Merge pull request #76 from logicabrity/clean-up-bin-dir

Clean up bin dir

Author: logicabrity

Diff for: fix_load_path_mac.py renamed to bin/fix_load_path_mac.py

@@ -1,3 +1,8 @@
+"""
+Creates working dylibs on Mac OS X by adding the full path to referenced libraries.
+This fixes ImportErrors that may appear starting with SUNDIALS 2.6.
+
+"""
 import os
 import glob
 import re
@@ -27,4 +32,4 @@ def extract_library(so_file):
 
 for so in sos:
     extract_library(so)
-    print("Done for %s!"%so)
+    print("Done for %s!"%so)

Diff for: bin/install-python-packages.sh

@@ -0,0 +1 @@
+pip install --upgrade cython psutil ipywidgets

Diff for: bin/install-sundials-2.5.sh

@@ -1,4 +1,7 @@
 # required to compile fidimag
-apt-get install python-pip python-numpy python-dev python-scipy cmake
-# required for tests and running it
-apt-get install python-pytest python-pyvtk ipython python-matplotlib
+deps_compilation="python-pip python-numpy python-dev python-scipy cmake"
+
+# required for tests and running fidimag
+deps_live="python-pytest python-pyvtk ipython python-matplotlib"
+
+apt-get install $deps_compilation $deps_live

Diff for: bin/install-ubuntu-packages.sh

@@ -1,15 +1,13 @@
 echo "Super user authentication required to add packages (you will be \
 prompted for confirmation)."
 sudo bash install-ubuntu-packages.sh
+sudo bash install-python-packages.sh
 bash install-fftw.sh
 bash install-sundials.sh
-sudo pip install cython --upgrade
-sudo pip install psutil ipywidgets
 pushd .. > /dev/null
 make
 
-# Adds Fidimag environment variables to profile.d, if they're not already
-# there.
+# Adds fidimag environment variables to profile.d, if they're not already there.
 FIDIMAG_PROFILE_PATH=/etc/profile.d/fidimag.sh
 if [ ! -e "$FIDIMAG_PROFILE_PATH" ]; then
     echo "Warning: Adding Fidimag to path at $FIDIMAG_PROFILE_PATH."

Diff for: bin/ubuntu_install_script.sh

@@ -259,7 +259,7 @@ which can be seen by using ``otool -L fidimag/extensions/clib.so``, ::
     /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
     /opt/local/lib/libgcc/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 
-A solution is to change these path manually with ``install_name_tool``, so we have provided a python script (``fix_load_path_mac.py``) to do this.
+A solution is to change these path manually with ``install_name_tool``, so we have provided a python script (``bin/fix_load_path_mac.py``) to do this.
 After run the script, the library path is fixed, for example, the output of the cmd ``otool -L fidimag/extensions/clib.so`` gives ::
 
   fidimag/extensions/neb_clib.so: