Opened 4 months ago
Last modified 4 days ago
#28298 new enhancement
py3: final polishing of the last failing doctests
Reported by: | chapoton | Owned by: | |
---|---|---|---|
Priority: | major | Milestone: | sage-8.9 |
Component: | python3 | Keywords: | |
Cc: | vklein, embray, jmantysalo, gh-timokau, jhpalmieri, dcoudert, etn40ff, arojas | Merged in: | |
Authors: | Reviewers: | ||
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
After #26212, there remains only a few failing doctests (not using any optional package).
Fixed:
- 1 in src/sage/tests/books/computational-mathematics-with-sagemath/graphtheory_doctest.py #28300
- 1 in src/sage/tests/books/computational-mathematics-with-sagemath/sol/graphtheory_doctest.py #28300
- (A) 1 in src/sage/combinat/root_system/non_symmetric_macdonald_polynomials.py #28305
- (D) 1 in src/sage/tests/cmdline.py #28320
- (C) 1 in src/sage/symbolic/expression.pyx #28219 #28412
- (K) 2 in src/sage/crypto/block_cipher/present.py #28403
- (B) 7 in src/sage/combinat/root_system/weyl_group.py #27967 #28351
- (E) 1 at line 597 in src/sage/libs/eclib/interface.py #28454 #28472
- (G) src/sage/rings/polynomial/polynomial_rational_flint.pyx #28334 #28649
- (H) 1 in src/sage/libs/singular/function.pyx #28622
- (I) 2 in src/sage/numerical/backends/generic_backend.pyx #28622
- (J) 4 in src/sage/repl/attach.py #28622
Those that are not yet handled are the following.
*On several machines*:
- (F) 1 in src/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py (not seen since some time. random ? could be ignored ?)
but not on these machines: macOS mojave (several different machines)
OS X only:
- (K) 2 in src/sage/symbolic/expression.py #28489
- (L) 1 in src/sage/numerical/linear_tensor_element.pyx #28559
Table summary:
Issue | ref. patchbot | ubuntu, debian | OS X |
(F) | fail ? | ||
(K) | fail (intermittent) | ||
(L) | fail (intermittent) |
Change History (60)
comment:1 Changed 4 months ago by
- Cc dcoudert added
comment:2 Changed 4 months ago by
- Description modified (diff)
comment:3 Changed 4 months ago by
- Description modified (diff)
comment:4 Changed 4 months ago by
- Cc etn40ff added
comment:5 Changed 4 months ago by
- Description modified (diff)
comment:6 Changed 4 months ago by
comment:7 Changed 4 months ago by
the flint one has been reported by several people on sage-release
comment:8 Changed 4 months ago by
The flint one is strange, since flint doesn't depend on Python. So either the error occurs also in Python 2, or there is something strange going on with the flint interface.
comment:9 Changed 4 months ago by
- Description modified (diff)
comment:10 Changed 4 months ago by
Maybe this is a stupid question, but are we sure that the errors that are unique to the patchbot are machine-specific (i.e. reproducible on that machine) or is there a chance this could be fixed by doing a clean install?
comment:11 Changed 4 months ago by
I have just "make distclean" that precise patchbot machine. It is currently running, and we will see the results in 2 hours. This machine has a fairly stable configuration, and the remaining failing doctests have been there since many releases.
Some of these errors pass when each file is doctested alone. Some look like a mis-synchronized (pexpect ?) interface.
Of course, we will have to make the decision when we claim "all doctests pass", in spite of the remaining quantum noise..
comment:12 Changed 4 months ago by
- Description modified (diff)
comment:13 Changed 4 months ago by
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comment:14 Changed 4 months ago by
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comment:15 Changed 4 months ago by
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comment:16 Changed 4 months ago by
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comment:17 follow-up: ↓ 22 Changed 4 months ago by
Please add your machine results in the table, to help understand the remaining errors.
comment:18 Changed 4 months ago by
- Description modified (diff)
comment:19 Changed 4 months ago by
I have access to three different OS X Mojave machines: an iMac Pro, an iMac, and a MacBook Air, and I see the same failures on all three. I've updated the table correspondingly.
comment:21 follow-up: ↓ 24 Changed 4 months ago by
Frédéric, if you have a machine with the flint problem, can you try to track it down? Eric G thought it dated back at least to 8.8.rc3, but I don't see that in his report on sage-release. Emmanuel first reported it for 8.9.beta2 and provided a report for 8.9.beta1 without this failure, so maybe it happened between 8.9.beta1 and 8.9.beta2.
