Fix doctests #19

saraedum · 2018-04-04T21:58:33Z

It would be great to make sage -tp src pass. (And sage -tp --long src as well.)

A GitLab CI pipeline runs these doctests, the results of the latest run are:

227 failing individual doctests

No modules are failing entirely at the moment.

For reference, here are the corresponding numbers in Debian (for --long doctests.)

TODO:

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

isuruf · 2018-06-01T20:33:37Z

Added a TODO

saraedum · 2018-06-11T20:27:18Z

I have not tried to find out yet what's the issue…

UnsatisfiableError: The following specifications were found to be in conflict:
  - gcc
  - sage 8.2*

isuruf · 2018-06-11T20:28:11Z

Probably mpfr.

saraedum · 2018-06-11T20:31:37Z

True. gcc does not come from conda-forge. Any workaround?

isuruf · 2018-06-11T20:33:17Z

Use the system package manager?

saraedum · 2018-06-11T20:34:54Z

Haha, sorry, for asking such dumb questions ;)

saraedum · 2018-06-12T15:09:53Z

One killed and one timeout less. And a few thousand fewer doctests failing.

isuruf · 2018-06-12T15:27:55Z

Did you have jmol installed? Does jmol work in a headless image?

isuruf · 2018-06-17T18:41:09Z

Newest build https://gitlab.com/isuruf/conda-sagelib-tests/-/jobs/75426947

saraedum · 2018-06-21T08:50:35Z

@isuruf: I just gave you access to my gitlab repo so we can work on the same fork.

isuruf · 2018-06-21T14:03:21Z

I just pushed to your repo. Here's the latest build.
https://isuruf.gitlab.io/-/conda-sagelib-tests/-/jobs/76387946/artifacts/sagemath/doctest.txt

There are some issues with cddlib

saraedum · 2018-06-21T14:15:23Z

The output of cddlib has changed in a recent version. I just released 0.94j which together with https://trac.sagemath.org/ticket/25344 should fix these.

saraedum · 2018-06-21T14:35:09Z

Or let's just pin it to the right version rather ;) see conda-forge/sage-feedstock#19.

saraedum · 2018-06-21T14:59:37Z

We can not pin to 0.94g because it's not in conda-forge. So should we patch Sage's parser or backport the uppgrade to 0.94j?

saraedum · 2018-06-21T15:07:03Z

Debian's debian/patches/u1-version-cddlib-094h.patch should do the trick. I'll create a PR.

isuruf · 2018-06-24T16:38:36Z

That worked. Down to 123 failures

saraedum · 2018-07-04T19:19:54Z

Unfortunately, we know hit the 3h limit on gitlab.

saraedum · 2018-07-04T19:20:08Z

Let's use some private runners then…

saraedum · 2018-07-07T00:13:25Z

❯ conda list |grep r-base
r-base                    3.4.1                         4    conda-forge

saraedum · 2018-07-08T15:00:34Z

It appears that pexpect is making the difference. Sage uses 4.1.0, conda has 4.6.0. Strangely everything appears to work if I shorten sage's R prompt from __SAGE_R_PROMPT> to __SAGE__> .

saraedum · 2018-07-09T08:47:37Z

There is an upstream ticket about the 4.6.0 upgrade: https://trac.sagemath.org/ticket/25700

kiwifb · 2018-07-09T09:02:29Z

Have you ever adopted this patch originally from debian? https://github.com/cschwan/sage-on-gentoo/blob/master/sci-mathematics/sage/files/dt-r-no-readline.patch

saraedum · 2018-07-09T09:10:43Z

Interesting. Thanks, I was not aware of that one.

kiwifb · 2018-07-09T09:12:30Z

It helped me with readline 7.0 but I am wondering if it would help here as well. Haven't looked at pexpect 4.6.0 in gentoo yet. Mostly because it isn't in the main tree.

saraedum · 2018-07-09T09:20:36Z

And it actually makes things work. See https://trac.sagemath.org/ticket/25806 for upstreaming this.

saraedum · 2018-08-17T01:07:57Z

@isuruf why did you install numpy 1.13 in 0b2f6d3b05d7bfb767a2e385a2d916ab5f5bcac9? This seems to cause errors, see CI

ImportError: numpy.core.multiarray failed to import

Locally with 1.14 these imports work fine.

saraedum · 2018-08-17T01:34:39Z

This is now conda-forge/sage-feedstock#23.

isuruf · 2018-08-17T01:51:17Z

I installed 1.13 because the printing of arrays changed and there were doctests failing. I guess the new sage versions fixed the doctests

saraedum · 2018-08-17T01:56:04Z

I see. Do you mean these?

