Add component/ocropy and scipy to erp5

Needed for receipt_recognition module. It contain the ocropy library and its binarization, segementation and recognition tools, as well as the scipy library containing the ndimage and stats module used in receipt_recognition_module for the binarization and inside ocropy. 

This is separated in 3 commits:
The first one add ocropy and dependancies inside slapos component;
The second one add the ocropy component to stack/erp5 buildout config file, and add gcc to the binaries callable from erp5 (needed by ocropy);
The third  is only required for the module to work without installing the wendelin software.

Edit: To keep discussions posts, i wont rebase in master, to see the rebased final commits: https://lab.nexedi.com/francois.lecorre/slapos/commits/rebased_branch

/reviewed-on nexedi/slapos!153

component/matplotlib/buildout.cfg

@@ -29,7 +29,10 @@ CFLAGS = -I${libpng:location}/include -I${freetype:location}/include
 recipe = zc.recipe.egg:custom
 egg = matplotlib
 environment = matplotlib-env
-setup-eggs = ${numpy:egg}
+setup-eggs =
+  cycler
+  python-dateutil
+  ${numpy:egg}
 rpath =
   ${libpng:location}/lib
   ${freetype:location}/lib

component/ocropy/buildout.cfg

+[buildout]
+extends =
+  ../git/buildout.cfg
+  ../gzip/buildout.cfg
+  ../scipy/buildout.cfg
+  ../lxml-python/buildout.cfg
+  ../matplotlib/buildout.cfg
+  ../numpy/buildout.cfg
+  ../patch/buildout.cfg
+  ../pillow/buildout.cfg
+  ../numpy/buildout.cfg
+
+parts = ocropy
+
+[ocropy-eng-traineddata]
+recipe = hexagonit.recipe.download
+filename = en-default.pyrnn.gz
+md5sum = cedd140c7d7650e910f0550ad0f04727
+download-only = true
+url = http://www.tmbdev.net/en-default.pyrnn.gz
+
+[ocropy-env]
+OCROPY_MODEL_PATH = ${ocropy-eng-traineddata:location}/${ocropy-eng-traineddata:filename}
+HOME = ${ocropy:egg}
+
+[ocropy]
+recipe = zc.recipe.egg:custom
+egg = ocropy
+setup-eggs =
+  ${numpy:egg}
+  ${scipy:egg}
+  ${matplotlib:egg}
+  ${pillow-python:egg}
+patches =
+  ${:_profile_base_location_}/ocropy.patch
+patch-options = -p0
+patch-binary = ${patch:location}/bin/patch
+environment = ocropy-env
+find-links = https://github.com/tmbdev/ocropy/tarball/4efbddca22bb2f0c639af0694e7a1386f2f097b5/ocropy-1.0.tar.gz
+md5sum = 240b8866dd7248816e01af469a328c09

