Opened 12 years ago
Closed 12 years ago
#11298 closed defect (fixed)
Extend the capabilities of Sage's introspection
Reported by: | SimonKing | Owned by: | jason |
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Priority: | major | Milestone: | sage-4.7.2 |
Component: | misc | Keywords: | edit sageinspect |
Cc: | jsrn, nthiery, saliola | Merged in: | sage-4.7.2.alpha1 |
Authors: | Simon King | Reviewers: | John Palmieri |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | #9976, #11287 | Stopgaps: |
Description (last modified by )
The following used to fail:
sage: x?? Error getting source: could not find class definition sage: P.<x,y> = QQ[] sage: P?? Error getting source: could not find class definition sage: I?? Error getting source: could not find class definition
Similarly, the edit command did not work in these case.
With my patch, all that works. Moreover, both sage.misc.edit_module and sage.misc.sageinspect are put into the reference manual.
Note that this may be related with #11287: sage.misc.sage_getfile
and sage_getsourcelines
could be a reliable tool to get information on how and from where to import a given object. Therefore Cc to the participants of that ticket.
Moreover, Cc to #9976. Reason:
Depends on #9976
Apply
Attachments (5)
Change History (45)
comment:1 Changed 12 years ago by
Status: | new → needs_review |
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comment:3 Changed 12 years ago by
Note that, with the patch, functools.partial
objects can be reasonably edited as well:
edit(sage.combinat.partition_algebra.SetPartitionsAk,'vim')
opens vim at line 31 of sage/combinat/partition_algebra.py:
def create_set_partition_function(letter, k): """ EXAMPLES:: sage: from sage.combinat.partition_algebra import create_set_partition_function sage: create_set_partition_function('A', 3) Set partitions of {1, ..., 3, -1, ..., -3} """ from sage.functions.all import floor if isinstance(k, (int, Integer)): if k > 0: return globals()['SetPartitions' + letter + 'k_k'](k) elif is_RealNumber(k): if k - math.floor(k) == 0.5: return globals()['SetPartitions' + letter + 'khalf_k'](floor(k)) raise ValueError, "k must be an integer or an integer + 1/2"
and indeed that is the underlying definition of SetPartitionsAk
; see line 53, which is
SetPartitionsAk = functools.partial(create_set_partition_function,"A")
comment:4 Changed 12 years ago by
I found one more case where source code inspection failed: the (lib)singular_standard_options wrapper.
With the new patch, we have
sage: P.<x,y> = QQ[] sage: I = P*[x,y] sage: edit(I.interreduced_basis,'vim') ... @singular_standard_options @libsingular_standard_options def interreduced_basis(self): r""" If this ideal is spanned by `(f_1, ..., f_n)` this method returns `(g_1, ..., g_s)` such that: - `(f_1,...,f_n) = (g_1,...,g_s)` - `LT(g_i) != LT(g_j)` for all `i != j` ...
which would previously just show the code of the wrapper, not of the wrapped method.
I wonder why the patchbot complains. In particular, why does the patchbot mention my patch from trac ticket #11115 - it shouldn't be a dependency, or should it? Let's see.
For now:
Depends on #9976
comment:5 Changed 12 years ago by
I just verified: In my patch queue, the patches from #11115 come after trac11298_introspection_and_edit.patch
In other words, the behaviour of the patchbot seems very strange to me.
comment:6 Changed 12 years ago by
comment:7 Changed 12 years ago by
Adding "r" to one doc string (for making the documentation nicely formatted) and correcting one doc test.
The tests in sage.misc and in sage.rings.polynomial all pass. Next, I'll run long tests.
Depends on #9976
comment:8 Changed 12 years ago by
Status: | needs_review → needs_work |
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I'll try to trigger the patchbot by changing to "needs work"...
comment:10 Changed 12 years ago by
Status: | needs_work → needs_review |
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Changed 12 years ago by
Attachment: | trac11298_introspection_and_edit.patch added |
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Extend the capabilities of introspection and interactive source code edition
comment:11 Changed 12 years ago by
OK, that did not help. Hence, I submitted the patches again. I wish the red blob would finally vanish!
