#12415 closed enhancement (fixed)
Update doctesting framework
Reported by:  robertwb  Owned by:  jdemeyer 

Priority:  major  Milestone:  sage5.9 
Component:  doctest framework  Keywords:  
Cc:  kini, ohanar, jhpalmieri  Merged in:  sage5.9.beta0 
Authors:  David Roe, Robert Bradshaw, Jeroen Demeyer  Reviewers:  Jeroen Demeyer, David Roe 
Report Upstream:  N/A  Work issues:  
Branch:  Commit:  
Dependencies:  #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, #14254, #14242, #14253  Stopgaps: 
Description (last modified by )
There are several improvements that would be good to make, including but not limited to:
 Forking rather than starting up a new Sage each time.
 Customizable comparison rather than mutating doctests into new doctests (e.g. followup to #10952).
 Eliminate need to write temporary files for every doctested file.
 Constant headaches caused by the difference in doctesting library vs. nonlibrary files.
 The ability to drop into a debugger if a doctest raises an exception.
Robert's code is at
http://code.google.com/p/sagemathtimer/
Apply 12415_framework.patch, 12415_doctest_fixes.patch, 12415_doc.patch, 12415_review.patch, 12415_test.patch, 12415_review_review.patch, 12415_review3.patch, 12415_manifest.patch, 12415_rebase_58.patch
Apply 12415_script.patch and 12415_script_review.patch to the scripts repo
Apply 12415_spkg_bin_sage.patch to the root repo
For followup or other doctestrelated tickets see #11337.
Attachments (13)
Change History (326)
comment:1 Changed 8 years ago by
 Description modified (diff)
comment:2 Changed 8 years ago by
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comment:3 Changed 8 years ago by
 Description modified (diff)
comment:4 Changed 8 years ago by
 Description modified (diff)
comment:5 Changed 8 years ago by
 Description modified (diff)
comment:6 Changed 8 years ago by
 Dependencies set to #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384
comment:7 Changed 8 years ago by
 Dependencies changed from #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384 to #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384
comment:8 Changed 8 years ago by
 Cc kini added
comment:9 Changed 8 years ago by
12415_2.patch seems to contain a lot of tempfile changes, could you split out the doctest changes into a separate patch (or are these affecting doctests?)
comment:10 Changed 8 years ago by
 Cc ohanar added
comment:11 Changed 8 years ago by
apparently even I forget my trac username is not what it should be
comment:12 Changed 8 years ago by
 Dependencies changed from #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384 to #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384
comment:13 Changed 8 years ago by
 Dependencies changed from #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384 to #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384
comment:14 Changed 8 years ago by
 Dependencies changed from #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384
comment:15 Changed 8 years ago by
I've moved the patches dealing with temporary files to #13147.
comment:16 Changed 8 years ago by
 Cc jhpalmieri added
comment:17 Changed 8 years ago by
 Description modified (diff)
comment:18 Changed 8 years ago by
 Description modified (diff)
comment:19 Changed 8 years ago by
 Status changed from new to needs_review
Ready for review!
There are still a few known issues:
 valgrinding under sage t doesn't work. I haven't used valgrind much and don't know how to resolve this.
 The fix at #13147 probably needs work: I'm getting a failure in
sage.rings.polynomial.multi_polynomial_libsingular
to do with garbage collection. I'm working on it.  I'm in the process of updating the developer guide.
But I wanted to get some other people involved in reviewing.
comment:20 Changed 8 years ago by
This may be a silly question, but how do I use the new framework? Don't we need changes to the scripts repo, too? (If I just run sage t FILES
, I don't see the various messages, like Doctesting ...
, that should be printed by run_doctests
are not printed, so sage t
is not yet using the new framework.)
One of the patches also didn't apply cleanly to 5.1.beta5:
hg qimport P ~/Downloads/12415_stderr.patch adding 12415_stderr.patch to series file applying 12415_stderr.patch patching file sage/lfunctions/lcalc.py Hunk #1 FAILED at 226 1 out of 2 hunks FAILED  saving rejects to file sage/lfunctions/lcalc.py.rej patch failed, unable to continue (try v) patch failed, rejects left in working dir errors during apply, please fix and refresh 12415_stderr.patch
comment:21 Changed 8 years ago by
comment:22 Changed 8 years ago by
 Description modified (diff)
comment:23 Changed 8 years ago by
The description is updated: let me know if you have any more problems. I think you need to apply 12415_stderr_vs_51b5.patch instead of 12415_stderr.patch.
comment:24 Changed 8 years ago by
Regarding 12415_spkg_bin_sage.patch, the file in question should be part of the root repo.
comment:25 Changed 8 years ago by
One regression: with the old setup, running sage tp FILES
(with no argument for tp
) would choose the number of threads automatically. With the new setup, this command gives an error, because FILES
is not an integer. Therefore I think that, for example, make ptestlong
will fail. (The file sageruntests says that the default value for nthreads is 1, but I don't think optparse is dealing with the missing argument properly here. Also, passing the argument 0 causes doctests to never happen: maybe it's using 0 threads instead of minimum(8, cpu_count())
.
comment:26 Changed 8 years ago by
I would suggest the following two changes: for the scripts repo:

sageruntests
diff git a/sageruntests b/sageruntests
a b import optparse, os, sys 5 5 if __name__ == "__main__": 6 6 parser = optparse.OptionParser() 7 7 8 parser.add_option("p", "nthreads", type= int, default=1, metavar="N", help="tests in parallel using N threads with 0 interpreted as minimum(8, cpu_count())")8 parser.add_option("p", "nthreads", type="string", default=1, metavar="N", help="tests in parallel using N threads with 0 interpreted as minimum(8, cpu_count())") 9 9 parser.add_option("serial", action="store_true", default=False, help="run tests in a single process in series") 10 10 parser.add_option("timeout", type=int, default=1, help="timeout (in seconds) for doctesting one file") 11 11 parser.add_option("a", "all", action="store_true", default=False, help="test all files in the Sage library") … … if __name__ == "__main__": 49 49 parser.add_option("stats_path", "statspath", default=os.path.join(os.path.expanduser("~/.sage/timings2.json")), \ 50 50 help="path to a json dictionary for the latest run storing a timing for each file") 51 51 52 options, args = parser.parse_args() 53 try: 54 options.nthreads = int(options.nthreads) 55 except ValueError: 56 args.insert(0, options.nthreads.strip()) 57 options.nthreads = 0 58 59 if options.nthreads == 0: 60 try: 61 options.nthreads = int(os.environ['SAGE_NUM_THREADS_PARALLEL']) 62 except KeyError: 63 options.nthreads = 1 64 52 65 from sage.doctest.control import DocTestController 53 DC = DocTestController( *parser.parse_args())66 DC = DocTestController(options, args) 54 67 err = DC.run() 55 68 sys.exit(err)
and for the Sage library:

sage/doctest/control.py
diff git a/sage/doctest/control.py b/sage/doctest/control.py
a b class DocTestController(SageObject): 433 433 else: 434 434 nother += 1 435 435 if nfiles + ndbsources + nother: 436 self.log("Doctesting %s."%(", ".join((["%s file%s"%(nfiles, "s" if nfiles > 1 else "")] if nfiles else []) + 437 (["%s other sources"%nother] if nother else [])))) 436 self.log("Doctesting %s"%(", ".join((["%s file%s"%(nfiles, "s" if nfiles > 1 else "")] if nfiles else []) + 437 (["%s other sources"%nother] if nother else []))) 438 + " using %s threads."%self.options.nthreads if self.options.nthreads > 1 else ".") 438 439 self.reporter = DocTestReporter(self) 439 440 self.dispatcher = DocTestDispatcher(self) 440 441 try:
Or something like that. I guess you should also print the number of threads when you print "Doctesting entire Sage library.", etc.
comment:27 Changed 8 years ago by
I've updated the option parsing to allow p to take no options (though I used a callback so that the p doesn't have to be last). I changed 12415_spkg_bin_sage.patch to be an actual patch against the root repository. I also made a small change to the debug functionality (printing the doctest that failed before dropping into the debugger).
Since I'm modifying four repositories, I'll just update the patches rather than creating lots of referee patches (unless the referee objects!).
comment:28 Changed 8 years ago by
 Description modified (diff)
comment:29 Changed 8 years ago by
sage/parallel/decorate.py
: Use
Unhandled SIG...
(on systems, this would give a SIGBUS: Bus Error instead)
comment:30 Changed 8 years ago by
Please explain why you're adding nodoctest
to some of the files in doc/
?
comment:31 Changed 8 years ago by
Are all the options in sageruntests
actually implemented? (it seems some of them are meant for #12720, these should not be added here)
comment:32 Changed 8 years ago by
I guess you're no longer using the scripts sagetest
, sageptest
, sagedoctest
, sagemaketest
, perhaps sagetestnew
and sagetestimport
. Remove these.
comment:33 followup: ↓ 34 Changed 8 years ago by
Why does the doctesting framework need to be imported from sage.all
?
comment:34 in reply to: ↑ 33 Changed 8 years ago by
Replying to jdemeyer:
Why does the doctesting framework need to be imported from
sage.all
?
I don't think it needs to be, but it makes it easy to test (and debug) doctests from within Sage:
sage: run_doctests(sage.rings.integer) ...
comment:35 Changed 8 years ago by
You have two instances of
except:
in the new code.
The one for os.kill()
should just catch OSError
, for the other one replace
except KeyboardInterrupt: pass except:
by
except Exception:
comment:36 Changed 8 years ago by
Replace
import multiprocessing options.nthreads = os.getenv('SAGE_NUM_THREADS_PARALLEL',min(8, multiprocessing.cpu_count()))
by
options.nthreads = int(os.getenv('SAGE_NUM_THREADS_PARALLEL', 1))
(don't reinvent the sagenumthreads.py
wheel)
comment:37 Changed 8 years ago by
 Status changed from needs_review to needs_work
comment:38 followup: ↓ 42 Changed 8 years ago by
 Reviewers set to Jeroen Demeyer
Planning to make a reviewer patch, so hang on...
comment:39 Changed 8 years ago by
comment:40 Changed 8 years ago by
This actually fails on the very first thing I tried (after applying all patches and doing sage b
):
jdemeyer@sage:/release/sage5.1.beta5doctest$ ./sage t devel/sage/sage/rings/padics/ argv ['/release/sage5.1.beta5doctest/local/bin/sageruntests', 'devel/sage/sage/rings/padics/'] Traceback (most recent call last): File "/release/sage5.1.beta5doctest/local/bin/sageruntests", line 68, in <module> DC = DocTestController(*parser.parse_args()) File "/release/sage5.1.beta5doctest/local/lib/python2.7/sitepackages/sage/doctest/control.py", line 116, in __init__ if options.nthreads == 0: AttributeError: Values instance has no attribute 'nthreads'
Am I doing something wrong?
comment:41 Changed 8 years ago by
Building from scratch and doing make ptest
gives:
argv ['/release/merger/sage5.1.beta512415/local/bin/sageruntests', 'p', 'sagenb', 'devel/sage/doc/common', 'devel/sage/doc/de', 'devel/sage/doc/en', 'devel/sage/doc/fr', 'devel/sage/doc/ru', 'devel/sage/doc/tr', 'devel/sage/sage'] next_arg: sagenb Running doctests with ID 20120625125722d71deecd. Doctesting the Sage notebook. Doctesting 2067 files using 6 threads Usage: sage docbuild [OPTIONS] DOCUMENT (FORMAT  COMMAND) sageruntests: error: no such option: p ********************************************************************** File "programming", line 620, in programming Failed example: for i in range(5): Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 572, in _run compileflags, 1) File "<doctest programming[0]>", line 1 for i in range(5): ^ SyntaxError: unexpected EOF while parsing ********************************************************************** 1 items had failures: 1 of 113 in programming ***Test Failed*** 1 failures. ********************************************************************** File "programming", line 578, in programming Failed example: for i in range(5): Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 572, in _run compileflags, 1) File "<doctest programming[0]>", line 1 for i in range(5): ^ SyntaxError: unexpected EOF while parsing ********************************************************************** 1 items had failures: 1 of 113 in programming ***Test Failed*** 1 failures. ********************************************************************** File "sage.misc.sh", line 20, in sage.misc.sh.Sh.eval Failed example: sh.eval('''echo "Hello there"\nif [ $? eq 0 ]; then\necho "good"\nfi''') Expected: /... '' Got: Hello there good /release/merger/sage5.1.beta512415 '' ********************************************************************** File "interfaces", line 331, in interfaces Failed example: maxima.plot3d("[cos(x)*(3 + y*cos(x/2)), sin(x)*(3 + y*cos(x/2)),\ y*sin(x/2)]", "[x, 4, 4]", "[y, 4, 4]",\ '[plot_format, openmath]') # not tested Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 572, in _run compileflags, 1) File "<doctest interfaces[0]>", line 2 maxima.plot3d("[cos(x)*(3 + y*cos(x/2)), sin(x)*(3 + y*cos(x/2)),\ y*sin(x/2)]", "[x, 4, 4]", "[y, 4, 4]",\ ^ SyntaxError: unexpected character after line continuation character ********************************************************************** 1 items had failures: 1 of 57 in interfaces ***Test Failed*** 1 failures. ********************************************************************** 1 items had failures: 1 of 1 in sage.misc.sh.Sh.eval ***Test Failed*** 1 failures. ********************************************************************** File "sage.doctest.control", line 246, in sage.doctest.control.DocTestController.add_files Failed example: DC = DocTestController(DD, []) Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 573, in _run self.execute(example, compiled, test.globs) File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 835, in execute exec compiled in globs File "<doctest sage.doctest.control.DocTestController.add_files[2]>", line 1, in <module> DC = DocTestController(DD, []) File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/control.py", line 127, in __init__ self.logfile = open(options.logfile, 'a') IOError: [Errno 2] No such file or directory: '/release/merger/sage5.1.beta512415/home/.sage//tmp/test.log' ********************************************************************** File "sage.doctest.control", line 247, in sage.doctest.control.DocTestController.add_files Failed example: DC.add_files() Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 573, in _run self.execute(example, compiled, test.globs) File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 835, in execute exec compiled in globs File "<doctest sage.doctest.control.DocTestController.add_files[3]>", line 1, in <module> DC.add_files() NameError: name 'DC' is not defined ********************************************************************** File "sage.doctest.control", line 249, in sage.doctest.control.DocTestController.add_files Failed example: (os.path.join(os.environ['SAGE_ROOT'], 'devel', 'sage', 'sage'), True) in DC.files Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 573, in _run self.execute(example, compiled, test.globs) File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 835, in execute exec compiled in globs File "<doctest sage.doctest.control.DocTestController.add_files[4]>", line 1, in <module> (os.path.join(os.environ['SAGE_ROOT'], 'devel', 'sage', 'sage'), True) in DC.files NameError: name 'DC' is not defined ********************************************************************** File "sage.doctest.control", line 418, in sage.doctest.control.DocTestController.run_doctests Failed example: DC.run_doctests() Expected: Doctesting 1 file. sage t .../sage/rings/homset.py [... tests, ... s]  All tests passed!  Total time for all tests: ... seconds cpu time: ... seconds cumulative wall time: ... seconds Got: . sage t /release/merger/sage5.1.beta512415/devel/sage/sage/rings/homset.py [15 tests, 0.3 s]  All tests passed!  Total time for all tests: 0.8 seconds cpu time: 0.1 seconds cumulative wall time: 0.3 seconds ********************************************************************** File "interfaces", line 318, in interfaces Failed example: maxima.plot3d("[cos(x)*(3 + y*cos(x/2)), sin(x)*(3 + y*cos(x/2)),\ y*sin(x/2)]", "[x, 4, 4]", "[y, 4, 4]",\ '[plot_format, openmath]') # not tested Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 572, in _run compileflags, 1) File "<doctest interfaces[0]>", line 2 maxima.plot3d("[cos(x)*(3 + y*cos(x/2)), sin(x)*(3 + y*cos(x/2)),\ y*sin(x/2)]", "[x, 4, 4]", "[y, 4, 4]",\ ^ SyntaxError: unexpected character after line continuation character ********************************************************************** 1 items had failures: 1 of 57 in interfaces ***Test Failed*** 1 failures. ********************************************************************** File "sage.doctest.control", line 479, in sage.doctest.control.DocTestController.cleanup Failed example: DC.run() Expected: Running doctests with ID ... Doctesting 1 file. sage t .../rings/infinity.py [... tests, ... s]  All tests passed!  Total time for all tests: ... seconds cpu time: ... seconds cumulative wall time: ... seconds 0 Got: Running doctests with ID 20120625125735cf5e164b. . sage t /release/merger/sage5.1.beta512415/devel/sage/sage/rings/infinity.py [220 tests, 12.8 s]  All tests passed!  Total time for all tests: 13.8 seconds cpu time: 1.0 seconds cumulative wall time: 12.8 seconds 0 ********************************************************************** File "sage.doctest.control", line 619, in sage.doctest.control.DocTestController.run Failed example: DC.run() Expected: Running doctests with ID ... Doctesting 1 file. sage t .../sage/sets/non_negative_integers.py [... tests, ... s]  All tests passed!  Total time for all tests: ... seconds cpu time: ... seconds cumulative wall time: ... seconds 0 Got: Running doctests with ID 20120625125749f475b4d8. . sage t /release/merger/sage5.1.beta512415/devel/sage/sage/sets/non_negative_integers.py [41 tests, 0.5 s]  All tests passed!  Total time for all tests: 1.4 seconds cpu time: 0.1 seconds cumulative wall time: 0.5 seconds 0 ********************************************************************** File "sage.doctest.control", line 660, in sage.doctest.control.run_doctests Failed example: run_doctests(sage.rings.infinity) Expected: Doctesting .../sage/rings/infinity.py Running doctests with ID ... Doctesting 1 file. sage t .../sage/rings/infinity.py [... tests, ... s]  All tests passed!  Total time for all tests: ... seconds cpu time: ... seconds cumulative wall time: ... seconds Got: Doctesting /release/merger/sage5.1.beta512415/devel/sage/sage/rings/infinity.py Running doctests with ID 2012062512575038f106c7. . sage t /release/merger/sage5.1.beta512415/devel/sage/sage/rings/infinity.py [220 tests, 20.3 s]  All tests passed!  Total time for all tests: 22.3 seconds cpu time: 1.0 seconds cumulative wall time: 20.3 seconds ********************************************************************** 5 items had failures: 3 of 13 in sage.doctest.control.DocTestController.add_files 1 of 10 in sage.doctest.control.DocTestController.cleanup 1 of 6 in sage.doctest.control.DocTestController.run 1 of 7 in sage.doctest.control.DocTestController.run_doctests 1 of 1 in sage.doctest.control.run_doctests ***Test Failed*** 7 failures. ********************************************************************** File "sage.parallel.decorate", line 559, in sage.parallel.decorate.fork Failed example: g() Expected: <BLANKLINE>  Unhandled SIGSEGV: A segmentation fault occurred in Sage. This probably occurred because a *compiled* component of Sage has a bug in it and is not properly wrapped with sig_on(), sig_off(). You might want to run Sage under gdb with 'sage gdb' to debug this. Sage will now terminate.  