py3: failing doctest in graph_database.py with interactive_query #27435

dcoudert · 2019-03-07T12:02:04Z

sage -t --long src/sage/graphs/graph_database.py
**********************************************************************
File "src/sage/graphs/graph_database.py", line 1081, in sage.graphs.graph_database.GraphDatabase.interactive_query
Failed example:
    D.interactive_query(display_cols=['graph6', 'num_vertices', 'degree_sequence'], num_edges=5, max_degree=3)
Exception raised:
    Traceback (most recent call last):
      File "/Users/dcoudert/sage3/sage/local/lib/python3.6/inspect.py", line 1119, in getfullargspec
        sigcls=Signature)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.6/inspect.py", line 2186, in _signature_from_callable
        raise TypeError('{!r} is not a callable object'.format(obj))
    TypeError: 0 is not a callable object

    The above exception was the direct cause of the following exception:

    Traceback (most recent call last):
      File "/Users/dcoudert/sage3/sage/local/lib/python3.6/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.6/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.graph_database.GraphDatabase.interactive_query[1]>", line 1, in <module>
        D.interactive_query(display_cols=['graph6', 'num_vertices', 'degree_sequence'], num_edges=Integer(5), max_degree=Integer(3))
      File "/Users/dcoudert/sage3/sage/local/lib/python3.6/site-packages/sage/graphs/graph_database.py", line 1087, in interactive_query
        interact(f)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.6/site-packages/sage/misc/decorators.py", line 343, in my_wrap
        return func(*args)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.6/site-packages/sagenb/notebook/interact.py", line 2636, in interact
        (args, varargs, varkw, defaults) = inspect.getargspec(f)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.6/inspect.py", line 1073, in getargspec
        getfullargspec(func)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.6/inspect.py", line 1125, in getfullargspec
        raise TypeError('unsupported callable') from ex
    TypeError: unsupported callable

CC: @dimpase @jdemeyer

Component: graph theory

Author: Ewan Davies, David Coudert

Branch/Commit: 10fd0e8

Reviewer: Frédéric Chapoton, John Palmieri

Issue created by migration from https://trac.sagemath.org/ticket/27435

The text was updated successfully, but these errors were encountered:

dcoudert · 2019-03-07T12:02:23Z

comment:1

I don't know how to fix it.

sheldoncooper07 · 2019-03-08T11:08:45Z

comment:2

Hi, I am Piyush, I am new to sage, I was wondering if I could be of some help here.

I am not able to replicate this test. Is there something that I am missing? I am using Ubuntu 16.04

$ ./sage -t --long src/sage/graphs/graph_database.py
Running doctests with ID 2019-03-08-11-03-04-40b4d48a.
Git branch: develop
Using --optional=dochtml,memlimit,mpir,python2,sage
Doctesting 1 file.
sage -t --long src/sage/graphs/graph_database.py
    [50 tests, 0.49 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 0.6 seconds
    cpu time: 0.5 seconds
    cumulative wall time: 0.5 seconds

dcoudert · 2019-03-08T11:55:50Z

comment:3

The problem is with Python 3. We are working hard on the transition from Python 2 to Python 3.

embray · 2019-03-25T10:56:15Z

comment:4

Ticket retargeted after milestone closed (if you don't believe this ticket is appropriate for the Sage 8.8 release please retarget manually)

ed359 · 2019-05-13T04:42:35Z

comment:5

I may have managed to fix this error. I don't know anything about the origins of the code but the error arises in in graph_database._gen_interact_func where it seems a string defining a function called _ is run with exec.

I tried changing the name of the function that gets defined and ran into a different python3-related bug in the sagenb python package (maintained out of the main sage tree): it still uses xrange in sagenb.notebook.interact at line 1185.

I downloaded the source for that package, changed the uses of xrange, and now the doctest passes on my machine, but the bar for passing is simply emitting a string starting and finishing with <html> and </html>.

I'm not sure what to suggest for this ticket, the doctest in question has something to do with the old sage notebook (sagenb). The function interactive_query returns some html that doesn't appear do anything in jupyter, and I can't use the old notebook on python3 (an error related to Twisted). Is the old notebook formally deprecated? See #22431 and in particular the 'side remark' about the graph database explorer.

If my changes to _gen_interact_func and the sagenb package are wanted I can send patches, but as I can't run the notebook myself on python3 I can't even verify that it's a proper fix.

dcoudert · 2019-05-13T06:14:36Z

comment:6

Let's ask the author of #22431 if anything was said about graph_editor and interactive queries in graph_database.

