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bump up numpy min version to 1.20 #3737

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merged 5 commits into from
Jul 5, 2022
Merged

bump up numpy min version to 1.20 #3737

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5c4db42
bump up numpy min version to 1.20
IAlibay Jun 27, 2022
7c5dc14
update changelog
IAlibay Jun 27, 2022
85d1b1f
Merge branch 'develop' into numpy-1.20
IAlibay Jun 30, 2022
5b7e8dd
Pin arm64 darwin to 1.21, bump min for py3.10
IAlibay Jun 30, 2022
75cf13f
update changelog
IAlibay Jul 4, 2022
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2 changes: 1 addition & 1 deletion .github/workflows/gh-ci.yaml
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Expand Up @@ -57,7 +57,7 @@ jobs:
full-deps: false
install_hole: false
codecov: false
numpy: numpy=1.19.0
numpy: numpy=1.20.0
- name: asv_check
os: ubuntu-latest
python-version: 3.8
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2 changes: 1 addition & 1 deletion .travis.yml
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Expand Up @@ -44,7 +44,7 @@ matrix:
group: edge
if: type = cron
before_install:
- python -m pip install cython "numpy>=1.19.2" scipy
- python -m pip install cython "numpy>=1.20.0" scipy
- python -m pip install --no-build-isolation hypothesis matplotlib packaging pytest pytest-cov pytest-xdist tqdm threadpoolctl fasteners
install:
- cd package
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8 changes: 4 additions & 4 deletions azure-pipelines.yml
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Expand Up @@ -40,25 +40,25 @@ jobs:
PYTHON_VERSION: '3.9'
PYTHON_ARCH: 'x64'
BUILD_TYPE: 'wheel'
NUMPY_MIN: '1.19.3'
NUMPY_MIN: '1.20.0'
imageName: 'windows-2019'
Win-Python38-64bit-full-wheel:
PYTHON_VERSION: '3.8'
PYTHON_ARCH: 'x64'
BUILD_TYPE: 'wheel'
NUMPY_MIN: '1.19.0'
NUMPY_MIN: '1.20.0'
imageName: 'windows-2019'
Linux-Python39-64bit-full-wheel:
PYTHON_VERSION: '3.9'
PYTHON_ARCH: 'x64'
BUILD_TYPE: 'wheel'
NUMPY_MIN: '1.19.3'
NUMPY_MIN: '1.20.0'
imageName: 'ubuntu-latest'
Linux-Python38-64bit-full-wheel:
PYTHON_VERSION: '3.8'
PYTHON_ARCH: 'x64'
BUILD_TYPE: 'wheel'
NUMPY_MIN: '1.19.3'
NUMPY_MIN: '1.20.0'
imageName: 'ubuntu-latest'
pool:
vmImage: $(imageName)
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2 changes: 1 addition & 1 deletion maintainer/conda/environment.yml
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Expand Up @@ -16,7 +16,7 @@ dependencies:
- mmtf-python
- mock
- networkx
- numpy>=1.19
- numpy>=1.20
- pytest
- python==3.8
- scikit-learn
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1 change: 1 addition & 0 deletions package/CHANGELOG
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Expand Up @@ -29,6 +29,7 @@ Enhancements
(CZI Performance track, PR #3683)

Changes
* Minimum supported NumPy version is now 1.20 as per NEP29 (PR #3737)
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* Narrowed variable scope to reduce use of OpenMP `private` clause (PR #3706, PR
#3728)

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9 changes: 3 additions & 6 deletions package/pyproject.toml
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Expand Up @@ -4,13 +4,10 @@ requires = [
"Cython>=0.28",
"packaging",
# lowest NumPy we can use for a given Python,
# except for more exotic platforms (linux/Mac ARM flavors)
"numpy==1.19; python_version=='3.8' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_machine!='aarch64'",
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@tylerjereddy I wasn't 100% sure of the logic here, we seem to have entries specfic for "not ((arm64 or Darwin) and aarch64)" and "arm64 and Darwin" but nothing for aarch64. Is there a specific reason we were restricting aarch64 to py3.10 only?

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Older Python versions should be "ok" with aarch64 I think. This is a good reference as always: https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg#L29

Of course, there's no substitute for actually trying it with pip install .., but my original draft was probably incomplete anyway, especially for the more exotic platforms.

"numpy==1.19.3; python_version=='3.9' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_machine!='aarch64'",
# arm65 on Darwin supports py3.8 and above and requires numpy>=1.20.0
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Is "arm65" a thing? OR should this be "arm64"?

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typo definitely

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Suggested change
# arm65 on Darwin supports py3.8 and above and requires numpy>=1.20.0
# arm64 on Darwin supports py3.8 and above and requires numpy>=1.21.0

and then change below

"numpy==1.20.0; python_version=='3.8'",
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Suggested change
"numpy==1.20.0; python_version=='3.8'",
"numpy==1.21.0; python_version=='3.8'",

"numpy==1.20.0; python_version=='3.9'",
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Suggested change
"numpy==1.20.0; python_version=='3.9'",
"numpy==1.21.0; python_version=='3.9'",

"numpy==1.21.4; python_version=='3.10' and platform_python_implementation != 'PyPy'",
"setuptools",
"wheel",
# arm64 on Darwin supports Python 3.8 and above and requires numpy>=1.20.0
"numpy==1.20.0; python_version=='3.8' and platform_machine=='arm64' and platform_system=='Darwin'",
"numpy==1.20.0; python_version=='3.9' and platform_machine=='arm64' and platform_system=='Darwin'",
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I remember this tripping up a user on Discord because it forces a from-source build of NumPy on M1 macs--perhaps we should consider doing the same thing as oldest-supported-numpy and just requiring 1.21.0 as described here: https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg#L37 ?

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Yeah reading the comment re: universal2 I'm pretty happy bumping up the darwin + arm64 requirements to 1.21.0.

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Sounds sensible.

And thank you @tylerjereddy for linking to the setup.cfg... might be good to keep the link around somewhere.... maybe a wiki page of tips of the trade for packaging? ;-)

]
2 changes: 1 addition & 1 deletion package/requirements.txt
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Expand Up @@ -11,7 +11,7 @@ mmtf-python
msmb_theme==1.2.0
netcdf4
networkx
numpy>=1.19.0
numpy>=1.20.0
packaging
parmed
pytest
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6 changes: 3 additions & 3 deletions package/setup.py
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Expand Up @@ -190,7 +190,7 @@ def get_numpy_include():
import numpy as np
except ImportError:
print('*** package "numpy" not found ***')
print('MDAnalysis requires a version of NumPy (>=1.19.0), even for setup.')
print('MDAnalysis requires a version of NumPy (>=1.20.0), even for setup.')
print('Please get it from http://numpy.scipy.org/ or install it through '
'your package manager.')
sys.exit(-1)
Expand Down Expand Up @@ -597,7 +597,7 @@ def long_description(readme):
exts, cythonfiles = extensions(config)

install_requires = [
'numpy>=1.19.0',
'numpy>=1.20.0',
'biopython>=1.71',
'networkx>=2.0',
'GridDataFormats>=0.4.0',
Expand Down Expand Up @@ -646,7 +646,7 @@ def long_description(readme):
# all standard requirements are available through PyPi and
# typically can be installed without difficulties through setuptools
setup_requires=[
'numpy>=1.19.0',
'numpy>=1.20.0',
'packaging',
],
install_requires=install_requires,
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