Re: [sage-devel] Re: python3 report (end of august 2018)
I could do this for elliptic curves, but not this week as I'm at a meeting. John On Mon, 27 Aug 2018 at 00:02, John H Palmieri wrote: > First, thank you, Frédéric, for all of the work you've done on this. > > Second, to everyone else: if you're an expert in, say, toric varieties or > elliptic curves, try building Sage with Python 3 and then fixing doctests > on the appropriate directory. Some of these will be easy for anyone, but > some may require expertise in the particular mathematics. > > (Third, by the way, most of the errors in steenrod_algebra.py were fixed > by https://trac.sagemath.org/ticket/25927, which already has a positive > review. Most of the remaining failures just have to do with different > sorting in Python 2 vs. Python 3 when printing dictionaries.) > > John > > > > On Sunday, August 26, 2018 at 8:47:01 AM UTC-7, Frédéric Chapoton wrote: >> >> Dear all, here is a short python3 status report. >> >> There is a patchbot report with python3 for 8.4.b2 somewhere on the page >> : https://patchbot.sagemath.org/ticket/0/ >> (@ patchbot breeders, please update your patchbot so that we know if it >> builds and runs sage with python2 or python3.) >> >> We are now hopefully getting close to making the documentation (html and >> pdf) build with python3. One good step in this direction would be to merge >> the 4 waiting pull requests in sagenb (and then upgrade the sagenb spkg, >> see https://trac.sagemath.org/ticket/25837). >> >> Otherwise, some progress has been made on the hash issue ( >> https://trac.sagemath.org/ticket/24551). There remains in particular the >> controversial question of the hash issue for groups. There is no general >> agreement on the meaning of equality for groups, and this will probably >> make the definition of hash difficult. >> >> The patchbot report on sage+python3 for 8.4.b2 has still *many* (and I >> mean *many*) failing doctests. But it also stops badly in the way shown >> below, complaining that too many files are open. Could somebody investigate >> this issue, please ? >> >> And I would like to know if some buildbot is using the python3 make >> target that is now available ? >> >> Frédéric >> >> sage -t --long src/sage/combinat/crystals/kac_modules.py # 3 doctests >> failed >> sage -t --long src/sage/matroids/matroids_plot_helpers.py # 1 doctest >> failed >> sage -t --long src/sage/libs/gap/element.pyx # 2 doctests failed >> sage -t --long src/sage/groups/conjugacy_classes.py # 2 doctests failed >> sage -t --long src/sage/docs/instancedoc.pyx # 1 doctest failed >> sage -t --long src/sage/rings/padics/factory.py # 104 doctests failed >> Doctests interrupted: 843/3700 files tested >> -- >> Total time for all tests: 6360.5 seconds >> cpu time: 10897.2 seconds >> cumulative wall time: 12855.4 seconds >> Traceback (most recent call last): >> File "/home/u1/chapoton/sage3/src/bin/sage-runtests", line 156, in >> >> err = DC.run() >> File >> "/home/u1/chapoton/sage3/local/lib/python3.6/site-packages/sage/doctest/control.py" >> , line 1187, in run >> self.run_doctests() >> File >> "/home/u1/chapoton/sage3/local/lib/python3.6/site-packages/sage/doctest/control.py" >> , line 915, in run_doctests >> self.dispatcher.dispatch() >> File >> "/home/u1/chapoton/sage3/local/lib/python3.6/site-packages/sage/doctest/forker.py" >> , line 1912, in dispatch >> self.parallel_dispatch() >> File >> "/home/u1/chapoton/sage3/local/lib/python3.6/site-packages/sage/doctest/forker.py" >> , line 1809, in parallel_dispatch >> w.start() # This might take some time >> File >> "/home/u1/chapoton/sage3/local/lib/python3.6/site-packages/sage/doctest/forker.py" >> , line 2095, in start >> super(DocTestWorker, self).start() >> File >> "/home/u1/chapoton/sage3/local/lib/python3.6/multiprocessing/process.py", >> line 105, in start >> self._popen = self._Popen(self) >> File >> "/home/u1/chapoton/sage3/local/lib/python3.6/multiprocessing/context.py", >> line 223, in _Popen >> return _default_context.get_context().Process._Popen(process_obj) >> File >> "/home/u1/chapoton/sage3/local/lib/python3.6/multiprocessing/context.py", >> line 277, in _Popen >> return Popen(process_obj) >> File >> "/home/u1/chapoton/sage3/local/lib/python3.6/multiprocessing/popen_fork.py" >> , line 19, in __init__ >> self._launch(process_obj) >> File >> "/home/u1/chapoton/sage3/local/lib/python3.6/multiprocessing/popen_fork.py" >> , line 65, in _launch >> parent_r, child_w = os.pipe() >> OSError: [Errno 24] Too many open files >> >> >> By the way, here are the worst offenders, those having hundreds of >> failing doctests: >> >> sage -t --long src/sage/schemes/elliptic_curves/ell_number_field.py # >> 107 doctests failed >> sage -t --long src/sage/modular/pollack_stevens/modsym.py # 199 >> doctests failed >> sage -t --long src/sage/schemes/hyperelliptic_curves/ >>
[sage-devel] Re: trac questions
