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:  sage9.4 
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: 
Description (last modified by )
The upgrade to 1.20.x https://numpy.org/devdocs/release/1.20.0notes.html require dropping support for Python 3.6
 1.20.0rc1 released 20201203  https://pypi.org/project/numpy/#history
Change History (20)
comment:1 Changed 22 months ago by
Branch:  → u/arojas/upgrade_numpy_to_1_20_x____needs_python____3_7 

comment:2 Changed 22 months ago by
Authors:  → Antonio Rojas 

Cc:  François Bissey added 
Commit:  → 022d34a10e3969bf0b5489893814174d9690b8dd 
Status:  new → needs_review 
comment:3 Changed 22 months ago by
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:5 Changed 20 months ago by
Branch:  u/arojas/upgrade_numpy_to_1_20_x____needs_python____3_7 → u/mkoeppe/upgrade_numpy_to_1_20_x____needs_python____3_7 

comment:6 Changed 20 months ago by
Authors:  Antonio Rojas → Antonio Rojas, Matthias Koeppe 

Commit:  022d34a10e3969bf0b5489893814174d9690b8dd → 57338c1cc0a835b9ac7fb027ffa99bb5f77a45fc 
Dependencies:  #30551 #31364 → #30551 
Description:  modified (diff) 
Summary:  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 
Last 10 new commits:
66c2987  build/pkgs/{sage_sws2rst,sage_docbuild}/installrequires.txt: New

7f8ec6c  build/pkgs/sagelib/src/tox.ini: Add factor sitepackages

0283da5  build/make/Makefile.in: Add wheel, setuptools_wheel to PYTHON_TOOLCHAIN to make sure that PEP 517 packages have a complete build system

f720722  build/pkgs/sagelib/src/tox.ini: Add factor nobuildisolation

c451b31  src/setup.cfg.m4 (install_requires): Add sage_conf

6700223  Merge tag '9.3.rc0' into t/30913/sagelib__add_setup_cfg__install_requires_

04da2c6  build/pkgs/ipywidgets: Patch out declaring installrequires of nbformat and jupyterlabwidgets

815c944  Merge #30913

b06731c  Remove Python 3.6 support from metadata and documentation

57338c1  Update numpy to 1.20.2, scipy to 1.6.2, networkx to 2.5.1

comment:7 Changed 19 months ago by
Commit:  57338c1cc0a835b9ac7fb027ffa99bb5f77a45fc → 02f68482174d6a4b49d0a8cd1e3575ee3c007fc5 

comment:8 Changed 19 months ago by
Summary:  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 

comment:9 Changed 19 months ago by
Reviewers:  → https://github.com/mkoeppe/sage/actions/runs/873204088 

comment:11 Changed 18 months ago by
On this GH Actions run, I merged many tickets. All failures are of the form
[sagelib9.3] building 'sage.rings.padics.padic_relaxed_element' extension [sagelib9.3] Executing 1 command (using 1 thread) [sagelib9.3] [1/1] gcc Wnounusedresult Wsigncompare DNDEBUG g fwrapv O2 Wall g fstackprotectorstrong Wformat Werror=formatsecurity 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/sitepackages/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.linuxx86_643.8/build/cythonized/sage/rings/padics/padic_relaxed_element.o fnostrictaliasing DCYTHON_CLINE_IN_TRACEBACK=1 std=c99 [sagelib9.3] 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 [sagelib9.3] 5174  #include "sage/libs/linkages/padics/relaxed/flint_helper.c" [sagelib9.3]  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [sagelib9.3] compilation terminated.
Not sure which one caused this
comment:12 Changed 18 months ago by
Dependencies:  #30551 → #31860 

comment:13 Changed 18 months ago by
Reviewers:  https://github.com/mkoeppe/sage/actions/runs/873204088 → https://github.com/mkoeppe/sage/actions/runs/903785429 

comment:15 Changed 18 months ago by
Reviewers:  https://github.com/mkoeppe/sage/actions/runs/903785429 → https://github.com/mkoeppe/sage/actions/runs/904444329 

comment:16 Changed 18 months ago by
Reviewers:  https://github.com/mkoeppe/sage/actions/runs/904444329 → https://github.com/mkoeppe/sage/actions/runs/904504331 

comment:18 Changed 18 months ago by
Reviewers:  https://github.com/mkoeppe/sage/actions/runs/904504331 → Dima Pasechnik 

Status:  needs_review → positive_review 
lgtm
comment:20 Changed 18 months ago by
Branch:  u/mkoeppe/upgrade_numpy_to_1_20_x____needs_python____3_7 → 02f68482174d6a4b49d0a8cd1e3575ee3c007fc5 

Resolution:  → fixed 
Status:  positive_review → closed 
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The type aliases
numpy.int
,numpy.complex
andnumpy.float
are now deprecatedNew commits:
Don't use deprecated numpy type aliases
Update numpy to 1.20.1