better devel

.gitignore

@@ -2,3 +2,13 @@
 __pycache__/
 *.egg-info
 build/
+dist
+.coverage
+cache
+junit
+joblib
+__pycache__
+.mypy_cache
+coverage.xml
+_version.py
+*.sublime-*

Makefile

@@ -0,0 +1,22 @@
+clean:
+	-rm -rf build
+	-rm -rf dist
+	-rm -rf *.egg-info
+	-rm -rf .coverage
+	-rm -rf cache
+	-rm -rf junit
+	-rm -rf joblib
+	-rm -rf __pycache__
+	-rm -rf .mypy_cache
+	# -rm -rf .pytest_cache
+
+test: clean
+	pytest wsi \
+		--doctest-modules \
+		--junitxml=junit/test-results.xml \
+		--cov=wsi \
+		--cov-report=xml \
+		--cov-report=html
+
+install: clean
+	python -m pip install -e .

wsi/tests/test_wsi.py

@@ -19,7 +19,7 @@ def get_test_slide():
     path = Path(tempfile.NamedTemporaryFile().name)
 
     with open(path, "wb") as file:
-        for chunk in requests.get(url, stream=True).iter_content(chunk_size=1024):
+        for chunk in requests.get(url, stream=True).iter_content(chunk_size=1024 * 4):
             file.write(chunk)
     return path
 

wsi/wsi.py

@@ -29,6 +29,7 @@
 
 # TODO: replace contours_tumor with a generic label field
 # TODO: make function to plot contours (colored by label field)
+# TODO: replace pickle with geojson or hdf5
 
 
 class WholeSlideImage(object):