'NO DATA' Got: /release/merger/sage5.1.beta512415/local/lib/libcsage.so(print_backtrace+0x2b)[0x2b39ebbaf66e] /release/merger/sage5.1.beta512415/local/lib/libcsage.so(sigdie+0x14)[0x2b39ebbaf69b] /release/merger/sage5.1.beta512415/local/lib/libcsage.so(sage_signal_handler+0x20b)[0x2b39ebbaf189] /lib/libpthread.so.0[0x2b39e86417d0] /lib/libc.so.6(strlen+0x30)[0x2b39e8f532f0] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyString_FromString+0x1b)[0x2b39e82e486b] /release/merger/sage5.1.beta512415/home/.sage//temp/sage.math.washington.edu/28931//spyx//_release_merger_sage_5_1_beta5_12415_home__sage_temp_sage_math_washington_edu_28931_tmp_0_spyx/_release_merger_sage_5_1_beta5_12415_home__sage_temp_sage_math_washington_edu_28931_tmp_0_spyx_0.so[0x2aaaaaab0abd] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5a63)[0x2b39e833b2a3] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0x2b39e833d312] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82c1979] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b39e82942c8] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x37bf)[0x2b39e8338fff] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82b6b09] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82c952d] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82c9acb] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82f0568] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b39e82942c8] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x1299)[0x2b39e8336ad9] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0x2b39e833d312] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5ae4)[0x2b39e833b324] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0x2b39e833d312] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x2b39e833d432] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x714e)[0x2b39e833c98e] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0x2b39e833d312] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5ae4)[0x2b39e833b324] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0x2b39e833d312] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5ae4)[0x2b39e833b324] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0x2b39e833d312] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82c1979] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b39e82942c8] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82a487f] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b39e82942c8] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82f563a] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b39e82942c8] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x37bf)[0x2b39e8338fff] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0x2b39e833d312] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82c1979] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b39e82942c8] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82a487f] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b39e82942c8] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82f523c] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82f0568] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b39e82942c8] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x1299)[0x2b39e8336ad9] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0x2b39e833d312] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82c1979] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b39e82942c8] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82a487f] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b39e82942c8] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82f523c] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0[0x2b39e82f0568] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b39e82942c8] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x1299)[0x2b39e8336ad9] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x69c5)[0x2b39e833c205] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0x2b39e833d312] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x2b39e833d432] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyRun_FileExFlags+0xc1)[0x2b39e83611b1] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0x1f9)[0x2b39e8361489] /release/merger/sage5.1.beta512415/local/lib/libpython2.7.so.1.0(Py_Main+0xb15)[0x2b39e8373e65] /lib/libc.so.6(__libc_start_main+0xf4)[0x2b39e8ef61f4] python[0x400679] <BLANKLINE>  Unhandled SIGSEGV: A segmentation fault occurred in Sage. This probably occurred because a *compiled* component of Sage has a bug in it and is not properly wrapped with sig_on(), sig_off(). You might want to run Sage under gdb with 'sage gdb' to debug this. Sage will now terminate.  'NO DATA' ********************************************************************** 1 items had failures: 1 of 17 in sage.parallel.decorate.fork ***Test Failed*** 1 failures. ********************************************************************** File "sage.tests.startup", line 6, in sage.tests.startup Failed example: if os.uname()[1] == 'sage.math.washington.edu': print float(os.popen("sage startuptime>/dev/null; sage startuptimegrep sage.all").readlines()[0].split()[1]) < 2.0 else: print True # nothing when not on sage.math Expected: True Got: False ********************************************************************** File "sage.rings.polynomial.multi_polynomial_libsingular", line 420, in sage.rings.polynomial.multi_polynomial_libsingular.MPolynomialRing_libsingular.__copy__ Failed example: len(ring_refcount_dict) == n Expected: True Got: False ********************************************************************** File "sage.rings.polynomial.plural", line 2738, in sage.rings.polynomial.plural.new_NRing Failed example: z*x Expected: x*z Got: Exception KeyError: (The ring pointer 0x2b3a04886e90,) in 'sage.libs.singular.ring.singular_ring_delete' ignored x*z ********************************************************************** File "sage.rings.polynomial.plural", line 2856, in sage.rings.polynomial.plural.SCA Failed example: E = SCA(QQ, ['x', 'y', 'z'], [0, 1], order = 'degrevlex') Expected nothing Got: Exception KeyError: (The ring pointer 0x2b3a048af1a0,) in 'sage.libs.singular.ring.singular_ring_delete' ignored ********************************************************************** File "sage.matrix.benchmark", line 11, in sage.matrix.benchmark Failed example: b.report([b.det_ZZ], 'Test', systems=['sage']) Expected: ====================================================================== Test ====================================================================== ... ====================================================================== Got: Linux sage.math.washington.edu 2.6.2428server #1 SMP Fri Feb 11 18:08:32 UTC 2011 x86_64 GNU/Linux ====================================================================== Test ====================================================================== <BLANKLINE> <BLANKLINE>  Dense integer determinant over ZZ. Given an n x n matrix A over ZZ with random entries between min and max, inclusive, compute det(A). <BLANKLINE> ********************************************************************** 2 items had failures: 1 of 8 in sage.rings.polynomial.plural.SCA 1 of 17 in sage.rings.polynomial.plural.new_NRing ***Test Failed*** 2 failures. INPUT: <BLANKLINE>  ``n``  matrix dimension (default: ``200``)  ``min``  minimal value for entries of matrix (default: ``1``)  ``max``  maximal value for entries of matrix (default: ``100``)  ``system``  either 'sage' or 'magma' (default: 'sage') <BLANKLINE> EXAMPLES:: <BLANKLINE> sage: import sage.matrix.benchmark as b sage: ts = b.det_ZZ(200) sage: tm = b.det_ZZ(200, system='magma') # optional  magma sage 1.560 ====================================================================== ********************************************************************** 1 items had failures: 1 of 16 in sage.rings.polynomial.multi_polynomial_libsingular.MPolynomialRing_libsingular.__copy__ ***Test Failed*** 1 failures. ********************************************************************** 1 items had failures: 1 of 2 in sage.tests.startup ***Test Failed*** 1 failures. ********************************************************************** File "sage.matrix.benchmark", line 38, in sage.matrix.benchmark.report Failed example: b.report([b.det_ZZ], 'Test', systems=['sage']) Expected: ====================================================================== Test ====================================================================== ... ====================================================================== Got: Linux sage.math.washington.edu 2.6.2428server #1 SMP Fri Feb 11 18:08:32 UTC 2011 x86_64 GNU/Linux ====================================================================== Test ====================================================================== <BLANKLINE> <BLANKLINE>  Dense integer determinant over ZZ. Given an n x n matrix A over ZZ with random entries between min and max, inclusive, compute det(A). <BLANKLINE> INPUT: <BLANKLINE>  ``n``  matrix dimension (default: ``200``)  ``min``  minimal value for entries of matrix (default: ``1``)  ``max``  maximal value for entries of matrix (default: ``100``)  ``system``  either 'sage' or 'magma' (default: 'sage') <BLANKLINE> EXAMPLES:: <BLANKLINE> sage: import sage.matrix.benchmark as b sage: ts = b.det_ZZ(200) sage: tm = b.det_ZZ(200, system='magma') # optional  magma sage 1.330 ====================================================================== ********************************************************************** File "sage.doctest.forker", line 925, in sage.doctest.forker.SageDocTestRunner.report_unexpected_exception Failed example: "ArithmeticError" in tb Expected: True Got: False ********************************************************************** File "sage.doctest.forker", line 1185, in sage.doctest.forker.DocTestWorker.__init__ Failed example: run_doctests(sage.rings.big_oh) # indirect doctest Expected: Doctesting .../sage/rings/big_oh.py Running doctests with ID ... Doctesting 1 file. sage t .../sage/rings/big_oh.py [... tests, ... s]  All tests passed!  Total time for all tests: ... seconds cpu time: ... seconds cumulative wall time: ... seconds Got: Doctesting /release/merger/sage5.1.beta512415/devel/sage/sage/rings/big_oh.py Running doctests with ID 20120625125929e5a039b5. . sage t /release/merger/sage5.1.beta512415/devel/sage/sage/rings/big_oh.py [17 tests, 1.4 s]  All tests passed!  Total time for all tests: 1.9 seconds cpu time: 0.4 seconds cumulative wall time: 1.4 seconds ********************************************************************** File "sage.doctest.forker", line 1211, in sage.doctest.forker.DocTestWorker.run Failed example: run_doctests(sage.symbolic.units) # indirect doctest Expected: Doctesting .../sage/symbolic/units.py Running doctests with ID ... Doctesting 1 file. sage t .../sage/symbolic/units.py [... tests, ... s]  All tests passed!  Total time for all tests: ... seconds cpu time: ... seconds cumulative wall time: ... seconds Got: Doctesting /release/merger/sage5.1.beta512415/devel/sage/sage/symbolic/units.py Running doctests with ID 20120625125931e804e534. . sage t /release/merger/sage5.1.beta512415/devel/sage/sage/symbolic/units.py [82 tests, 0.4 s]  All tests passed!  Total time for all tests: 0.7 seconds cpu time: 0.2 seconds cumulative wall time: 0.4 seconds ********************************************************************** 3 items had failures: 1 of 1 in sage.doctest.forker.DocTestWorker.__init__ 1 of 1 in sage.doctest.forker.DocTestWorker.run 1 of 18 in sage.doctest.forker.SageDocTestRunner.report_unexpected_exception ***Test Failed*** 3 failures. ********************************************************************** File "sage.tests.cmdline", line 270, in sage.tests.cmdline.test_executable Failed example: ret Expected: 0 Got: 1 ********************************************************************** File "sage.tests.cmdline", line 272, in sage.tests.cmdline.test_executable Failed example: out.find("All tests passed!") >= 0 Expected: True Got: False ********************************************************************** File "sage.tests.cmdline", line 275, in sage.tests.cmdline.test_executable Failed example: ret Expected: 0 Got: 1 ********************************************************************** File "sage.tests.cmdline", line 277, in sage.tests.cmdline.test_executable Failed example: out.find("All tests passed!") >= 0 Expected: True Got: False ********************************************************************** File "sage.tests.cmdline", line 291, in sage.tests.cmdline.test_executable Failed example: ret Expected: 128 Got: 1 ********************************************************************** File "sage.tests.cmdline", line 293, in sage.tests.cmdline.test_executable Failed example: out.find("1 items had failures:") >= 0 Expected: True Got: False ********************************************************************** 1 items had failures: 6 of 183 in sage.tests.cmdline.test_executable ***Test Failed*** 6 failures. ********************************************************************** File "sage.matrix.benchmark", line 566, in sage.matrix.benchmark.report_GF Failed example: b.report_GF(systems=['sage']) Expected: ====================================================================== Dense benchmarks over GF with prime 16411 ====================================================================== ... ====================================================================== Got: Linux sage.math.washington.edu 2.6.2428server #1 SMP Fri Feb 11 18:08:32 UTC 2011 x86_64 GNU/Linux ====================================================================== Dense benchmarks over GF with prime 16411 ====================================================================== <BLANKLINE> <BLANKLINE>  Rank over GF(p): Given a n x (n+10) matrix over GF(p) with random entries, compute the rank. <BLANKLINE> INPUT: <BLANKLINE>  ``n``  matrix dimension (default: 300)  ``p``  prime number (default: ``16411``)  ``system``  either 'magma' or 'sage' (default: 'sage') <BLANKLINE> EXAMPLES:: <BLANKLINE> sage: import sage.matrix.benchmark as b sage: ts = b.rank_GF(1000) sage: tm = b.rank_GF(1000, system='magma') # optional  magma sage 0.160  Rank over GF(p): Given a (n + 10) x n matrix over GF(p) with random entries, compute the rank. <BLANKLINE> INPUT: <BLANKLINE>  ``n``  matrix dimension (default: 300)  ``p``  prime number (default: ``16411``)  ``system``  either 'magma' or 'sage' (default: 'sage') <BLANKLINE> EXAMPLES:: <BLANKLINE> sage: import sage.matrix.benchmark as b sage: ts = b.rank2_GF(500) sage: tm = b.rank2_GF(500, system='magma') # optional  magma sage 0.170  Given a n+1 x n matrix over GF(p) with random entries, compute the nullspace. <BLANKLINE> INPUT: <BLANKLINE>  ``n``  matrix dimension (default: 300)  ``p``  prime number (default: ``16411``)  ``system``  either 'magma' or 'sage' (default: 'sage') <BLANKLINE> EXAMPLES:: <BLANKLINE> sage: import sage.matrix.benchmark as b sage: ts = b.nullspace_GF(300) sage: tm = b.nullspace_GF(300, system='magma') # optional  magma sage 0.820  Given a n x n matrix over GF with random entries, compute the charpoly. <BLANKLINE> INPUT: <BLANKLINE>  ``n``  matrix dimension (default: 100)  ``p``  prime number (default: ``16411``)  ``system``  either 'magma' or 'sage' (default: 'sage') <BLANKLINE> EXAMPLES:: <BLANKLINE> sage: import sage.matrix.benchmark as b sage: ts = b.charpoly_GF(100) sage: tm = b.charpoly_GF(100, system='magma') # optional  magma sage 0.060  Given an n x n matrix A over GF(p) with random entries, compute A * (A+1). <BLANKLINE> INPUT: <BLANKLINE>  ``n``  matrix dimension (default: 100)  ``p``  prime number (default: ``16411``)  ``system``  either 'magma' or 'sage' (default: 'sage')  ``times``  number of experiments (default: ``3``) <BLANKLINE> EXAMPLES:: <BLANKLINE> sage: import sage.matrix.benchmark as b sage: ts = b.matrix_multiply_GF(100, p=19) sage: tm = b.matrix_multiply_GF(100, p=19, system='magma') # optional  magma sage 0.003  Dense determinant over GF(p). Given an n x n matrix A over GF with random entries compute det(A). <BLANKLINE> INPUT: <BLANKLINE>  ``n``  matrix dimension (default: 300)  ``p``  prime number (default: ``16411``)  ``system``  either 'magma' or 'sage' (default: 'sage') <BLANKLINE> EXAMPLES:: <BLANKLINE> sage: import sage.matrix.benchmark as b sage: ts = b.det_GF(1000) sage: tm = b.det_GF(1000, system='magma') # optional  magma sage 0.090 ====================================================================== ********************************************************************** 3 items had failures: 1 of 2 in sage.matrix.benchmark 1 of 2 in sage.matrix.benchmark.report 1 of 2 in sage.matrix.benchmark.report_GF ***Test Failed*** 3 failures.  Doctests interrupted: 0/2067 files tested  Total time for all tests: 181.4 seconds cpu time: 0.0 seconds cumulative wall time: 0.0 seconds Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/bin/sageruntests", line 69, in <module> err = DC.run() File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/control.py", line 645, in run self.run_doctests() File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/control.py", line 446, in run_doctests self.dispatcher.dispatch() File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 1130, in dispatch self._parallel_dispatch() File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 1072, in _parallel_dispatch w.start() File "/release/merger/sage5.1.beta512415/local/lib/python/multiprocessing/process.py", line 130, in start self._popen = Popen(self) File "/release/merger/sage5.1.beta512415/local/lib/python/multiprocessing/forking.py", line 120, in __init__ self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory
comment:42 in reply to: ↑ 38 Changed 8 years ago by
Replying to jdemeyer:
Planning to make a reviewer patch
...after you guys fix the more serious errors.
comment:43 followup: ↓ 47 Changed 8 years ago by
Some of these are due to a bug in the change I just made to p. I'm working on fixing those.
Some look like you didn't apply the patch to the sagenb repo. Did you forget, or is something else going on?
Some are due to the fact that in your tests, os.system calls are happening before the python process gets far enough, so results that were printed to the screen in the wrong order. I'm guessing this may relate to the fact that you're running on /release, since my tests on sage.math didn't show the same behavior.
I'm in the process of fixing stuff.
comment:44 Changed 8 years ago by
There's some code in the current doctesting code to output xml results, which I'm not currently duplicating. Is this used somewhere?
comment:45 Changed 8 years ago by
Currently sage t new is broken. I'm trying to figure out why.
comment:46 followup: ↓ 78 Changed 8 years ago by
Alright, I'm going to start running tests. There are still some remaining issues, but the patches are in a state where someone else might want to look at them. :)
Remaining problems:
 #13145 needs work, generating some doctest failures related to deallocating multivariate polynomials
 hg_sage seems to be broken, causing the new option to fail
 valgrinding
sage t
doesn't work; I'm not sure whether it did before  The new code doesn't support xml output
I'll see if I find more when running sage t all
.
comment:47 in reply to: ↑ 43 Changed 8 years ago by
Replying to roed:
Some are due to the fact that in your tests, os.system calls are happening before the python process gets far enough, so results that were printed to the screen in the wrong order.
