Merge pull request #63 from KVSlab/update-ci

Change CI from TravisCI to CircleCI

Author: hkjeldsberg

.circleci/config.yml

@@ -0,0 +1,58 @@
+version: 2.1
+workflows:
+  version: 2
+  test:
+    jobs:
+      - install-and-test
+jobs:
+  install-and-test:
+    docker:
+      - image: cimg/python:3.6
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - run:
+          name: Install miniconda
+          command: |
+            # Install anaconda
+            wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
+            bash ~/miniconda.sh -b -p $HOME/miniconda
+      - run:
+          name: Setup environment and run tests
+          command: |
+            # Export path
+            export PATH="$HOME/miniconda/bin:$PATH"
+            hash -r
+
+            # Set conda parameters
+            conda config --set restore_free_channel true
+            conda config --set always_yes yes --set changeps1 no
+            conda config --add channels vmtk
+            conda config --add channels morphman
+
+            # Set up environment
+            conda create -n morphman morphman pytest llvm=3.3
+
+            # Activate environment
+            source activate morphman
+
+            # Useful for debugging any issues with conda
+            conda info -a
+
+            # Dependencies for code coverage
+            pip install pytest-cov codecov
+
+            # Edit VMTK files
+            sed -i -e 's/len(self.SourcePoints)\/3/len\(self.SourcePoints\)\/\/3/g' $HOME/miniconda/envs/morphman/lib/python3.6/site-packages/vmtk/vmtkcenterlines.py
+            sed -i -e 's/len(self.TargetPoints)\/3/len\(self.TargetPoints\)\/\/3/g' $HOME/miniconda/envs/morphman/lib/python3.6/site-packages/vmtk/vmtkcenterlines.py
+            sed -i -e 's/(len(values) - 1)\/2/\(len\(values\) - 1\)\/\/2/g' $HOME/miniconda/envs/morphman/lib/python3.6/site-packages/vmtk/vmtksurfacecurvature.py
+
+            # Run tests
+            cd test
+            pytest --cov=./
+
+      # store artifacts (for example logs, binaries, etc)
+      # to be available in the web app or through the API
+      - store_artifacts:
+          path: test-reports
+

.travis.yml

@@ -1,7 +1,7 @@
 ## [morphMan - Morphological Manipulation](https://morphman.readthedocs.io)
 
 [![Documentation Status](https://readthedocs.org/projects/morphman/badge/?version=latest)](https://morphman.readthedocs.io/en/latest/?badge=latest)
-[![Build Status](https://travis-ci.org/KVSlab/morphMan.svg?branch=master)](https://travis-ci.org/KVSlab/morphMan)
+[![CircleCI](https://circleci.com/gh/KVSlab/morphMan/tree/master.svg?style=svg)](https://circleci.com/gh/KVSlab/morphMan/tree/master)
 [![Build status](https://ci.appveyor.com/api/projects/status/2k6q32hqg6g5oopc?svg=true)](https://ci.appveyor.com/project/hkjeldsberg/morphman-s1s38)
 [![DOI](http://joss.theoj.org/papers/10.21105/joss.01065/status.svg)](https://doi.org/10.21105/joss.01065)
 [![codecov](https://codecov.io/gh/KVSlab/morphMan/branch/master/graph/badge.svg)](https://codecov.io/gh/KVSlab/morphMan)

README.md

@@ -1,6 +1,6 @@
 import setuptools
 
-with open("README.md", "r") as fh:
+with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 DEPENDENCIES = []  # 'scipy', 'numpy', 'vtk']