From 605f05942f6ec7ffff544f6160f5f3e9807a705c Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Tue, 3 Feb 2015 14:58:57 +1100
Subject: [PATCH 01/10] Move RAG files to skimage.future

---
 skimage/{graph => future}/_ncut.py          | 0
 skimage/{graph => future}/_ncut_cy.pyx      | 0
 skimage/{graph => future}/graph_cut.py      | 0
 skimage/{graph => future}/graph_merge.py    | 0
 skimage/{graph => future}/rag.py            | 0
 skimage/{graph => future}/tests/test_rag.py | 0
 6 files changed, 0 insertions(+), 0 deletions(-)
 rename skimage/{graph => future}/_ncut.py (100%)
 rename skimage/{graph => future}/_ncut_cy.pyx (100%)
 rename skimage/{graph => future}/graph_cut.py (100%)
 rename skimage/{graph => future}/graph_merge.py (100%)
 rename skimage/{graph => future}/rag.py (100%)
 rename skimage/{graph => future}/tests/test_rag.py (100%)

diff --git a/skimage/graph/_ncut.py b/skimage/future/_ncut.py
similarity index 100%
rename from skimage/graph/_ncut.py
rename to skimage/future/_ncut.py
diff --git a/skimage/graph/_ncut_cy.pyx b/skimage/future/_ncut_cy.pyx
similarity index 100%
rename from skimage/graph/_ncut_cy.pyx
rename to skimage/future/_ncut_cy.pyx
diff --git a/skimage/graph/graph_cut.py b/skimage/future/graph_cut.py
similarity index 100%
rename from skimage/graph/graph_cut.py
rename to skimage/future/graph_cut.py
diff --git a/skimage/graph/graph_merge.py b/skimage/future/graph_merge.py
similarity index 100%
rename from skimage/graph/graph_merge.py
rename to skimage/future/graph_merge.py
diff --git a/skimage/graph/rag.py b/skimage/future/rag.py
similarity index 100%
rename from skimage/graph/rag.py
rename to skimage/future/rag.py
diff --git a/skimage/graph/tests/test_rag.py b/skimage/future/tests/test_rag.py
similarity index 100%
rename from skimage/graph/tests/test_rag.py
rename to skimage/future/tests/test_rag.py

From 1b748668eecfd22e69ac7fa70356c8cdf917ad96 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Tue, 3 Feb 2015 15:06:27 +1100
Subject: [PATCH 02/10] Move package to skimage.future.graph

---
 skimage/future/__init__.py                   |  0
 skimage/future/graph/__init__.py             | 12 ++++++++++++
 skimage/future/{ => graph}/_ncut.py          |  0
 skimage/future/{ => graph}/_ncut_cy.pyx      |  0
 skimage/future/{ => graph}/graph_cut.py      |  0
 skimage/future/{ => graph}/graph_merge.py    |  0
 skimage/future/{ => graph}/rag.py            |  2 +-
 skimage/future/{ => graph}/tests/test_rag.py |  0
 skimage/graph/__init__.py                    |  4 ----
 9 files changed, 13 insertions(+), 5 deletions(-)
 create mode 100644 skimage/future/__init__.py
 create mode 100644 skimage/future/graph/__init__.py
 rename skimage/future/{ => graph}/_ncut.py (100%)
 rename skimage/future/{ => graph}/_ncut_cy.pyx (100%)
 rename skimage/future/{ => graph}/graph_cut.py (100%)
 rename skimage/future/{ => graph}/graph_merge.py (100%)
 rename skimage/future/{ => graph}/rag.py (99%)
 rename skimage/future/{ => graph}/tests/test_rag.py (100%)