Also I don't know if these tools have users. If not, we may simply deprecate the parts involving sagenb. Otherwise, someone with enough knowledge in notebooks should try to solve the issues.

dimpase · 2019-05-13T07:19:30Z

comment:7

Replying to @ed359:

I may have managed to fix this error. I don't know anything about the origins of the code but the error arises in in graph_database._gen_interact_func where it seems a string defining a function called _ is run with exec.

I tried changing the name of the function that gets defined and ran into a different python3-related bug in the sagenb python package (maintained out of the main sage tree): it still uses xrange in sagenb.notebook.interact at line 1185.

I downloaded the source for that package, changed the uses of xrange, and now the doctest passes on my machine, but the bar for passing is simply emitting a string starting and finishing with <html> and </html>.

I'm not sure what to suggest for this ticket, the doctest in question has something to do with the old sage notebook (sagenb). The function interactive_query returns some html that doesn't appear do anything in jupyter, and I can't use the old notebook on python3 (an error related to Twisted). Is the old notebook formally deprecated? See #22431 and in particular the 'side remark' about the graph database explorer.

If my changes to _gen_interact_func and the sagenb package are wanted I can send patches, but as I can't run the notebook myself on python3 I can't even verify that it's a proper fix.

As long as these changes don't break sagenb on python2, it is fine.
Please send a PR on https://github.com/sagemath/sagenb
(perhaps they are already fixed in the 4 most recent open PRs there.)

As to functionality to be removed, I don't know.

ed359 · 2019-05-13T18:06:20Z

Branch: u/gh-ed359/py3__failing_doctest_in_graph_database_py_with_interactive_query

kcrisman · 2019-05-13T18:41:49Z

comment:9

Thanks. We may need to think about how to deal with this in the eventual removal of sagenb, as the interact should in principle still be able to work in e.g. Jupyter notebooks, but would have to import from elsewhere. Cc:ing Jeroen as he knows a lot about how that is implemented in Jupyter and where things might need to import from now.

New commits:

`2d05ce8`	`graph_database.py: fix doctest on python3`

kcrisman · 2019-05-13T18:41:49Z

Commit: 2d05ce8

dcoudert · 2019-05-30T15:59:52Z

comment:10

Now the error is in sagenb (tested over 8.8.beta6).

sage -t --long src/sage/graphs/graph_database.py
**********************************************************************
File "src/sage/graphs/graph_database.py", line 1082, in sage.graphs.graph_database.GraphDatabase.interactive_query
Failed example:
    D.interactive_query(display_cols=['graph6', 'num_vertices', 'degree_sequence'], num_edges=5, max_degree=3)
Exception raised:
    Traceback (most recent call last):
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1105, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.graph_database.GraphDatabase.interactive_query[1]>", line 1, in <module>
        D.interactive_query(display_cols=['graph6', 'num_vertices', 'degree_sequence'], num_edges=Integer(5), max_degree=Integer(3))
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/graphs/graph_database.py", line 1088, in interactive_query
        interact(f)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/misc/decorators.py", line 343, in my_wrap
        return func(*args)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sagenb/notebook/interact.py", line 2643, in interact
        for i, arg in enumerate(args)]
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sagenb/notebook/interact.py", line 2643, in <listcomp>
        for i, arg in enumerate(args)]
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sagenb/notebook/interact.py", line 3093, in render
        to_value=self.__to_value, width=self.__width)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sagenb/notebook/interact.py", line 1185, in __init__
        default_value = [[default_value[i * columns + j] for j in xrange(columns)] for i in xrange(rows)]
    NameError: name 'xrange' is not defined
**********************************************************************

embray · 2019-06-14T14:54:19Z

comment:11

As the Sage-8.8 release milestone is pending, we should delete the sage-8.8 milestone for tickets that are not actively being worked on or that still require significant work to move forward. If you feel that this ticket should be included in the next Sage release at the soonest please set its milestone to the next release milestone (sage-8.9).

jhpalmieri · 2019-07-10T18:52:16Z

comment:13

If the problem is with sagenb, then can we mark the doctest as "# py2", since my understanding is that sagenb is not compatible with Python 3? That is, keep the proposed changes here, but also tag the doctest as py2 only.

dimpase · 2019-07-10T19:10:33Z

comment:14

can't we just skip installing sagenb on Python3?

jhpalmieri · 2019-07-10T19:24:55Z

comment:15

I think that sagenb as a whole does not work with Python 3, but parts of it do, and parts are imported into the Sage library in various places. If we don't install it, some things may break. Some of the imports:

src/sage/graphs/graph_editor.py:    import sagenb.notebook.interact
src/sage/interacts/library.py:        import sagenb.notebook.interact
src/sage/interacts/debugger.py:        from sagenb.notebook.interact import slider, input_box, selector

dcoudert · 2019-07-10T20:36:46Z

comment:16

I agree with the proposal of marking this doctest as # py2, but we should also add that there is known issue with py3, no ? This way, we don't await for a decision about sagenb.

dcoudert · 2019-07-11T09:44:46Z

comment:17

I added proposed modification and pushed the code to a new branch in public. Feel free to modify it if needed.

