Upgrade NumPy to 1.18.5, scipy to 1.4.1, add pybind11 package

[mkoeppe]

Follow-up from the update of numpy to 1.16.6 (#29429):

We update

• NumPy to the latest release, 1.18.5
• scipy to latest release, 1.4.1.
  (latest as of 2020-06-05; both versions (and also the upcoming numpy 1.19) support python >= 3.6)

Depends on #29480

CC: @isuruf @dimpase @jdemeyer @embray @slel @vbraun

Component: porting

Author: Matthias Koeppe

Branch/Commit: u/mkoeppe/trac/local_conda_forge_macos_standard__build_error_with_numpy @ 56a6fe1

Reviewer: Isuru Fernando, Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/29425

[isuruf]

comment:1

Can you try setting NPY_DISTUTILS_APPEND_FLAGS=1 in the numpy build script?

[mkoeppe]

comment:2

This didn't make a difference

[mkoeppe]

comment:3

Upgrading numpy to 1.18.2 fixes it; but this will require a Cython upgrade too

[mkoeppe]

Branch: u/mkoeppe/local_conda_forge_macos_standard__build_error_with_numpy

[mkoeppe]

Commit: 6170b87

[mkoeppe]

Author: Matthias Koeppe

[mkoeppe]

New commits:

adf988d	build/pkgs/cython: Update to 0.29.16
6170b87	build/pkgs/numpy: Update numpy to 1.18.2, back out numpy-1.10.2-no-hardcode-blas.patch (does not apply)

[mkoeppe]

comment:7

Tests run at https://github.com/mkoeppe/sage/actions/runs/66127777

[isuruf]

comment:8

Cython URL can be set to https://pypi.io/packages/source/C/Cython/Cython-VERSION.tar.gz

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

078a653

build/pkgs/cython/checksums.ini: Use predictable URL for upstream_url pattern

[sagetrac-git]

Changed commit from 6170b87 to 078a653

[mkoeppe]

comment:10

Thanks!

[isuruf]

Reviewer: Isuru Fernando

[mkoeppe]

comment:12

Breaks py2 builds

Traceback (most recent call last):
  File "setup.py", line 32, in <module>
    raise RuntimeError("Python version >= 3.5 required.")
RuntimeError: Python version >= 3.5 required.
}}

[mkoeppe]

comment:13

Setting milestone to 9.2, which is presumably the first py3-only release

[dimpase]

Commit: c005562

[dimpase]

comment:45

Replying to @mkoeppe:

Filtering out doctest warnings was done on one of the recent glpk tickets

added the last commit to suppress the warning in the proper Pythonic way. The rest stays (mod rebase)

[vbraun]

comment:46

I'm getting various test failures

[mkoeppe]

comment:47

An upgrade ticket like this really needs to be run on the GitHub test infrastructure...

[dimpase]

comment:48

running GH Actions test here https://github.com/dimpase/sage/pull/9

[dimpase]

comment:49

Replying to @mkoeppe:

An upgrade ticket like this really needs to be run on the GitHub test infrastructure...

Unfortunately there seem to be problems with runner setups, e.g. here
https://github.com/dimpase/sage/runs/740349791?check_suite_focus=true

• this is docker (archlinux-latest, standard-gcc_spkg)
  I see

2020-06-04T22:39:01.9688082Z Suggested packages:
2020-06-04T22:39:01.9688790Z   python3-pytest python-setuptools-doc

and a lot of

2020-06-05T03:08:41.2134392Z Failure: ModuleNotFoundError (No module named 'pytest') ... ERROR

which seems to suggest that python3-pytest is a requirement.

Do you know how to fix this?

(there are other errors pointing at internal problems of runners)

Can we easily extend setup to use our own runners?

[mkoeppe]

comment:50

Apparently, running the testsuite of networkx requires pytest. Let's discuss this on #29766.

I don't think this has anything to do with GitHub.

[mkoeppe]

comment:51

In the meantime, numpy 1.18.5 has appeared

[mkoeppe]

Changed branch from u/dimpase/trac/local_conda_forge_macos_standard__build_error_with_numpy to u/mkoeppe/trac/local_conda_forge_macos_standard__build_error_with_numpy

[mkoeppe]

Changed commit from c005562 to 56a6fe1

[mkoeppe]

comment:53

Tests (with #29766) run at https://github.com/mkoeppe/sage/pull/38/checks

---

New commits:

56a6fe1

build/pkgs/numpy: Update to 1.18.5

[mkoeppe]

comment:56

Can this ticket be tested successfully by itself or only as part of the networkx upgrade in #29766? If the latter, then let's close this ticket and merge it into #29766.

[dimpase]

comment:57

Replying to @mkoeppe:

Can this ticket be tested successfully by itself or only as part of the networkx upgrade in #29766? If the latter, then let's close this ticket and merge it into #29766.

no, this one does not need #29766

[mkoeppe]

comment:58

OK, running a new test without #29766 at https://github.com/mkoeppe/sage/pull/39/checks

[mkoeppe]

comment:59

Replying to @dimpase:

Replying to @mkoeppe:

Can this ticket be tested successfully by itself or only as part of the networkx upgrade in #29766? If the latter, then let's close this ticket and merge it into #29766.

no, this one does not need #29766

Actually, on ubuntu-xenial-standard (https://github.com/mkoeppe/sage/runs/745921419), I see lots of failures from the networkx testsuite such as this one:

File "/sage/local/var/tmp/sage/build/networkx-2.2/src/networkx/drawing/nx_pylab.py", line 249, in networkx.drawing.nx_pylab.draw_networkx
Failed example:
    nx.draw(G)
Exception raised:
    Traceback (most recent call last):
      File "/sage/local/lib/python3.7/doctest.py", line 1329, in __run
        compileflags, 1), test.globs)
      File "<doctest networkx.drawing.nx_pylab.draw_networkx[1]>", line 1, in <module>
        nx.draw(G)
      File "/sage/local/var/tmp/sage/build/networkx-2.2/src/networkx/drawing/nx_pylab.py", line 126, in draw
        draw_networkx(G, pos=pos, ax=ax, **kwds)
      File "/sage/local/var/tmp/sage/build/networkx-2.2/src/networkx/drawing/nx_pylab.py", line 278, in draw_networkx
        edge_collection = draw_networkx_edges(G, pos, arrows=arrows, **kwds)
      File "/sage/local/var/tmp/sage/build/networkx-2.2/src/networkx/drawing/nx_pylab.py", line 611, in draw_networkx_edges
        if cb.is_numlike(alpha):
    AttributeError: module 'matplotlib.cbook' has no attribute 'is_numlike'

[mkoeppe]

comment:60

Therefore, let's close this ticket and continue on #29766.