Depends on #9976
comment:12 Changed 12 years ago by
Dependencies: | → #9976 |
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Ooops, I forgot that since recently there is a form field in which to state dependencies. Let's try it!
comment:13 Changed 12 years ago by
FWIW, long tests pass for me, and I believe that the patchbot has a serious flaw if it can not even deal with a single dependency.
comment:14 Changed 12 years ago by
comment:15 Changed 12 years ago by
Status: | needs_review → needs_work |
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Work issues: | → Fix crash at docbuild |
I noticed that building the documentation crashes when the second patch is applied. It is as follows:
Running Sphinx v1.0.4 loading pickled environment... done building [html]: targets for 39 source files that are out of date updating environment: 0 added, 39 changed, 0 removed reading sources... [ 33%] sage/rings/polynomial/multi_polynomial_ideal_libsingular Exception occurred: File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/Sphinx-1.0.4-py2.6.egg/sphinx/config.py", line 207, in __getattr__ raise AttributeError('No such config value: %s' % name) AttributeError: No such config value: autodoc_default_flags The full traceback has been saved in /tmp/sphinx-err-1tNBmd.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. Either send bugs to the mailing list at <http://groups.google.com/group/sphinx-dev/>, or report them in the tracker at <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks! Build finished. The built documents can be found in /mnt/local/king/SAGE/sage-4.7.rc2/devel/sage/doc/output/html/en/reference
and the traceback is
# Sphinx version: 1.0.4 # Docutils version: 0.5 release # Jinja2 version: 2.5.5 Traceback (most recent call last): File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/Sphinx-1.0.4-py2.6.egg/sphinx/cmdline.py", line 173, in main app.build(force_all, filenames) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/Sphinx-1.0.4-py2.6.egg/sphinx/application.py", line 207, in build self.builder.build_update() File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/Sphinx-1.0.4-py2.6.egg/sphinx/builders/__init__.py", line 198, in build_update 'out of date' % len(to_build)) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/Sphinx-1.0.4-py2.6.egg/sphinx/builders/__init__.py", line 218, in build purple, length): File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/Sphinx-1.0.4-py2.6.egg/sphinx/builders/__init__.py", line 120, in status_iterator for item in iterable: File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/Sphinx-1.0.4-py2.6.egg/sphinx/environment.py", line 518, in update_generator self.read_doc(docname, app=app) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/Sphinx-1.0.4-py2.6.egg/sphinx/environment.py", line 658, in read_doc pub.publish() File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/core.py", line 204, in publish self.settings) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/readers/__init__.py", line 69, in read self.parse() File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/readers/__init__.py", line 75, in parse self.parser.parse(self.input, document) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/__init__.py", line 157, in parse self.statemachine.run(inputlines, document, inliner=self.inliner) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 170, in run input_source=document['source']) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/statemachine.py", line 232, in run context, state, transitions) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/statemachine.py", line 420, in check_line return method(match, context, next_state) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 2658, in underline self.section(title, source, style, lineno - 1, messages) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 308, in section self.new_subsection(title, lineno, messages) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 376, in new_subsection node=section_node, match_titles=1) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 266, in nested_parse node=node, match_titles=match_titles) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 195, in run results = StateMachineWS.run(self, input_lines, input_offset) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/statemachine.py", line 232, in run context, state, transitions) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/statemachine.py", line 420, in check_line return method(match, context, next_state) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 2241, in explicit_markup self.explicit_list(blank_finish) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 2269, in explicit_list match_titles=self.state_machine.match_titles) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 300, in nested_list_parse node=node, match_titles=match_titles) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 195, in run results = StateMachineWS.run(self, input_lines, input_offset) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/statemachine.py", line 232, in run context, state, transitions) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/statemachine.py", line 420, in check_line return method(match, context, next_state) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 2542, in explicit_markup nodelist, blank_finish = self.explicit_construct(match) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 2251, in explicit_construct return method(self, expmatch) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 1994, in directive directive_class, match, type_name, option_presets) File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/docutils/parsers/rst/states.py", line 2043, in run_directive result = directive_instance.run() File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/Sphinx-1.0.4-py2.6.egg/sphinx/ext/autodoc.py", line 1154, in run if flag in self.env.config.autodoc_default_flags and \ File "/mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/Sphinx-1.0.4-py2.6.egg/sphinx/config.py", line 207, in __getattr__ raise AttributeError('No such config value: %s' % name) AttributeError: No such config value: autodoc_default_flags
I have no idea how this can be debugged.
comment:16 Changed 12 years ago by
Perhaps it would be worth while to follow a more conceptual approach.
Currently, singular_standard_options
and magma_standard_options
applied to a method func
simply return a function wrapper
, that does not know about func
(except its doc string, but I think that's a bad idea as well since copying that string costs time). So, introspection does not work. I tried to provide wrapper
with the tools needed to make it work, but apparently it was not so easy.
But there is the sage_wraps
factory, and I think I should try to use it!
Changed 12 years ago by
Attachment: | trac11298_singular_standard_options.patch added |
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Introspection for sage.misc.decorators.sage_wraps, applied for singular_standard_options. Put decorators into references.
comment:17 Changed 12 years ago by
Status: | needs_work → needs_review |
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Work issues: | Fix crash at docbuild |
The second patch has now been updated.