component/ocropy/ocropy.patch

+diff --git ocrolib/__init__.py ocrolib/__init__.py
+index 1e0d627..81e85fb 100644
+--- ocrolib/__init__.py
++++ ocrolib/__init__.py
+@@ -1,7 +1,7 @@
+ __all__ = [
+     "binnednn","cairoextras","common","components","dbtables",
+     "fgen","gmmtree","gtkyield","hocr","lang","native",
+-    "mlp","multiclass","default","lineest"
++    "mlp","multiclass","default","lineest", "psegutils"
+ ]
+ 
+ ################################################################
+@@ -9,5 +9,6 @@ __all__ = [
+ ################################################################
+ 
+ import default
++from psegutils import *
+ from common import *
+ from default import traceback as trace
+diff --git ocrolib/common.py ocrolib/common.py
+index 27c0f26..14f088f 100644
+--- ocrolib/common.py
++++ ocrolib/common.py
+@@ -14,6 +14,7 @@ import unicodedata
+ import inspect
+ import glob
+ import cPickle
++import gzip
+ from ocrolib.exceptions import (BadClassLabel, BadInput, FileNotFound,
+                                 OcropusException)
+ 
+@@ -428,6 +429,7 @@ def unpickle_find_global(mname,cname):
+         exec "import "+mname
+     return getattr(sys.modules[mname],cname)
+ 
++
+ def load_object(fname,zip=0,nofind=0,verbose=0):
+     """Loads an object from disk. By default, this handles zipped files
+     and searches in the usual places for OCRopus. It also handles some
+@@ -439,8 +441,7 @@ def load_object(fname,zip=0,nofind=0,verbose=0):
+     if zip==0 and fname.endswith(".gz"):
+         zip = 1
+     if zip>0:
+-        # with gzip.GzipFile(fname,"rb") as stream:
+-        with os.popen("gunzip < '%s'"%fname,"rb") as stream:
++        with gzip.GzipFile(fname,"rb") as stream:
+             unpickler = cPickle.Unpickler(stream)
+             unpickler.find_global = unpickle_find_global
+             return unpickler.load()
+@@ -618,7 +619,7 @@ def ocropus_find_file(fname, gz=True):
+ 
+     possible_prefixes.append(os.path.normpath(os.path.join(
+         os.path.dirname(inspect.getfile(inspect.currentframe())),
+-        os.pardir, os.pardir, os.pardir, os.pardir, "share", "ocropus")))
++        os.pardir, "share", "ocropus")))
+ 
+     possible_prefixes.append("/usr/local/share/ocropus")
+ 
+diff --git ocrolib/native.py ocrolib/native.py
+index b7a207f..240450b 100644
+--- ocrolib/native.py
++++ ocrolib/native.py
+@@ -44,6 +44,7 @@ class CompileError(Exception):
+ 
+ def compile_and_find(c_string,prefix=".pynative",opt="-g -O4",libs="-lm",
+                      options="-shared -fopenmp -std=c99 -fPIC",verbose=0):
++    prefix = os.path.join(os.path.dirname(__file__), prefix)
+     if not os.path.exists(prefix):
+         os.mkdir(prefix)
+     m = hashlib.md5()
+diff --git setup.py setup.py
+index 2ec5832..6697b12 100644
+--- setup.py
++++ setup.py
+@@ -10,7 +10,9 @@ assert sys.version_info[0]==2 and sys.version_info[1]>=7,\
+ from distutils.core import setup #, Extension, Command
+ #from distutils.command.install_data import install_data
+ 
+-if not os.path.exists("models/en-default.pyrnn.gz"):
++models = os.environ.get('OCROPY_MODEL_PATH', '').split(':') or \
++    [c for c in glob.glob("models/*pyrnn.gz")]
++if not models:
+     print()
+     print("You should download the default model 'en-default.pyrnn.gz'")
+     print("and put it into ./models.")
+@@ -18,16 +20,23 @@ if not os.path.exists("models/en-default.pyrnn.gz"):
+     print("Check https://github.com/tmbdev/ocropy for the location")
+     print("of model files.")
+     print()
++    sys.exit(1)
+ 
+-models = [c for c in glob.glob("models/*pyrnn.gz")]
+ scripts = [c for c in glob.glob("ocropus-*") if "." not in c and "~" not in c]
+ 
++# compile pynative files now and include them in the build
++sys.path.insert(0, os.curdir)
++import ocrolib.nutils
++pynative_files = [os.path.join(*c.split(os.path.sep)[1:]) \
++    for c in glob.glob('ocrolib/.pynative/*')]
++
+ setup(
+     name = 'ocropy',
+     version = 'v1.0',
+     author = "Thomas Breuel",
+     description = "The OCRopy RNN-based Text Line Recognizer",
+     packages = ["ocrolib"],
+-    data_files= [('share/ocropus', models)],
++    package_data = {'ocrolib': pynative_files},
++    data_files= [('share/ocropus', models), ("", ["LICENSE"])],
+     scripts = scripts,
+     )

component/python-2.7/buildout.cfg

@@ -56,9 +56,10 @@ configure-options =
 make-binary =
 make-targets = make profile-opt && make install
 