diff --git a/skimage/future/__init__.py b/skimage/future/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/skimage/future/graph/__init__.py b/skimage/future/graph/__init__.py
new file mode 100644
index 00000000..6b7e0aaa
--- /dev/null
+++ b/skimage/future/graph/__init__.py
@@ -0,0 +1,12 @@
+from .graph_cut import cut_threshold, cut_normalized
+from .rag import rag_mean_color, RAG, draw_rag
+from .graph_merge import merge_hierarchical
+ncut = cut_normalized
+
+__all__ = ['rag_mean_color',
+           'cut_threshold',
+           'cut_normalized',
+           'ncut',
+           'draw_rag',
+           'merge_hierarchical',
+           'RAG']
diff --git a/skimage/future/_ncut.py b/skimage/future/graph/_ncut.py
similarity index 100%
rename from skimage/future/_ncut.py
rename to skimage/future/graph/_ncut.py
diff --git a/skimage/future/_ncut_cy.pyx b/skimage/future/graph/_ncut_cy.pyx
similarity index 100%
rename from skimage/future/_ncut_cy.pyx
rename to skimage/future/graph/_ncut_cy.pyx
diff --git a/skimage/future/graph_cut.py b/skimage/future/graph/graph_cut.py
similarity index 100%
rename from skimage/future/graph_cut.py
rename to skimage/future/graph/graph_cut.py
diff --git a/skimage/future/graph_merge.py b/skimage/future/graph/graph_merge.py
similarity index 100%
rename from skimage/future/graph_merge.py
rename to skimage/future/graph/graph_merge.py
diff --git a/skimage/future/rag.py b/skimage/future/graph/rag.py
similarity index 99%
rename from skimage/future/rag.py
rename to skimage/future/graph/rag.py
index 120e9e91..e3d52875 100644
--- a/skimage/future/rag.py
+++ b/skimage/future/graph/rag.py
@@ -14,7 +14,7 @@ import numpy as np
 from scipy.ndimage import filters
 from scipy import ndimage as nd
 import math
-from .. import draw, measure, segmentation, util, color
+from ... import draw, measure, segmentation, util, color
 try:
     from matplotlib import colors
     from matplotlib import cm
diff --git a/skimage/future/tests/test_rag.py b/skimage/future/graph/tests/test_rag.py
similarity index 100%
rename from skimage/future/tests/test_rag.py
rename to skimage/future/graph/tests/test_rag.py
diff --git a/skimage/graph/__init__.py b/skimage/graph/__init__.py
index f93708c9..89260f1f 100644
--- a/skimage/graph/__init__.py
+++ b/skimage/graph/__init__.py
@@ -1,9 +1,5 @@
 from .spath import shortest_path
 from .mcp import MCP, MCP_Geometric, MCP_Connect, MCP_Flexible, route_through_array
-from .graph_cut import cut_threshold, cut_normalized
-from .rag import rag_mean_color, RAG, draw_rag
-from .graph_merge import merge_hierarchical
-ncut = cut_normalized
 
 
 __all__ = ['shortest_path',

From eeaf7662912d83a4417d53127c4db6f33b7adc33 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Tue, 3 Feb 2015 15:08:12 +1100
Subject: [PATCH 03/10] Update bento file to moved RAG code

---
 bento.info | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/bento.info b/bento.info
index a36a4ebb..bfc607a8 100644
--- a/bento.info
+++ b/bento.info
@@ -33,7 +33,8 @@ UseBackends: Waf
 Library:
     Packages:
         skimage, skimage.color, skimage.data, skimage.draw, skimage.exposure,
-        skimage.feature, skimage.filters, skimage.graph, skimage.io,
+        skimage.feature, skimage.filters, skimage.future, skimage.future.graph,
+        skimage.graph, skimage.io,
         skimage.io._plugins, skimage.measure, skimage.morphology,
         skimage.scripts, skimage.restoration, skimage.segmentation,
         skimage.transform, skimage.util
@@ -151,9 +152,9 @@ Library:
     Extension: skimage.feature._hessian_det_appx
         Sources:
             skimage/exposure/_hessian_det_appx.pyx
-    Extension: skimage.graph._ncut_cy
+    Extension: skimage.future.graph._ncut_cy
         Sources:
-            skimage/graph/_ncut_cy.pyx
+            skimage/future/graph/_ncut_cy.pyx
     Extension: skimage.external.tifffile._tifffile
         Sources:
             skimage/external/tifffile/_tifffile.c

