Merge pull request #21 from kavli-ntnu/swb_development

Switch `sep` to optional

README.rst

@@ -19,9 +19,10 @@ Installing in this way requires having `git`, this can be acquired from
 
     https://git-scm.com/download/win
 
-Installing the required python package `sep` requires the Microsoft Visual C++ Build Tools, these can be downloaded from
+Opexebo has an optional dependency, `sep`, that is not installed by default. To be able to install it, you require a C++ compiler installed on your system. On Linux, `gcc` will do the job. On Windows, the the Microsoft Visual C++ Build Tools fulfil the same role (https://www.microsoft.com/en-us/download/details.aspx?id=48159). To force installation of all optional depencies, append `[full]` to the install command, for example
+
+    pip install git+https://github.com/kavli-ntnu/opexebo.git#egg=v0.3.3[full]
 
-    https://www.microsoft.com/en-us/download/details.aspx?id=48159
 
 
 Usage example

dev-requirements.txt

@@ -1,5 +1,5 @@
-pip==19.1.1
-bumpversion==0.5.3
+pip>=19.0.0
+bumpversion>=0.5.3
 wheel>=0.31.0,<0.32
 flake8==3.5.0
 tox>=3.2.0,<3.3

opexebo/__init__.py

@@ -18,4 +18,4 @@
 
 __author__ = """Simon Ball"""
 __email__ = 'simon.ball@ntnu.no'
-__version__ = '0.3.2'
+__version__ = '0.3.3'

opexebo/general/peakSearch.py

@@ -1,9 +1,14 @@
 import numpy as np
+import warnings
 import opexebo.defaults as default
 from skimage import measure, morphology
-import sep
 
 
+#import sep
+# NOTE!! Due to how annoying it is to install sep, I have moved this dependency 
+# into the method that uses it. This will allow users that struggle to install it
+# to proceed with other methods that do not rely on it
+
 # TODO! Decide what, if any, parameters need to move over to Defaults
 
 
@@ -58,7 +63,7 @@ def peak_search(image, **kwargs):
     if search_method == default.search_method:
         peak_coords = _peak_search_skimage(image, **kwargs)
     elif search_method == "sep":
-        peak_coords = _peak_search_sep(image, **kwargs)
+        peak_coords = _peak_search_sep_wrapper(image, **kwargs)
     else:
         raise NotImplementedError("The search method you have requested (%s) is"\
                                   " not yet implemented" % search_method)
@@ -104,8 +109,26 @@ def _peak_search_skimage(image, **kwargs):
     return peak_coords
 
 
-
-
+def _peak_search_sep_wrapper(firing_map, **kwargs):
+    ''' Wrapper around the 'sep' Peak Search method
+    Because the 'sep' package is a nightmare to install, and not used for most
+    analysis routines, this wrapper allows most users to ignore it
+    
+    If the user tries to invoke the 'sep' routines, this will try to do so
+    If it fails due to ModuleNotFound, it will use the default algorithm instead
+    with a warning to the user
+    
+    '''
+    algorithm = _peak_search_sep
+    try:
+        import sep
+    except ModuleNotFoundError:
+        warnings.warn("Package 'sep' not installed in this environment."\
+                      " Using the default peak search algorithm instead")
+        algorithm = _peak_search_skimage
+    return algorithm(firing_map, **kwargs)
+
+
 
 def _peak_search_sep(firing_map, **kwargs):
     '''Peak search using sep, a Python wrapper for a standard astronomy library.
@@ -120,6 +143,8 @@ def _peak_search_sep(firing_map, **kwargs):
          'tetrode': 6,
          'cell': 23}
     '''
+    import sep
+
     mask = kwargs.get("mask", np.zeros(firing_map.shape, dtype=bool))
     null_background = kwargs.get("null_background", False)
     threshold = kwargs.get("threshold", 0.2)

optional-requirements.txt

@@ -0,0 +1 @@
+sep>=1.0.3

requirements.txt

@@ -1,4 +1,3 @@
-sep>=1.0.3
 astropy>=3.1.2
 numpy>=1.15.0
 scipy>=1.3.0

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.2
+current_version = 0.3.3
 commit = False
 tag = False
 

setup.py

@@ -16,6 +16,9 @@
 with open(path.join(here, 'requirements.txt')) as f:
     requirements = f.read().split()
 
+with open(path.join(here, 'optional-requirements.txt')) as f:
+    optional_requirements = f.read().split()
+
 setup_requirements = [ ]
 
 test_requirements = [ ]
@@ -35,12 +38,13 @@
     ],
     description="Collection of python code in Kavli lab.",
     install_requires=requirements,
+    extras_require={"full": optional_requirements},
     long_description=readme + '\n\n' + history,
     include_package_data=True,
     keywords='neuroscience kavli gridscore',
     name='opexebo',
     packages=find_packages(include=['opexebo*']),
     url='https://github.com/kavli-ntnu/opexebo',
-    version='0.3.2',
+    version='0.3.3',
     zip_safe=False,
 )