Topic/cythonized modules

.gitignore

@@ -9,3 +9,4 @@ pip-selfcheck.json
 *.venv/*
 *.ipynb_checkpoints
 .idea/
+*.so

.travis.yml

@@ -1,12 +1,14 @@
 language: python
 
 python:
-- '3.4'
 - '3.5'
+- '3.6'
 
 install:
 - pip install --upgrade pip
+- pip install numpy
 - pip install .[test]
+- python setup.py build_ext --inplace
 
 script: pytest
 
@@ -20,7 +22,7 @@ deploy:
   user: klsmith-usgs
   password:
     secure: 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
+  distributions: sdist bdist_wheel
   on:
-    distributions: sdist bdist_wheel
     repo: USGS-EROS/lcmap-pyccd
     branch: master

MANIFEST.in

@@ -0,0 +1,4 @@
+include ccd/models/lasso.pxd
+include ccd/models/robust_fit.pxd
+include ccd/models/tmask.pxd
+include ccd/procedures.pxd

Makefile

@@ -1,2 +1,11 @@
 profile:
 	kernprof -v -l pytest
+
+build_cython:
+	python setup.py build_ext --inplace
+
+clean_cython:
+	rm ccd/*.c
+	rm ccd/*.so
+	rm ccd/models/*.c
+	rm ccd/models/*.so

README.md

@@ -84,6 +84,9 @@ System requirements (Centos)
 * graphviz
 * python-virtualenv
 
+Python requirements
+* numpy (for install of C compiled extensions)
+
 It's highly recommended to do all your development & testing in a virtual environment.
 ```bash
 user@dev:/home/user/$ mkdir pyccd

ccd/__init__.py

@@ -148,9 +148,14 @@ def detect(dates, blues, greens, reds, nirs,
     dates = np.asarray(dates)
     quality = np.asarray(quality)
 
-    spectra = np.stack((blues, greens,
-                        reds, nirs, swir1s,
-                        swir2s, thermals))
+    spectra = np.stack((np.asarray(blues, dtype=np.int16),
+                        np.asarray(greens, dtype=np.int16),
+                        np.asarray(reds, dtype=np.int16),
+                        np.asarray(nirs, dtype=np.int16),
+                        np.asarray(swir1s, dtype=np.int16),
+                        np.asarray(swir2s, dtype=np.int16),
+                        np.asarray(thermals, dtype=np.int16)
+                        ))
 
     __check_inputs(dates, quality, spectra)