From 483d7d669baa37b79605f594db3f5884f1806832 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Tue, 3 Feb 2015 15:10:54 +1100
Subject: [PATCH 04/10] Update plot_rag examples to use skimage.future

---
 doc/examples/plot_rag.py            | 2 +-
 doc/examples/plot_rag_draw.py       | 3 ++-
 doc/examples/plot_rag_mean_color.py | 3 ++-
 doc/examples/plot_rag_merge.py      | 3 ++-
 4 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/doc/examples/plot_rag.py b/doc/examples/plot_rag.py
index e44f4094..d4f2711c 100644
--- a/doc/examples/plot_rag.py
+++ b/doc/examples/plot_rag.py
@@ -14,7 +14,7 @@ The example below also shows how to use a custom function to select the larger
 weight instead.
 
 """
-from skimage.graph import rag
+from skimage.future.graph import rag
 import networkx as nx
 from matplotlib import pyplot as plt
 import numpy as np
diff --git a/doc/examples/plot_rag_draw.py b/doc/examples/plot_rag_draw.py
index 0c1e1abc..bdc39678 100644
--- a/doc/examples/plot_rag_draw.py
+++ b/doc/examples/plot_rag_draw.py
@@ -6,7 +6,8 @@ Drawing Region Adjacency Graphs (RAGs)
 This example constructs a Region Adjacency Graph (RAG) and draws it with
 the `rag_draw` method.
 """
-from skimage import graph, data, segmentation
+from skimage import data, segmentation
+from skimage.future import graph
 from matplotlib import pyplot as plt, colors
 
 
diff --git a/doc/examples/plot_rag_mean_color.py b/doc/examples/plot_rag_mean_color.py
index ab962e65..4b2bfcae 100644
--- a/doc/examples/plot_rag_mean_color.py
+++ b/doc/examples/plot_rag_mean_color.py
@@ -9,7 +9,8 @@ difference in mean color. We then join regions with similar mean color.
 
 """
 
-from skimage import graph, data, io, segmentation, color
+from skimage import data, io, segmentation, color
+from skimage.future import graph
 from matplotlib import pyplot as plt
 
 
diff --git a/doc/examples/plot_rag_merge.py b/doc/examples/plot_rag_merge.py
index d454a096..37712d5b 100644
--- a/doc/examples/plot_rag_merge.py
+++ b/doc/examples/plot_rag_merge.py
@@ -10,7 +10,8 @@ until no highly similar region pairs remain.
 
 """
 
-from skimage import graph, data, io, segmentation, color
+from skimage import data, io, segmentation, color
+from skimage.future import graph
 import numpy as np
 
 

From 5bd36730fc2cd2aa160ef00246fb3635cf334a0a Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Tue, 3 Feb 2015 15:13:02 +1100
Subject: [PATCH 05/10] Update plot_ncut example to use skimage.future

---
 doc/examples/plot_ncut.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/examples/plot_ncut.py b/doc/examples/plot_ncut.py
index 6b8a62ab..5596a297 100644
--- a/doc/examples/plot_ncut.py
+++ b/doc/examples/plot_ncut.py
@@ -12,7 +12,8 @@ References
        Pattern Analysis and Machine Intelligence,
        IEEE Transactions on, vol. 22, no. 8, pp. 888-905, August 2000.
 """
-from skimage import graph, data, io, segmentation, color
+from skimage import data, io, segmentation, color
+from skimage.future import graph
 from matplotlib import pyplot as plt
 
 

From d2d50e93911693c326b057a4c48f0a47d520f0a1 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Tue, 3 Feb 2015 15:20:57 +1100
Subject: [PATCH 06/10] Add package docstring for skimage.future

---
 skimage/future/__init__.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/skimage/future/__init__.py b/skimage/future/__init__.py
index e69de29b..121ff925 100644
--- a/skimage/future/__init__.py
+++ b/skimage/future/__init__.py
@@ -0,0 +1,6 @@
+"""Functionality with an experimental API. Although you can count on the
+functions in this package being around in the future, the API may change with
+any version update **and will not follow the skimage two-version deprecation
+path**. Therefore, use the functions herein with care, and do not use them in
+production code that will depend on updated skimage versions.
+"""

