Bug 251626 - math/py-numpy: update to 1.19.4 (compatible with Python 3.9)
Summary: math/py-numpy: update to 1.19.4 (compatible with Python 3.9)
Status: New
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Many People
Assignee: Port Management Team
URL:
Keywords: patch
Depends on: 251412 252540
Blocks:
  Show dependency treegraph
 
Reported: 2020-12-06 00:11 UTC by Greg V
Modified: 2021-01-09 09:58 UTC (History)
3 users (show)

See Also:
bugzilla: maintainer-feedback? (python)
lbartoletti: exp-run?


Attachments
numpy1194.patch (7.53 KB, patch)
2020-12-06 00:11 UTC, Greg V
no flags Details | Diff
Numpy 1.9.0 and bump dependent ports (145.82 KB, patch)
2020-12-27 10:18 UTC, Loïc Bartoletti
no flags Details | Diff
numpy 1.9 and dependent ports v2 (119.43 KB, patch)
2021-01-04 06:21 UTC, Loïc Bartoletti
no flags Details | Diff

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Description Greg V 2020-12-06 00:11:11 UTC
Created attachment 220299 [details]
numpy1194.patch

The version of numpy currently in ports doesn't work with python 3.9, here's an update that does.

--- notes ---

The `${REINPLACE_CMD} -e '\|_examples/$$|d' ${_PYTHONPKGLIST}` line prevents the automatic plist from distutils from including a directory, which would crash pkg, see https://github.com/freebsd/pkg/issues/1911 / https://github.com/freebsd/pkg/pull/1912

The big chunk of files/patch-numpy-distutils-system_info.py that doesn't apply anymore has been removed — I don't think any change like that is necessary now? I have tried both openblas and atlas, make test does run tests with both.
Comment 1 Loïc Bartoletti freebsd_committer 2020-12-24 10:02:53 UTC
Thanks Greg,

AFAIK, NumPy >= 1.19.0 is python 3 only and you should add USES= python:3.6+ instead of USES= python
Comment 2 Antoine Brodin freebsd_committer 2020-12-24 10:28:08 UTC
(In reply to Loïc Bartoletti from comment #1)
And if it's the case,  all ports depending on it have to be changed to python:3.6+ too
Comment 3 Loïc Bartoletti freebsd_committer 2020-12-27 10:18:03 UTC
Created attachment 220988 [details]
Numpy 1.9.0 and bump dependent ports
Comment 4 Loïc Bartoletti freebsd_committer 2020-12-27 10:25:16 UTC
You're right, I updated all the ports. 

A note for math/plot, I tested this port with python:3.6+ and it compiles by adapting the plist.

Can you run an exp-run, please? Thanks
Comment 5 Antoine Brodin freebsd_committer 2020-12-28 13:53:47 UTC
More ports that need to be adjusted:

[00:01:53] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package vera++-1.3.0_14 from devel/vera++ -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:01:55] Error: compute_deps_pkg failed to lookup pkgname for math/py-matplotlib2@py27 processing package vtk6-6.2.0_13 from math/vtk6 -- Is SUBDIR+=py-matplotlib2@py27 missing in math/Makefile and does the port provide the 'py27' FLAVOR?

[00:01:56] Error: compute_deps_pkg failed to lookup pkgname for devel/py-game@py27 processing package py27-kaa-base-0.6.0_12 from multimedia/py-kaa-base -- Is SUBDIR+=py-game@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:01:56] Error: compute_deps_pkg failed to lookup existing pkgname for devel/py-game@py27 processing package py27-kaa-base-0.6.0_12

[00:01:56] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package ceph12-12.2.12_2 from net/ceph12 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:01] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package py27-tagpy-2013.1_21 from audio/py-tagpy@py27 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:01] Error: compute_deps_pkg failed to lookup pkgname for math/py-pandas@py27 processing package py27-pandas-charm-0.3.0_1 from biology/py-pandas-charm@py27 -- Is SUBDIR+=py-pandas@py27 missing in math/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:01] Error: compute_deps_pkg failed to lookup existing pkgname for math/py-pandas@py27 processing package py27-pandas-charm-0.3.0_1

[00:02:01] Error: compute_deps_pkg failed to lookup pkgname for cad/py-gdspy@py27 processing package py27-phidl-1.0.1_1 from cad/py-phidl@py27 -- Is SUBDIR+=py-gdspy@py27 missing in cad/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:01] Error: compute_deps_pkg failed to lookup existing pkgname for cad/py-gdspy@py27 processing package py27-phidl-1.0.1_1

