cschwan / sage-on-gentoo

(Unofficial) Gentoo Overlay for Sage- and Sage-related ebuilds
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doctesting `sage-9.3.beta` failures #628

Closed strogdon closed 3 years ago

strogdon commented 3 years ago

This is a fresh install of s-o-g and I have some odd failures.

sage -t --long --random-seed=0 /usr/share/doc/sage-9999/html/en/prep/_sources/Quickstarts/Number-Theory.rst  # 1 doctest failed
sage -t --long --random-seed=0 /usr/share/doc/sage-9999/html/en/constructions/_sources/interface_issues.rst  # 1 doctest failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/calculus/calculus.py  # 1 doctest failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/calculus/wester.py  # 1 doctest failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/cpython/dict_del_by_value.pyx  # 2 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/features/__init__.py  # 1 doctest failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/functions/airy.py  # 37 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/functions/error.py  # 33 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/functions/bessel.py  # 79 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/functions/gamma.py  # 14 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/functions/log.py  # 22 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/functions/hypergeometric.py  # 26 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/functions/orthogonal_polys.py  # 38 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/functions/exp_integral.py  # 93 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/functions/jacobi.py  # 94 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/functions/special.py  # 33 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/functions/transcendental.py  # 11 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/interfaces/maxima_lib.py  # 3 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/interfaces/tests.py  # 1 doctest failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/libs/mpmath/ext_libmp.pyx  # 7 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/libs/mpmath/ext_impl.pyx  # 2 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/libs/mpmath/ext_main.pyx  # 38 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/libs/mpmath/utils.pyx  # 39 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/libs/pynac/pynac.pyx  # 17 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/matrix/matrix_double_dense.pyx  # 1 doctest failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/misc/lazy_import.pyx  # 1 doctest failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/misc/sageinspect.py  # 2 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/numerical/optimize.py  # 2 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/plot/line.py  # 1 doctest failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/plot/plot.py  # 3 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/repl/ipython_kernel/kernel.py  # 1 doctest failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/rings/complex_arb.pyx  # 1 doctest failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/schemes/riemann_surfaces/riemann_surface.py  # 45 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/structure/coerce.pyx  # 2 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/symbolic/function.pyx  # 6 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/tests/book_stein_ent.py  # 1 doctest failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/symbolic/expression.pyx  # 3 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/symbolic/integration/integral.py  # 6 doctests failed
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/tests/books/computational-mathematics-with-sagemath/integration_doctest.py  # 2 doctests failed
sage -t --long --random-seed=0 /usr/share/doc/sage-9999/html/fr/tutorial/_sources/tour_algebra.rst  # 3 doctests failed
sage -t --long --random-seed=0 /usr/share/doc/sage-9999/html/en/tutorial/_sources/tour_algebra.rst  # 3 doctests failed

I may have missed some items but when doctesting TypeError: Cannot convert mpz to sage.rings.integer.Integer seems to be pervasive, i.e.

**********************************************************************
File "/usr/lib/python3.9/site-packages/sage/calculus/calculus.py", line 372, in sage.calculus.calculus
Failed example:
    [f[0].n() for f in _.coefficients()]  # numerical coefficients to make comparison easier; Maple 12 gives same answer
Exception raised:
    Traceback (most recent call last):
      File "sage/symbolic/expression.pyx", line 6186, in sage.symbolic.expression.Expression.numerical_approx (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/symbolic/expression.cpp:37044)
        x = x._convert(kwds)
      File "sage/symbolic/expression.pyx", line 1495, in sage.symbolic.expression.Expression._convert (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/symbolic/expression.cpp:10452)
        cdef GEx res = self._gobj.evalf(0, kwds)
      File "sage/libs/pynac/pynac.pyx", line 2139, in sage.libs.pynac.pynac.py_psi2 (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/pynac/pynac.cpp:25307)
        return mpmath_utils.call(mpmath.psi, n, x, prec=prec)
      File "sage/libs/mpmath/utils.pyx", line 439, in sage.libs.mpmath.utils.call (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:7129)
        y = mpmath_to_sage(y, prec)
      File "sage/libs/mpmath/utils.pyx", line 272, in sage.libs.mpmath.utils.mpmath_to_sage (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:5518)
        mpfr_from_mpfval(y.value, x._mpf_)
      File "sage/libs/mpmath/utils.pyx", line 167, in sage.libs.mpmath.utils.mpfr_from_mpfval (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:4702)
        sign, man, exp, bc = x
    TypeError: Cannot convert mpz to sage.rings.integer.Integer

