included submodule SPGL1 in automatic installation

MANIFEST.in

@@ -1,8 +1,9 @@
 # Include the license file
 include LICENSE.txt
 
-# Include the data files
-recursive-include movies *
+# Include the submodule files
+recursive-include SPGL1_python_port *.py
+#exclude movies*/demo*/docs*/examples*
 
 # If using Python 2.6 or less, then have to include package data, even though
 # it's already declared in setup.py

build.sh

@@ -1,2 +1,5 @@
+#Python command to install the script.
+$PYTHON setup.py install  # --single-version-externally-managed --record=record.txt
+
+
 
-$PYTHON setup.py install  # --single-version-externally-managed --record=record.txt   Python command to install the script.

ca_source_extraction/deconvolution.py

@@ -15,8 +15,8 @@
 #import time
 #import sys    
 
-from spgl1 import spg_bpdn
-import spgl_aux as spg
+from SPGL1_python_port.spgl1 import spg_bpdn
+from SPGL1_python_port import spgl_aux as spg
 
 #%%
 def constrained_foopsi(fluor, bl = None,  c1 = None, g = None,  sn = None, p = None, method = 'spgl1', bas_nonneg = True,  

meta.yaml

@@ -7,15 +7,13 @@ source:
   #git_rev: 0.03
   #git_url: https://github.com/agiovann/Constrained_NMF.git
   path: ../Constrained_NMF 
+
 requirements:
   build:
     - python <3
     - setuptools
     - pip 
 
-#    - tifffile >=0.7.0    
-#    - joblib >=0.8.4
-#    - pico >=1.1.1
 
   run:
     - python <3
@@ -29,14 +27,17 @@ requirements:
     - jupyter 
     - bokeh
     - cvxopt 
-#    - tifffile >=0.7.0    
-#    - joblib >=0.8.4
-#    - pico >=1.1.1
+    - joblib >=0.8.4
+#    - tifffile >=0.7.0        
+#    - picos >=1.1.1
 
 
-test:
+#test:
+#    files:
+#      - movies/demoMovie.tif    
+#      - demo.py
+#      - demoCNMF.ipynb
 
-
 about:
   home: http://agiovann.github.io/Constrained_NMF
   license: GPL2

setup.py

@@ -4,13 +4,10 @@
 #import numpy as np
 
 
-"""A setuptools based setup module.
-See:
-https://packaging.python.org/en/latest/distributing.html
-https://github.com/pypa/sampleproject
 """
-
-# Always prefer setuptools over distutils
+    Installation script for anaconda installers
+    
+"""
 here = path.abspath(path.dirname(__file__))
 
 with open('README.md','r') as rmf:
@@ -47,7 +44,7 @@
     'Programming Language :: Python :: 2.7',
     ],
     keywords = 'fluorescence calcium ca imaging deconvolution ROI identification',
-    packages = ['ca_source_extraction'],
+    packages = ['ca_source_extraction','SPGL1_python_port'],
     data_files = [	('', ['LICENSE.txt']),
                   ('', ['README.md'])],
     install_requires = [ 'python==2.7.*'],#'matplotlib', 'scikit-learn', 'scikit-image', 'ipyparallel','scikit-learn','ipython','scipy','numpy'],#,'bokeh','jupyter','tifffile','cvxopt','picos', 'joblib>=0.8.4'],