[00:02:01] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package py27-YouCompleteMe-g20191130_1 from devel/youcompleteme@py27 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:01] Error: compute_deps_pkg failed to lookup pkgname for devel/py-game@py27 processing package py27-hypatia_engine-0.3.1_4 from games/hypatia_engine@py27 -- Is SUBDIR+=py-game@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:01] Error: compute_deps_pkg failed to lookup existing pkgname for devel/py-game@py27 processing package py27-hypatia_engine-0.3.1_4

[00:02:01] Error: compute_deps_pkg failed to lookup pkgname for devel/py-game@py27 processing package py27-pyspacewar-1.1.1_1 from games/pyspacewar@py27 -- Is SUBDIR+=py-game@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for devel/py-game@py27 processing package py27-pyspacewar-1.1.1_1

[00:02:02] Error: compute_deps_pkg failed to lookup pkgname for graphics/py-gdal@py27 processing package py27-Fiona-1.8.18 from graphics/py-fiona@py27 -- Is SUBDIR+=py-gdal@py27 missing in graphics/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for graphics/py-gdal@py27 processing package py27-Fiona-1.8.18

[00:02:02] Error: compute_deps_pkg failed to lookup pkgname for devel/py-game@py27 processing package py27-pyganim-0.9.2_3 from graphics/py-pyganim@py27 -- Is SUBDIR+=py-game@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for devel/py-game@py27 processing package py27-pyganim-0.9.2_3

[00:02:02] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package py27-piranha-0.11_7 from math/py-piranha@py27 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup pkgname for math/py-pandas@py27 processing package py27-pandas-datareader-0.8.1 from math/py-pandas-datareader@py27 -- Is SUBDIR+=py-pandas@py27 missing in math/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for math/py-pandas@py27 processing package py27-pandas-datareader-0.8.1

[00:02:02] Error: compute_deps_pkg failed to lookup pkgname for misc/py-onnx@py27 processing package py27-onnx-tf-1.6.0 from misc/py-onnx-tf@py27 -- Is SUBDIR+=py-onnx@py27 missing in misc/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for misc/py-onnx@py27 processing package py27-onnx-tf-1.6.0

[00:02:02] Error: compute_deps_pkg failed to lookup pkgname for devel/py-flatbuffers@py27 processing package py27-tflite-2.3.0 from misc/py-tflite@py27 -- Is SUBDIR+=py-flatbuffers@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for devel/py-flatbuffers@py27 processing package py27-tflite-2.3.0

[00:02:02] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package py27-libtorrent-rasterbar-1.2.10 from net-p2p/py-libtorrent-rasterbar@py27 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup pkgname for science/py-netCDF4@py27 processing package py27-netcdf-flattener-1.2.0 from science/py-netcdf-flattener@py27 -- Is SUBDIR+=py-netCDF4@py27 missing in science/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for science/py-netCDF4@py27 processing package py27-netcdf-flattener-1.2.0

[00:02:02] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package py27-dlib-19.21 from science/py-dlib@py27 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup pkgname for textproc/py-elasticsearch6@py27 processing package py27-elasticsearch-dsl-6.4.0_1 from textproc/py-elasticsearch-dsl@py27 -- Is SUBDIR+=py-elasticsearch6@py27 missing in textproc/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for textproc/py-elasticsearch6@py27 processing package py27-elasticsearch-dsl-6.4.0_1

[00:02:02] Error: compute_deps_pkg failed to lookup pkgname for textproc/py-elasticsearch6@py27 processing package py27-elasticsearch-curator-5.6.0_1 from textproc/py-elasticsearch-curator@py27 -- Is SUBDIR+=py-elasticsearch6@py27 missing in textproc/Makefile and does the port provide the 'py27' FLAVOR?

[00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for textproc/py-elasticsearch6@py27 processing package py27-elasticsearch-curator-5.6.0_1
Comment 6 Loïc Bartoletti freebsd_committer 2021-01-04 06:21:39 UTC
Created attachment 221265 [details]
numpy 1.9 and dependent ports v2

Here is the updated version which includes the latest python commits.
Comment 8 Rainer Hurling freebsd_committer 2021-01-06 08:20:35 UTC
(In reply to Antoine Brodin from comment #7)
Regarding the log file for py-pandas: There is a bug #251412 with an update for py-pandas from 0.24.2 to 1.15.0, ready to commit ;)

Maybe the error with the undeclared identifier 'NUMPY_IMPORT_ARRAY_RETVAL' does not occur with this version of py-pandas (untested)?
Comment 9 Loïc Bartoletti freebsd_committer 2021-01-09 07:32:08 UTC
(In reply to Rainer Hurling from comment #8)
I tried your patch of py-pandas and it built fine with numpy 1.9, please commit it :)