Expected:
    array([[[ 1.,  1.,  1.],
            [ 1.,  1.,  1.],
            [ 1.,  1.,  1.]],
    <BLANKLINE>
           [[ 1.,  1.,  1.],
            [ 0.,  0.,  0.],
            [ 1.,  1.,  1.]],
    <BLANKLINE>
           [[ 1.,  1.,  1.],
            [ 1.,  1.,  1.],
            [ 1.,  1.,  1.]]])
Got:
    array([[[1., 1., 1.],
            [1., 1., 1.],
            [1., 1., 1.]],
    <BLANKLINE>
           [[1., 1., 1.],
            [0., 0., 0.],
            [1., 1., 1.]],
    <BLANKLINE>
           [[1., 1., 1.],
            [1., 1., 1.],
            [1., 1., 1.]]])

If so, let me try to make the tests less strict upstream.

saraedum · 2018-08-17T01:57:19Z

~~Seems like a NORMALIZE_WHITESPACE would fix these.~~ No, actually not.

isuruf · 2018-08-17T02:00:16Z

Yes, doctests like that failed

saraedum · 2018-08-17T02:15:48Z

Nice, numpy has a legacy printing mode to print like 1.13 :)

saraedum · 2018-08-23T04:36:21Z

@isuruf: Any idea where these floating point errors that crash Sage could come from?

isuruf · 2018-08-25T02:18:57Z

Also needs sagemath/sagenb#450 and https://trac.sagemath.org/ticket/26117

saraedum · 2018-09-03T22:53:01Z

@isuruf: We are now having trouble with maxima not being run with the same ecl that it was built with: RuntimeError: ECL says: Module error: Don't know how to REQUIRE MAXIMA. Apparently we need to pin exactly when building something with ecl.

Sage 8.3 runs into trouble with ecl 16.1.3 and to require maxima from within Sage, we need to build and run maxima with the same version it seems. Fixes conda-forge#9; see also conda-forge/sagelib-feedstock#19.

timokau · 2018-09-04T09:45:23Z

That error occurs when ecl can't find maxima.fas. You could try explicitly setting the MAXIMA_FAS environment variable to the correct location. Maybe that'll work without rebuilding ecl.

saraedum · 2018-10-04T17:26:39Z

With conda-forge/maxima-feedstock#10 we are now down to 8 modules timing out and 340 failing tests.

isuruf · 2018-10-04T19:20:23Z

Most of these errors are due to latest versions of numpy and networkx

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saraedum mentioned this issue Jun 2, 2018

Add jmol conda-forge/staged-recipes#5996

Merged

saraedum mentioned this issue Jul 10, 2018

Sage Notebook does not open properly when installed using Conda conda-forge/sage-feedstock#21

Closed

isuruf mentioned this issue Aug 3, 2018

Segfault on Travis symengine/symengine.py#239

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saraedum added the upstream: needs review There is a an upstream issue on trac.sagemath.org that "Needs Review" by anybody who feels qualified label Aug 15, 2018

saraedum removed the upstream: needs review There is a an upstream issue on trac.sagemath.org that "Needs Review" by anybody who feels qualified label Aug 17, 2018

saraedum mentioned this issue Aug 23, 2018

Floating point exceptions #44

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saraedum mentioned this issue Sep 4, 2018

Downgrade ecl to 16.1.2 and pin exactly conda-forge/maxima-feedstock#10

Merged

saraedum mentioned this issue Oct 14, 2018

Pass --no-readline to R sagemath/sage#25806

Closed

Fix doctests #19

Fix doctests #19

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