setuptools dependency on Mac OS X

src/shorah/amplicon.py

@@ -38,7 +38,6 @@
 
 import logging
 import logging.handlers
-from pkg_resources import resource_filename
 
 from Bio import SeqIO
 
@@ -53,10 +52,16 @@
     from . import shorah_snv
 
 # Try fetching diri and b2w exe with pkg resources
-diri_exe = resource_filename(__name__, 'bin/diri_sampler')
-b2w_exe = resource_filename(__name__, 'bin/b2w')
+try:
+    from pkg_resources import resource_filename
+except ModuleNotFoundError:
+    diri_exe = None
+    b2w_exe = None
+else:
+    diri_exe = resource_filename(__name__, 'bin/diri_sampler')
+    b2w_exe = resource_filename(__name__, 'bin/b2w')
 # Try fetching diri and b2w exe with bash 'which'
-if not (os.path.exists(diri_exe) and os.path.exists(b2w_exe)):
+if not (diri_exe and b2w_exe) or not (os.path.exists(diri_exe) and os.path.exists(b2w_exe)):
     diri_exe = shutil.which('diri_sampler')
     b2w_exe = shutil.which('b2w')
     if not (diri_exe and b2w_exe):

src/shorah/cli.py

@@ -42,6 +42,7 @@
 import sys
 
 
+use_pkg_resources = False;
 all_dirs = os.path.abspath(__file__).split(os.sep)
 base_dir = os.sep.join(all_dirs[:-all_dirs[::-1].index('shorah')])
 version_fname = os.path.join(base_dir, '.version')
@@ -57,6 +58,8 @@
     except DistributionNotFound:
         __version__ = 'unknown'
         print("cannot find version", file=sys.stderr)
+    else:
+        use_pkg_resources = True;
 
 # manipulate path to import functions
 parent_dir = os.path.join(base_dir, 'src')

src/shorah/shorah_snv.py

@@ -44,12 +44,15 @@
 
 import logging
 
-from pkg_resources import resource_filename
-
 # Try fetching fil exe with pkg resources
-fil_exe = resource_filename(__name__, 'bin/fil')
+try:
+    from pkg_resources import resource_filename
+except ModuleNotFoundError:
+    fil_exe = None
+else:
+    fil_exe = resource_filename(__name__, 'bin/fil')
 # Try fetching fil exe with bash 'which'
-if not os.path.exists(fil_exe):
+if not fil_exe or not os.path.exists(fil_exe):
     fil_exe = shutil.which('fil')
     if not fil_exe:
         # Try fetching fil exe based on directory structure

src/shorah/shotgun.py

@@ -35,7 +35,6 @@
 import sys
 import shlex
 import logging
-from pkg_resources import resource_filename
 import re
 import shutil
 
@@ -52,10 +51,16 @@
     from . import shorah_snv
 
 # Try fetching diri and b2w exe with pkg resources
-diri_exe = resource_filename(__name__, 'bin/diri_sampler')
-b2w_exe = resource_filename(__name__, 'bin/b2w')
+try:
+    from pkg_resources import resource_filename
+except ModuleNotFoundError:
+    diri_exe = None
+    b2w_exe = None
+else:
+    diri_exe = resource_filename(__name__, 'bin/diri_sampler')
+    b2w_exe = resource_filename(__name__, 'bin/b2w')
 # Try fetching diri and b2w exe with bash 'which'
-if not (os.path.exists(diri_exe) and os.path.exists(b2w_exe)):
+if not (diri_exe and b2w_exe) or not (os.path.exists(diri_exe) and os.path.exists(b2w_exe)):
     diri_exe = shutil.which('diri_sampler')
     b2w_exe = shutil.which('b2w')
     if not (diri_exe and b2w_exe):