On Tuesday, August 28, 2018 at 4:41:32 AM UTC+10, John H Palmieri wrote: > > Is it possible to configure trac.sagemath.org so that > > - it is not possible to select "Needs review" if the author field is > blank? (or it gives an immediate error message if you try to select "Needs > review" with blank author field) > > We shouldn't do that because of invalid/wont-fix tickets (or only allow a blank author field when that milestone has been set). > - it is not possible to select "Positive review" if author and/or reviewer > fields are blank? > +1 but with some kind of message saying why it is grayed out. Best, Travis -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] trac questions
Is it possible to configure trac.sagemath.org so that - it is not possible to select "Needs review" if the author field is blank? (or it gives an immediate error message if you try to select "Needs review" with blank author field) - it is not possible to select "Positive review" if author and/or reviewer fields are blank? -- John -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] python3 report (end of august 2018)
Another easy diagnostic: look at /proc/$PID/fd/* and see which file(-descriptors) are open. On Monday, August 27, 2018 at 7:21:45 AM UTC+2, Snark wrote: > > That probably means the doctesting framework is leaking file > descriptors, ie: it opens each and every file but never closes them. > > I would search: > (1) either a single piece of code which does all the opening and never > closes anything during the whole run (the least likely scenario) > (2) or a piece of code forking correct workers (ie: they would > open+close correctly) but leaking them (so the closing part doesn't > happen) (the most likely scenario). > > Someone familiar with the code should probably have a look and would be > more efficient at spotting the problem. > > jpuydt on irc.debian.org > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] r-3.4.4.p0 configure/install error
Sorry for the delay in getting back. I could not install libpaper as non root. I don't have root privileges on the machine I am working on. I have requested our IT person to get that installed. I will update promptly once I get that installed and run make again. On Mon, Aug 27, 2018, 1:27 AM Dima Pasechnik wrote: > if you still have the failed Sage install, all you need to do after > libpaper installation is to run make again. > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-devel@googlegroups.com. > Visit this group at https://groups.google.com/group/sage-devel. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] 3D plots in Jupyter notebook broken since Sage 8.4.beta0
Le lundi 27 août 2018 12:21:15 UTC+2, François Bissey a écrit : > > https://trac.sagemath.org/ticket/26114 should be in the next beta and fix > this issue. > > OK very good. Thanks! Eric. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] 3D plots in Jupyter notebook broken since Sage 8.4.beta0
https://trac.sagemath.org/ticket/26114 should be in the next beta and fix this issue. François > On 27/08/2018, at 22:18, Eric Gourgoulhon wrote: > > Hi, > > Since Sage 8.4.beta0, the default 3D viewer (Jmol) seems broken in Jupyter > notebooks. For instance, typing > sphere() > results in a blank screen, with the following message in the console: > [W 12:14:53.681 NotebookApp] 404 GET /nbextensions/jsmol/JSmol.min.js > (127.0.0.1) 16.30ms referer=None > > Running instead > sphere(viewer='threejs') > works fine. > > Everything is OK with Sage 8.3. > > Eric. > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-devel@googlegroups.com. > Visit this group at https://groups.google.com/group/sage-devel. > For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] 3D plots in Jupyter notebook broken since Sage 8.4.beta0
Hi, Since Sage 8.4.beta0, the default 3D viewer (Jmol) seems broken in Jupyter notebooks. For instance, typing sphere() results in a blank screen, with the following message in the console: [W 12:14:53.681 NotebookApp] 404 GET /nbextensions/jsmol/JSmol.min.js (127.0.0.1) 16.30ms referer=None Running instead sphere(viewer='threejs') works fine. Everything is OK with Sage 8.3. Eric. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: recommendation: delete local/share/mathjax/mathjax, run make doc-clean, then make