New commits:

`d5074f9`	`trac #27435: Merged with 8.9.beta2`
`10fd0e8`	`trac #27435: mark doctest as py2 only and add warning block`

dcoudert · 2019-07-11T09:44:46Z

Author: Ewan Davies, David Coudert

dcoudert · 2019-07-11T09:44:46Z

Changed branch from u/gh-ed359/py3__failing_doctest_in_graph_database_py_with_interactive_query to public/graphs/27435_doctest_in_graph_database

dcoudert · 2019-07-11T09:44:46Z

Changed commit from 2d05ce8 to 10fd0e8

jhpalmieri · 2019-07-17T21:02:22Z

comment:18

This is fine with me. Anyone else have any comments? Objections to setting to positive review?

fchapoton · 2019-07-18T07:14:20Z

Reviewer: Frédéric Chapoton, John Palmieri

fchapoton · 2019-07-18T07:14:20Z

comment:19

ok..

vbraun · 2019-07-20T09:10:54Z

Changed branch from public/graphs/27435_doctest_in_graph_database to 10fd0e8

dcoudert added this to the sage-8.7 milestone Mar 7, 2019

dcoudert added c: graph theory labels Mar 7, 2019

embray modified the milestones: sage-8.7, sage-8.8 Mar 25, 2019

embray removed this from the sage-8.8 milestone Jun 14, 2019

dcoudert added this to the sage-8.9 milestone Jun 15, 2019

dcoudert added the s: needs review label Jul 11, 2019

fchapoton added s: positive review and removed s: needs review labels Jul 18, 2019

vbraun removed the s: positive review label Jul 20, 2019

vbraun closed this as completed in f20bcce Jul 20, 2019

fchapoton mentioned this issue Jan 1, 2020

py3: make all tests pass #26212

Closed

dcoudert mentioned this issue Jun 20, 2020

Meta-ticket: make graphs compatible with Python 3 #26640

Closed

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py3: failing doctest in graph_database.py with interactive_query #27435

py3: failing doctest in graph_database.py with interactive_query #27435

dcoudert commented Mar 7, 2019

dcoudert commented Mar 7, 2019

sheldoncooper07 mannequin commented Mar 8, 2019

dcoudert commented Mar 8, 2019

embray commented Mar 25, 2019

ed359 commented May 13, 2019

dcoudert commented May 13, 2019

dimpase commented May 13, 2019

ed359 commented May 13, 2019

kcrisman commented May 13, 2019

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dcoudert commented May 30, 2019

embray commented Jun 14, 2019

jhpalmieri commented Jul 10, 2019

dimpase commented Jul 10, 2019

jhpalmieri commented Jul 10, 2019

dcoudert commented Jul 10, 2019

dcoudert commented Jul 11, 2019

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dcoudert commented Jul 11, 2019

jhpalmieri commented Jul 17, 2019

fchapoton commented Jul 18, 2019

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vbraun commented Jul 20, 2019

py3: failing doctest in graph_database.py with interactive_query #27435

py3: failing doctest in graph_database.py with interactive_query #27435

Comments

dcoudert commented Mar 7, 2019

dcoudert commented Mar 7, 2019

sheldoncooper07 mannequin commented Mar 8, 2019

dcoudert commented Mar 8, 2019

embray commented Mar 25, 2019

ed359 commented May 13, 2019

dcoudert commented May 13, 2019

dimpase commented May 13, 2019

ed359 commented May 13, 2019

kcrisman commented May 13, 2019

kcrisman commented May 13, 2019

dcoudert commented May 30, 2019

embray commented Jun 14, 2019

jhpalmieri commented Jul 10, 2019

dimpase commented Jul 10, 2019

jhpalmieri commented Jul 10, 2019

dcoudert commented Jul 10, 2019

dcoudert commented Jul 11, 2019

dcoudert commented Jul 11, 2019

dcoudert commented Jul 11, 2019

dcoudert commented Jul 11, 2019

jhpalmieri commented Jul 17, 2019

fchapoton commented Jul 18, 2019

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vbraun commented Jul 20, 2019