Can you use git bisect
to try to locate the problem? Could it have been #28048? (I don't see why, but I'm looking at the tickets merged in 8.9.beta2, trying to see what could possibly be related. Could accents in SAGE_LOCAL
be causing this?)
comment:22 in reply to: ↑ 17 Changed 4 months ago by
Replying to chapoton:
Please add your machine results in the table, to help understand the remaining errors.
For my laptop (Ubuntu 18.04.2, Core i7-6700HQ, 16 GB RAM), the results are identical to those marked as "laptop ch".
comment:23 Changed 4 months ago by
I guess the OS of the machine is important to understand the failures. Then what OS are the reference patchbot and "laptop ch"?
comment:24 in reply to: ↑ 21 ; follow-up: ↓ 25 Changed 4 months ago by
Replying to jhpalmieri:
Frédéric, if you have a machine with the flint problem, can you try to track it down? Eric G thought it dated back at least to 8.8.rc3, but I don't see that in his report on sage-release. Emmanuel first reported it for 8.9.beta2 and provided a report for 8.9.beta1 without this failure, so maybe it happened between 8.9.beta1 and 8.9.beta2.
Oh, I see, the relevant folder wasn't in python3-known-passing-test.txt
until 8.9.beta2, so it may have been failing for some time before that.
comment:25 in reply to: ↑ 24 Changed 4 months ago by
Replying to jhpalmieri:
Replying to jhpalmieri:
Frédéric, if you have a machine with the flint problem, can you try to track it down? Eric G thought it dated back at least to 8.8.rc3, but I don't see that in his report on sage-release. Emmanuel first reported it for 8.9.beta2 and provided a report for 8.9.beta1 without this failure, so maybe it happened between 8.9.beta1 and 8.9.beta2.
Oh, I see, the relevant folder wasn't in
python3-known-passing-test.txt
until 8.9.beta2, so it may have been failing for some time before that.
Yes I confirm. I've still a working version of Python3 8.8.rc3 (on Ubuntu 18.04) and the flint issue is already there.
comment:26 Changed 4 months ago by
- Description modified (diff)
I don't have any solutions, but let's track the flint problem at #28334.
comment:27 Changed 4 months ago by
- Description modified (diff)
comment:28 Changed 4 months ago by
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comment:29 Changed 4 months ago by
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comment:30 Changed 3 months ago by
- Description modified (diff)
I expect (K) to fail on all machines due to the nature of the problem, but I've only tested on OS X.
comment:31 Changed 3 months ago by
- Description modified (diff)
comment:32 Changed 3 months ago by
Got a patchbot report from another machine, with similar results as for the reference machine:
https://patchbot.sagemath.org/log/0/Ubuntu/18.04/x86_64/4.15.0-54-generic/petitbonum/2019-08-29%2012:45:45?short
namely
sage -t --long src/sage/symbolic/expression.pyx # 1 doctest failed sage -t --long src/sage/combinat/root_system/weyl_group.py # 7 doctests failed sage -t --long src/sage/rings/polynomial/polynomial_rational_flint.pyx # 1 doctest failed sage -t --long src/sage/libs/eclib/interface.py # 1 doctest failed sage -t --long src/sage/crypto/block_cipher/present.py # 2 doctests failed sage -t --long src/sage/repl/attach.py # 4 doctests failed sage -t --long src/sage/libs/singular/function.pyx # 1 doctest failed sage -t --long src/sage/numerical/backends/generic_backend.pyx # 2 doctests failed
comment:33 Changed 3 months ago by
- Cc arojas added
comment:36 Changed 3 months ago by
- Description modified (diff)
comment:37 Changed 3 months ago by
At this point, it begins to be useful to widen the scope of our checks. I proceeded to make ptestalllong
on two different machines (but very close), with a few optional packages, both running 8.9.beta9.
Please let me know if this isn't the right place to post this kind of reports...
TL;DR:
make ptestalllong
gives failures on 22 packages total (20 on one machine, 19 on the other);- Most of these failure cannot be reproduced when running the test standalone (whether
MAKE
is defined or not). Three file persist to fail when ran standalone:- src/sage/combinat/root_system/weyl_group.py (known)
- src/sage/libs/eclib/interface.py (also known)
- src/sage/tests/gap_packages.py (not known but optional package, fails only on one of my machines).
I have no explanation for the intermachines differences; one is a Debian testing desktop (core i7, 8 GB RAM), the other is a Debian testing laptop (core i7, 16 GB RAM).
The large number of transient failures let me think that some parts of the libraries are not as reentrant as we might wish them to be...
