Opened 2 years ago

Closed 18 months ago

#31008 closed enhancement (fixed)

Upgrade NumPy to 1.20.3, SciPy 1.6.3, networkx 2.5.1

Reported by: Matthias Köppe Owned by:
Priority: major Milestone: sage-9.4
Component: packages: standard Keywords:
Cc: Samuel Lelièvre, François Bissey Merged in:
Authors: Antonio Rojas, Matthias Koeppe Reviewers: Dima Pasechnik
Report Upstream: N/A Work issues:
Branch: 02f6848 (Commits, GitHub, GitLab) Commit: 02f68482174d6a4b49d0a8cd1e3575ee3c007fc5
Dependencies: #31860 Stopgaps:

Status badges

Description (last modified by Matthias Köppe)

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

Change History (20)

comment:1 Changed 22 months ago by Antonio Rojas

Branch: u/arojas/upgrade_numpy_to_1_20_x____needs_python____3_7

comment:2 Changed 22 months ago by Antonio Rojas

Authors: Antonio Rojas
Cc: François Bissey added
Commit: 022d34a10e3969bf0b5489893814174d9690b8dd
Status: newneeds_review

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

comment:3 Changed 22 months ago by Matthias Köppe

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

comment:4 Changed 22 months ago by Antonio Rojas

Dependencies: #30551#30551 #31364

Done, #31364

comment:5 Changed 20 months ago by Matthias Köppe

Branch: u/arojas/upgrade_numpy_to_1_20_x____needs_python____3_7u/mkoeppe/upgrade_numpy_to_1_20_x____needs_python____3_7

comment:6 Changed 20 months ago by Matthias Köppe

Authors: Antonio RojasAntonio Rojas, Matthias Koeppe
Commit: 022d34a10e3969bf0b5489893814174d9690b8dd57338c1cc0a835b9ac7fb027ffa99bb5f77a45fc
Dependencies: #30551 #31364#30551
Description: modified (diff)
Summary: Upgrade NumPy to 1.20.x -- needs python >= 3.7Upgrade NumPy to 1.20.x, SciPy 1.6.2, networkx 2.5.1 -- needs python >= 3.7

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

comment:7 Changed 19 months ago by git

Commit: 57338c1cc0a835b9ac7fb027ffa99bb5f77a45fc02f68482174d6a4b49d0a8cd1e3575ee3c007fc5

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

comment:8 Changed 19 months ago by Matthias Köppe

Summary: Upgrade NumPy to 1.20.x, SciPy 1.6.2, networkx 2.5.1 -- needs python >= 3.7Upgrade NumPy to 1.20.3, SciPy 1.6.3, networkx 2.5.1

comment:9 Changed 19 months ago by Matthias Köppe

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

comment:10 Changed 18 months ago by Dima Pasechnik

all GH tests failed here, restart them, maybe?

comment:11 Changed 18 months ago by Matthias Köppe

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

comment:12 Changed 18 months ago by Matthias Köppe

Dependencies: #30551#31860

comment:13 Changed 18 months ago by Matthias Köppe

Reviewers: https://github.com/mkoeppe/sage/actions/runs/873204088https://github.com/mkoeppe/sage/actions/runs/903785429

comment:14 Changed 18 months ago by Matthias Köppe

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

comment:15 Changed 18 months ago by Matthias Köppe

Reviewers: https://github.com/mkoeppe/sage/actions/runs/903785429https://github.com/mkoeppe/sage/actions/runs/904444329

comment:16 Changed 18 months ago by Matthias Köppe

Reviewers: https://github.com/mkoeppe/sage/actions/runs/904444329https://github.com/mkoeppe/sage/actions/runs/904504331

comment:17 Changed 18 months ago by Matthias Köppe

Now there are useful reports from GH Actions.

comment:18 Changed 18 months ago by Dima Pasechnik

Reviewers: https://github.com/mkoeppe/sage/actions/runs/904504331Dima Pasechnik
Status: needs_reviewpositive_review

lgtm

comment:19 Changed 18 months ago by Matthias Köppe

Thanks!

comment:20 Changed 18 months ago by Volker Braun

Branch: u/mkoeppe/upgrade_numpy_to_1_20_x____needs_python____3_702f68482174d6a4b49d0a8cd1e3575ee3c007fc5
Resolution: fixed
Status: positive_reviewclosed
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