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Export/Import of GML/Graphml/Yaml files through NetworkX #9731

Open 6bdad4c1-1e26-4f2f-a442-a01a2292c181 opened 14 years ago

6bdad4c1-1e26-4f2f-a442-a01a2292c181 commented 14 years ago

Thanks to Ben's update of NetworkX, these methods can now be used through Sage... This patch updates the constructor method for Graph, and adds write_* methods to export graphs.

This patch requires #9567

Nathann

CC: @sagetrac-bedwards

Component: graph theory

Issue created by migration from https://trac.sagemath.org/ticket/9731

6bdad4c1-1e26-4f2f-a442-a01a2292c181 commented 14 years ago
comment:1

Attachment: trac_9731.patch.gz

89c6e537-b2e3-45e6-882d-d4957b74ffe5 commented 13 years ago
comment:2
sage -t -long ./sage/graphs/generic_graph.py
**********************************************************************
File "/home/rlmill/sage-4.6.1.alpha2/devel/sage-main/sage/graphs/generic_graph.py", line 14430:
    sage: g.is_isomorphic(h)
Expected:
    True
Got:
    False
**********************************************************************
File "/home/rlmill/sage-4.6.1.alpha2/devel/sage-main/sage/graphs/generic_graph.py", line 14444:
    sage: g.write_yaml(SAGE_TMP+"/g.yml")
Exception raised:
    Traceback (most recent call last):
      File "/home/rlmill/sage-4.6.1.alpha2/local/bin/ncadoctest.py", line 1231, in run_one_test
        self.run_one_example(test, example, filename, compileflags)
      File "/home/rlmill/sage-4.6.1.alpha2/local/bin/sagedoctest.py", line 38, in run_one_example
        OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
      File "/home/rlmill/sage-4.6.1.alpha2/local/bin/ncadoctest.py", line 1172, in run_one_example
        compileflags, 1) in test.globs
      File "<doctest __main__.example_217[3]>", line 1, in <module>
        g.write_yaml(SAGE_TMP+"/g.yml")###line 14444:
    sage: g.write_yaml(SAGE_TMP+"/g.yml")
      File "/home/rlmill/sage-4.6.1.alpha2/local/lib/python/site-packages/sage/graphs/generic_graph.py", line 14451, in write_yaml
        networkx.write_yaml(self.networkx_graph(copy = False), filename)
      File "/home/rlmill/sage-4.6.1.alpha2/local/lib/python2.6/networkx/readwrite/nx_yaml.py", line 40, in write_yaml
        "write_yaml() requires PyYAML: http://pyyaml.org/ "
    ImportError: write_yaml() requires PyYAML: http://pyyaml.org/
**********************************************************************

There are more, but...

89c6e537-b2e3-45e6-882d-d4957b74ffe5 commented 13 years ago
comment:3

By the way, those showed up with sage-4.6.1.alpha2 plus the patches here, if that is relevant.

6bdad4c1-1e26-4f2f-a442-a01a2292c181 commented 13 years ago
comment:4

Not only that, but once the yaml export is removed the graphml docstring does not pass because of stupid edge labels set by default (if you write a file without any edge label, the one you get has its endpoints as labels) with weird 'u' before the vertices' name... O_o

Nathann