Use sys.stdout.flush()
(and/or the same for stderr
) before os.system()
to overcome this. The difference is probably that my output was sent to a pipe, as opposed to directly to the terminal. In the latter case, flushing is automatic.
True, I might not have applied all patches correctly.
comment:48 followup: ↓ 49 Changed 8 years ago by
comment:49 in reply to: ↑ 48 Changed 8 years ago by
Replying to kini:
It doesn't make sense to patch the old notebook. Please work with the flask notebook instead (i.e. make this ticket depend on #11080 and preferably #13121).
I agree that it doesn't make much sense to patch the old notebook, but if this can get a positive review quickly I'd rather not wait on #11080 and #13121. The changes to the old notebook are pretty minor.
comment:50 followups: ↓ 52 ↓ 53 Changed 8 years ago by
Design question: when running tests in parallel, failed examples are printed as they arise, meaning that examples from different files are intermingled. Is this a problem that needs to be fixed?
comment:51 Changed 8 years ago by
 Status changed from needs_work to needs_review
The only tests I have failing on sage.math are sage.tests.startup
and sage.rings.polynomial.multi_polynomial_libsingular
(due to #13145).
comment:52 in reply to: ↑ 50 Changed 8 years ago by
Replying to roed:
Design question: when running tests in parallel, failed examples are printed as they arise, meaning that examples from different files are intermingled. Is this a problem that needs to be fixed?
It might not be truly a problem, but I prefer the current model where the tests for one file are grouped.
comment:53 in reply to: ↑ 50 Changed 8 years ago by
Replying to roed:
Design question: when running tests in parallel, failed examples are printed as they arise, meaning that examples from different files are intermingled. Is this a problem that needs to be fixed?
Even better might be an option to show only the first failure in each file.
comment:54 Changed 8 years ago by
I've updated the code to group results for each file, and added an option (sage t initial
) so that only the first failure is reported.
comment:55 Changed 8 years ago by
The following is cut from a make ptestlong
run:
sage t devel/sage/sage/symbolic/expression.pyx [1960 tests, 38.2 s] sage t devel/sage/sage/pl********************************************************************** File "sage.schemes.elliptic_curves.ell_rational_field", line 1468, in sage.schemes.elliptic_curves.ell_rational_field.EllipticCurve_ration al_field.simon_two_descent Failed example: E.simon_two_descent() # long time (9s on sage.math, 2011) Expected: (5, 5, [(5 : 8 : 1), (4 : 9 : 1), (3 : 11 : 1), (1 : 20 : 1), (6 : 25 : 1)]) Got: Saturation index bound = 265 WARNING: saturation at primes p > 97 will not be done; points may be unsaturated at primes between 97 and index bound Failed to saturate MW basis at primes [ ] Saturation index bound = 265 WARNING: saturation at primes p > 199 will not be done; points may be unsaturated at primes between 199 and index bound Failed to saturate MW basis at primes [ ] (5, 5, [(5 : 8 : 1), (4 : 9 : 1), (3 : 11 : 1), (1 : 20 : 1), (6 : 25 : 1)]) ********************************************************************** 1 items had failures: 1 of 38 in sage.schemes.elliptic_curves.ell_rational_field.EllipticCurve_rational_field.simon_two_descent ***Test Failed*** 1 failures. ot/plot3d/implicit_plot3d.py [57 tests, 26.9 s] sage t devel/sage/sage/modular/modsym/ambient.py [397 tests, 26.4 s]
There are 3 issues:
 The doctest failure itself.
 The fact that
sage t foo
is written instead ofsage t long foo
.
 Output flushing: note the
sage t devel/sage/sage/pl
and then later
ot/plot3d/implicit_plot3d.py [57 tests, 26.9 s]
By all means please keep working on this, it already looks very cool!
comment:56 Changed 8 years ago by
Some more doctest failures from make ptest
:
sage t devel/sage/doc/common/__init__.py [0 tests, 0.0 s] sage t devel/sage/doc/common/build_optiUsage: sage docbuild [OPTIONS] DOCUMENT (FORMAT  COMMAND) sageruntests: error: no such option: p ons.py [0 tests, 0.0 s] sage t devel/sage/doc/common/builder.py Bad exit: 2 Tests run before process failed: sage t devel/sage/doc/common/conf.py [0 tests, 0.0 s]
sage t devel/sage/doc/de/tutorial/interactive_shell.rst Error: TAB character found at line 656 [8 tests, 0.2 s] sage t devel/sage/doc/en/tutorial/interactive_shell.rst [8 tests, 0.2 s] sage t devel/sage/doc/en/bordeaux_2008/birds_other.rst [26 tests, 5.2********************************************************************** File "interfaces", line 331, in interfaces Failed example: maxima.plot3d("[cos(x)*(3 + y*cos(x/2)), sin(x)*(3 + y*cos(x/2)),\ y*sin(x/2)]", "[x, 4, 4]", "[y, 4, 4]",\ '[plot_format, openmath]') # not tested Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 590, in _run compileflags, 1) File "<doctest interfaces[0]>", line 2 maxima.plot3d("[cos(x)*(3 + y*cos(x/2)), sin(x)*(3 + y*cos(x/2)),\ y*sin(x/2)]", "[x, 4, 4]", "[y, 4, 4]",\ ^ SyntaxError: unexpected character after line continuation character ********************************************************************** 1 items had failures: 1 of 57 in interfaces ***Test Failed*** 1 failures. ********************************************************************** File "interfaces", line 318, in interfaces Failed example: maxima.plot3d("[cos(x)*(3 + y*cos(x/2)), sin(x)*(3 + y*cos(x/2)),\ y*sin(x/2)]", "[x, 4, 4]", "[y, 4, 4]",\ '[plot_format, openmath]') # not tested Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 590, in _run compileflags, 1) File "<doctest interfaces[0]>", line 2 maxima.plot3d("[cos(x)*(3 + y*cos(x/2)), sin(x)*(3 + y*cos(x/2)),\ y*sin(x/2)]", "[x, 4, 4]", "[y, 4, 4]",\ ^ SyntaxError: unexpected character after line continuation character ********************************************************************** 1 items had failures: 1 of 57 in interfaces ***Test Failed*** 1 failures. s] sage t devel/sage/doc/fr/tutorial/interactive_shell.rst [8 tests, 0.2 s]
(why is the filename simply "interfaces")
sage t devel/sage/doc/en/reference/probability.rst [0 tests, 0.0 s] sage t de********************************************************************** File "programming", line 620, in programming Failed example: for i in range(5): Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 590, in _run compileflags, 1) File "<doctest programming[0]>", line 1 for i in range(5): ^ SyntaxError: unexpected EOF while parsing ********************************************************************** 1 items had failures: 1 of 113 in programming ***Test Failed*** 1 failures.
sage t devel/sage/doc/en/reference/rings_standard.rst [0 tests, 0.0 s] sage t devel/sage/doc/en/reference/combinat/root_syste********************************************************************** File "programming", line 578, in programming Failed example: for i in range(5): Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 590, in _run compileflags, 1) File "<doctest programming[0]>", line 1 for i in range(5): ^ SyntaxError: unexpected EOF while parsing ********************************************************************** 1 items had failures: 1 of 113 in programming ***Test Failed*** 1 failures. ms.rst [0 tests, 0.0 s]
sage t devel/sage/sage/databases/odlyzko.py [0 tests, 0.0 s] sag********************************************************************** File "sage.doctest.reporting", line 93, in sage.doctest.reporting.DocTestReporter.report Failed example: DTR.report(FDS, True, 0, None, "Output so far...") Expected: sage t .../devel/sage/sage/doctest/reporting.py Timed out! Output so far... Got: sage t /release/merger/sage5.1.beta512415/devel/sage/sage/doctest/reporting.py Timed out! Tests run before process froze: Output so far... ********************************************************************** File "sage.doctest.reporting", line 102, in sage.doctest.reporting.DocTestReporter.report Failed example: DTR.report(FDS, False, 3, None, "Output before bad exit") Expected: sage t .../devel/sage/sage/doctest/reporting.py Bad exit: 3 Output before bad exit Got: sage t /release/merger/sage5.1.beta512415/devel/sage/sage/doctest/reporting.py Bad exit: 3 Tests run before process failed: Output before bad exit ********************************************************************** File "sage.doctest.reporting", line 215, in sage.doctest.reporting.DocTestReporter.finalize Failed example: DTR.report(FDS, True, 0, None, "Output so far...") Expected: sage t .../devel/sage/sage/doctest/reporting.py Timed out! Output so far... Got: sage t /release/merger/sage5.1.beta512415/devel/sage/sage/doctest/reporting.py Timed out! Tests run before process froze: Output so far... ********************************************************************** File "sage.doctest.reporting", line 219, in sage.doctest.reporting.DocTestReporter.finalize Failed example: DTR.report(FDS, False, 3, None, "Output before bad exit") Expected: sage t .../devel/sage/sage/doctest/reporting.py Bad exit: 3 Output before bad exit Got: sage t /release/merger/sage5.1.beta512415/devel/sage/sage/doctest/reporting.py Bad exit: 3 Tests run before process failed: Output before bad exit ********************************************************************** 2 items had failures: 2 of 26 in sage.doctest.reporting.DocTestReporter.finalize 2 of 23 in sage.doctest.reporting.DocTestReporter.report ***Test Failed*** 4 failures. e t devel/sage/sage/databases/sloane.py [1 tests, 0.1 s]
sage t devel/sage/sage/ext/cdefs.pxi [0 tests, 0.0 s] sage t devel/sage/sage/docte********************************************************************** File "sage.doctest.control", line 252, in sage.doctest.control.DocTestController.add_files Failed example: DC = DocTestController(DD, []) Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 591, in _run self.execute(example, compiled, test.globs) File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 873, in execute exec compiled in globs File "<doctest sage.doctest.control.DocTestController.add_files[2]>", line 1, in <module> DC = DocTestController(DD, []) File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/control.py", line 132, in __init__ print "Unable to open logfile at %s\nProceeding without logging."%(self.logfile) AttributeError: 'DocTestController' object has no attribute 'logfile' **********************************************************************
sage t devel/sage/sage/misc/profiler.py [0 tests, 0.0 s] sage t devel/sage/********************************************************************** File "sage.matrix.benchmark", line 11, in sage.matrix.benchmark Failed example: print "starting"; b.report([b.det_ZZ], 'Test', systems=['sage']) Expected: starting... ====================================================================== Test ====================================================================== ... ====================================================================== Got: Linux sage.math.washington.edu 2.6.2428server #1 SMP Fri Feb 11 18:08:32 UTC 2011 x86_64 GNU/Linux starting ====================================================================== Test ====================================================================== <BLANKLINE> <BLANKLINE>  Dense integer determinant over ZZ. Given an n x n matrix A over ZZ with random entries between min and max, inclusive, compute det(A). <BLANKLINE> INPUT: <BLANKLINE>  ``n``  matrix dimension (default: ``200``)  ``min``  minimal value for entries of matrix (default: ``1``)  ``max``  maximal value for entries of matrix (default: ``100``)  ``system``  either 'sage' or 'magma' (default: 'sage') <BLANKLINE> EXAMPLES:: <BLANKLINE> sage: import sage.matrix.benchmark as b sage: ts = b.det_ZZ(200) sage: tm = b.det_ZZ(200, system='magma') # optional  magma sage 1.370 ====================================================================== **********************************************************************
comment:57 Changed 8 years ago by
Another annoyance, compare in the output:
sage t devel/sage/sage/rings/polynomial/padics/polynomial_padic_capped_relative_dense.py
sage t /release/merger/sage5.1.beta512415/devel/sagenbmain/sagenb/interfaces/expect.py
Why a relative path in the first case but a full path in the second case? Also with a
, only absolute paths are shown. I would prefer all paths to be relative to the current directory.
comment:58 Changed 8 years ago by
jdemeyer@sage:/release/merger/sage5.1.beta512415$ ./sage tp 1000000000 devel/sage/sage/rings/padics/ Running doctests with ID 201206261158023accd40f. Doctesting 32 files using 1000000000 threads
The previous doctester would reduce the number of threads to be at most the number of files to test.
comment:59 Changed 8 years ago by
A very useful feature from the previous doctester which is missing here is that verbose
actually shows the output as the test is running. So when it gets stuck somewhere, you actually see that it gets stuck. Currently, the whole test result is simply dumped at the end.
One more featurerequest: with verbose
, show the time taken for each single test, i.e. I would like
Trying: EllipticCurve('900d1').integral_points() Expecting: [(11 : 27 : 1), (4 : 34 : 1), (4 : 18 : 1), (16 : 54 : 1)] ok [0.10s] Trying: E=EllipticCurve([879984,319138704]) Expecting nothing ok [1.92s] Trying: P1=E.point((540,1188)); P2=E.point((576,1836)) Expecting nothing ok [4.59s]
comment:60 followup: ↓ 65 Changed 8 years ago by
What does the serial
option do and how is it different from p 1
?
comment:61 Changed 8 years ago by
I would expect sage t f
not to need any filename arguments (similarly to a
), just run all the failed tests.
However:
jdemeyer@sage:/release/merger/sage5.1.beta512415$ ./sage t f Usage: sage t [options] filenames
comment:62 followup: ↓ 66 Changed 8 years ago by
Perhaps add a T
option as a synonym for timeout
?
comment:63 followups: ↓ 68 ↓ 71 Changed 8 years ago by
I'm collecting some "special cases" for doctests in http://boxen.math.washington.edu/home/jdemeyer/doctest/ (maybe these should eventually become "metadoctests").
The doctesting framework seems to hang on
jdemeyer@sage:/release/merger/sage5.1.beta512415$ ./sage t /home/jdemeyer/doctest/sigdie.py Running doctests with ID 20120626141255fbefc7c4. Doctesting 1 file.
While the following gives an error inside the doctesting framework (this also used to fail before):
jdemeyer@sage:/release/merger/sage5.1.beta512415$ ./sage t /home/jdemeyer/doctest/keyboardinterrupt.py Running doctests with ID 20120626141238b70e54c4. Doctesting 1 file. sage t /home/jdemeyer/doctest/keyboardinterrupt.py Traceback (most recent call last): File "/release/merger/sage5.1.beta512415/local/lib/python2.7/sitepackages/sage/doctest/reporting.py", line 146, in report ntests, runner = results TypeError: 'NoneType' object is not iterable  Doctests interrupted: 0/1 files tested  Total time for all tests: 1.0 seconds cpu time: 0.0 seconds cumulative wall time: 0.0 seconds
The following should report an error but doesn't:
jdemeyer@sage:/release/merger/sage5.1.beta512415$ ./sage t /home/jdemeyer/doctest/sig_on.py Running doctests with ID 2012062614140806a01dbf. Doctesting 1 file. sage t /home/jdemeyer/doctest/sig_on.py [1 tests, 1.1 s]  All tests passed!  Total time for all tests: 2.1 seconds cpu time: 0.1 seconds cumulative wall time: 1.1 seconds
comment:64 Changed 8 years ago by
I'm working on fixing these. Thanks for the feedback!
comment:65 in reply to: ↑ 60 ; followup: ↓ 80 Changed 8 years ago by
Replying to jdemeyer:
What does the
serial
option do and how is it different fromp 1
?
The p 1
has one worker: there's another thread which collates and prints answers. p 1
is the default.
comment:66 in reply to: ↑ 62 Changed 8 years ago by
Replying to jdemeyer:
Perhaps add a
T
option as a synonym fortimeout
?
Done. Are there other options that should have a short form? Maybe L
for long
? I'd like to avoid too much mixing of upper and lower case....
comment:67 Changed 8 years ago by
There doesn't seem to be an objection to diverting stderr
, so I'm going to not worry about keeping changes resulting from that decision separate (I don't want to update that patch since it requires rebuilding a lot of files).
comment:68 in reply to: ↑ 63 ; followups: ↓ 69 ↓ 74 Changed 8 years ago by
Replying to jdemeyer:
The following should report an error but doesn't:
jdemeyer@sage:/release/merger/sage5.1.beta512415$ ./sage t /home/jdemeyer/doctest/sig_on.py Running doctests with ID 2012062614140806a01dbf. Doctesting 1 file. sage t /home/jdemeyer/doctest/sig_on.py [1 tests, 1.1 s]  All tests passed!  Total time for all tests: 2.1 seconds cpu time: 0.1 seconds cumulative wall time: 1.1 seconds
If I do cython('sig_on()')
at the command line nothing happens. Is it supposed to crash Sage?
comment:69 in reply to: ↑ 68 Changed 8 years ago by
Replying to roed:
Replying to jdemeyer:
The following should report an error but doesn't:
jdemeyer@sage:/release/merger/sage5.1.beta512415$ ./sage t /home/jdemeyer/doctest/sig_on.py Running doctests with ID 2012062614140806a01dbf. Doctesting 1 file. sage t /home/jdemeyer/doctest/sig_on.py [1 tests, 1.1 s]  All tests passed!  Total time for all tests: 2.1 seconds cpu time: 0.1 seconds cumulative wall time: 1.1 secondsIf I do
cython('sig_on()')
at the command line nothing happens. Is it supposed to crash Sage?
I can even run sage commands afterward, like factor(2^1991)
. But if I hit CtlC, I get a segfault (and it screws up my terminal).
comment:70 followup: ↓ 72 Changed 8 years ago by
New version posted. sage t long a
passes all tests except the one related to #13145.
