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Remove deprecated 'center' aliases in GenomeDiagram

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commit d508b01d4cfc83bbc09005ec2690d443396ebb1f 1 parent 472aae3
Peter Cock peterjc authored
14 Bio/Graphics/GenomeDiagram/_AbstractDrawer.py
View
@@ -433,20 +433,6 @@ def __init__(self, parent, pagesize='A3', orientation='landscape',
else:
self.cross_track_links = cross_track_links
- @property
- def xcentre(self):
- """Backwards compatible alias for xcenter (DEPRECATED)"""
- warnings.warn("The .xcentre attribute is deprecated, use .xcenter instead",
- Bio.BiopythonDeprecationWarning)
- return self.xcenter
-
- @property
- def ycentre(self):
- """Backwards compatible alias for ycenter (DEPRECATED)"""
- warnings.warn("The .ycentre attribute is deprecated, use .ycenter instead",
- Bio.BiopythonDeprecationWarning)
- return self.ycenter
-
def set_page_size(self, pagesize, orientation):
""" set_page_size(self, pagesize, orientation)
14 Bio/Graphics/GenomeDiagram/_Graph.py
View
@@ -86,7 +86,7 @@ class GraphData(object):
"""
def __init__(self, id=None, data=None, name=None, style='bar',
color=colors.lightgreen, altcolor=colors.darkseagreen,
- center=None, colour=None, altcolour=None, centre=None):
+ center=None, colour=None, altcolour=None):
"""__init__(self, id=None, data=None, name=None, style='bar',
color=colors.lightgreen, altcolor=colors.darkseagreen)
@@ -107,8 +107,7 @@ def __init__(self, id=None, data=None, name=None, style='bar',
values (some styles only) (overridden by backwards
compatible argument with UK spelling, colour).
- o center Value at which x-axis crosses y-axis (overridden by
- backwards comparible argument with UK spelling, centre).
+ o center Value at which x-axis crosses y-axis.
"""
@@ -117,8 +116,6 @@ def __init__(self, id=None, data=None, name=None, style='bar',
color = colour
if altcolour is not None:
altcolor = altcolour
- if centre is not None:
- center = centre
self.id = id # Unique identifier for the graph
self.data = {} # holds values, keyed by sequence position
@@ -133,13 +130,6 @@ def __init__(self, id=None, data=None, name=None, style='bar',
self.linewidth = 2 # linewidth to use in line graphs
self.center = center # value at which x-axis crosses y-axis
- @property
- def centre(self):
- """Backwards compatible alias for center (DEPRECATED)."""
- warnings.warn("The .centre attribute is deprecated, use .center instead",
- Bio.BiopythonDeprecationWarning)
- return self.center
-
def set_data(self, data):
""" set_data(self, data)
6 DEPRECATED
View
@@ -177,9 +177,9 @@ GenomeDiagram originally used colour and centre (UK spelling of color and
center) for argument names. As part of its integration into Biopython 1.50,
this will support both colour and color, and both centre and center, to help
people port existing scripts written for the standalone version of
-GenomeDiagram. However, these were deprecated in Release 1.55 final, and we
-intend to eventually remove support for colour and centre in later releases
-of Biopython.
+GenomeDiagram. However, these were deprecated in Release 1.55 final.
+Support for centre was removed in Release 1.62, and we intend to eventually
+remove support for colour in later releases of Biopython.
Bio.AlignAce and Bio.MEME
=========================
7 Doc/Tutorial.tex
View
@@ -80,7 +80,7 @@
\author{Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, \\
Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczy\'{n}ski}
-\date{Last Update -- 22 March 2013 (Biopython 1.61+)}
+\date{Last Update -- 12 July 2013 (Biopython 1.61+)}
%Hack to get the logo at the start of the HTML front page:
%(hopefully this isn't going to be too wide for most people)
@@ -15408,9 +15408,8 @@ \subsection{Converting old code}
you will have to make a few changes - most importantly to your import statements.
Also, the older version of GenomeDiagram used only the UK spellings of color and
-center (colour and centre). As part of the integration into Biopython, both
-forms can now be used for argument names. However, at some point in the future the
-UK spellings may be deprecated.
+center (colour and centre). You will need to change to the American spellings,
+although for several years the Biopython version of GenomeDiagram supported both.
For example, if you used to have:
\begin{verbatim}
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