Details of failing files:
| Test file | Laptop | Desktop | Standalone | |---------------------------------------------------------+--------+---------+------------| | src/sage/graphs/generators/smallgraphs.py | Y | N | N | | src/sage/combinat/posets/posets.py | Y | Y | N | | src/sage/combinat/root_system/weyl_group.py | Y | Y | Y | | src/sage/plot/animate.py | Y | Y | N | | src/sage/doctest/forker.py | Y | N | N | | src/sage/libs/eclib/interface.py | Y | Y | Y | | src/sage/combinat/matrices/hadamard_matrix.py | Y | Y | N | | src/sage/rings/polynomial/polynomial_rational_flint.pyx | Y | Y | N | | src/sage/symbolic/integration/external.py | Y | Y | N | | src/sage/misc/latex.py | Y | Y | N | | src/sage/coding/databases.py | Y | Y | N | | src/sage/misc/persist.pyx | Y | Y | N | | src/sage/databases/oeis.py | Y | Y | N | | src/sage/tests/gap_packages.py | Y | N | Y | | src/sage/repl/load.py | Y | Y | N | | src/sage/graphs/graph_latex.py | Y | Y | N | | src/sage/combinat/designs/ext_rep.py | Y | N | N | | src/sage/misc/remote_file.py | Y | Y | N | | src/sage/databases/findstat.py | Y | Y | N | | src/sage/interfaces/magma_free.py | N | Y | N | | src/sage/interfaces/mathematica.py | N | Y | N |
Details on the failures on request (including the full logs...).
HTH,
comment:38 follow-up: ↓ 39 Changed 3 months ago by
- Description modified (diff)
Description modified according to the report https://groups.google.com/d/msg/sage-release/M1JjXhXfsU4/TuPETvGUAgAJ
comment:39 in reply to: ↑ 38 Changed 3 months ago by
Replying to egourgoulhon:
Description modified according to the report https://groups.google.com/d/msg/sage-release/M1JjXhXfsU4/TuPETvGUAgAJ
See however https://trac.sagemath.org/ticket/28334#comment:11 for a possible further update of the summary table.
comment:40 Changed 3 months ago by
- Description modified (diff)
I may have accidentally found a fix for the eclib/interface.py
problem. See #28454. Needs testing and, more importantly, some understanding of whether this is a valid fix.
comment:41 Changed 3 months ago by
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comment:42 Changed 3 months ago by
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comment:43 Changed 3 months ago by
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comment:45 Changed 3 months ago by
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comment:46 Changed 3 months ago by
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comment:47 Changed 3 months ago by
- Description modified (diff)
comment:48 follow-up: ↓ 51 Changed 2 months ago by
Regarding (H), (I), (J): I don't see them ordinarily on OS X, even when running make ptestlong
, but I do see them on my OS X patchbot. Is there something different about patchbots which could lead to these failures?
comment:49 Changed 2 months ago by
- Description modified (diff)
comment:50 Changed 2 months ago by
- Description modified (diff)
comment:51 in reply to: ↑ 48 Changed 7 weeks ago by
- Description modified (diff)
Replying to jhpalmieri:
Regarding (H), (I), (J): I don't see them ordinarily on OS X, even when running
make ptestlong
, but I do see them on my OS X patchbot. Is there something different about patchbots which could lead to these failures?
I really think this is the case. I've opened #28622 for this, not that I have any ideas how to fix it.
comment:52 Changed 7 weeks ago by
These failures seem to also occur outside of the patchbot, but they are very repeatable when using the patchbot, as described at #28622, so I hope if we can fix the patchbot problems, it will either fix them outside of the patchbot or at least give us some clues.
comment:53 follow-up: ↓ 55 Changed 6 weeks ago by
I still don't know if anyone else has seen (K) or (L). (F) maybe hasn't been seen for a long time. Things are looking good!
comment:54 Changed 6 weeks ago by
If all remaining failures are transient, maybe its time to switch the betas over to py3 and do some more extensive testing?
comment:55 in reply to: ↑ 53 Changed 6 weeks ago by
Replying to jhpalmieri:
I still don't know if anyone else has seen (K) or (L).
I can reproduce (K) on macOS reliably, but have not seen (L).
comment:56 Changed 6 weeks ago by
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comment:57 Changed 3 weeks ago by
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comment:58 Changed 3 weeks ago by
I haven't seen (L) in a while. I haven't heard any other reports of it, either. So I would put a very low priority on it.
comment:59 Changed 4 days ago by
I propose to clear up (F), (K), and (L) here. They are all intermittent failures with obscure causes, and do not seem likely to get any solution in the near future, and just blocking sage on python 3. They can change to regular tickets. Any one object?
comment:60 Changed 4 days ago by
These are not blocking anything. The switch to python3 is happening.
Are all of the failures "on some machines" actually on the same machine? Can these be reproduced by anyone else?