/home/jdemeyer/doctest/keyboardinterrupt.py
passes if you remove the trailing colon. I've updated the framework to recover a bit more gracefully if a doctest raises an unexpected KeyboardInterrupt?, but it behaves a bit strangely since it's difficult to distinguish between an actual interrupt (in which case the testing should terminate) and one raised by a doctest (in which case tests of other files could continue). I think the new behavior is actually fairly reasonable: try it on your file without removing the colon.
comment:71 in reply to: ↑ 63 ; followup: ↓ 73 Changed 8 years ago by
Replying to jdemeyer:
The doctesting framework seems to hang on
jdemeyer@sage:/release/merger/sage5.1.beta512415$ ./sage t /home/jdemeyer/doctest/sigdie.py Running doctests with ID 20120626141255fbefc7c4. Doctesting 1 file.
Is this behavior acceptable? Eventually the test will time out (you can try running sage t T 5 /home/jdemeyer/doctest/sigdie.py
) and the ending summary will be printed with a time out.
comment:72 in reply to: ↑ 70 ; followup: ↓ 75 Changed 8 years ago by
Replying to roed:
it's difficult to distinguish between an actual interrupt (in which case the testing should terminate) and one raised by a doctest (in which case tests of other files could continue).
A "real" interrupt would interrupt also the master process, a fake doctestinterrupt only the child process. That's an easy way to distinguish.
comment:73 in reply to: ↑ 71 ; followup: ↓ 76 Changed 8 years ago by
Replying to roed:
Replying to jdemeyer:
The doctesting framework seems to hang on
jdemeyer@sage:/release/merger/sage5.1.beta512415$ ./sage t /home/jdemeyer/doctest/sigdie.py Running doctests with ID 20120626141255fbefc7c4. Doctesting 1 file.Is this behavior acceptable?
Not really. One should get a message that Sage crashed (compare with the old doctesting framework).
comment:74 in reply to: ↑ 68 ; followup: ↓ 77 Changed 8 years ago by
Replying to roed:
If I do
cython('sig_on()')
at the command line nothing happens. Is it supposed to crash Sage?
Let me elaborate: #10030 added a check to the doctesting code which checks
sage: sig_on_count() 0
after each doctest (i.e. it appends this to every doctest), to ensure there are no unbalanced sig_on()
s. Could you add this also to your doctesting framework?
comment:75 in reply to: ↑ 72 ; followup: ↓ 79 Changed 8 years ago by
Replying to jdemeyer:
Replying to roed:
it's difficult to distinguish between an actual interrupt (in which case the testing should terminate) and one raised by a doctest (in which case tests of other files could continue).
A "real" interrupt would interrupt also the master process, a fake doctestinterrupt only the child process. That's an easy way to distinguish.
Sure, and for reporting what happened to the user this is fine. But from the child process' perspective, an unexpected KeyboardInterrupt
has been raised and it should stop testing that file. The parent process can continue the doctests though....
comment:76 in reply to: ↑ 73 Changed 8 years ago by
Replying to jdemeyer:
Replying to roed:
Replying to jdemeyer:
The doctesting framework seems to hang on
jdemeyer@sage:/release/merger/sage5.1.beta512415$ ./sage t /home/jdemeyer/doctest/sigdie.py Running doctests with ID 20120626141255fbefc7c4. Doctesting 1 file.Is this behavior acceptable?
Not really. One should get a message that Sage crashed (compare with the old doctesting framework).
Okay, I will look into it. I assume that the underlying process has terminated and I should be able to get at the exit code somehow.
comment:77 in reply to: ↑ 74 Changed 8 years ago by
Replying to jdemeyer:
Replying to roed:
If I do
cython('sig_on()')
at the command line nothing happens. Is it supposed to crash Sage?Let me elaborate: #10030 added a check to the doctesting code which checks
sage: sig_on_count() 0after each doctest (i.e. it appends this to every doctest), to ensure there are no unbalanced
sig_on()
s. Could you add this also to your doctesting framework?
This shouldn't be too hard.
comment:78 in reply to: ↑ 46 Changed 8 years ago by
Replying to roed:
Alright, I'm going to start running tests. There are still some remaining issues, but the patches are in a state where someone else might want to look at them. :)
Remaining problems:
 #13145 needs work, generating some doctest failures related to deallocating multivariate polynomials
 hg_sage seems to be broken, causing the new option to fail
 valgrinding
sage t
doesn't work; I'm not sure whether it did before The new code doesn't support xml output
I'll see if I find more when running
sage t all
.
I'm going to sleep; let me know which of these need to be fixed in order for this ticket to get a positive review. I will also keep working on the tests in /home/jdemeyer/doctest/
. And of course if you find more problems or have other feature requests, keep those coming too!
comment:79 in reply to: ↑ 75 ; followup: ↓ 83 Changed 8 years ago by
Replying to roed:
Sure, and for reporting what happened to the user this is fine. But from the child process' perspective, an unexpected
KeyboardInterrupt
has been raised and it should stop testing that file.
Okay, I see what you mean. I would propose not to specialcase KeyboardInterrupt
at all in the child process. When the parent process gets a KeyboardInterrupt
, kill all child processes (without showing their output) and exit.
(note: since the old doctesting framework didn't do this either, I don't consider this a prerequisite for positive review, but a nice feature to have.)
comment:80 in reply to: ↑ 65 ; followup: ↓ 81 Changed 8 years ago by
comment:81 in reply to: ↑ 80 ; followups: ↓ 82 ↓ 163 Changed 8 years ago by
Replying to jdemeyer:
Replying to roed:
Replying to jdemeyer:
What does the
serial
option do and how is it different fromp 1
?The
p 1
has one worker: there's another thread which collates and prints answers.p 1
is the default.I suppose you mean "process", not thread? Still, I don't see the point of
serial
.
The main point of serial
is that it allows you to debug problems in the doctesting framework without worrying about multiprocessing. :)
I'm fine making it less prominent (having it not show up in the help display for sage t
for example, and not using it for verbose
mode). But I think it should stick around since it currently exists, and it makes some kinds of bugs much easier to track down.
comment:82 in reply to: ↑ 81 ; followup: ↓ 233 Changed 8 years ago by
Replying to roed:
Replying to jdemeyer:
Replying to roed:
Replying to jdemeyer:
What does the
serial
option do and how is it different fromp 1
?The
p 1
has one worker: there's another thread which collates and prints answers.p 1
is the default.I suppose you mean "process", not thread? Still, I don't see the point of
serial
.The main point of
serial
is that it allows you to debug problems in the doctesting framework without worrying about multiprocessing. :)I'm fine making it less prominent (having it not show up in the help display for
sage t
for example, and not using it forverbose
mode). But I think it should stick around since it currently exists, and it makes some kinds of bugs much easier to track down.
I'm also using it for gdb
since it makes the tracebacks simpler, though I'm not sure that's necessary.
Do you ever use sage t
with valgrind? I'm not sure exactly what's wrong with sage t valgrind <FILENAME>
.
comment:83 in reply to: ↑ 79 Changed 8 years ago by
Replying to jdemeyer:
Replying to roed:
Sure, and for reporting what happened to the user this is fine. But from the child process' perspective, an unexpected
KeyboardInterrupt
has been raised and it should stop testing that file.Okay, I see what you mean. I would propose not to specialcase
KeyboardInterrupt
at all in the child process. When the parent process gets aKeyboardInterrupt
, kill all child processes (without showing their output) and exit.(note: since the old doctesting framework didn't do this either, I don't consider this a prerequisite for positive review, but a nice feature to have.)
I just tried changing the interrupt handling so that KeyboardInterrupt
is handled in the parent process and it doesn't work as well: there's extraneous printing happening when the doctest framework thinks it's just printing an unexpected exception, and I don't see a good way to get rid of it.
I think the current handling of KeyboardInterrupts? is fine.
comment:84 Changed 8 years ago by
I'm going to be offline until Tuesday. More feedback while I'm gone would be great. :)
comment:85 Changed 8 years ago by
As far as I understand it, this new framework should allow for the same commands (e.g., sage tp 6 long devel/sage/sage/matrix/
). In addition, though, there are new commandline options to sageruntest
, which should available through sage t ...
, right? Which of these new options should be documented in the help messages usage
and/or usage_advanced
at the top of spkg/bin/sage
? Which should be documented in the developer's guide?
comment:86 Changed 8 years ago by
I'm back, and I've been working on a patch to the developer's guide. I'll post something soon, and more comments on which options will be shown in usage.
comment:87 Changed 8 years ago by
I'm going to build and test Sage again with these patches. Stay tuned...
comment:88 Changed 8 years ago by
 Description modified (diff)
comment:89 followup: ↓ 90 Changed 8 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871
 Status changed from needs_review to needs_work
Needs to be rebased to #11871.
comment:90 in reply to: ↑ 89 Changed 8 years ago by
comment:91 Changed 8 years ago by
The change to 12415_script.patch fixes a problem with interrupting doctests on sage.math.
comment:92 Changed 8 years ago by
When doing make ptest
and make ptestlong
, all doctests are run but there is no summary at the end. The processes end with exit code 132 (which usually means an Illegal Instruction but probably not here).
The following are the last lines output by make ptest
and make ptestlong
:
sage t devel/sage/doc/en/thematic_tutorials/lie/weyl_groups.rst [44 tests, 4.6 s] sage t devel/sage/doc/fr/tutorial/tour_plotting.rst [35 tests, 9.2 s] sage t devel/sage/doc/de/tutorial/tour_plotting.rst [51 tests, 10.7 s] sage t devel/sage/doc/en/tutorial/tour_plotting.rst [51 tests, 10.9 s] sage t devel/sage/doc/ru/tutorial/tour_plotting.rst [46 tests, 10.9 s]
and
sage t long devel/sage/sage/combinat/crystals/__init__.py [0 tests, 0.0 s] sage t long devel/sage/sage/gsl/callback.pyx [0 tests, 0.0 s] sage t long devel/sage/sage/ext/python_module.pxi [0 tests, 0.0 s] sage t long devel/sage/sage/groups/perm_gps/all.py [0 tests, 0.0 s] sage t long devel/sage/doc/en/bordeaux_2008/modular_forms_and_hecke_operators.rst [0 tests, 0.0 s]
comment:93 Changed 8 years ago by
Then I get the following make ptestlong
failures:
Running doctests with ID 201207082357280d45df42. Doctesting the Sage notebook. Sorting sources by runtime so that slower doctests are run first.... Doctesting 2067 files using 6 threads. Usage: sage docbuild [OPTIONS] DOCUMENT (FORMAT  COMMAND) sageruntests: error: no such option: p sage t long devel/sage/doc/common/builder.py Bad exit: 2 ******************************************************************************** Tests run before process failed: ******************************************************************************** sage t long devel/sage/sage/tests/interrupt.pyx [80 tests, 15.0 s]
sage t long devel/sage/sage/matrix/matrix2.pyx [1980 tests, 24.9 s] ********************************************************************** File "devel/sage/sage/tests/cmdline.py", line 272, in sage.tests.cmdline.test_executable Failed example: out.find("All tests passed!") >= 0 Expected: True Got: False ********************************************************************** File "devel/sage/sage/tests/cmdline.py", line 277, in sage.tests.cmdline.test_executable Failed example: out.find("All tests passed!") >= 0 Expected: True Got: False ********************************************************************** 1 items had failures: 2 of 185 in sage.tests.cmdline.test_executable ***Test Failed*** 2 failures. sage t long devel/sage/sage/tests/cmdline.py [184 tests, 23.0 s]
********************************************************************** File "devel/sage/sage/doctest/control.py", line 263, in sage.doctest.control.DocTestController.add_files Failed example: DC = DocTestController(DD, []) Exception raised: Traceback (most recent call last): File "/release/merger/sage5.1.rc012415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 590, in _run self.execute(example, compiled, test.globs) File "/release/merger/sage5.1.rc012415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 881, in execute exec compiled in globs File "<doctest sage.doctest.control.DocTestController.add_files[2]>", line 1, in <module> DC = DocTestController(DD, []) File "/release/merger/sage5.1.rc012415/local/lib/python2.7/sitepackages/sage/doctest/control.py", line 142, in __init__ print "Unable to open logfile at %s\nProceeding without logging."%(self.logfile) AttributeError: 'DocTestController' object has no attribute 'logfile' **********************************************************************
+ errors related to #13145.
comment:94 followup: ↓ 98 Changed 8 years ago by
 Status changed from needs_work to needs_review
I thought I'd solved the sporadic problem in sage.tests.interrupt by increasing the delays in test_sig_block_outside_sig_on
: after the change I ran sage tp sagenb long devel/sage/doc/common devel/sage/doc/[az][az] devel/sage/sage
10 times with no failures (where before there had been 5 failures in interrupt.pyx
). But I just got another one. Maybe it has to do with the load on sage.math? There are more processes running now than when I ran the test earlier.
Jeroen, would you be willing to take a look at it since you wrote the tests in that file?
All the other tests pass for me, with the exception of startup.py.
comment:95 Changed 8 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195
comment:96 Changed 8 years ago by
Rebased the scripts patch to sage5.1.
comment:97 Changed 8 years ago by
The sagenb patch doesn't apply to the new notebook (#11080).
comment:98 in reply to: ↑ 94 ; followup: ↓ 99 Changed 8 years ago by
Replying to roed:
I thought I'd solved the sporadic problem in sage.tests.interrupt by increasing the delays in
test_sig_block_outside_sig_on
The tests should be designed in such a way that they work regardless of the delay.
comment:99 in reply to: ↑ 98 Changed 8 years ago by
Replying to jdemeyer:
Replying to roed:
I thought I'd solved the sporadic problem in sage.tests.interrupt by increasing the delays in
test_sig_block_outside_sig_on
The tests should be designed in such a way that they work regardless of the delay.
Agreed, but I'm at a loss for what's causing the problem, and it's difficult to debug since it's sporadic and a segfault.
comment:100 Changed 8 years ago by
I have added some changes to local/bin/.hgignore
to the scripts patch. I discovered there was a problem when I put the file sageruntests
in local/bin
without adding it using hg
. Surprisingly, hg status
didn't show sageruntests
.
comment:102 Changed 8 years ago by
 Description modified (diff)
I imported the patch: https://github.com/sagemath/sagenb/pull/84
I'll cut a sagenb 0.10.2 release with this fix in it (and put it on #13121). Jeroen, are you aware of any other tickets with bugfixtype patches to sagenb which I could merge at the same time?
comment:103 followup: ↓ 104 Changed 8 years ago by
Actually, since this doctest fix actually breaks doctests with the current doctesting framework, should I leave this patch for sagenb 0.11 or something? How close would you say this ticket is to positive review? I notice it's set to milestone 5.3, whereas I'm hoping that #13121 can get into 5.2, so maybe that is the way to go.
comment:104 in reply to: ↑ 103 Changed 8 years ago by
Replying to kini:
Actually, since this doctest fix actually breaks doctests with the current doctesting framework, should I leave this patch for sagenb 0.11 or something?
Yes please.
How close would you say this ticket is to positive review?
I think it's mostly finished, but since this is a big change, I'm certainly not merging it in sage5.2. Also, there is a good chance that various small issues will come up here.
I notice it's set to milestone 5.3, whereas I'm hoping that #13121 can get into 5.2, so maybe that is the way to go.
Yes.
comment:105 followup: ↓ 110 Changed 8 years ago by
 Status changed from needs_review to needs_work
Just one failure remaining related to this ticket:
********************************************************************** File "devel/sage/sage/doctest/control.py", line 258, in sage.doctest.control.DocTestController.add_files Failed example: DC = DocTestController(DD, []) Expected nothing Got: Unable to open logfile at /release/merger/sage5.112415/home/.sage//tmp/test.log Proceeding without logging. sage t devel/sage/sage/ext/gmp.pxi [0 tests, 0.0 s] ********************************************************************** 1 items had failures: 1 of 15 in sage.doctest.control.DocTestController.add_files ***Test Failed*** 1 failures. sage t devel/sage/sage/doctest/control.py [115 tests, 3.6 s]
But also the formatting of the above failure looks strange:
1) Why does
sage t devel/sage/sage/ext/gmp.pxi [0 tests, 0.0 s]
appear in the middle of the failure?
2) Could you format the output as
sage t devel/sage/sage/doctest/control.py ********************************************************************** [...failure...] ********************************************************************** 1 items had failures: 1 of 15 in sage.doctest.control.DocTestController.add_files ***Test Failed*** 1 failures. [115 tests, 3.6 s]
I would even shorten the last two lines to
[115 tests, 1 failed, 3.6 s]
And I would add a function like
def count_noun(number, noun): if number == 1: return "1 %s"%noun else: return "%d %ss"%(number,noun)
So you can do
print count_noun(n, 'item'), "had failures"
comment:106 followup: ↓ 109 Changed 8 years ago by
The KeyboardInterrupt
example http://boxen.math.washington.edu/home/jdemeyer/doctest/keyboardinterrupt.py still doesn't work correctly:
Running doctests with ID 20120713105302ed232e22. Doctesting 1 file. sage t /home/jdemeyer/doctest/keyboardinterrupt.py Unexpected KeyboardInterrupt raised in file ******************************************************************************** Tests run before interrupt: sage: raise KeyboardInterrupt ## line 2 ## ********************************************************************************  sage t /home/jdemeyer/doctest/keyboardinterrupt.py # Unhandled KeyboardInterrupt  Total time for all tests: 1.1 seconds cpu time: 0.0 seconds cumulative wall time: 0.0 seconds
The expected result is that the test passes. I don't mind if you don't fix this (currently, it's also broken), but I thought you should know...
comment:107 Changed 8 years ago by
Concerning the logfile error: I think you are making the mistaken assumption that $SAGE_TESTDIR
is an existing directory. But I also find it strange that a doctest writes to a logfile inside SAGE_TESTDIR
, I don't really like that.
comment:108 Changed 8 years ago by
When testing sage/tests/interrupt.pyx
verbosely, I regularly get errors of the form
[...] Trying (line 637): test_try_finally_signal() Expecting: Traceback (most recent call last): ... RuntimeError: Aborted ok [0.23s] Trying (line 100631): sig_on_count() Expecting: 0 ok [0.00s] sage t long devel/sage/sage/tests/interrupt.pyx Traceback (most recent call last): File "/release/merger/sage5.112415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 1634, in __call__ File "/release/merger/sage5.112415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 725, in run File "/release/merger/sage5.112415/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 556, in _run AttributeError: Example instance has no attribute 'options'  sage t long devel/sage/sage/tests/interrupt.pyx # AttributeError in loading  Total time for all tests: 12.7 seconds cpu time: 0.0 seconds cumulative wall time: 0.0 seconds
This looks like a bug in the doctesting framework (unless somehow the interrupt tests corrupt the doctest process?)
comment:109 in reply to: ↑ 106 Changed 8 years ago by
Replying to jdemeyer:
The
KeyboardInterrupt
example http://boxen.math.washington.edu/home/jdemeyer/doctest/keyboardinterrupt.py still doesn't work correctly:Running doctests with ID 20120713105302ed232e22. Doctesting 1 file. sage t /home/jdemeyer/doctest/keyboardinterrupt.py Unexpected KeyboardInterrupt raised in file ******************************************************************************** Tests run before interrupt: sage: raise KeyboardInterrupt ## line 2 ## ********************************************************************************  sage t /home/jdemeyer/doctest/keyboardinterrupt.py # Unhandled KeyboardInterrupt  Total time for all tests: 1.1 seconds cpu time: 0.0 seconds cumulative wall time: 0.0 secondsThe expected result is that the test passes. I don't mind if you don't fix this (currently, it's also broken), but I thought you should know...
