Implement xarray <-> dataset

.travis.yml

@@ -6,6 +6,9 @@ os:
   - linux
   - osx
 osx_image: xcode9.1
+dist: xenial
+services:
+  - xvfb
 install:
   - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
         MINICONDA_VERSION=2 ;

.travis/build.sh

@@ -19,6 +19,7 @@ check () {
 conda create -n imagej -y python=$TRAVIS_PYTHON_VERSION
 source activate imagej
 conda env update -f environment.yml
+conda install pytest
 
 # -- ensure supporting tools are available --
 check curl git unzip
@@ -41,7 +42,7 @@ fi
 case "$(uname -s),$(uname -m)" in
 	Linux,x86_64) launcher=ImageJ-linux64 ;;
 	Linux,*) launcher=ImageJ-linux32 ;;
-	Darwin,*) launcher=Contents/MacOS/ImageJ-macosx ;;
+	Darwin,*) launcher=Contents/MacOS/ImageJ-macosx; skipGUI=1 ;;
 	MING*,*) launcher=ImageJ-win32.exe ;;
 	*) die "Unknown platform" ;;
 esac
@@ -62,7 +63,9 @@ python setup.py install
 unset JAVA_HOME
 
 # -- run tests with local Fiji.app --
-python -O test/test_imagej.py --ij "$ij_dir"
+python -m pytest --ij="$ij_dir"
+test "$skipGUI" || python -m pytest --ij="$ij_dir" --headless=false
 
 # -- run tests with ImageJ from Maven repository --
-python -m unittest discover test -v
+python -m pytest
+

conftest.py

@@ -0,0 +1,48 @@
+import imagej
+import pytest
+import argparse
+
+
+def pytest_addoption(parser):
+    """
+    Set up the command line parser for IJ location and headless mode
+    :param parser: pytest's parser, passed in automatically
+    :return: None
+    """
+    parser.addoption(
+        "--ij", action="store", default=None, help="directory to IJ"
+    )
+    parser.addoption(
+        "--headless", type=str2bool, action="store", default=True, help="Start in headless mode"
+    )
+
+
+@pytest.fixture(scope='session')
+def ij_fixture(request):
+    """
+    Create an ImageJ instance to be used by the whole testing environment
+    :param request: Pytest variable passed in to fixtures
+    :return: pyimageJ instance
+    """
+    ij_dir = request.config.getoption('--ij')
+    headless = request.config.getoption('--headless')
+
+    ij_wrapper = imagej.init(ij_dir, headless=headless)
+
+    return ij_wrapper
+
+
+def str2bool(v):
+    """
+    Convert string inputs into bool
+    :param v: A string
+    :return: Corresponding boolean
+    """
+    if isinstance(v, bool):
+        return v
+    if v.lower() in ('yes', 'true', 't', 'y', '1'):
+        return True
+    elif v.lower() in ('no', 'false', 'f', 'n', '0'):
+        return False
+    else:
+        raise argparse.ArgumentTypeError('Boolean value expected')

environment.yml

@@ -10,3 +10,4 @@ dependencies:
   - scyjava
   - pillow # for server
   - requests # for server
+  - xarray