From 008775853fb1a4e0a648f26dfe7cceb60ced7a76 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Tue, 3 Feb 2015 15:34:56 +1100
Subject: [PATCH 07/10] Fix setup.py cascade

---
 skimage/future/graph/setup.py | 30 ++++++++++++++++++++++++++++++
 skimage/future/setup.py       | 12 ++++++++++++
 skimage/graph/setup.py        |  3 ---
 skimage/setup.py              |  1 +
 4 files changed, 43 insertions(+), 3 deletions(-)
 create mode 100644 skimage/future/graph/setup.py
 create mode 100644 skimage/future/setup.py

diff --git a/skimage/future/graph/setup.py b/skimage/future/graph/setup.py
new file mode 100644
index 00000000..059a0779
--- /dev/null
+++ b/skimage/future/graph/setup.py
@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+
+from skimage._build import cython
+import os.path
+
+base_path = os.path.abspath(os.path.dirname(__file__))
+
+
+def configuration(parent_package='', top_path=None):
+    from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
+
+    config = Configuration('graph', parent_package, top_path)
+    config.add_data_dir('tests')
+
+    # This function tries to create C files from the given .pyx files.  If
+    # it fails, try to build with pre-generated .c files.
+    cython(['_ncut_cy.pyx'], working_path=base_path)
+    config.add_extension('_ncut_cy', sources=['_ncut_cy.c'],
+                         include_dirs=[get_numpy_include_dirs()])
+    return config
+
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(maintainer='scikit-image Developers',
+          maintainer_email='scikit-image@googlegroups.com',
+          description='Graph-based Image-processing Algorithms',
+          url='https://github.com/scikit-image/scikit-image',
+          license='Modified BSD',
+          **(configuration(top_path='').todict())
+          )
diff --git a/skimage/future/setup.py b/skimage/future/setup.py
new file mode 100644
index 00000000..aaded0c7
--- /dev/null
+++ b/skimage/future/setup.py
@@ -0,0 +1,12 @@
+
+def configuration(parent_package='skimage', top_path=None):
+    from numpy.distutils.misc_util import Configuration
+    config = Configuration('future', parent_package, top_path)
+    config.add_subpackage('graph')
+    return config
+
+if __name__ == "__main__":
+    from numpy.distutils.core import setup
+
+    config = configuration(top_path='').todict()
+    setup(**config)
diff --git a/skimage/graph/setup.py b/skimage/graph/setup.py
index edc7b653..4c6aba06 100644
--- a/skimage/graph/setup.py
+++ b/skimage/graph/setup.py
@@ -17,7 +17,6 @@ def configuration(parent_package='', top_path=None):
     cython(['_spath.pyx'], working_path=base_path)
     cython(['_mcp.pyx'], working_path=base_path)
     cython(['heap.pyx'], working_path=base_path)
-    cython(['_ncut_cy.pyx'], working_path=base_path)
 
     config.add_extension('_spath', sources=['_spath.c'],
                          include_dirs=[get_numpy_include_dirs()])
@@ -25,8 +24,6 @@ def configuration(parent_package='', top_path=None):
                          include_dirs=[get_numpy_include_dirs()])
     config.add_extension('heap', sources=['heap.c'],
                          include_dirs=[get_numpy_include_dirs()])
-    config.add_extension('_ncut_cy', sources=['_ncut_cy.c'],
-                         include_dirs=[get_numpy_include_dirs()])
     return config
 
 if __name__ == '__main__':
diff --git a/skimage/setup.py b/skimage/setup.py
index 94d00ea8..b33f5e81 100644
--- a/skimage/setup.py
+++ b/skimage/setup.py
@@ -14,6 +14,7 @@ def configuration(parent_package='', top_path=None):
     config.add_subpackage('feature')
     config.add_subpackage('restoration')
     config.add_subpackage('filters')
+    config.add_subpackage('future')
     config.add_subpackage('graph')
     config.add_subpackage('io')
     config.add_subpackage('measure')