That's because your expected output has an extra colon. If you delete the trailing colon it passes tests.
With the extra colon it's an unexpected KeyboardInterrupt
.
comment:110 in reply to: ↑ 105 Changed 8 years ago by
Replying to jdemeyer:
Just one failure remaining related to this ticket:
********************************************************************** File "devel/sage/sage/doctest/control.py", line 258, in sage.doctest.control.DocTestController.add_files Failed example: DC = DocTestController(DD, []) Expected nothing Got: Unable to open logfile at /release/merger/sage5.112415/home/.sage//tmp/test.log Proceeding without logging. sage t devel/sage/sage/ext/gmp.pxi [0 tests, 0.0 s] ********************************************************************** 1 items had failures: 1 of 15 in sage.doctest.control.DocTestController.add_files ***Test Failed*** 1 failures. sage t devel/sage/sage/doctest/control.py [115 tests, 3.6 s]But also the formatting of the above failure looks strange:
1) Why does
sage t devel/sage/sage/ext/gmp.pxi [0 tests, 0.0 s]appear in the middle of the failure?
2) Could you format the output as
sage t devel/sage/sage/doctest/control.py ********************************************************************** [...failure...] ********************************************************************** 1 items had failures: 1 of 15 in sage.doctest.control.DocTestController.add_files ***Test Failed*** 1 failures. [115 tests, 3.6 s]I would even shorten the last two lines to
[115 tests, 1 failed, 3.6 s]And I would add a function like
def count_noun(number, noun): if number == 1: return "1 %s"%noun else: return "%d %ss"%(number,noun)So you can do
print count_noun(n, 'item'), "had failures"
Cool. I will work on these.
I'm going to be mostly (or entirely) out of communication for the next few days. Hopefully I'll have some changes available on Monday.
comment:111 followup: ↓ 112 Changed 8 years ago by
From a discussion on sagecombinatdevel: would it be possible to optionally print extra information after doctesting: how many optional doctests were skipped, and perhaps how they were labeled? ("skipped 5 doctests marked "optional  bug")
comment:112 in reply to: ↑ 111 Changed 8 years ago by
Replying to jhpalmieri:
From a discussion on sagecombinatdevel: would it be possible to optionally print extra information after doctesting: how many optional doctests were skipped, and perhaps how they were labeled? ("skipped 5 doctests marked "optional  bug")
Yeah, that shouldn't be a problem. But I'd like to put a feature freeze on this ticket and open a new ticket for it: I'm already regretting adding the new debugging feature since I'm struggling with debugging its interaction with KeyboardInterrupts
.
I just opened #13278 for this.
comment:113 Changed 7 years ago by
Ping  should this still be needs_work?
comment:114 Changed 7 years ago by
There's still the interrupt.pyx
failures which need to be investigated (probably by me since I know most about interrupts).
comment:115 Changed 7 years ago by
If you could look at those it would be great. My computer is currently being repaired, but I can try to take another shot at this next week.
comment:116 Changed 7 years ago by
Alright, I've rebased this against 5.4.rc1 and made the suggested changes in #13147. There's still an intermittent failure in sage.tests.interrupt and I'm at a loss for what's causing it. Help would be appreciated.
comment:117 Changed 7 years ago by
I've put the output before segfault from a case where interrupt.pyx failed at http://pastebin.com/Yvs8Ev68 (expiring in 1 month).
comment:118 Changed 7 years ago by
 Work issues set to intermittent interrupt.pyx failure
I've moved the debug functionality that triggers on an incorrect result to #13610 since I was struggling to get the interrupt handling working correctly (IPython embedded shells intercept KeyboardInterrupts
). With this change the only work issue I'm aware of on this ticket is the intermittent failure in interrupt.pyx. Testing just interrupt.pyx doesn't trigger this failure (or at least does so rarely); run sage t sage/tests/parigp.py sage/tests/interrupt.pyx
for example.
comment:119 Changed 7 years ago by
Ok, I found another issue which I'm not going to fix tonight. The code that parses a file and generates the tests has a bug somewhere that means some files with tests are not getting tested. I need to track down the bug and add some doctests to make sure this kind of thing doesn't happen again.
comment:120 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121
 Description modified (diff)
Alright, I fixed a bunch of bugs in the parsing of files. I added two new patches since the old ones were getting big. Sorry for the huge size of this ticket: some of the changes in 12415_more_doctest_fixes.patch can be split off into new tickets, but many of them need to be made along with the switch to the new testing code.
comment:121 Changed 7 years ago by
Here's my current status on the interrupt.pyx
problem.
 It occurs only if
interrupt.pyx
is not the first file being tested (sosage t rings/big_oh.py tests/interrupt.pyx
will show it for example)  The segfault is actually caused by the test at line 694 of
interrupt.pyx
:sage: test_sig_block()
I tried looking into the signal handling code but got lost. Any ideas?
comment:122 Changed 7 years ago by
 Work issues changed from intermittent interrupt.pyx failure to interrupt.pyx failure
comment:123 Changed 7 years ago by
I can have a look at the interrupt code, but not now...
comment:124 Changed 7 years ago by
Fair enough. Do you have any idea when you might have a chance? Or any suggestions for debugging it myself?
comment:125 Changed 7 years ago by
 Description modified (diff)
comment:126 Changed 7 years ago by
I have no idea what's going on, but to follow up on David's comment: on an OS X 10.8 machine, if I run sage t rings/big_oh.py tests/interrupt.pyx
, I get an error at line 744. If I make either of the following two changes, the error goes away:

sage/tests/interrupt.pyx
diff git a/sage/tests/interrupt.pyx b/sage/tests/interrupt.pyx
a b def test_sig_block(long delay = DEFAULT_ 691 691 TESTS:: 692 692 693 693 sage: from sage.tests.interrupt import * 694 sage: test_sig_block()695 42696 694 """ 697 695 cdef volatile_int v = 0 698 696
or

sage/tests/interrupt.pyx
diff git a/sage/tests/interrupt.pyx b/sage/tests/interrupt.pyx
a b def test_signal_during_malloc(long delay 741 741 742 742 TESTS:: 743 743 744 sage: from sage.tests.interrupt import *745 sage: for i in range(4): # Several times to reduce chances of false positive746 ... test_signal_during_malloc()747 744 """ 748 745 signal_after_delay(SIGINT, delay) 749 746 try:
For the second one, I still get the error if I keep line 744,
sage: from sage.tests.interrupt import *
but remove the actual doctest. Does this have any significance for anyone?
comment:127 Changed 7 years ago by
The problem seems to be caused by
sage: test_sig_block() 42
but it only shows up if enough time is taken up by later tests. So you can delete
sage: from sage.tests.interrupt import * sage: for i in range(4): # Several times to reduce chances of false positive ... test_signal_during_malloc()
and add something else, and you still get the error.
comment:128 Changed 7 years ago by
By commenting out most of the tests in that file, I can get the following error message:
Fatal Python error: GC object already tracked
I still get a SIGABRT, but now the bad exit code is 6 rather than 11.
comment:129 Changed 7 years ago by
Alright. I have a minimal example that doesn't rely on the doctesting framework. Of course, I still don't know how to resolve the issue, but at least it should be easier to work on. See #13748.
comment:130 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121,#13748
comment:131 followup: ↓ 132 Changed 7 years ago by
If the issue isn't related to the new doctesting framework, but is a preexisting condition revealed by it, then it shouldn't be a dependency, but a separate issue. If that was the only issue with this ticket, then this ticket could be merged, right?
comment:132 in reply to: ↑ 131 Changed 7 years ago by
Replying to jhpalmieri:
If the issue isn't related to the new doctesting framework, but is a preexisting condition revealed by it, then it shouldn't be a dependency, but a separate issue. If that was the only issue with this ticket, then this ticket could be merged, right?
I have no problem with that interpretation. But in some sense it is related to the new doctesting framework since we weren't using Python's multiprocessing module before.
So, does anyone want to give this ticket a positive review?
comment:133 Changed 7 years ago by
 Description modified (diff)
comment:134 Changed 7 years ago by
Rebased and merged the two doctest patches.
comment:135 Changed 7 years ago by
 Description modified (diff)
comment:136 Changed 7 years ago by
Merged the two framework patches, removed the change to sage/tests/interrupt.pyx
comment:137 Changed 7 years ago by
I still don't like the DocTestWorker.annihilate()
method which parses ps
output to figure out which processes to kill.
comment:138 followup: ↓ 145 Changed 7 years ago by
Robert wrote that code. :) I think the issue is that some doctests may spawn new processes that can survive their death. Do you have an alternate approach to suggest?
I'm very happy that you found the problem in #13748; I will try to take a look at this while I'm at the Joint meetings next week. In general I have very little time this month....
comment:139 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121,#13748 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121,#13748, #13899
 Work issues interrupt.pyx failure deleted
comment:140 Changed 7 years ago by
There are various new doctest errors, all of them look easy to fix. But also two errors in the doctest framework itself:
sage t long devel/sage/sage/doctest/sources.py ********************************************************************** File "devel/sage/sage/doctest/sources.py", line 177, in sage.doctest.sources.DocTestSource._process_doc Failed example: doctests == manual_doctests Expected: True Got: False ********************************************************************** File "devel/sage/sage/doctest/sources.py", line 655, in sage.doctest.sources.FileDocTestSource._test_enough_doctests Failed example: for path, dirs, files in itertools.chain(os.walk(sage_loc), os.walk(doc_loc)): # long time path = os.path.relpath(path) for F in files: _, ext = os.path.splitext(F) if ext in ('.py', '.pyx', '.sage', '.spyx', '.rst', '.tex'): filename = os.path.join(path, F) FDS = FileDocTestSource(filename, True, True, True, False) FDS._test_enough_doctests(verbose=False) Expected: There are 3 unexpected tests being run in .../sage/doctest/parsing.py There are 1 tests in .../sage/ext/c_lib.pyx that are not being run There are 2 tests in .../sage/server/notebook/worksheet.py that are not being run There are 5 tests in .../doc/en/tutorial/interfaces.rst that are not being run Got: There are 2 tests in devel/sage/sage/server/notebook/worksheet.py that are not being run There are 2 unexpected tests being run in devel/sage/sage/misc/cython.py There are 1 tests in devel/sage/sage/ext/c_lib.pyx that are not being run There are 3 unexpected tests being run in devel/sage/sage/doctest/parsing.py There are 5 tests in devel/sage/doc/en/tutorial/interfaces.rst that are not being run There are 1130 tests in devel/sage/doc/output/latex/en/reference/reference.tex that are not being run There are 51 tests in devel/sage/doc/output/latex/en/tutorial/SageTutorial.tex that are not being run There are 4 tests in devel/sage/doc/output/latex/en/thematic_tutorials/thematic_tutorials.tex that are not being run There are 6 tests in devel/sage/doc/output/latex/en/prep/prep_tutorials.tex that are not being run There are 2 tests in devel/sage/doc/output/latex/en/numerical_sage/numerical_sage.tex that are not being run There are 15 tests in devel/sage/doc/output/latex/en/developer/developer.tex that are not being run There are 16 tests in devel/sage/doc/output/latex/en/constructions/constructions.tex that are not being run There are 51 tests in devel/sage/doc/output/latex/ru/tutorial/SageTutorial_ru.tex that are not being run There are 51 tests in devel/sage/doc/output/latex/fr/tutorial/tutorialfr.tex that are not being run There are 51 tests in devel/sage/doc/output/latex/de/tutorial/SageTutorialde.tex that are not being run **********************************************************************
Also, the directory devel/sagenb/sagenb/data
should probably not be tested, as there are failures because of TAB characters in the MathJax rst documentation.
comment:141 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121,#13748, #13899 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899
comment:142 followup: ↓ 148 Changed 7 years ago by
Do you guys consider it a feature or a bug that
""" sage: 1e16 # relative tol 1e10 10^16 """
doesn't work? See #12815.
comment:143 followup: ↓ 146 Changed 7 years ago by
What I'm missing in this patchbomb is a highlevel overview of how everything works. To me, it looks like a large lump of code (which seems to work pretty well) which is hard to understand.
comment:144 Changed 7 years ago by
Typo:
Comparison ist just comparison of the underlying lists.
comment:145 in reply to: ↑ 138 Changed 7 years ago by
Replying to roed:
Robert wrote that code. :) I think the issue is that some doctests may spawn new processes that can survive their death. Do you have an alternate approach to suggest?
There is some commentedout code mentioning process groups, it would be a good idea to make that work.
But I'm also a bit lost on how the fork()ing actually works and how many Sage sessions are involved.
comment:146 in reply to: ↑ 143 Changed 7 years ago by
Replying to jdemeyer:
What I'm missing in this patchbomb is a highlevel overview of how everything works. To me, it looks like a large lump of code (which seems to work pretty well) which is hard to understand.
I will add somw top level documentation next week.
comment:147 Changed 7 years ago by
#13908 might also help with proper killing.
comment:148 in reply to: ↑ 142 Changed 7 years ago by
comment:149 Changed 7 years ago by
Looks like I have to depend on this for the numpy1.7 upgrade at #11334, so I am tagging along :)
comment:150 Changed 7 years ago by
It is interesting. With each new version of numpy we seem to have new instances of
Warning: divide by zero encountered in divide
appearing in doctests. This suggest that numpy sometimes mixes stderr and stdout or that they are very intent to tell you about these warnings. All the instances of this warning that are fixed in 12415_stderr_vs_51b5.patch also appears with the upgrade to numpy 1.7.0  plus some more.
comment:151 Changed 7 years ago by
 Description modified (diff)
Combined 12415_stderr_vs_51b5.patch and 12415_doctest_fixes.patch and rebased.
12415_framework.patch needs to be rebased but displayhook.py
changed substantially in #12719, so I don't know what to do.
comment:152 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155
comment:153 followup: ↓ 154 Changed 7 years ago by
Is this because of the displayhook?
File "devel/sage/sage/combinat/cluster_algebra_quiver/quiver.py", line 996, in sage.combinat.cluster_algebra_quiver.quiver.ClusterQuiver.mutation_sequence Failed example: [T.b_matrix() for T in seq] Expected: [ [ 0 1 0 0] [ 0 1 0 0] [ 0 1 1 0] [1 0 1 0] [ 1 0 1 0] [1 0 1 0] [ 0 1 0 1] [ 0 1 0 1] [ 1 1 0 1] [ 0 0 1 0], [ 0 0 1 0], [ 0 0 1 0] ] Got: [[ 0 1 0 0] [1 0 1 0] [ 0 1 0 1] [ 0 0 1 0], [ 0 1 0 0] [ 1 0 1 0] [ 0 1 0 1] [ 0 0 1 0], [ 0 1 1 0] [1 0 1 0] [ 1 1 0 1] [ 0 0 1 0]]
comment:154 in reply to: ↑ 153 Changed 7 years ago by
Replying to jdemeyer:
Is this because of the displayhook?
File "devel/sage/sage/combinat/cluster_algebra_quiver/quiver.py", line 996, in sage.combinat.cluster_algebra_quiver.quiver.ClusterQuiver.mutation_sequence Failed example: [T.b_matrix() for T in seq] Expected: [ [ 0 1 0 0] [ 0 1 0 0] [ 0 1 1 0] [1 0 1 0] [ 1 0 1 0] [1 0 1 0] [ 0 1 0 1] [ 0 1 0 1] [ 1 1 0 1] [ 0 0 1 0], [ 0 0 1 0], [ 0 0 1 0] ] Got: [[ 0 1 0 0] [1 0 1 0] [ 0 1 0 1] [ 0 0 1 0], [ 0 1 0 0] [ 1 0 1 0] [ 0 1 0 1] [ 0 0 1 0], [ 0 1 1 0] [1 0 1 0] [ 1 1 0 1] [ 0 0 1 0]]
Yeah, that's the kind of error that would occur because of displayhook. I'll take a look.
comment:155 Changed 7 years ago by
All other files (except 12415_framework.patch) have been rebased to sage5.7.beta1.
comment:156 followup: ↓ 157 Changed 7 years ago by
Great. I'm building a copy of sage5.7.beta1 now and will try to rebase 12415_framework.patch to it later today.
comment:157 in reply to: ↑ 156 Changed 7 years ago by
Replying to roed:
Great. I'm building a copy of sage5.7.beta1 now and will try to rebase 12415_framework.patch to it later today.
That would be great!