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/usr/lib/python3.9/site-packages/sage/doctest/forker.py", line 714, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.9/site-packages/sage/doctest/forker.py", line 1133, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.calculus.calculus[101]>", line 1, in <module>
        [f[Integer(0)].n() for f in _.coefficients()]  # numerical coefficients to make comparison easier; Maple 12 gives same answer
      File "<doctest sage.calculus.calculus[101]>", line 1, in <listcomp>
        [f[Integer(0)].n() for f in _.coefficients()]  # numerical coefficients to make comparison easier; Maple 12 gives same answer
      File "sage/structure/element.pyx", line 885, in sage.structure.element.Element.n (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/structure/element.c:8385)
        return self.numerical_approx(prec, digits, algorithm)
      File "sage/symbolic/expression.pyx", line 6190, in sage.symbolic.expression.Expression.numerical_approx (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/symbolic/expression.cpp:37117)
        x = x._convert(kwds)
      File "sage/symbolic/expression.pyx", line 1495, in sage.symbolic.expression.Expression._convert (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/symbolic/expression.cpp:10452)
        cdef GEx res = self._gobj.evalf(0, kwds)
      File "sage/libs/pynac/pynac.pyx", line 2139, in sage.libs.pynac.pynac.py_psi2 (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/pynac/pynac.cpp:25307)
        return mpmath_utils.call(mpmath.psi, n, x, prec=prec)
      File "sage/libs/mpmath/utils.pyx", line 439, in sage.libs.mpmath.utils.call (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:7129)
        y = mpmath_to_sage(y, prec)
      File "sage/libs/mpmath/utils.pyx", line 272, in sage.libs.mpmath.utils.mpmath_to_sage (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:5518)
        mpfr_from_mpfval(y.value, x._mpf_)
      File "sage/libs/mpmath/utils.pyx", line 167, in sage.libs.mpmath.utils.mpfr_from_mpfval (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:4702)
        sign, man, exp, bc = x
    TypeError: Cannot convert mpz to sage.rings.integer.Integer
kiwifb commented 3 years ago

I see there is a new version of mpmath in the tree, what is your version? I have 1.1.0 here.

strogdon commented 3 years ago

I'm using 1.2.1.

kiwifb commented 3 years ago

Can you downgrade to check if that's it?

strogdon commented 3 years ago

It's no longer in the tree but I think I can do a local overlay.

kiwifb commented 3 years ago

I see, it was stabilized on Monday and 1.1.0 was removed in the same sweep https://packages.gentoo.org/packages/dev-python/mpmath/changelog. My tree still has it as unstable, the Australian mirror has been a bit laggy lately. I will investigate locally because if, as I suspect, it is the cause, the damage will be widespread.

kiwifb commented 3 years ago

OK, because of my time zone it was probably Tuesday for me, which makes it not quite as laggy.

kiwifb commented 3 years ago

Yes definitely the cause.

kiwifb commented 3 years ago

I suspect this

Compatibility:

* Enable sage backend by default only if SAGE_ROOT is set (Pauli Virtanen)

in https://github.com/fredrik-johansson/mpmath/blob/master/CHANGES

kiwifb commented 3 years ago
fbissey@moonloop ~ $ sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/calculus/calculus.py 
too many failed tests, not using stored timings
Running doctests with ID 2021-03-18-13-14-48-fb25a05d.
Using --optional=dochtml,memlimit,pip,sage
Doctesting 1 file.
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/calculus/calculus.py
**********************************************************************
File "/usr/lib/python3.9/site-packages/sage/calculus/calculus.py", line 372, in sage.calculus.calculus
Failed example:
    [f[0].n() for f in _.coefficients()]  # numerical coefficients to make comparison easier; Maple 12 gives same answer
Exception raised:
    Traceback (most recent call last):
      File "sage/symbolic/expression.pyx", line 6186, in sage.symbolic.expression.Expression.numerical_approx (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/symbolic/expression.cpp:37043)
        x = x._convert(kwds)
      File "sage/symbolic/expression.pyx", line 1495, in sage.symbolic.expression.Expression._convert (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/symbolic/expression.cpp:10451)
        cdef GEx res = self._gobj.evalf(0, kwds)
      File "sage/libs/pynac/pynac.pyx", line 2139, in sage.libs.pynac.pynac.py_psi2 (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/pynac/pynac.cpp:25306)
        return mpmath_utils.call(mpmath.psi, n, x, prec=prec)
      File "sage/libs/mpmath/utils.pyx", line 439, in sage.libs.mpmath.utils.call (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:7129)
        y = mpmath_to_sage(y, prec)
      File "sage/libs/mpmath/utils.pyx", line 272, in sage.libs.mpmath.utils.mpmath_to_sage (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:5518)
        mpfr_from_mpfval(y.value, x._mpf_)
      File "sage/libs/mpmath/utils.pyx", line 167, in sage.libs.mpmath.utils.mpfr_from_mpfval (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:4702)
        sign, man, exp, bc = x
    TypeError: Cannot convert mpz to sage.rings.integer.Integer

