#12806: upgrade of spkg networkx-1.2.p2 to 1.6
---------------------------------------------------+------------------------
Reporter: dkrenn | Owner: jason,
ncohen, rlm
Type: defect | Status:
needs_review
Priority: major | Milestone: sage-5.2
Component: graph theory | Resolution:
Keywords: spkg networkx graphs | Work issues:
Report Upstream: N/A | Reviewers: Keshav
Kini
Authors: Daniel Krenn, Javier López Peña | Merged in:
Dependencies: | Stopgaps:
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Changes (by jlopez):
* status: needs_work => needs_review
Old description:
> When upgrading the networkx package to 1.6, there arise a lot of doctest
> errors, see discussion on [http://groups.google.com/group/sage-
> devel/browse_thread/thread/60e2704e68cad4f4 sage-devel].
> This ticket should contain everything that is necessary to do so.
>
> To get the doctests passing, the following modifications have been made:
> 1. Fixed the calls in `graph.py` to conform to the new API for
> `betweennness_centrality`. Also exposed the new options.
> 2. Failing doctest in `digraph.py` was shocasing a bug that isn't there
> anymore. Fixed and documented it, and exposed the previously offending
> implementation to sage
> 3. Two failures in `graph_generators.py` were due to changes in
> randomized methods, so just changed the tests to conform to the new
> output, the rest were due to a bad-parameter case that was used to raise
> an exception but now degenerates gracefully. Fixed the corresponding
> doctests to account for that.
> 4. Failures in `graph_generic.py` were due to a change in the output of
> clustering coefficients for weighted graphs. Added an optional parameter
> to use the new output, implemented the old behaviour as it was in
> NetworkX 1.2, and set the old behaviour to default with a deprecation
> warning.
>
> To review this ticket:
> 1. Install [http://www.math.tugraz.at/~krenn/whatever/networkx-1.6.spkg
> this spkg]
> 2. Apply
> [http://trac.sagemath.org/sage_trac/attachment/ticket/12806/trac_12806_doctest_fixes.patch
> this patch] and
> [http://trac.sagemath.org/sage_trac/attachment/ticket/12806/trac_12806.reviewer.patch
> this patch]
New description:
When upgrading the networkx package to 1.6, there arise a lot of doctest
errors, see discussion on [http://groups.google.com/group/sage-
devel/browse_thread/thread/60e2704e68cad4f4 sage-devel].
This ticket should contain everything that is necessary to do so.
To get the doctests passing, the following modifications have been made:
1. Fixed the calls in `graph.py` to conform to the new API for
`betweennness_centrality`. Also exposed the new options.
2. Failing doctest in `digraph.py` was shocasing a bug that isn't there
anymore. Fixed and documented it, and exposed the previously offending
implementation to sage
3. Two failures in `graph_generators.py` were due to changes in randomized
methods, so just changed the tests to conform to the new output, the rest
were due to a bad-parameter case that was used to raise an exception but
now degenerates gracefully. Fixed the corresponding doctests to account
for that.
4. Failures in `graph_generic.py` were due to a change in the output of
clustering coefficients for weighted graphs. Added an optional parameter
to use the new output, implemented the old behaviour as it was in NetworkX
1.2, and set the old behaviour to default with a deprecation warning.
To review this ticket:
1. Install [http://www.math.tugraz.at/~krenn/whatever/networkx-1.6.spkg
this spkg]
2. Apply
[http://trac.sagemath.org/sage_trac/attachment/ticket/12806/trac_12806_doctest_fixes.patch
this patch],
[http://trac.sagemath.org/sage_trac/attachment/ticket/12806/trac_12806.reviewer.patch
this patch] and
[http://trac.sagemath.org/sage_trac/attachment/ticket/12806/trac_12806_docbuild_fix.patch
this patch]
--
Comment:
I think the documentation building problem is fixed; `sage --docbuild
reference pdf` gives me no errors. Needs review just for the docbuild
patch.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/12806#comment:19>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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