I would really like to finish this ticket. I feel that we're almost there, the main thing I would like to change is the handling of subprocesses (including but not limited to killing).
comment:158 Changed 7 years ago by
I think I've fixed the display hook problem. I just ran make ptestlong and found some errors; I'm looking into them and will report back.
I'm working on some general documentation, but some help on the annihilate
method would be useful, since I know nothing about process control groups.
comment:159 Changed 7 years ago by
There are still doctest failures in the doctest framework, see comment 140.
comment:160 Changed 7 years ago by
More doctest framework doctest failures:
sage t long devel/sage/sage/doctest/control.py ********************************************************************** File "devel/sage/sage/doctest/control.py", line 566, in sage.doctest.control.DocTestController.cleanup Failed example: DC.run() Exception raised: Traceback (most recent call last): File "/release/sage5.7.beta3doctest/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 595, in _run self.execute(example, compiled, test.globs) File "/release/sage5.7.beta3doctest/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 980, in execute exec compiled in globs File "<doctest sage.doctest.control.DocTestController.cleanup[8]>", line 1, in <module> DC.run() File "/release/sage5.7.beta3doctest/local/lib/python2.7/sitepackages/sage/doctest/control.py", line 725, in run self.test_safe_directory() File "/release/sage5.7.beta3doctest/local/lib/python2.7/sitepackages/sage/doctest/control.py", line 270, in test_safe_directory .format(os.getcwd())) RuntimeError: refusing to run doctests from the current directory '/home/jdemeyer/.sage/temp/sage.math.washington.edu/10273/dir_2B_1k4/test' since untrusted users could put files in this directory, making it unsafe to run Sage code from **********************************************************************
Then there is a bunch of
/release/sage5.7.beta3doctest/local/lib/python2.7/sitepackages/Cython/Build/Dependencies.py:229: UnicodeWarning: Unicode equal comparis on failed to convert both arguments to Unicode  interpreting them as being unequal if code[q1] == u'\\':
in between the tests, for example:
sage t long devel/sage/sage/combinat/species/empty_species.py [38 tests, 0.1 s] sage t long devel/sage/sage/combinat/sf/kfpoly.py [60 tests, 0.1 s] sage t long devel/sage/sage/combinat/words/shuffle_product.py [63 tests, 0.1 s] /release/sage5.7.beta3doctest/local/lib/python2.7/sitepackages/Cython/Build/Dependencies.py:229: UnicodeWarning: Unicode equal comparis on failed to convert both arguments to Unicode  interpreting them as being unequal if code[q1] == u'\\': sage t long devel/sage/sage/categories/algebra_modules.py [9 tests, 0.1 s] sage t long devel/sage/sage/numerical/backends/ppl_backend.pyx [167 tests, 0.1 s] sage t long devel/sagenbmain/sagenb/misc/misc.py [36 tests, 0.0 s]
comment:161 Changed 7 years ago by
Quick question: how many DocTestWorker
instances are created? Just one? Or N if we set MAKE=make jN
?
comment:162 Changed 7 years ago by
There is a lot of
if output_semaphore is not None: output_semaphore.acquire()
in the code which could be simplified assuming that output_semaphore
is never None
. Could we ensure that?
In fact, the whole block
try: if output_semaphore is not None: output_semaphore.acquire() do_something() finally: if output_semaphore is not None: output_semaphore.release()
could be simplified to
with output_semaphore: do_something()
comment:163 in reply to: ↑ 81 Changed 7 years ago by
Replying to roed:
The main point of
serial
is that it allows you to debug problems in the doctesting framework without worrying about multiprocessing. :)
I vote to completely remove the serial
option since for me the only effect is that it makes the code more complicated. Consider for example:
except KeyboardInterrupt: if result_pipe is None: # We're in serial mode raise # Otherwise, we've been started by a worker: we'll return the result in the finally block result = 0, DictAsObject(dict(err='ctlC')), "" [...] finally: if result_pipe is None: return result else: result_pipe.put(result, False)
If I want to fix KeyboardInterrupt
s in doctests, I now have to think about two code paths instead of one.
comment:164 Changed 7 years ago by
 Description modified (diff)
comment:165 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070
comment:166 Changed 7 years ago by
Any clue where this failure comes from?
sage t long devel/sagenbmain/sagenb/notebook/worksheet.py ********************************************************************** File "devel/sagenbmain/sagenb/notebook/worksheet.py", line 197, in sagenb.notebook.worksheet.Worksheet.? Failed example: sagenb.notebook.misc.notebook = nb Exception raised: Traceback (most recent call last): File "/release/sage5.7.beta3doctest/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 595, in _run self.execute(example, compiled, test.globs) File "/release/sage5.7.beta3doctest/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 980, in execute exec compiled in globs File "<doctest sagenb.notebook.worksheet.Worksheet.?[2]>", line 1, in <module> sagenb.notebook.misc.notebook = nb AttributeError: 'module' object has no attribute 'misc' **********************************************************************
comment:167 Changed 7 years ago by
Answering my own question, it seems that N DocTestWorkers
are started with make j N
.
But I don't understand the design choice of having two levels of multiprocessing: one from the master process to the DocTestWorker
and one from the DocTestWorker
to the DocTestTask
.
I surely need to think more about this, but I propose a redesign with only one level of multiprocessing, completely bypassing the DocTestWorker
class. This would give the benefits of "serial" processing while still allowing parallel doctests.
comment:168 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079
comment:169 followup: ↓ 170 Changed 7 years ago by
I would love to cooperate on this ticket, but I'm having a really hard time to understand everything. As I said before, this absolutely needs some highlevel documentation explaining the various classes involved and their interrelations (in particular, the classes in forker.py
).
comment:170 in reply to: ↑ 169 ; followup: ↓ 171 Changed 7 years ago by
Replying to jdemeyer:
I would love to cooperate on this ticket, but I'm having a really hard time to understand everything. As I said before, this absolutely needs some highlevel documentation explaining the various classes involved and their interrelations (in particular, the classes in
forker.py
).
Hi Jeroen, Sorry for the slow response time: I've had a visitor here in Calgary who's leaving this evening. I've started writing up overall documentation, and will work on it tonight.
In answer to your question about two layers of multiprocessing, the reason is to insulate the controlling process from segfaults and serious failures in the files being tested. If we come up with a design that satisfies that goal and also allows testing with multiple processes through sage t p N
I'm happy to change things. I certainly wouldn't call myself an expert on writing multiprocess code.
I'll write more this evening, and also review #14079 and #14080.
comment:171 in reply to: ↑ 170 ; followup: ↓ 172 Changed 7 years ago by
Replying to roed:
In answer to your question about two layers of multiprocessing, the reason is to insulate the controlling process from segfaults and serious failures in the files being tested. If we come up with a design that satisfies that goal and also allows testing with multiple processes through
sage t p N
I'm happy to change things.
We obviously need one level of multiprocessing to allow segmentation faults. But my idea would be to skip the first level of multiprocessing and move the code which is currently in DocTestWorker
to the toplevel process. I think that would simplify the code substantially.
comment:172 in reply to: ↑ 171 ; followup: ↓ 173 Changed 7 years ago by
Replying to jdemeyer:
Replying to roed:
In answer to your question about two layers of multiprocessing, the reason is to insulate the controlling process from segfaults and serious failures in the files being tested. If we come up with a design that satisfies that goal and also allows testing with multiple processes through
sage t p N
I'm happy to change things.We obviously need one level of multiprocessing to allow segmentation faults. But my idea would be to skip the first level of multiprocessing and move the code which is currently in
DocTestWorker
to the toplevel process. I think that would simplify the code substantially.
How would you run multiple files in parallel then?
comment:173 in reply to: ↑ 172 Changed 7 years ago by
Replying to roed:
How would you run multiple files in parallel then?
Like I said. Have one master process doing the jobs of the current master process + the current DocTestWorker
. That master process would start child processes for every file to be doctested, check for timeouts and crashes of the child processes.
And use #14079 to manage everything without busywaiting.
comment:174 followup: ↓ 175 Changed 7 years ago by
comment:175 in reply to: ↑ 174 ; followup: ↓ 176 Changed 7 years ago by
Replying to roed:
how can I be useful?
There are still some doctest failures left. I fixed a few in my reviewer patch (and #14070) but there are some I couldn't immediately fix. There is also the issue with TAB characters in devel/sagenb/sagenb/data
, ideally that directory would be skipped from doctesting.
But try not to change forker.py
too much, as I'm thinking of substantial changes there.
comment:176 in reply to: ↑ 175 Changed 7 years ago by
Replying to jdemeyer:
Replying to roed:
how can I be useful?
There are still some doctest failures left. I fixed a few in my reviewer patch (and #14070) but there are some I couldn't immediately fix. There is also the issue with TAB characters in
devel/sagenb/sagenb/data
, ideally that directory would be skipped from doctesting.But try not to change
forker.py
too much, as I'm thinking of substantial changes there.
Sounds good. I'll work on fixing doctest failures.
comment:177 followup: ↓ 180 Changed 7 years ago by
I also don't like this:
except IOError: # File doesn't exist result = 0, DictAsObject(dict(err='file')), ""
You assume that any IOError
comes from the fact that the doctested file doesn't exist. But it could also be a problem instead with the temporary file used for output (no space on /tmp
for example). Then the error message "File not found" would be very confusing. I think we need to explicitly check the existence of the doctested file and not handle IOError
specially.
comment:178 followup: ↓ 179 Changed 7 years ago by
In "normal" mode (nonverbose, nondebug, nonserial), does the DocTestTask
or DocTestRunner
ever print something to the real (unspoofed) stdout/stderr?
comment:179 in reply to: ↑ 178 Changed 7 years ago by
Replying to jdemeyer:
In "normal" mode (nonverbose, nondebug, nonserial), does the
DocTestTask
orDocTestRunner
ever print something to the real (unspoofed) stdout/stderr?
I don't think so.
comment:180 in reply to: ↑ 177 Changed 7 years ago by
Replying to jdemeyer:
I also don't like this:
except IOError: # File doesn't exist result = 0, DictAsObject(dict(err='file')), ""You assume that any
IOError
comes from the fact that the doctested file doesn't exist. But it could also be a problem instead with the temporary file used for output (no space on/tmp
for example). Then the error message "File not found" would be very confusing. I think we need to explicitly check the existence of the doctested file and not handleIOError
specially.
Fair enough.
comment:181 followups: ↓ 182 ↓ 184 Changed 7 years ago by
I think the word "output" is badly overused (there is the standard output, the file output=os.tmpfile()
, the string output
referring to the contents of the output
file and delayed_output
).
I propose to rename:
delayed_output
tomessages
output
(the file) toouttmpfile
(ortmpoutfile
?)
And am I right that delayed_output
is empty in normal mode when there are no doctest failures?
comment:182 in reply to: ↑ 181 Changed 7 years ago by
Replying to jdemeyer:
Can I replace "
delayed_output
" by "messages
" because I think the word "output" is overused (there is the standard output, the fileoutfile=os.tmpfile()
anddelayed_output
).And am I right that
delayed_output
is empty in normal mode when there are no doctest failures?
Sure, either "messages
" or "delayed_messages
" is fine. It should be empty in normal mode with no failures.
comment:183 Changed 7 years ago by
 Owner changed from mvngu to jdemeyer
Edited 181 because I noticed there is output
the file and output
the contents of the file.
comment:184 in reply to: ↑ 181 Changed 7 years ago by
Replying to jdemeyer:
I think the word "output" is badly overused (there is the standard output, the file
output=os.tmpfile()
, the stringoutput
referring to the contents of theoutput
file anddelayed_output
).I propose to rename:
delayed_output
tomessages
output
(the file) toouttmpfile
(ortmpoutfile
?)
I like outtmpfile
.
comment:185 followup: ↓ 186 Changed 7 years ago by
First version of my updated doctesting framework.
comment:186 in reply to: ↑ 185 ; followup: ↓ 187 Changed 7 years ago by
Replying to jdemeyer:
First version of my updated doctesting framework.
Some comments:
 For compatibility with Python's
doctest
module,summarize
should takeverbose
as the first argument andmsgfile
as an optional second argument.  It's
sage.ext.pselecter
rather than `sage.ext.pselect, unless you changed #14079.  Currently I get a timeout whenever I run tests on a file.
 Why did you disable the code that sets
following
in_parallel_dispatch
?
Overall, I think the changes are good ones.
comment:187 in reply to: ↑ 186 Changed 7 years ago by
Replying to roed:
 For compatibility with Python's
doctest
module,summarize
should takeverbose
as the first argument andmsgfile
as an optional second argument.
Fair enough. I never considered this compatibility, so it is quite possible that I introduced more incompatibilities.
 It's
sage.ext.pselecter
rather than `sage.ext.pselect, unless you changed #14079.
Yes, I did change #14079 but didn't realise that I hadn't uploaded the new patch. Anyway, I am looking into the problem on OS X.
 Currently I get a timeout whenever I run tests on a file.
Could be the same OSdependent problem as the one you reported in #14079.
 Why did you disable the code that sets
following
in_parallel_dispatch
?
Simply because it is work in progress, new tests are needed. My DocTestWorker
has a substantially different function from the old DocTestWorker
, so I cannot recycle the tests.
comment:188 Changed 7 years ago by
Updated patch (I haven't looked at the OS X specific issue).
comment:189 followup: ↓ 190 Changed 7 years ago by
I noticed a change in behaviour and I'm wondering whether it is intentional.
Old doctesting framework outputs like:
sage t file.py <messages> [4.1 s]
New doctesting framework outputs like:
<messages> sage t file.py [1 test, 1 failure, 1.7 s]
I dislike the last way of outputting, especially in verbose
mode, because there is no mention of what file is being tested. You see:
Running doctests with ID 20130213125539de348564. Doctesting 1 file. Trying (line 2): cython('sig_on()') Expecting nothing ok [1.61 s] ...
"line 2" of which file?...
comment:190 in reply to: ↑ 189 ; followup: ↓ 191 Changed 7 years ago by
Replying to jdemeyer:
I noticed a change in behaviour and I'm wondering whether it is intentional.
Old doctesting framework outputs like:
sage t file.py <messages> [4.1 s]New doctesting framework outputs like:
<messages> sage t file.py [1 test, 1 failure, 1.7 s]I dislike the last way of outputting, especially in
verbose
mode, because there is no mention of what file is being tested. You see:Running doctests with ID 20130213125539de348564. Doctesting 1 file. Trying (line 2): cython('sig_on()') Expecting nothing ok [1.61 s] ..."line 2" of which file?...
Adding the number of tests and number of failures was intentional (to which I assume you don't object). The change in order is an artifact of the code that delayed printing. When there are lots of processes running parallel, you can't output
sage t file.py
before starting testing, since the messages will get mixed up. I agree that the line describing which file is being tested should come at the beginning.
comment:191 in reply to: ↑ 190 ; followup: ↓ 192 Changed 7 years ago by
Replying to roed:
I agree that the line describing which file is being tested should come at the beginning.
OK, so you agree with
sage t file.py <messages> [1 test, 1 failure, 1.7 s]
I would move the part of report()
which prints the "sage t ..." header to a new function report_start()
(for example) and then correct the logic in forker.py
to call that function at the appropriate time. Does that sound good?
comment:192 in reply to: ↑ 191 Changed 7 years ago by
Replying to jdemeyer:
Replying to roed:
I agree that the line describing which file is being tested should come at the beginning.
OK, so you agree with
sage t file.py <messages> [1 test, 1 failure, 1.7 s]I would move the part of
report()
which prints the "sage t ..." header to a new functionreport_start()
(for example) and then correct the logic inforker.py
to call that function at the appropriate time. Does that sound good?
Sounds good. Presumably it will get printed to the msgfile
before all of the other messages and then actually printed to the screen in whatever way is appropriate.
comment:193 followup: ↓ 194 Changed 7 years ago by
 Description modified (diff)
 Milestone changed from sage5.7 to sage5.8
Could you please review 12415_doctest_review.patch? It contains all my reviewer changes for doctests in the Sage library (i.e. all changes not for the doctest framework).
comment:194 in reply to: ↑ 193 ; followup: ↓ 195 Changed 7 years ago by
Replying to jdemeyer:
Could you please review 12415_doctest_review.patch? It contains all my reviewer changes for doctests in the Sage library (i.e. all changes not for the doctest framework).
I'm running tests on OS X 10.6.8 with sage 5.7.beta1.
 Your changes to
sage.calculus.test_sympy
break doctests on my machine: they were correct before the change. Presumably these results are system dependent and should be changed somehow.  I get a bad exit in sage.misc.interpreter at line 132 (in
get_test_shell()
): it prints out a bunch of help text from IPython, ending with[SageTerminalApp] Bad config encountered during initialization: [SageTerminalApp] Unrecognized flag: 'all'
I'm not really sure what's happening here: perhaps it's related to the IPython upgrade?
 The same thing happens in
sage.misc.sage_extension
at line 22.  There's still an error in
sagenb.notebook.worksheet
line 196:sagenb.notebook
has no attributemisc
. I've seen this before and it should be easy to fix.  There are problems running some tests in
sage.doctest.control
that may go away with your new code. If not I have fixes for them.
How is 12415_review.patch coming along?
comment:195 in reply to: ↑ 194 ; followup: ↓ 196 Changed 7 years ago by
Replying to roed:
Replying to jdemeyer:
Could you please review 12415_doctest_review.patch? It contains all my reviewer changes for doctests in the Sage library (i.e. all changes not for the doctest framework).
I'm running tests on OS X 10.6.8 with sage 5.7.beta1.
 Your changes to
sage.calculus.test_sympy
break doctests on my machine: they were correct before the change. Presumably these results are system dependent and should be changed somehow.
The difference is between plain ASCII characters and some fancy Unicode characters for the display. Not sure what to do with this.
 I get a bad exit in sage.misc.interpreter at line 132 (in
get_test_shell()
):
Did you apply #14070?
 There's still an error in
sagenb.notebook.worksheet
line 196:sagenb.notebook
has no attributemisc
. I've seen this before and it should be easy to fix.
