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Upgrade NumPy to 1.20.3, SciPy 1.6.3, networkx 2.5.1 #31008

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mkoeppe opened this issue Dec 5, 2020 · 28 comments
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Upgrade NumPy to 1.20.3, SciPy 1.6.3, networkx 2.5.1 #31008

mkoeppe opened this issue Dec 5, 2020 · 28 comments
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c: packages: standard p: major / 3 t: enhancement
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sage-9.4

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@mkoeppe
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mkoeppe commented Dec 5, 2020

The upgrade to 1.20.x https://numpy.org/devdocs/release/1.20.0-notes.html require dropping support for Python 3.6

Depends on #31860

CC: @slel @kiwifb

Component: packages: standard

Author: Antonio Rojas, Matthias Koeppe

Branch/Commit: 02f6848

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/31008
@mkoeppe mkoeppe added this to the sage-9.4 milestone Dec 5, 2020
@antonio-rojas
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Branch: u/arojas/upgrade_numpy_to_1_20_x____needs_python____3_7

@antonio-rojas
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Author: Antonio Rojas

@antonio-rojas
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comment:2

The type aliases numpy.int, numpy.complex and numpy.float are now deprecated

New commits:

55fb295Don't use deprecated numpy type aliases
022d34aUpdate numpy to 1.20.1

@antonio-rojas
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Commit: 022d34a

@mkoeppe
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mkoeppe commented Feb 8, 2021

comment:3

Assuming the fixes to src/sage also work for 1.19.x, I'd suggest to put them on a separate ticket so we can get them in Sage 9.3. The upgrade itself will have to wait as it requires dropping python3.6 support

@antonio-rojas
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Changed dependencies from #30551 to #30551 #31364

@antonio-rojas
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comment:4

Done, #31364

@mkoeppe
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mkoeppe commented Apr 19, 2021

Changed branch from u/arojas/upgrade_numpy_to_1_20_x____needs_python____3_7 to u/mkoeppe/upgrade_numpy_to_1_20_x____needs_python____3_7

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mkoeppe commented Apr 19, 2021

Last 10 new commits:

66c2987build/pkgs/{sage_sws2rst,sage_docbuild}/install-requires.txt: New
7f8ec6cbuild/pkgs/sagelib/src/tox.ini: Add factor sitepackages
0283da5build/make/Makefile.in: Add wheel, setuptools_wheel to PYTHON_TOOLCHAIN to make sure that PEP 517 packages have a complete build system
f720722build/pkgs/sagelib/src/tox.ini: Add factor nobuildisolation
c451b31src/setup.cfg.m4 (install_requires): Add sage_conf
6700223Merge tag '9.3.rc0' into t/30913/sagelib__add_setup_cfg__install_requires_
04da2c6build/pkgs/ipywidgets: Patch out declaring install-requires of nbformat and jupyterlab-widgets
815c944Merge #30913
b06731cRemove Python 3.6 support from metadata and documentation
57338c1Update numpy to 1.20.2, scipy to 1.6.2, networkx to 2.5.1

@mkoeppe
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mkoeppe commented Apr 19, 2021

Changed dependencies from #30551 #31364 to #30551

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mkoeppe commented Apr 19, 2021

Changed commit from 022d34a to 57338c1

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@mkoeppe
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mkoeppe commented Apr 19, 2021

Changed author from Antonio Rojas to Antonio Rojas, Matthias Koeppe

@mkoeppe mkoeppe changed the title Upgrade NumPy to 1.20.x -- needs python >= 3.7 Upgrade NumPy to 1.20.x, SciPy 1.6.2, networkx 2.5.1 -- needs python >= 3.7 Apr 19, 2021
@sagetrac-git
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sagetrac-git mannequin commented May 12, 2021

Changed commit from 57338c1 to 02f6848

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sagetrac-git mannequin commented May 12, 2021

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

ac49be0build/pkgs/numpy: Update to 1.20.3
02f6848build/pkgs/scipy: Update to 1.6.3

@mkoeppe mkoeppe changed the title Upgrade NumPy to 1.20.x, SciPy 1.6.2, networkx 2.5.1 -- needs python >= 3.7 Upgrade NumPy to 1.20.3, SciPy 1.6.3, networkx 2.5.1 May 12, 2021
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mkoeppe commented May 25, 2021

Reviewer: https://github.com/mkoeppe/sage/actions/runs/873204088

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dimpase commented Jun 3, 2021

comment:10

all GH tests failed here, restart them, maybe?

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mkoeppe commented Jun 3, 2021

comment:11

On this GH Actions run, I merged many tickets. All failures are of the form

  [sagelib-9.3]   building 'sage.rings.padics.padic_relaxed_element' extension
  [sagelib-9.3]   Executing 1 command (using 1 thread)
  [sagelib-9.3]   [1/1] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -O2 -g -march=native -fPIC -I./sage/libs/flint -I./sage/cpython -Isage/libs/flint -I/sage/build/pkgs/sagelib/src -I/usr/include/python3.8 -I/sage/local/lib/python3.8/site-packages/numpy/core/include -Ibuild/cythonized -I/sage/local/include -I/usr/include/python3.8 -c build/cythonized/sage/rings/padics/padic_relaxed_element.c -o build/temp.linux-x86_64-3.8/build/cythonized/sage/rings/padics/padic_relaxed_element.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c99
  [sagelib-9.3]   build/cythonized/sage/rings/padics/padic_relaxed_element.c:5174:10: fatal error: sage/libs/linkages/padics/relaxed/flint_helper.c: No such file or directory
  [sagelib-9.3]    5174 | #include "sage/libs/linkages/padics/relaxed/flint_helper.c"
  [sagelib-9.3]         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  [sagelib-9.3]   compilation terminated.

Not sure which one caused this

@mkoeppe
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mkoeppe commented Jun 3, 2021

Changed dependencies from #30551 to #31860

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mkoeppe commented Jun 3, 2021

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/873204088 to https://github.com/mkoeppe/sage/actions/runs/903785429

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mkoeppe commented Jun 3, 2021

comment:14

Already 9.4.beta0 is broken with the same error - see #31903

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mkoeppe commented Jun 3, 2021

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/903785429 to https://github.com/mkoeppe/sage/actions/runs/904444329

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mkoeppe commented Jun 3, 2021

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/904444329 to https://github.com/mkoeppe/sage/actions/runs/904504331

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mkoeppe commented Jun 4, 2021

comment:17

Now there are useful reports from GH Actions.

@dimpase
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dimpase commented Jun 7, 2021

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/904504331 to Dima Pasechnik

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dimpase commented Jun 7, 2021

comment:18

lgtm

@mkoeppe
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mkoeppe commented Jun 7, 2021

comment:19

Thanks!

@vbraun
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vbraun commented Jun 19, 2021

Changed branch from u/mkoeppe/upgrade_numpy_to_1_20_x____needs_python____3_7 to 02f6848

@vbraun vbraun closed this as completed in 4363ed9 Jun 19, 2021
@embray embray mentioned this issue Jan 3, 2021
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