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/usr/lib/python3.9/site-packages/sage/doctest/forker.py", line 714, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.9/site-packages/sage/doctest/forker.py", line 1133, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.calculus.calculus[101]>", line 1, in <module>
        [f[Integer(0)].n() for f in _.coefficients()]  # numerical coefficients to make comparison easier; Maple 12 gives same answer
      File "<doctest sage.calculus.calculus[101]>", line 1, in <listcomp>
        [f[Integer(0)].n() for f in _.coefficients()]  # numerical coefficients to make comparison easier; Maple 12 gives same answer
      File "sage/structure/element.pyx", line 885, in sage.structure.element.Element.n (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/structure/element.c:8385)
        return self.numerical_approx(prec, digits, algorithm)
      File "sage/symbolic/expression.pyx", line 6190, in sage.symbolic.expression.Expression.numerical_approx (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/symbolic/expression.cpp:37116)
        x = x._convert(kwds)
      File "sage/symbolic/expression.pyx", line 1495, in sage.symbolic.expression.Expression._convert (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/symbolic/expression.cpp:10451)
        cdef GEx res = self._gobj.evalf(0, kwds)
      File "sage/libs/pynac/pynac.pyx", line 2139, in sage.libs.pynac.pynac.py_psi2 (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/pynac/pynac.cpp:25306)
        return mpmath_utils.call(mpmath.psi, n, x, prec=prec)
      File "sage/libs/mpmath/utils.pyx", line 439, in sage.libs.mpmath.utils.call (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:7129)
        y = mpmath_to_sage(y, prec)
      File "sage/libs/mpmath/utils.pyx", line 272, in sage.libs.mpmath.utils.mpmath_to_sage (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:5518)
        mpfr_from_mpfval(y.value, x._mpf_)
      File "sage/libs/mpmath/utils.pyx", line 167, in sage.libs.mpmath.utils.mpfr_from_mpfval (/dev/shm/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/mpmath/utils.c:4702)
        sign, man, exp, bc = x
    TypeError: Cannot convert mpz to sage.rings.integer.Integer
**********************************************************************
1 item had failures:
   1 of 113 in sage.calculus.calculus
    [429 tests, 1 failure, 9.93 s]
----------------------------------------------------------------------
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/calculus/calculus.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 10.0 seconds
    cpu time: 10.6 seconds
    cumulative wall time: 9.9 seconds
fbissey@moonloop ~ $ SAGE_ROOT=1 sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/calculus/calculus.py 
too many failed tests, not using stored timings
Running doctests with ID 2021-03-18-13-18-15-7c4bcb36.
Using --optional=dochtml,memlimit,pip,sage
Doctesting 1 file.
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/calculus/calculus.py
    [429 tests, 9.94 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 10.0 seconds
    cpu time: 10.7 seconds
    cumulative wall time: 9.9 seconds
kiwifb commented 3 years ago

Hum, sage may have to changed in too many places to make viable as a patch in sage-on-gentoo. But we may still try something basic.

strogdon commented 3 years ago

As you indicated on https://github.com/fredrik-johansson/mpmath/pull/466 setting MPMATH_SAGE=1 seems to work. Any harm in setting MPMATH_SAGE globally?

kiwifb commented 3 years ago

Because the potential change to make is in a pyx file, a rebuild of sage is required for testing my idea. Due to my current schedule I won't know if it is helpful for several hours. I am trying this simple patch to sage

diff --git a/sage/libs/mpmath/utils.pyx b/sage/libs/mpmath/utils.pyx
index d6c9eee..e7fdec2 100644
--- a/sage/libs/mpmath/utils.pyx
+++ b/sage/libs/mpmath/utils.pyx
@@ -419,6 +419,8 @@ def call(func, *args, **kwargs):
         3.141592653589793j

     """
+    import os
+    os.environ['MPMATH_SAGE'] = 1
     from mpmath import mp
     orig = mp.prec
     prec = kwargs.pop('prec', orig)
kiwifb commented 3 years ago

In answer to your question, that makes it the default behavior when sage is installed which may or may not be desirable. In fact, I am fairly sure it not being the default behavior when there is a system sage installed was upstream's intention.

strogdon commented 3 years ago

I think, if patching is to work, os.environ['MPMATH_SAGE'] = 1 should be os.environ['MPMATH_SAGE'] = "1".