Good, then please fix it.
How is 12415_review.patch coming along?
I think it works well for normal testing. I still have to think about debug
and things like gdb
. It seems it will be necessary to have a serial mode for example for gdb
, so I have to put that back in. I would also like to force serial
when debug
is used, mainly to simplify the code.
But first I'm going to look at #14079 on OS X.
comment:196 in reply to: ↑ 195 ; followup: ↓ 197 Changed 7 years ago by
 Your changes to
sage.calculus.test_sympy
break doctests on my machine: they were correct before the change. Presumably these results are system dependent and should be changed somehow.The difference is between plain ASCII characters and some fancy Unicode characters for the display. Not sure what to do with this.
I fixed it by temporarily turning off unicode in pretting printing. I updated the patch with this change.
 I get a bad exit in sage.misc.interpreter at line 132 (in
get_test_shell()
):Did you apply #14070?
Nope: applying #14070 fixed the problem.
 There's still an error in
sagenb.notebook.worksheet
line 196:sagenb.notebook
has no attributemisc
. I've seen this before and it should be easy to fix.Good, then please fix it.
Okay, the easy fix I remembered is to add a line to sagenb.notebook.worksheet:
EXAMPLES: We test the constructor via an indirect doctest:: sage: nb = sagenb.notebook.notebook.Notebook(tmp_dir()+'.sagenb') + sage: import sagenb.notebook.misc sage: sagenb.notebook.misc.notebook = nb sage: W = nb.create_new_worksheet('Test with unicode ěščřžýáíéďĎ', 'admin') sage: W
I haven't made any changes to sagenb
for a long time. I assume this would require a new spkg?
How is 12415_review.patch coming along?
I think it works well for normal testing. I still have to think about
debug
and things likegdb
. It seems it will be necessary to have a serial mode for example forgdb
, so I have to put that back in. I would also like to forceserial
whendebug
is used, mainly to simplify the code.
Makes sense.
But first I'm going to look at #14079 on OS X.
Good luck.
comment:197 in reply to: ↑ 196 Changed 7 years ago by
Replying to roed:
I haven't made any changes to
sagenb
for a long time. I assume this would require a new spkg?
No, sagenb is now officially a separate project. I have sent a patch to "upstream" sagenb.
comment:198 Changed 7 years ago by
 Description modified (diff)
New major update of my code. Now adds support for debug
.
I removed SagePdb
since the motivation of the outputredirection in the Python doctesting framework seems to be doctesting Pdb
itself, not running a debugger inside the doctesting framework. For the new doctesting framework, we just need to stop spoofing before entering the debugger and start spoofing after the debugger is finished and that's all.
comment:199 Changed 7 years ago by
I fixed a few doctests errors, now the only remaining failure is
sage t long devel/sage/sage/doctest/sources.py ********************************************************************** File "devel/sage/sage/doctest/sources.py", line 653, in sage.doctest.sources.FileDocTestSource._test_enough_doctests Failed example: for path, dirs, files in itertools.chain(os.walk(sage_loc), os.walk(doc_loc)): # long time path = os.path.relpath(path) for F in files: _, ext = os.path.splitext(F) if ext in ('.py', '.pyx', '.sage', '.spyx', '.rst', '.tex'): filename = os.path.join(path, F) FDS = FileDocTestSource(filename, True, True, True, False) FDS._test_enough_doctests(verbose=False) Expected: There are 3 unexpected tests being run in .../sage/doctest/parsing.py There are 1 tests in .../sage/ext/c_lib.pyx that are not being run There are 2 tests in .../sage/server/notebook/worksheet.py that are not being run There are 5 tests in .../doc/en/tutorial/interfaces.rst that are not being run Got: doctest:229: UnicodeWarning: Unicode equal comparison failed to convert both arguments to Unicode  interpreting them as being unequal There are 2 tests in devel/sage/sage/server/notebook/worksheet.py that are not being run There are 2 unexpected tests being run in devel/sage/sage/misc/cython.py There are 9 tests in devel/sage/sage/graphs/graph_plot.py that are not being run There are 1 tests in devel/sage/sage/ext/c_lib.pyx that are not being run There are 3 unexpected tests being run in devel/sage/sage/doctest/parsing.py There are 5 tests in devel/sage/doc/en/tutorial/interfaces.rst that are not being run There are 1152 tests in devel/sage/doc/output/latex/en/reference/reference.tex that are not being run There are 51 tests in devel/sage/doc/output/latex/en/tutorial/SageTutorial.tex that are not being run There are 4 tests in devel/sage/doc/output/latex/en/thematic_tutorials/thematic_tutorials.tex that are not being run There are 6 tests in devel/sage/doc/output/latex/en/prep/prep_tutorials.tex that are not being run There are 2 tests in devel/sage/doc/output/latex/en/numerical_sage/numerical_sage.tex that are not being run There are 15 tests in devel/sage/doc/output/latex/en/developer/developer.tex that are not being run There are 16 tests in devel/sage/doc/output/latex/en/constructions/constructions.tex that are not being run There are 51 tests in devel/sage/doc/output/latex/ru/tutorial/SageTutorial_ru.tex that are not being run There are 51 tests in devel/sage/doc/output/latex/fr/tutorial/tutorialfr.tex that are not being run There are 51 tests in devel/sage/doc/output/latex/de/tutorial/SageTutorialde.tex that are not being run **********************************************************************
And there are still messages about TABs in sagenb/data
.
comment:200 followup: ↓ 201 Changed 7 years ago by
I have been thinking about the encoding warnings (and encodings in doctests in general). I think there are two options:
 either we ignore the Cython warnings and continue working with pure strings,
 or we make the doctester completely Unicodeaware.
I don't really see any middle ground. I'm inclined to go for the first option initially, but eventually migrating to the second option in a different ticket.
But I'm open to opinions on this.
comment:201 in reply to: ↑ 200 Changed 7 years ago by
Replying to jdemeyer:
I have been thinking about the encoding warnings (and encodings in doctests in general). I think there are two options:
 either we ignore the Cython warnings and continue working with pure strings,
 or we make the doctester completely Unicodeaware.
I don't really see any middle ground. I'm inclined to go for the first option initially, but eventually migrating to the second option in a different ticket.
But I'm open to opinions on this.
Sounds like a good plan to me. I prefer to avoid unicode when I can.
comment:202 Changed 7 years ago by
With these patches + the patched sagenb (https://github.com/sagemath/sagenb/pull/84), I get just one sporadic failure:
sage t long devel/sage/sage/homology/simplicial_complex.py ********************************************************************** File "devel/sage/sage/homology/simplicial_complex.py", line 2188, in sage.homology.simplicial_complex.SimplicialComplex.is_cohen_macaulay Failed example: S.is_cohen_macaulay(ncpus=3) Expected: False Got: Exception OSError: (10, 'No child processes') in <generator object __call__ at 0x646f1e0> ignored False **********************************************************************
I have not investigated, but I assume it must be some strange interaction between the DocTestWorker
processes and the cohen_macaulay
subprocesses.
Since bsd.math
has been down for a while (now it is back up), I haven't been able to look into the OS X issues.
I guess the only remaining issue is gdb
(and valgrind
...) support.
comment:203 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150
comment:204 Changed 7 years ago by
 Reviewers changed from Jeroen Demeyer to Jeroen Demeyer, David Roe
comment:205 Changed 7 years ago by
 Description modified (diff)
comment:206 Changed 7 years ago by
So is this ready for review by me?
comment:207 Changed 7 years ago by
Parallel testing still doesn't work on OS X. 1process testing (p 1
) works.
comment:208 Changed 7 years ago by
Do you know why parallel testing doesn't work?
comment:209 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158
comment:210 followup: ↓ 213 Changed 7 years ago by
What's the point of running optional tests without optional "sage" tests? Because that would badly fail with code like
sage: a = some_object() sage: a.some_standard_method() sage: a.use_mypackage() # optional: mypackage
(only the last line would be executed)
Are all doctests supposed to be written like
sage: a = some_object() sage: a.some_standard_method() sage: a = some_object() # optional: mypackage sage: a.use_mypackage() # optional: mypackage
comment:211 Changed 7 years ago by
 Description modified (diff)
comment:212 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182
comment:213 in reply to: ↑ 210 ; followup: ↓ 214 Changed 7 years ago by
Replying to jdemeyer:
What's the point of running optional tests without optional "sage" tests? Because that would badly fail with code like
sage: a = some_object() sage: a.some_standard_method() sage: a.use_mypackage() # optional: mypackage(only the last line would be executed)
Are all doctests supposed to be written like
sage: a = some_object() sage: a.some_standard_method() sage: a = some_object() # optional: mypackage sage: a.use_mypackage() # optional: mypackage
I agree that the current implementation is kinda dumb. But I could see wanting to run sage t all optional gap
and have only files with optional gap tests be run.
comment:214 in reply to: ↑ 213 ; followup: ↓ 215 Changed 7 years ago by
Replying to roed:
I agree that the current implementation is kinda dumb. But I could see wanting to run
sage t all optional gap
and have only files with optional gap tests be run.
So this is basically an option waiting for a better future implementation?
comment:215 in reply to: ↑ 214 Changed 7 years ago by
Replying to jdemeyer:
Replying to roed:
I agree that the current implementation is kinda dumb. But I could see wanting to run
sage t all optional gap
and have only files with optional gap tests be run.So this is basically an option waiting for a better future implementation?
Yeah, that's how I see it. I don't really run optional tests very often, but it seems like it could be useful to quickly run the tests that directly depend on gap when you update an spkg or something. But I'm not really attached to the particulars of the interface, so feel free to change it.
comment:216 followup: ↓ 217 Changed 7 years ago by
A question about this new framework: at #13928, it was pointed out that if you (for whatever reason) put the Sage directory into a directory whose path contains "/." (like "/home/user/.Sagestuff/sage5.8.beta0/"), then it will refuse to doctest any files in the Sage library. Will that still be true with this new setup? Basically, I'm wondering if this ticket supersedes #13928.
comment:217 in reply to: ↑ 216 Changed 7 years ago by
Replying to jhpalmieri:
A question about this new framework: at #13928, it was pointed out that if you (for whatever reason) put the Sage directory into a directory whose path contains "/." (like "/home/user/.Sagestuff/sage5.8.beta0/")
Hiding Sage from the boss?
then it will refuse to doctest any files in the Sage library. Will that still be true with this new setup?
No, see sage/doctest/control.py
, line 456.
comment:218 followup: ↓ 220 Changed 7 years ago by
Nathann has a reason for putting his entire Sage installation in a hidden directory. I can understand why we would skip testing files in directories within the Sage library that start with "." (like ".hg"), but why not just have that limitation and let the user put their Sage directory anywhere?
comment:219 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184
comment:220 in reply to: ↑ 218 ; followup: ↓ 223 Changed 7 years ago by
Replying to jhpalmieri:
Nathann has a reason for putting his entire Sage installation in a hidden directory. I can understand why we would skip testing files in directories within the Sage library that start with "." (like ".hg"), but why not just have that limitation
I believe that's precisely what we're doing, unless I am mistaken.
comment:221 Changed 7 years ago by
Sorry John, I misread your original question.
comment:222 followup: ↓ 224 Changed 7 years ago by
comment:223 in reply to: ↑ 220 Changed 7 years ago by
I can understand why we would skip testing files in directories within the Sage library that start with "." (like ".hg"), but why not just have that limitation
I believe that's precisely what we're doing, unless I am mistaken.
Sorry, but I don't get it O_o
After this patch is applied, will all files be skipped if SAGE_ROOT contains a /.
somewhere, even if it is not a /.hg
?
Nathann
comment:224 in reply to: ↑ 222 Changed 7 years ago by
comment:225 followup: ↓ 226 Changed 7 years ago by
What goes wrong with parallel testing on OS X? I've installed the patches on an OS X 10.8.2 box, and running ./sage tp devel/sage/sage/homology devel/sage/sage/parallel/
works fine, correctly detecting two cores, and completing testing faster than ./sage t ...
. Using ./sage tp 3 ...
runs even slightly faster.
comment:226 in reply to: ↑ 225 Changed 7 years ago by
Replying to jhpalmieri:
What goes wrong with parallel testing on OS X? I've installed the patches on an OS X 10.8.2 box, and running
./sage tp devel/sage/sage/homology devel/sage/sage/parallel/
works fine, correctly detecting two cores, and completing testing faster than./sage t ...
. Using./sage tp 3 ...
runs even slightly faster.
Jeroen said at #14079 that the parallel testing problem on OS X should be fixed now.
comment:227 Changed 7 years ago by
So far, OS X has not been my priority. I think it has to do with the way terminals are handled (try ./sage t ... </dev/null 2>&1  cat
for example, completely bypassing terminal I/O)
comment:228 Changed 7 years ago by
Concerning terminals, I also noted (on Linux) that piping output to less
(./sage t ...  less
) doesn't quite work properly.
comment:229 followup: ↓ 231 Changed 7 years ago by
Without applying any of the patches here, if a user modifies their configuration, say via #14188, some doctests may fail. I assume the same will be true after applying the patches here. My question: should make ptest
(etc.) run with the nodotsage
setting, while sage t ...
uses the user's configuration? Or should both use nodotsage
, or neither use it?
comment:230 Changed 7 years ago by
 Status changed from needs_work to needs_review
comment:231 in reply to: ↑ 229 Changed 7 years ago by
Replying to jhpalmieri:
Without applying any of the patches here, if a user modifies their configuration, say via #14188, some doctests may fail. I assume the same will be true after applying the patches here. My question: should
make ptest
(etc.) run with thenodotsage
setting, whilesage t ...
uses the user's configuration? Or should both usenodotsage
, or neither use it?
I would say that both should use it: I don't see why the user might need their custom configuration when doctesting.
comment:232 followup: ↓ 236 Changed 7 years ago by
I have a request/suggestion: move DOCTEST_MODE
out of plot.py and into a file in the doctest directory. Right now, importing from plot.py can be lead to circular imports, etc. Also, it never belonged in plot.py in the first place. Can we do that on this ticket, or should it be on a followup?
comment:233 in reply to: ↑ 82 Changed 7 years ago by
Replying to roed:
Do you ever use
sage t
with valgrind? I'm not sure exactly what's wrong withsage t valgrind <FILENAME>
.
It used to work and I used it at some point to deal with the nice random failures caused by the introduction of weak caches of #715. Note the optional spkg we currently propose is really old (and surely dysfunctional on most systems), but there's an update rotting at #13060. I wouldn't mind making valgrind working again a followup ticket as I'm not actively using it right now.
comment:234 Changed 7 years ago by
Concerning DOT_SAGE
: it's not as easy as you think. The problem is that the doctesting framework needs DOT_SAGE
in a few places, for example to store the timing information. So running
sage nodotsage t ...
is not an option.
Perhaps changing $IPYTHONDIR
is sufficient? That could be done within the doctesting framework.
comment:235 Changed 7 years ago by
 Description modified (diff)
comment:236 in reply to: ↑ 232 Changed 7 years ago by
Replying to jhpalmieri:
I have a request/suggestion: move
DOCTEST_MODE
out of plot.py and into a file in the doctest directory. Right now, importing from plot.py can be lead to circular imports, etc. Also, it never belonged in plot.py in the first place. Can we do that on this ticket, or should it be on a followup?
This ticket is already big enough, so I created the followup #14203.
Changed 7 years ago by
Changed 7 years ago by
comment:237 Changed 7 years ago by
 Description modified (diff)
comment:238 Changed 7 years ago by
All tests pass for me. I'm reading through 12415_review.patch.
comment:239 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054
comment:240 Changed 7 years ago by
Fixed a conflict (nothing serious) with #14054.
comment:241 Changed 7 years ago by
Still working through 12415_review.patch, but note that four functions in sage.doctest.forker don't have tests.
comment:242 Changed 7 years ago by
 Description modified (diff)
Here's a review patch which adds doctests for the four functions that were missing them and makes a few other minor changes. Other than this, I'm happy with Jeroen's changes.
comment:243 followup: ↓ 245 Changed 7 years ago by
In 12415_review_review.patch, line 693 of control.py, "sage.supp" got changed to "sage.sup". Was this intentional?
comment:244 followup: ↓ 246 Changed 7 years ago by
When I run make ptestlong
, things look fine on the screen, but I see some funny characters in ptestlong.log (this is on OS X 10.8.2):
Doctesting 2283 files using 2 threads. ^[[?1034hsage t long devel/sage/sage/misc/interpreter.py [107 tests, 12.0 s]
So far, this is the only instance of this in the file. Could it be some sort of terminal color escape sequence? I see it on one machine but not another, so maybe it was just a cosmic ray...
comment:245 in reply to: ↑ 243 Changed 7 years ago by
Replying to jhpalmieri:
In 12415_review_review.patch, line 693 of control.py, "sage.supp" got changed to "sage.sup". Was this intentional?
Nope: thanks for catching that.
comment:246 in reply to: ↑ 244 Changed 7 years ago by
Replying to jhpalmieri:
When I run
make ptestlong
, things look fine on the screen, but I see some funny characters in ptestlong.log (this is on OS X 10.8.2):Doctesting 2283 files using 2 threads. ^[[?1034hsage t long devel/sage/sage/misc/interpreter.py [107 tests, 12.0 s]So far, this is the only instance of this in the file. Could it be some sort of terminal color escape sequence?
Yes. It most likely comes from the import readline
I added in init_sage()
(this happens once, so it's normal you see it only once in ptestlong.log
). I have been fighting quite a bit with terminal I/O in this new doctester, and this is yet another manifestion of terminal issues :(
comment:247 followup: ↓ 252 Changed 7 years ago by
Could you do me a favour since I don't have access to an OS X 10.8 system:
Remove that import readline
statement and run
./sage btp N long devel/sage/sage/doctest devel/sage/sage/tests
in the following ways:
 Normal doctest run in the terminal, let it finish
 Interrupt (CTRLC) the tests somewhere in the middle of the run
 Pipe the output through
less
:./sage tp 2 ...  less
And all this both with p 1
and with p N
for some N > 1
.
comment:248 followup: ↓ 250 Changed 7 years ago by
David, I noticed that doc/en/developer/doctesting.rst
in 12415_doc.patch is full of TAB characters. Could you please replace those by 8 spaces?