The problem seems solved: I touched all files in sage/rings/polynomial, did sage -b
and then built the documentation without problem.
Moreover, I fixed some syntax error in the documentation, and I've put sage.misc.decorators into the reference manual.
So, it is needing review again!
Changed 12 years ago by
Attachment: | trac11298_singular_standard_options.rebase4.7.1.a1.patch added |
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rebased Simon's patch to 4.7.1.alpha1
comment:18 Changed 12 years ago by
Description: | modified (diff) |
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comment:19 Changed 12 years ago by
Thank you, Burcin!
For the patchbot, that seems to ignore the ticket description:
Apply trac11298_introspection_and_edit.patch, trac11298_singular_standard_options.rebase4.7.1.a1.patch
comment:20 follow-ups: 22 23 Changed 12 years ago by
This looks pretty good to me. I have one question: in sage_getsourcelines
, lines 1408-1411, you have the code
except IOError: if obj.__class__ != type: return sage_getsourcelines(obj.__class__) raise
What is type
here? Can you give me an example which will reach this code?
comment:22 Changed 12 years ago by
Replying to jhpalmieri:
This looks pretty good to me. I have one question: in
sage_getsourcelines
, lines 1408-1411, you have the code ...What is
type
here? Can you give me an example which will reach this code?
By type
, I mean the type type
, such as here:
sage: 1.__class__ <type 'sage.rings.integer.Integer'> sage: 1.__class__.__class__ <type 'type'>
The idea of the code lines in question is as follows:
Let obj
be the object whose source lines we want to determine. It is not necessarily true that the correct source lines for obj
coincide with the source lines of its class (notorious counter example: decorated methods). Therefore, we need to try harder.
- First, it is attempted to get the position of the source code from what
inspect.getdoc
returns (lines 1400-1401)
- Second (if "first" fails), the same is attempted with what
_sage_getdoc_unformatted
returns (lines 1403-1404). For a reason that I don't understand, one can not replace the first step by the second step: The comment that I inserted states that a mysterious import error would occur at startup.
- Third (if "second" fails as well), it is tested whether the inspect module can provide the source lines of the object
obj
(line 1407).
- Last resort (if "third" fails), we replace
obj
byobj.__class__
. That is not desired for decorated methods, but these are supposed to provide the source lines in a different way, so that one of the first three methods should succeed. I think as a last resort it is ok... (line 1410).
There is one obvious problem with the "last resort". If the source lines of obj.__class__
can not be found (e.g., if obj.__class__
is defined in an spkg, not in the Sage library) then as a last resort one would try to get obj.__class__.__class__
, but that is the type type
(see example above), which is defined in the Python spkg and can thus not be found. Infinite recursion.
In order to avoid the infinite recursion, an error is raised if obj.__class__
is the type type
, which is, in particular, the case if obj
is not a class instance but a class.
I hope that answers your question...
comment:23 Changed 12 years ago by
Replying to jhpalmieri:
What is
type
here? Can you give me an example which will reach this code?
A concrete example (using the meataxe wrapper from my cohomology spkg):
sage: from sage.misc.sageinspect import sage_getsourcelines sage: from pGroupCohomology.mtx import MTX sage: M = MTX(5,[[1,2],[3,4]]) sage: sage_getsourcelines(M) --------------------------------------------------------------------------- IOError Traceback (most recent call last) /home/king/<ipython console> in <module>() /mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/sage/misc/sageinspect.pyc in sage_getsourcelines(obj, is_binary) 1407 if pos is None: 1408 try: -> 1409 return inspect.getsourcelines(obj) 1410 except IOError: 1411 if obj.__class__ != type: /mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python/inspect.pyc in getsourcelines(object) 676 original source file the first line of code was found. An IOError is 677 raised if the source code cannot be retrieved.""" --> 678 lines, lnum = findsource(object) 679 680 if ismodule(object): return lines, 0 /mnt/local/king/SAGE/sage-4.7.rc2/local/lib/python2.6/site-packages/IPython/ultraTB.pyc in findsource(object) 175 return lines, candidates[0][1] 176 else: --> 177 raise IOError('could not find class definition') 178 179 if ismethod(object): IOError: could not find class definition
Since M
can not provide its source lines, the source lines of M.__class__
(i.e., of MTX
) are sought.
Since the source lines of MTX
can not be found (with the first three methods), the inspect module raises a IOError
. It is caught, but reraised, since MTX.__class__
is the type type
and hence an infinite recursion must be prevented.
comment:24 follow-up: 26 Changed 12 years ago by
Reviewers: | → John Palmieri |
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Okay, I'm happy with this. I'm attaching a referee's patch with a few small changes. If you're happy with my changes, please switch the ticket to "positive review".