On Sat, Aug 25, 2018 at 3:39 PM Sébastien Labbé wrote: > > On one machine, I get this: > > $ du -s -h local/share/doc/sage > 20G/local/share/doc/sage > > on the other, I get this: > > $ du -s -h local/share/doc/sage > 1,9Glocal/share/doc/sage > > I do not know why the bug affects only one? Thanks for sharing. This bug is already fixed, but if you did a build on the first machine with a version where the bug did exist (specifically in the sagenb package) then it will persist until and unless you delete $SAGE_LOCAL/share/mathjax and reinstall the mathjax package. Otherwise you'll just never see it in the first place. > On Thursday, August 23, 2018 at 10:13:11 PM UTC+2, John H Palmieri wrote: >> >> I found that my Sage documentation directory was taking up 15GB of hard >> drive space, because of a bug (which I think has been fixed, but I don't >> remember where). The bug was caused by a recursive symlink >> >> local/share/mathjax/mathjax -> local/share/mathjax >> >> When the contents of local/share/mathjax were copied to various _static >> directories in the html documentation, rather than just reproducing the >> symlink, it created many layers of subdirectories; for example, >> ca/intro/_static/mathjax/mathjax/mathjax/... Basically mathjax all the way >> down. I don't know if this happened all at once, or once each time I built >> the documentation. >> >> To see if you have this problem, see if you have the symlink. You might also >> find out how much disk space local/share/doc/sage takes up (for example, "du >> -s -h /path/to/SAGE_ROOT/local/share/doc/sage"). On my computer, it is >> 1.9GB. If you are using up a lot more space than that, you might have hit >> this bug. >> >> To fix: remove the symlink SAGE_ROOT/local/share/mathjax/mathjax. Then run >> "make doc-clean" to remove the old documentation, and then run "make" to >> rebuild the documentation. >> >> Question: >> >> - has the bug been fixed, or is that symlink still being created? >> >> -- >> John >> > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-devel@googlegroups.com. > Visit this group at https://groups.google.com/group/sage-devel. > For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] python3 report (end of august 2018)
On Sun, Aug 26, 2018 at 5:47 PM Frédéric Chapoton wrote: > > Dear all, here is a short python3 status report. > > There is a patchbot report with python3 for 8.4.b2 somewhere on the page : > https://patchbot.sagemath.org/ticket/0/ > (@ patchbot breeders, please update your patchbot so that we know if it > builds and runs sage with python2 or python3.) > > We are now hopefully getting close to making the documentation (html and pdf) > build with python3. One good step in this direction would be to merge the 4 > waiting pull requests in sagenb (and then upgrade the sagenb spkg, see > https://trac.sagemath.org/ticket/25837). > > Otherwise, some progress has been made on the hash issue > (https://trac.sagemath.org/ticket/24551). There remains in particular the > controversial question of the hash issue for groups. There is no general > agreement on the meaning of equality for groups, and this will probably make > the definition of hash difficult. > > The patchbot report on sage+python3 for 8.4.b2 has still many (and I mean > many) failing doctests. But it also stops badly in the way shown below, > complaining that too many files are open. Could somebody investigate this > issue, please ? I'm not sure what's going on there--I haven't seen that before. But I also haven't merged 8.4.beta2 into my python3 branch yet. I think it's still based on 8.3.something. For comparison though, on my python3 branch, which admittedly I haven't updated in 2 or 3 weeks, but which has many fixes merged into it that are not yet merged into develop, I have: $ grep -R "doctests\? failed" logs/ptest.log | wc -l 465 or ~465 modules with failing doctests. Of those, most of them do not have hundreds of failures as in your report. Here are the top 10 in number of failures: $ grep 'doctests\? failed' logs/ptest.log | sort -k 5 -nr | head -10 sage -t src/sage/misc/explain_pickle.py # 71 doctests failed sage -t src/sage/graphs/generic_graph.py # 25 doctests failed sage -t src/sage/combinat/diagram_algebras.py # 25 doctests failed sage -t src/sage/combinat/finite_state_machine.py # 24 doctests failed sage -t src/sage/combinat/rigged_configurations/kr_tableaux.py # 23 doctests failed sage -t src/sage/matroids/matroid.pyx # 20 doctests failed sage -t src/sage/categories/finite_dimensional_algebras_with_basis.py # 18 doctests failed sage -t src/sage/modular/modsym/ambient.py # 17 doctests failed sage -t src/sage/categories/quantum_group_representations.py # 17 doctests failed sage -t src/sage/quadratic_forms/genera/normal_form.py # 16 doctests failed Of these, I know many of the failures to be due to slight ordering differences in the output, such as of things like sets, or results from graph algorithms that are not exactly deterministic (at least between Python versions). Of course, there are also still a number of outright exceptions: $ grep -R "Exception raised" logs/ptest.log | wc -l 613 To be clear, this was also with just `make ptest`, not `make ptestlong`. The numbers are probably a bit higher with some `# long time` tests. But I think what this shows is that we're in better shape on Python 3 than I think the OP suggests, at least in theory. We just need to get more of the existing fixes cleaned up so that they can be merged. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
