Update minimum numpy support to match 1.23[.2] (#4402)

* Update minimum numpy support to match 1.23.2 [NEP29]

.github/workflows/gh-ci.yaml

@@ -41,7 +41,7 @@ jobs:
               python-version: 3.9
               full-deps: false
               codecov: true
-              numpy: numpy=1.22.3
+              numpy: numpy=1.23.2
             - name: asv_check
               os: ubuntu-latest
               python-version: 3.9

.github/workflows/linters.yaml

@@ -145,7 +145,7 @@ jobs:
         with:
           micromamba: true
           full-deps: true
-          numpy: numpy=1.22.3
+          numpy: numpy=1.23.2
 
       - name: install
         run: |

azure-pipelines.yml

@@ -41,7 +41,7 @@ jobs:
           PYTHON_VERSION: '3.9'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.22.3'
+          NUMPY_MIN: '1.23.2'
           imageName: 'windows-2019'
         Linux-Python312-64bit-full-wheel:
           PYTHON_VERSION: '3.12'
@@ -53,7 +53,7 @@ jobs:
           PYTHON_VERSION: '3.9'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.22.3'
+          NUMPY_MIN: '1.23.2'
           imageName: 'ubuntu-latest'
   pool:
     vmImage: $(imageName)

maintainer/conda/environment.yml

@@ -18,7 +18,7 @@ dependencies:
   - mmtf-python
   - mock
   - networkx
-  - numpy>=1.22.3
+  - numpy>=1.23.2
   - pytest
   - python==3.9
   - pytng>=0.2.3

package/CHANGELOG

@@ -24,6 +24,9 @@ Fixes
 Enhancements
 
 Changes
+ * As per NEP29, the minimum version of numpy has been raised to 1.23.
+   We have opted to pin to 1.23.2 to ensure the same minimum numpy version
+   is used from python 3.9 to 3.11 (Issue #4401, PR #4402)
 
 Deprecations
 

package/pyproject.toml

@@ -5,15 +5,9 @@ requires = [
     "packaging",
     # lowest NumPy we can use for a given Python,
     # In part adapted from: https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
-    # except for more exotic platform (Mac Arm flavors)
-    # aarch64, AIX, s390x, and arm64 all support 1.21 so we can safely pin to this
-    # Note: MDA does not build with PyPy so we do not support it in the build system
-    # Scipy: On windows avoid 1.21.6, 1.22.0, and 1.22.1 because they were built on vc142
-    # Let's set everything to this version to make things clean, also avoids other issues
-    # on other archs
-    "numpy==1.22.3; python_version=='3.9' and platform_python_implementation != 'PyPy'",
-    "numpy==1.22.3; python_version=='3.10' and platform_python_implementation != 'PyPy'",
-    "numpy==1.23.2; python_version=='3.11' and platform_python_implementation != 'PyPy'",
+    # As per NEP29, we set the minimum version to 1.23.2 for Python <=3.11
+    # and 1.26.0 (first to support) for Python 3.12
+    "numpy==1.23.2; python_version<='3.11' and platform_python_implementation != 'PyPy'",
     "numpy==1.26.0; python_version=='3.12' and platform_python_implementation != 'PyPy'",
     # For unreleased versions of Python there is currently no known supported
     # NumPy version. In that case we just let it be a bare NumPy install
@@ -35,7 +29,7 @@ maintainers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    'numpy>=1.22.3',
+    'numpy>=1.23.2',
     'GridDataFormats>=0.4.0',
     'mmtf-python>=1.0.0',
     'joblib>=0.12',
@@ -109,4 +103,3 @@ Discord = 'https://discord.com/channels/807348386012987462/'
 Blog = 'https://www.mdanalysis.org/blog/'
 Twitter = 'https://twitter.com/mdanalysis'
 Source = 'https://github.com/mdanalysis/mdanalysis'
-

package/requirements.txt

@@ -10,7 +10,7 @@ matplotlib
 mmtf-python
 netcdf4
 networkx
-numpy>=1.22.3
+numpy>=1.23.2
 packaging
 parmed
 pytest

package/setup.py

@@ -591,7 +591,7 @@ def long_description(readme):
     exts, cythonfiles = extensions(config)
 
     install_requires = [
-          'numpy>=1.22.3',
+          'numpy>=1.23.2',
           'GridDataFormats>=0.4.0',
           'mmtf-python>=1.0.0',
           'joblib>=0.12',
@@ -637,7 +637,7 @@ def long_description(readme):
           # all standard requirements are available through PyPi and
           # typically can be installed without difficulties through setuptools
           setup_requires=[
-              'numpy>=1.21.0',
+              'numpy>=1.23.2',
               'packaging',
           ],
           install_requires=install_requires,