Fix freeze of segment on OS X

.gitignore

@@ -10,6 +10,7 @@ cover
 MANIFEST
 *spec
 !inselect.spec
+!segment.spec
 *tar.gz
 *dmg
 .directory

build.sh

@@ -43,10 +43,9 @@ if [[ "$OSTYPE" == "darwin"* ]]; then
         rm -rf $script.spec
         pyinstaller --onefile --hidden-import numpy inselect/scripts/$script.py
     done
-    # segment has an additional hidden import
-    rm -rf segment.spec
-    pyinstaller --onefile --hidden-import numpy \
-        --hidden-import sklearn.neighbors.typedefs inselect/scripts/segment.py
+
+    # segment has additional requirements so have its own spec file
+    pyinstaller --clean segment.spec
 
     # Add a few items to the PropertyList file generated by PyInstaller
     python -m bin.plist dist/inselect.app/Contents/Info.plist

inselect.spec

@@ -25,6 +25,10 @@ a = Analysis(['inselect.py'],
 # of manipulating Analysis.binaries.
 
 MISSING_DYLIBS = (
+    'libiomp5.dylib',
+    'libmkl_intel_lp64.dylib',
+    'libmkl_intel_thread.dylib',
+    'libmkl_core.dylib',
     'libQtCore.4.dylib',
     'libQtGui.4.dylib',
     'libpng16.16.dylib',

segment.spec

@@ -0,0 +1,51 @@
+# -*- mode: python -*-
+import sys
+
+from pathlib import Path
+
+block_cipher = None
+
+
+a = Analysis(['inselect/scripts/segment.py'],
+             pathex=['/Users/lawrence/projects/inselect'],
+             binaries=None,
+             datas=None,
+             hiddenimports=['numpy', 'sklearn.neighbors.typedefs'],
+             hookspath=[],
+             runtime_hooks=[],
+             excludes=[],
+             win_no_prefer_redirects=False,
+             win_private_assemblies=False,
+             cipher=block_cipher)
+
+# PyInstaller does not detect some dylibs, I think in some cases because they
+# are symlinked.
+# See Stack Overflow post http://stackoverflow.com/a/17595149 for example
+# of manipulating Analysis.binaries.
+MISSING_DYLIBS = (
+    'libiomp5.dylib',
+    'libmkl_intel_lp64.dylib',
+    'libmkl_intel_thread.dylib',
+    'libmkl_core.dylib',
+)
+
+# The lib directory associated with this environment
+LIB = Path(sys.argv[0]).parent.parent.joinpath('lib')
+
+# Find the source for each library and add it to the list of binaries
+a.binaries += TOC([
+    (lib, str(LIB.joinpath(lib).resolve()), 'BINARY') for lib in MISSING_DYLIBS
+])
+
+pyz = PYZ(a.pure, a.zipped_data,
+             cipher=block_cipher)
+exe = EXE(pyz,
+          a.scripts,
+          a.binaries,
+          a.zipfiles,
+          a.datas,
+          name='segment',
+          debug=False,
+          strip=False,
+          upx=True,
+          console=True )