starfish.display: unpin napari version, add tests, view masks separately

.travis.yml

@@ -47,9 +47,19 @@ jobs:
         - make install-dev slow-test
       after_success:
         - bash <(curl -s https://codecov.io/bash)
-    - name: Install Napari
+    - name: Install Napari & Test napari
       if: type = push and (branch = master or branch =~ /-alltest/)
-      script: pip install .[napari]
+      dist: xenial
+      before_install:
+        - sudo apt-get install -y libgl1-mesa-glx libqt5x11extras5 xvfb
+        - make install-dev
+        - pip install .[napari]
+        - export DISPLAY=:99
+        - Xvfb $DISPLAY -ac -screen 0 1024x768x24 &
+        - sleep 10
+      script:
+        - python -c "import vispy; print(vispy.sys_info())"
+        - make napari-test
     - name: Docker
       if: type = push and (branch = master or branch =~ /-alltest/)
       script: make docker
@@ -88,7 +98,7 @@ jobs:
       script: make TESTING=1 install-dev iss_pipeline.py
     - name: Released Notebooks
       if: type = cron and (branch = master or branch =~ /-alltest/)
-      script: make check-notebooks install-released-notebooks-support run-notebooks
+            script: make check-notebooks install-released-notebooks-support run-notebooks
 cache:
   directories:
   - $HOME/.cache/pip

Makefile

@@ -39,14 +39,20 @@ lint-non-init:
 lint-init:
 	flake8 --ignore 'E252, E301, E302, E305, E401, F401, W503, E731, F811' --filename='*__init__.py' $(MODULES)
 
+# note that napari tests shouldn't be run in parallel because Qt seems to intermittently fail when multiple QApplications are spawned on threads.
 test:
-	pytest -v -n 8 --cov starfish
+	pytest -v -n 8 --cov starfish -m 'not napari'
+	pytest -v --cov starfish -m 'napari'
 
 fast-test:
-	pytest -v -n 8 --cov starfish -m 'not slow'
+	pytest -v -n 8 --cov starfish -m 'not (slow or napari)'
 
 slow-test:
-	pytest -v -n 8 --cov starfish -m 'slow'
+	pytest -v -n 8 --cov starfish -m 'slow and (not napari)'
+
+# note that this shouldn't be run in parallel because Qt seems to intermittently fail when multiple QApplications are spawned on threads.
+napari-test:
+	pytest -v --cov starfish -m 'napari'
 
 mypy:
 	mypy --ignore-missing-imports $(MODULES)

REQUIREMENTS-CI.txt

@@ -5,7 +5,7 @@ mypy
 numpydoc
 nbencdec >= 0.0.5
 pycodestyle==2.5.0
-pytest>=3.6.3
+pytest>=4.4.0
 pytest-cov>=2.5.1
 pytest-xdist
 recommonmark

setup.py

@@ -19,7 +19,7 @@
     packages=setuptools.find_packages(),
     install_requires=install_requires,
     extras_require={
-        'napari': [f"napari=={napari_version}"],
+        'napari': [f"napari>={napari_version}"],
     },
     entry_points={
         'console_scripts': [

starfish/core/_display.py

@@ -4,6 +4,7 @@
 from typing import Iterable, List, Optional, Set, Tuple, Union
 
 import numpy as np
+from packaging.version import parse as parse_version
 
 from starfish.core.imagestack.imagestack import ImageStack
 from starfish.core.intensity_table.intensity_table import IntensityTable
@@ -16,7 +17,7 @@
     Viewer = None
 
 
-NAPARI_VERSION = "0.1.3"  # when changing this, update docs in display
+NAPARI_VERSION = "0.1.5"  # when changing this, update docs in display
 INTERACTIVE = not hasattr(__main__, "__file__")
 
 
@@ -127,7 +128,8 @@ def display(
         z_multiplier: float = 1
 ):
     """
-    Displays an image stack and/or detected spots using napari (https://github.com/napari/napari).
+    Display an image stack, detected spots, and masks using
+    `napari <https://github.com/napari/napari>`.
 
     Parameters
     ----------
@@ -193,20 +195,19 @@ def display(
 
     Notes
     -----
-    - To use in ipython, use the `%gui qt5` magic.
+    - To use in ipython, use the `%gui qt` magic.
     - napari axes currently cannot be labeled. Until such a time that they can, this function will
       order them by Round, Channel, and Z.
-    - Requires napari 0.1.3: install starfish using `pip install starfish[napari]` to install all
-      necessary requirements
+    - Requires at least napari 0.1.5: use `pip install starfish[napari]`
+      to install all necessary requirements
     """
-    if stack is None and spots is None:
-        # masks without stack or spots have no context so don't check for that
-        raise TypeError("expected a stack and/or spots; got nothing")
+    if stack is None and spots is None and masks is None:
+        raise TypeError("expected a stack, spots, or masks; got nothing")
 
     try:
         import napari
     except ImportError:
-        raise ImportError(f"Requires napari {NAPARI_VERSION}. "
+        raise ImportError(f"Requires at least napari {NAPARI_VERSION}. "
                           "Run `pip install starfish[napari]` "
                           "to install the necessary requirements.")
 
@@ -215,7 +216,7 @@ def display(
     except Exception as e:
         raise RuntimeError("Could not identify napari version") from e
 
-    if version != NAPARI_VERSION:
+    if parse_version(version) < parse_version(NAPARI_VERSION):
         raise ValueError(f"Incorrect version {version} of napari installed."
                          "Run `pip install starfish[napari]` "
                          "to install the necessary requirements.")

starfish/core/test/test_display.py

@@ -0,0 +1,54 @@
+import numpy as np
+import pytest
+
+from starfish import display, SegmentationMaskCollection
+from starfish.core.test.factories import SyntheticData
+from starfish.types import Coordinates
+
+
+sd = SyntheticData(
+    n_ch=2,
+    n_round=3,
+    n_spots=1,
+    n_codes=4,
+    n_photons_background=0,
+    background_electrons=0,
+    camera_detection_efficiency=1.0,
+    gray_level=1,
+    ad_conversion_bits=16,
+    point_spread_function=(2, 2, 2),
+)
+
+stack = sd.spots()
+spots = sd.intensities()
+masks = SegmentationMaskCollection.from_label_image(
+    np.random.rand(128, 128).astype(np.uint8),
+    {Coordinates.Y: np.arange(128), Coordinates.X: np.arange(128)}
+)
+
+
+@pytest.mark.napari
+@pytest.mark.parametrize('masks', [masks, None], ids=['masks', '     '])
+@pytest.mark.parametrize('spots', [spots, None], ids=['spots', '     '])
+@pytest.mark.parametrize('stack', [stack, None], ids=['stack', '     '])
+def test_display(stack, spots, masks):
+    import napari
+    from qtpy.QtCore import QTimer
+    from qtpy.QtWidgets import QApplication
+
+    def run():
+        app = QApplication.instance() or QApplication([])
+        viewer = napari.Viewer()
+        timer = QTimer()
+        timer.setInterval(500)
+        timer.timeout.connect(viewer.window.close)
+        timer.timeout.connect(app.quit)
+        timer.start()
+        display(stack, spots, masks, viewer=viewer)
+        app.exec_()
+
+    if stack is None and spots is None and masks is None:
+        with pytest.raises(TypeError):
+            run()
+    else:
+        run()