I agree with 12415_review_review.patch.
Did you also look at 12415_doctest_review.patch, 12415_script_review.patch and 12415_test.patch?
comment:249 followup: ↓ 251 Changed 7 years ago by
Sorry, too fast. This is dangerous:
sage: W.start() sage: W.join() sage: while W.rmessages is not None: ....: W.read_messages() sage: len(W.messages) > 0 True
You should read the messages while the worker is running, because otherwise the pipe buffer might get full, leading to a block. So put W.join()
at the end instead of at the beginning. Apart from that, it's a useful and good test.
comment:250 in reply to: ↑ 248 ; followup: ↓ 253 Changed 7 years ago by
Replying to jdemeyer:
David, I noticed that
doc/en/developer/doctesting.rst
in 12415_doc.patch is full of TAB characters. Could you please replace those by 8 spaces?
That's ironic. I replaced them, though I left the ones you're deleting in 12415_review.patch so that it applies cleanly.
Did you also look at 12415_doctest_review.patch, 12415_script_review.patch and 12415_test.patch?
12415_doctest_review.patch and 12415_script_review.patch both look fine.
For 12415_test.patch, you never run some of the files in the test directory (sig_on.rst
and sleep_and_raise.rst
). Otherwise they look good.
Changed 7 years ago by
comment:251 in reply to: ↑ 249 Changed 7 years ago by
Replying to jdemeyer:
Sorry, too fast. This is dangerous:
sage: W.start() sage: W.join() sage: while W.rmessages is not None: ....: W.read_messages() sage: len(W.messages) > 0 TrueYou should read the messages while the worker is running, because otherwise the pipe buffer might get full, leading to a block. So put
W.join()
at the end instead of at the beginning. Apart from that, it's a useful and good test.
Done. I also updated the tests for kill
and save_result_output
to be more robust.
comment:252 in reply to: ↑ 247 Changed 7 years ago by
Replying to jdemeyer:
Could you do me a favour since I don't have access to an OS X 10.8 system:
Is this useful for me to run on OS X 10.6.8?
Remove that
import readline
statement and run./sage btp N long devel/sage/sage/doctest devel/sage/sage/testsin the following ways:
 Normal doctest run in the terminal, let it finish
 Interrupt (CTRLC) the tests somewhere in the middle of the run
 Pipe the output through
less
:./sage tp 2 ...  less
And all this both with
p 1
and withp N
for someN > 1
.
comment:253 in reply to: ↑ 250 Changed 7 years ago by
Replying to roed:
For 12415_test.patch, you never run some of the files in the test directory (
sig_on.rst
andsleep_and_raise.rst
).
Well, I found sleep_and_raise.rst
useful for manual testing, so I left it.
And sig_on.rst
will be tested in the followup #14152 (which will be an easy ticket).
comment:254 followup: ↓ 255 Changed 7 years ago by
On OS X 10.8.2.
Running with sage btp 1 ...
:
sage t long devel/sage/sage/tests/french_book/polynomes.py /Users/palmieri/Desktop/Sage_stuff/sage_builds/sage5.8.beta2/local/lib/python2.7/sitepackages/Cython/Build/Dependencies.py:229: UnicodeWarning: Unicode equal comparison failed to convert both arguments to Unicode  interpreting them as being unequal if code[q1] == u'\\': [107 tests, 2.6 s]
Running with sage btp 2 ...
— note the random (?) placement of the unicode warning:
sage t long devel/sage/sage/tests/book_stein_modform.py [239 tests, 3.3 s] /Users/palmieri/Desktop/Sage_stuff/sage_builds/sage5.8.beta2/local/lib/python2.7/sitepackages/Cython/Build/Dependencies.py:229: UnicodeWarning: Unicode equal comparison failed to convert both arguments to Unicode  interpreting them as being unequal if code[q1] == u'\\': sage t long devel/sage/sage/tests/french_book/polynomes.py [107 tests, 2.3 s]
Without the import readline
statement, I got one nonrepeatable failure with sage btp 2 ...
(probably has nothing to do with readline, but have you seen this before?):
sage t long devel/sage/sage/doctest/forker.py ********************************************************************** File "devel/sage/sage/doctest/forker.py", line 1693, in sage.doctest.forker.DocTestWorker.read_messages Failed example: while W.rmessages is not None: W.read_messages() Exception raised: Traceback (most recent call last): File "/Users/palmieri/Desktop/Sage_stuff/sage_builds/sage5.8.beta2/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 436, in _run self.execute(example, compiled, test.globs) File "/Users/palmieri/Desktop/Sage_stuff/sage_builds/sage5.8.beta2/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 792, in execute exec compiled in globs File "<doctest sage.doctest.forker.DocTestWorker.read_messages[9]>", line 2, in <module> W.read_messages() File "/Users/palmieri/Desktop/Sage_stuff/sage_builds/sage5.8.beta2/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 1703, in read_messages s = os.read(self.rmessages, 4096) OSError: [Errno 4] Interrupted system call ********************************************************************** 1 item had failures: 1 of 13 in sage.doctest.forker.DocTestWorker.read_messages [384 tests, 1 failure, 17.3 s]
With or without the import readline
statement, I see this when piping through less
, with btp 1
or btp 2
:
Installing c_lib ESC[?1034hscons: `install' is up to date.
Except for the nonrepeatable failure, I see no difference with or without import readline
.
comment:255 in reply to: ↑ 254 Changed 7 years ago by
Replying to jhpalmieri:
sage t long devel/sage/sage/doctest/forker.py ********************************************************************** File "devel/sage/sage/doctest/forker.py", line 1693, in sage.doctest.forker.DocTestWorker.read_messages Failed example: while W.rmessages is not None: W.read_messages() Exception raised: Traceback (most recent call last): File "/Users/palmieri/Desktop/Sage_stuff/sage_builds/sage5.8.beta2/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 436, in _run self.execute(example, compiled, test.globs) File "/Users/palmieri/Desktop/Sage_stuff/sage_builds/sage5.8.beta2/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 792, in execute exec compiled in globs File "<doctest sage.doctest.forker.DocTestWorker.read_messages[9]>", line 2, in <module> W.read_messages() File "/Users/palmieri/Desktop/Sage_stuff/sage_builds/sage5.8.beta2/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 1703, in read_messages s = os.read(self.rmessages, 4096) OSError: [Errno 4] Interrupted system call ********************************************************************** 1 item had failures: 1 of 13 in sage.doctest.forker.DocTestWorker.read_messages [384 tests, 1 failure, 17.3 s]
That actually looks serious, I'll have a look.
Installing c_lib ESC[?1034hscons: `install' is up to date.
That's before the doctester starts, so it's not our problem.
Except for the nonrepeatable failure, I see no difference with or without
import readline
.
Is the [[?1034h
control code gone when you remove import readline
?
comment:256 followup: ↓ 258 Changed 7 years ago by
Is the [[?1034h control code gone when you remove import readline?
No, it's there either way.
comment:257 Changed 7 years ago by
Another random failure:
sage t devel/sage/sage/doctest/forker.py ********************************************************************** File "devel/sage/sage/doctest/forker.py", line 1729, in sage.doctest.forker.DocTestWorker.save_result_output Failed example: sorted(W.result[1].keys()) Expected: ['cputime', 'err', 'failures', 'walltime'] Got: ['err'] ********************************************************************** 1 item had failures: 1 of 14 in sage.doctest.forker.DocTestWorker.save_result_output [384 tests, 1 failure, 17.4 s]
comment:258 in reply to: ↑ 256 Changed 7 years ago by
Replying to jhpalmieri:
Is the [[?1034h control code gone when you remove import readline?
No, it's there either way.
In serial and in parallel?
comment:259 Changed 7 years ago by
 Status changed from needs_review to needs_work
Changed 7 years ago by
Changed 7 years ago by
comment:260 Changed 7 years ago by
 Description modified (diff)
 Milestone changed from sage5.8 to sage5.9
 Merged two doctest patches
 Merged the patches to the documentation into 12415_doc.patch and changed version numbers to sage5.9.
 12415_test.patch: removed unused
sig_on.rst
.
comment:261 Changed 7 years ago by
 Description modified (diff)
comment:262 followup: ↓ 263 Changed 7 years ago by
John: I think both your failures are due to not resetting the SIGCHLD
signal handler, that should be fixed now.
comment:263 in reply to: ↑ 262 Changed 7 years ago by
Replying to jdemeyer:
John: I think both your failures are due to not resetting the
SIGCHLD
signal handler, that should be fixed now.
I still get the following failures:
sage t sage/doctest/forker.py ********************************************************************** File "sage/doctest/forker.py", line 1777, in sage.doctest.forker.DocTestWorker.kill Failed example: W.kill() Exception raised: Traceback (most recent call last): File "/Users/roed/sage/sage5.8.beta0/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 432, in _run self.execute(example, compiled, test.globs) File "/Users/roed/sage/sage5.8.beta0/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 788, in execute exec compiled in globs File "<doctest sage.doctest.forker.DocTestWorker.kill[14]>", line 1, in <module> W.kill() File "/Users/roed/sage/sage5.8.beta0/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 1791, in kill os.killpg(self.pid, signal.SIGHUP) OSError: [Errno 3] No such process ********************************************************************** File "sage/doctest/forker.py", line 1781, in sage.doctest.forker.DocTestWorker.kill Failed example: W.kill() # Worker dies now Exception raised: Traceback (most recent call last): File "/Users/roed/sage/sage5.8.beta0/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 432, in _run self.execute(example, compiled, test.globs) File "/Users/roed/sage/sage5.8.beta0/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 788, in execute exec compiled in globs File "<doctest sage.doctest.forker.DocTestWorker.kill[17]>", line 1, in <module> W.kill() # Worker dies now File "/Users/roed/sage/sage5.8.beta0/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 1793, in kill os.killpg(self.pid, signal.SIGKILL) OSError: [Errno 1] Operation not permitted **********************************************************************
comment:264 Changed 7 years ago by
Got it! It's trying to kill the process group, but we're not sure at this point that the worker already changed its process group.
comment:265 Changed 7 years ago by
 Status changed from needs_work to needs_review
comment:266 Changed 7 years ago by
David: thanks for your added doctests. They really did expose some bugs.
Changed 7 years ago by
comment:267 Changed 7 years ago by
Excellent! I suspect there's more trouble somewhere, but I would suggest dealing with it in followup tickets.
The changes all look fine to me, but I haven't run full doctests (and am probably not going to be able to today since I'm traveling). I'm happy giving this positive review subject to all doctests passing.
Changed 7 years ago by
Doctest changes that are needed to account for differences in the new framework
comment:268 Changed 7 years ago by
 Status changed from needs_review to positive_review
Rebased again.
I take David's comment as meaning "positive review".
Changed 7 years ago by
comment:269 Changed 7 years ago by
 Status changed from positive_review to needs_work
comment:270 followup: ↓ 271 Changed 7 years ago by
 Description modified (diff)
 Status changed from needs_work to needs_review
12415_manifest.patch needs review.
comment:271 in reply to: ↑ 270 ; followup: ↓ 272 Changed 7 years ago by
 Status changed from needs_review to positive_review
Replying to jdemeyer:
12415_manifest.patch needs review.
It looks fine to me, though I don't see why it's relevant to doctesting.
comment:272 in reply to: ↑ 271 Changed 7 years ago by
Replying to roed:
I don't see why it's relevant to doctesting.
My patch adds .rst
files (mainly because I wanted to use something else than .py
files for a change).
comment:273 followup: ↓ 274 Changed 7 years ago by
 Description modified (diff)
Further testing revealed some more subtle problems. I will simply extend the file 12415_rebase_58.patch until this ticket is ready to be merged.
comment:274 in reply to: ↑ 273 Changed 7 years ago by
Replying to jdemeyer:
Further testing revealed some more subtle problems. I will simply extend the file 12415_rebase_58.patch until this ticket is ready to be merged.
Okay. Let me know when you want me to review it.
comment:275 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054 to #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605
comment:276 followup: ↓ 281 Changed 7 years ago by
While you were developing this, did you consider using Python's DocTestFinder to extract docstrings from Python files? The current code here doesn't use object.__doc__
, perhaps the Python doctest module does. I ask because #13605 added several classes with a dynamic __doc__
.
comment:277 Changed 7 years ago by
 Dependencies changed from #13147,#13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605 to #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111
comment:278 Changed 7 years ago by
 Description modified (diff)
comment:279 Changed 7 years ago by
 Dependencies changed from #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111 to #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, 13897
comment:280 Changed 7 years ago by
 Dependencies changed from #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, 13897 to #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111
comment:281 in reply to: ↑ 276 ; followup: ↓ 282 Changed 7 years ago by
Replying to jdemeyer:
While you were developing this, did you consider using Python's DocTestFinder to extract docstrings from Python files? The current code here doesn't use
object.__doc__
, perhaps the Python doctest module does. I ask because #13605 added several classes with a dynamic__doc__
.
I didn't, and it sounds like a good idea. We can override it to deal with Cython classes if necessary.
Do you think we should make this change on this ticket or a followup? I won't be able to work on it much until next week (I'm still in Hawaii after Sage Days 46).
comment:282 in reply to: ↑ 281 Changed 7 years ago by
Replying to roed:
Do you think we should make this change on this ticket or a followup?
Not on this ticket, it's already too big.
comment:283 Changed 7 years ago by
 Dependencies changed from #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111 to #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, #14254
comment:284 Changed 7 years ago by
 Dependencies changed from #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, #14254 to #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, #14254, #14242
comment:285 Changed 7 years ago by
 Dependencies changed from #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, #14254, #14242 to #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, #14254, #14242, #14253
Changed 7 years ago by
comment:286 Changed 7 years ago by
All well on the buildbots. So please do the final review of 12415_rebase_58.patch.
comment:287 Changed 7 years ago by
 Status changed from positive_review to needs_work
comment:288 Changed 7 years ago by
 Status changed from needs_work to needs_review
comment:289 followup: ↓ 290 Changed 7 years ago by
The only thing I'm concerned about is
There are 18 tests in sage/combinat/partition.py that are not being run There are 12 tests in sage/combinat/tableau.py that are not being run
Do you know why that changed?
comment:290 in reply to: ↑ 289 ; followup: ↓ 291 Changed 7 years ago by
comment:291 in reply to: ↑ 290 Changed 7 years ago by
 Description modified (diff)
 Status changed from needs_review to positive_review
comment:292 Changed 7 years ago by
 Description modified (diff)
comment:293 followup: ↓ 294 Changed 7 years ago by
 Merged in set to sage5.9.beta0
 Resolution set to fixed
 Status changed from positive_review to closed
comment:294 in reply to: ↑ 293 Changed 7 years ago by
Replying to jdemeyer:
Yay!
comment:295 Changed 7 years ago by
 Description modified (diff)
comment:296 Changed 7 years ago by
I'm working on #12281 and noticed that sage t debug
doesn't work for me on OS X 10.6.8 (it starts the tests but then just hangs). Strangely, the tests in sage.doctest.forker.SageDocTestRunner.report_unexpected_exception
seem to succeed. I haven't tried running tests in debug mode since Jeroen changed it in 12415_review.patch; can anyone else duplicate this problem on another platform?
comment:297 Changed 7 years ago by
 Description modified (diff)
comment:298 Changed 7 years ago by
 Description modified (diff)
comment:299 Changed 7 years ago by
 Description modified (diff)
comment:300 Changed 7 years ago by
 Dependencies changed from #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, #14254, #14242, #14253 to #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, #14254, #14242, #14253, #14307
comment:301 Changed 7 years ago by
 Dependencies changed from #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, #14254, #14242, #14253, #14307 to #13147, #13146, #13145, #12723, #12392, #12393, #12395, #12396, #12397, #12381, #12382, #12383, #12384, #11871, #13195, #13121, #13748, #13899, #12719, #5155, #14070, #14079, #14150, #14158, #14182, #14184, #14054, #14063, #13605, #14111, #14254, #14242, #14253
 Description modified (diff)
comment:302 Changed 7 years ago by
 Description modified (diff)
comment:303 Changed 7 years ago by
 Description modified (diff)
comment:304 Changed 7 years ago by
 Description modified (diff)
comment:305 Changed 7 years ago by
 Description modified (diff)
comment:306 Changed 7 years ago by
 Description modified (diff)
comment:307 Changed 7 years ago by
 Description modified (diff)
comment:308 Changed 7 years ago by
 Description modified (diff)
comment:309 Changed 7 years ago by
 Description modified (diff)
comment:310 Changed 7 years ago by
 Component changed from doctest to doctest framework
comment:311 Changed 7 years ago by
This patch breaks the fixdoctests script. The problem is that the strings which sagefixdoctests searches for in order to identify the line numbers have changed with the new output implemented in the current patch.
I have just uploaded the patch #10589 which makes sage fixdoctests
work properly with the new doctest output (as stated on the ticket for #10589, the main point of this patch is to fix some different problems with fixdoctests). This patch also adds a test to sage/tests/cmdline.py for the fixdoctests script so that the doctest framework now has a chance of identifying patches which break it in future.
comment:312 Changed 7 years ago by
Neither here nor on #14184 is there any public discussion of having removed onlyoptional
/only_optional
. The developer conventions have a nice unified way of testing examples, but it was very useful to just skip the "regular" tests. Did I miss a different place where this was disabled (and why? presumably technical)?
comment:313 Changed 7 years ago by
onlyoptional
was replaced by optional
. The old documentation was very unclear about what optional
and onlyoptional
did, so we basically just implemented what we could understand.
I'm working on this. Email me if you want to collaborate.