From 9cbeeca0df1233bbd0530a94c24158313281a2d3 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Tue, 3 Feb 2015 15:52:26 +1100
Subject: [PATCH 08/10] Update RAG doctest to use future

---
 skimage/future/graph/rag.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/skimage/future/graph/rag.py b/skimage/future/graph/rag.py
index e3d52875..9e882bae 100644
--- a/skimage/future/graph/rag.py
+++ b/skimage/future/graph/rag.py
@@ -251,7 +251,8 @@ def rag_mean_color(image, labels, connectivity=2, mode='distance',
 
     Examples
     --------
-    >>> from skimage import data, graph, segmentation
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
     >>> img = data.astronaut()
     >>> labels = segmentation.slic(img)
     >>> rag = graph.rag_mean_color(img, labels)

From e5fe82d6f32f75f03b2de7c24c667b345862f4a8 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Tue, 3 Feb 2015 16:20:15 +1100
Subject: [PATCH 09/10] Fix even more tests still importing skimage.graph

---
 skimage/future/graph/graph_cut.py      | 6 ++++--
 skimage/future/graph/rag.py            | 3 ++-
 skimage/future/graph/tests/test_rag.py | 2 +-
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/skimage/future/graph/graph_cut.py b/skimage/future/graph/graph_cut.py
index b4658bd1..d727eeac 100644
--- a/skimage/future/graph/graph_cut.py
+++ b/skimage/future/graph/graph_cut.py
@@ -37,7 +37,8 @@ def cut_threshold(labels, rag, thresh, in_place=True):
 
     Examples
     --------
-    >>> from skimage import data, graph, segmentation
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
     >>> img = data.astronaut()
     >>> labels = segmentation.slic(img)
     >>> rag = graph.rag_mean_color(img, labels)
@@ -107,7 +108,8 @@ def cut_normalized(labels, rag, thresh=0.001, num_cuts=10, in_place=True,
 
     Examples
     --------
-    >>> from skimage import data, graph, segmentation
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
     >>> img = data.astronaut()
     >>> labels = segmentation.slic(img, compactness=30, n_segments=400)
     >>> rag = graph.rag_mean_color(img, labels, mode='similarity')
diff --git a/skimage/future/graph/rag.py b/skimage/future/graph/rag.py
index 9e882bae..b0fd9240 100644
--- a/skimage/future/graph/rag.py
+++ b/skimage/future/graph/rag.py
@@ -365,7 +365,8 @@ def draw_rag(labels, rag, img, border_color=None, node_color='#ffff00',
 
     Examples
     --------
-    >>> from skimage import data, graph, segmentation
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
     >>> img = data.coffee()
     >>> labels = segmentation.slic(img)
     >>> g =  graph.rag_mean_color(img, labels)
diff --git a/skimage/future/graph/tests/test_rag.py b/skimage/future/graph/tests/test_rag.py
index cfa49cdf..1cac2b2d 100644
--- a/skimage/future/graph/tests/test_rag.py
+++ b/skimage/future/graph/tests/test_rag.py
@@ -1,5 +1,5 @@
 import numpy as np
-from skimage import graph
+from skimage.future import graph
 from skimage._shared.version_requirements import is_installed
 from numpy.testing.decorators import skipif
 from skimage import segmentation

From 0d1a2ef1faa6a732b59816bc07f281e519f3aa4f Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <juan.n@unimelb.edu.au>
Date: Wed, 4 Feb 2015 00:37:48 +1100
Subject: [PATCH 10/10] Import graph into future parent package

---
 skimage/future/__init__.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/skimage/future/__init__.py b/skimage/future/__init__.py
index 121ff925..0292a6ef 100644
--- a/skimage/future/__init__.py
+++ b/skimage/future/__init__.py
@@ -4,3 +4,7 @@ any version update **and will not follow the skimage two-version deprecation
 path**. Therefore, use the functions herein with care, and do not use them in
 production code that will depend on updated skimage versions.
 """
+
+from . import graph
+
+__all__ = ['graph']