>>> import os
>>> os.environ['MPMATH_SAGE'] = 1
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python-exec/python3.9/../../../lib/python3.9/os.py", line 684, in __setitem__
    value = self.encodevalue(value)
  File "/usr/lib/python-exec/python3.9/../../../lib/python3.9/os.py", line 756, in encode
    raise TypeError("str expected, not %s" % type(value).__name__)
TypeError: str expected, not int

I get confused about this.

kiwifb commented 3 years ago

That's an oversight on my part. You are obviously right. One sage install for nothing, it exhibit exactly the error you show above.

strogdon commented 3 years ago

OK, with 1 -> "1" I still get the failures. Perhaps MPMATH_SAGE could be set in the ebuild?

kiwifb commented 3 years ago

What would that achieve? Do you have problems during build? Or do you mean install an environment variable in /etc/env.d?

strogdon commented 3 years ago

Whatever is needed so that MPMATH_SAGE is present from a sage shell. After building with MPMATH_SAGE set correctly I have

(sage-sh) steven@hp-probook:~$ env | grep SAGE
SAGE_DEBUG=yes
SAGE_RC_FILE=/home/steven/.sage/sagerc
SAGE_STARTUP_FILE=/home/steven/.sage/init.sage
DOT_SAGE=/home/steven/.sage

but

$ MPMATH_SAGE=1 sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/calculus/calculus.py 
too many failed tests, not using stored timings
Running doctests with ID 2021-03-17-21-16-09-f330213e.
Using --optional=dochtml,memlimit,sage
Doctesting 1 file.
sage -t --long --random-seed=0 /usr/lib/python3.9/site-packages/sage/calculus/calculus.py
    [429 tests, 11.85 s]
----------------------------------------------------------------------
All tests passed!
kiwifb commented 3 years ago

Yes, make it a "true" sage variable that gets in the environment as well when sage is run. The variables you grepped above are explicitly setup in the sage executable and are only really used when you start sage with the "sage" executable. It wouldn't work if you import sage from a python shell which is also something you can do with sage-on-gentoo and in fact that you should be able to do now in vanilla sage, so long as you are using the right interpreter and possibly have the right PATHs set.

There may still be things to dig around using sage_conf.

kiwifb commented 3 years ago

Not really working. It looks like for now putting either SAGE_ROOT=bar or MPMATH_SAGE=foo in the environment is the quick fix. I may have to put it in sage ebuilds for now.

kiwifb commented 3 years ago

Now installing an env.d variable as a temporary fix. Hopefully something better will come along.

strogdon commented 3 years ago
$ cat /etc/env.d/99sage 
MPMATH_SAGE=1

This does not work here. I still see the

TypeError: Cannot convert mpz to sage.rings.integer.Integer

when doctesting. Also, I noticed that at least one doctest in comment:1 is not related to MPMATH.

sage -t --long --random -seed=0 /usr/lib/python3.9/site-packages/sage/misc/sageinspect.py

It seems odd to me because the failure mentions

ModuleNotFoundError: No module named '_home_steven__sage_temp_hp_probook_8631_tmp_md9yd6zb_pyx_0'

But I don't want to get side-tracked from the present issue.

kiwifb commented 3 years ago

Is MPMATH_SAGE in your environment? env should tell you, if not you may need a new terminal or to do a "env_update"

strogdon commented 3 years ago

No MPMATH_SAGE in my environment. And after env-update

# env | grep SAGE

is empty.

kiwifb commented 3 years ago

Hum, I had to run env-update as root, logout my ssh session and when I logged back in it was there.

strogdon commented 3 years ago

OK, logged out as root and then back in as root and the variable is there. The variable is not present when a new terminal is started as a normal user. However, if I ssh to myself (same machine) in this terminal then the variable is present. Something is not being sourced but not sure what it is.

kiwifb commented 3 years ago

This may be an issue with how your desktop environment start new terminals, new terminal tabs in konsole (kde) gets it. The way to get it as a user without restarting terminals is not env-update but . /etc/profile.

strogdon commented 3 years ago

I suspect that. If I remotely ssh to the machine the variable is present. If I login through one of the tty's then the variable is present. The variable is in profile.env.

strogdon commented 3 years ago

Had to logout of window manager and then in again to permanently fix the issue. Maybe a better way but I'm up to speed now - sourcing /etc/profile was only a terminal specific fix. Strange.

strogdon commented 3 years ago

If you don't have the sageinspect.py then I'll open another issue. I don't believe I have seen it previously.

kiwifb commented 3 years ago

sageinspect.py does take a long time here, but it does pass.

kiwifb commented 3 years ago

Upstream sage ticket https://trac.sagemath.org/ticket/25445 as I noted on sage-devel the kind of behavior we see is probably due to misuse of mpmath's API.

kiwifb commented 3 years ago

I am closing this. Not that there isn't much more to do but it is really out of scope of the overlay.