: orange3-single-cell
+
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+
+dependencies:
+  - orange3-bioinformatics==3.2.0
+  - pandas>=0.23
+  - fastdtw
+  - loompy
+  - networkx

orangecontrib/single_cell/tests/test_owscorecells.py renamed to orangecontrib/single_cell/tests/owscorecells.py

@@ -28,6 +28,7 @@
 
 PACKAGE_DATA = {
     'orangecontrib.single_cell.tutorials': ['*.ows', '*.tsv', '*.mtx', '*.tab.gz', '*.tab'],
+    'orangecontrib.single_cell.tests': ['*'],
     'orangecontrib.single_cell.launcher.icons': ['*.ows', '*.png'],
     'orangecontrib.single_cell.widgets.icons': ['*.ows']
 }