+extra-ldflags =
 # the entry "-Wl,-rpath=${file:location}/lib" below is needed by python-magic,
 # which would otherwise load the system libmagic.so with ctypes
 environment =
   PATH=${patch:location}/bin:${xz-utils:location}/bin:%(PATH)s
   CPPFLAGS=-I${zlib:location}/include -I${readline:location}/include -I${libexpat:location}/include -I${libffi:location}/include -I${ncurses:location}/include -I${ncurses:location}/include/ncursesw -I${bzip2:location}/include  -I${gdbm:location}/include -I${openssl:location}/include -I${sqlite3:location}/include -I${gettext:location}/include
-  LDFLAGS=-L${zlib:location}/lib -L${readline:location}/lib -L${libexpat:location}/lib -L${libffi:location}/lib -L${ncurses:location}/lib -L${bzip2:location}/lib -L${gdbm:location}/lib -L${openssl:location}/lib -L${sqlite3:location}/lib -Wl,-rpath=${zlib:location}/lib -Wl,-rpath=${readline:location}/lib -Wl,-rpath=${libexpat:location}/lib -Wl,-rpath=${libffi:location}/lib -Wl,-rpath=${ncurses:location}/lib -Wl,-rpath=${bzip2:location}/lib -Wl,-rpath=${gdbm:location}/lib -Wl,-rpath=${openssl:location}/lib -Wl,-rpath=${sqlite3:location}/lib -L${gettext:location}/lib -Wl,-rpath=${gettext:location}/lib -Wl,-rpath=${file:location}/lib
+  LDFLAGS=-L${zlib:location}/lib -L${readline:location}/lib -L${libexpat:location}/lib -L${libffi:location}/lib -L${ncurses:location}/lib -L${bzip2:location}/lib -L${gdbm:location}/lib -L${openssl:location}/lib -L${sqlite3:location}/lib -Wl,-rpath=${zlib:location}/lib -Wl,-rpath=${readline:location}/lib -Wl,-rpath=${libexpat:location}/lib -Wl,-rpath=${libffi:location}/lib -Wl,-rpath=${ncurses:location}/lib -Wl,-rpath=${bzip2:location}/lib -Wl,-rpath=${gdbm:location}/lib -Wl,-rpath=${openssl:location}/lib -Wl,-rpath=${sqlite3:location}/lib -L${gettext:location}/lib -Wl,-rpath=${gettext:location}/lib -Wl,-rpath=${file:location}/lib ${:extra-ldflags}

stack/erp5/buildout.cfg

@@ -9,6 +9,7 @@ extends =
   ../../component/dbus/buildout.cfg
   ../../component/file/buildout.cfg
   ../../component/fonts/buildout.cfg
+  ../../component/gcc/buildout.cfg
   ../../component/ghostscript/buildout.cfg
   ../../component/git/buildout.cfg
   ../../component/graphviz/buildout.cfg
@@ -27,6 +28,7 @@ extends =
   ../../component/matplotlib/buildout.cfg
   ../../component/mesa/buildout.cfg
   ../../component/numpy/buildout.cfg
+  ../../component/ocropy/buildout.cfg
   ../../component/onlyoffice-x2t/buildout.cfg
   ../../component/pandas/buildout.cfg
   ../../component/percona-toolkit/buildout.cfg
@@ -90,6 +92,8 @@ parts +=
   libreoffice-bin
   w3-validator
   tesseract
+  scipy
+  ocropy
   hookbox
   percona-toolkit
   zabbix-agent
@@ -136,6 +140,10 @@ parts +=
   ipython-notebook
   instance-jupyter
 
+# override python2.7 to add SlapOS libstdc++ in RPATH.
+[python2.7]
+extra-ldflags = -Wl,-rpath=${gcc:location}/lib -Wl,-rpath=${gcc:location}/lib64
+
 # override instance-jupyter not to render into default template.cfg
 [instance-jupyter]
 rendered = ${buildout:directory}/template-jupyter.cfg
@@ -437,11 +445,13 @@ eggs = ${neoppod:eggs}
   ${numpy:egg}
   ${matplotlib:egg}
   ${lxml-python:egg}
+  ${ocropy:egg}
   ${pandas:egg}
   ${pillow-python:egg}
   ${python-ldap-python:egg}
   ${pysvn-python:egg}
   ${pycrypto-python:egg}
+  ${scipy:egg}
   ${scikit-learn:egg}
   lock_file
   astor