Shapely install

[darribas]

Trying to work my way through the tutorial. Stuck at the install part. I've created the environment as suggested in install.md and it seems to work just fine until shapely. conda seems to install it correctly:

In [1]: import shapely

In [2]:

However, when I try the following, I the an OSError:

In [2]: import shapely.geos
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-2-298ab485fd08> in <module>()
----> 1 import shapely.geos

/Users/dani/anaconda/envs/scipygis/lib/python2.7/site-packages/shapely/geos.py in <module>()
     63     alt_paths = [os.path.join(sys.prefix, 'lib', 'libgeos_c.dylib')]
     64     _lgeos = load_dll('geos_c', fallbacks=alt_paths)
---> 65     free = load_dll('c').free
     66     free.argtypes = [c_void_p]
     67     free.restype = None

/Users/dani/anaconda/envs/scipygis/lib/python2.7/site-packages/shapely/geos.py in load_dll(libname, fallbacks)
     51     raise OSError(
     52         "Could not find library %s or load any of its variants %s" % (
---> 53             libname, fallbacks or []))
     54
     55

OSError: Could not find library c or load any of its variants []

In [3]:

Any idea on why this happens and, particularly, how I can fix it? All comments and help mostly appreciated. I'm running conda on Mavericks:

(scipygis)kokopelli:Desktop dani$ conda info
Current conda install:

             platform : osx-64
        conda version : 3.5.5
       python version : 2.7.8.final.0
     root environment : /Users/dani/anaconda  (writable)
  default environment : /Users/dani/anaconda/envs/scipygis
     envs directories : /Users/dani/anaconda/envs
        package cache : /Users/dani/anaconda/pkgs
         channel URLs : http://repo.continuum.io/pkgs/free/osx-64/
                        http://repo.continuum.io/pkgs/pro/osx-64/
          config file : None
    is foreign system : False

(scipygis)kokopelli:Desktop dani$

[carsonfarmer]

Hmm, not quite sure what would be causing this? I assume you have developer tools installed on your system? What about if you conda remove geos and try brew installing it instead, then pip installing shapely that way? You don't get the self-contained install that conda install affords, but it should work (this is usually what I do)?

[darribas]

Nope :-( I've found Kelsey's trick here and that allows me to import shapely.geos without complain. However, when I install cartopy and try one of their toy examples:

In [3]: import cartopy.crs as ccrs

In [4]: import matplotlib.pyplot as plt

In [5]:

In [5]: ax = plt.axes(projection=ccrs.PlateCarree())
Assertion failed: (0 != cs), function GEOSCoordSeq_getSize_r, file geos_ts_c.cpp, line 3612.
Abort trap: 6
(scipygis)kokopelli:~ dani$

And throws me out. It looks like this is a cartopy issue, not a shapely, but my hunch is that it all goes back to my GEOS installation. I've tried a couple of combinations (conda or brew for geos with cartopy from pip or conda), and I always get that issue.

Any comment or help most welcome, but I understand this might be my own crappy setup full of different installations and layers at this point.

[carsonfarmer]

Ah ok, yes I think this is a GEOS installation issue. I think I ran into the same problem at one point. Unfortunately, it looks like conda is using a very recent version of GEOS, whereas cartopy is expecting an older one (or vice versa). I've found that not using the conda versions and sticking with all pip versions works best for my system.

[darribas]

That did the trick... Wohooooooooo!!!

To recap, I removed anything dealing with conda that depends on geos:

conda remove geos, shapely, cartopy

Then installed geos with brew:

brew install geos

Added Kelsey's workaround to my .bash_profile:

export DYLD_FALLBACK_LIBRARY_PATH=$(HOME)/lib:/usr/local/lib:/lib:/usr/lib

And then pip'ed the two libraries:

pip install shapely
pip install git+git://github.com/SciTools/cartopy.git

Doing that in both the general setup and/or the scipygis virtual env seems to get cartopy to finally work. Closing the issue on this. Thank you very much for the advice!

[carsonfarmer]

Great, glad that worked (and good to know Kelsey's fix is also a key component).