This makes a very nice companion to #9976.
Changed 12 years ago by
Attachment: | trac_11298-ref.patch added |
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referee patch; apply on top of others
comment:25 Changed 12 years ago by
Description: | modified (diff) |
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(The only aspect of the referee's patch worth mentioning is the removal of the import of sage_getsource
. This is already done at the top-level of that file, so it doesn't need to be done again.)
comment:26 Changed 12 years ago by
Status: | needs_review → positive_review |
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Replying to jhpalmieri:
Okay, I'm happy with this. I'm attaching a referee's patch with a few small changes. If you're happy with my changes, please switch the ticket to "positive review".
I am happy with the changes. Thus I change it into a positive review. Thank you very much!
comment:27 Changed 12 years ago by
Milestone: | sage-4.7.1 → sage-4.7.2 |
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comment:28 Changed 12 years ago by
Status: | positive_review → needs_work |
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Work issues: | → rebase to #11287 |
This needs to be rebased to #11287.
comment:29 follow-up: 32 Changed 12 years ago by
After applying the patch at #11287, these still apply for me, although one does have fuzz. Is the fuzz an issue or are patches actually being rejected?
comment:30 Changed 12 years ago by
Status: | needs_work → needs_info |
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<Bump>
Jeroen, could you please elaborate why you think that it should be rebased?
comment:31 Changed 12 years ago by
(If all else fails, we can wait until 4.7.2.alpha0 and rebase it with respect to that.)
comment:32 follow-up: 33 Changed 12 years ago by
Replying to jhpalmieri:
After applying the patch at #11287, these still apply for me, although one does have fuzz. Is the fuzz an issue or are patches actually being rejected?
My personal opinion on applying patches with fuzz is that I allow patches with fuzz 1 but not with fuzz 2. I have seen at least two cases where a "fuzz 2" patch was actually wrongly merged (I don't remember which tickets).
comment:33 Changed 12 years ago by
Replying to jdemeyer:
My personal opinion on applying patches with fuzz is that I allow patches with fuzz 1 but not with fuzz 2. I have seen at least two cases where a "fuzz 2" patch was actually wrongly merged (I don't remember which tickets).
OK. Then I'll take care of it.
comment:34 Changed 12 years ago by
By the way: When I tried to import the patch from #11287 on top of sage-4.7.rc2, application to doc/en/reference/mist.rst failed. But if I understood correctly, the problem with the patch here is somewhere else, right? And moreover, I should probably get a more recent Sage version...
comment:35 follow-up: 36 Changed 12 years ago by
That's odd!
I applied the patches from #11251, then #11287. Then I had fuzz 2 for one of the patches from #9976 (but they are already merged in 4.7.1.alpha0), and then the patches from here applied cleanly and without fuzz.
So, it seems that I should get the latest rc or alpha version of sage, and try again.
comment:36 Changed 12 years ago by
Replying to SimonKing: Yes, sage-4.7.rc2 is in fact quite old, so please try sage-4.7.1.rc1 + #11287 (or wait until sage-4.7.2.alpha0 is released and rebase to that).
Changed 12 years ago by
Attachment: | trac11298_singular_standard_options.rebased.patch added |
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Introspection for sage.misc.decorators.sage_wraps, applied for singular_standard_options. Put decorators into references. Rebased against #11287
comment:37 Changed 12 years ago by
Dependencies: | #9976 → #9976, #11287 |
---|---|
Description: | modified (diff) |
Status: | needs_info → needs_review |
I've built sage-4.7.1.rc1 and rebased the patch.
Apply trac11298_introspection_and_edit.patch attachment:trac11298_singular_standard_options.rebased.patch attachment:trac_11298-ref.patch
comment:38 Changed 12 years ago by
Status: | needs_review → positive_review |
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The change of the patch concerns doc/en/misc.rst, and the reason for the change was the fact that the context of the inserted line has changed. In particular, the change in the patch has not changed code or doctests. Therefore I believe that it should be reverted to a positive review.
Apply trac11298_introspection_and_edit.patch trac11298_singular_standard_options.rebased.patch trac_11298-ref.patch
comment:39 Changed 12 years ago by
I believe that it should be reverted to a positive review.
I agree. If it's a simple rebase, no new review should be needed. Thanks for taking care of this.
comment:40 Changed 12 years ago by
Merged in: | → sage-4.7.2.alpha1 |
---|---|
Resolution: | → fixed |
Status: | positive_review → closed |
Work issues: | rebase to #11287 |
For the patchbot:
Depends on #9976