From 23456771851a23f54ed58c592251ca01048a783b Mon Sep 17 00:00:00 2001
From: IAlibay <ialibay@mdanalysis.org>
Date: Fri, 29 Dec 2023 15:02:21 +0000
Subject: [PATCH] Update minimum numpy support to match 1.23.2

---
 .github/workflows/gh-ci.yaml     | 2 +-
 .github/workflows/linters.yaml   | 2 +-
 azure-pipelines.yml              | 4 ++--
 maintainer/conda/environment.yml | 2 +-
 package/CHANGELOG                | 3 +++
 package/pyproject.toml           | 6 +++---
 package/requirements.txt         | 2 +-
 package/setup.py                 | 4 ++--
 8 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
index 578f4e4e845..79ac678c398 100644
--- a/.github/workflows/gh-ci.yaml
+++ b/.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
diff --git a/.github/workflows/linters.yaml b/.github/workflows/linters.yaml
index b4b9b061cb6..8a708169d1c 100644
--- a/.github/workflows/linters.yaml
+++ b/.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: |
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 61d58be7e95..4affb137b55 100644
--- a/azure-pipelines.yml
+++ b/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)
diff --git a/maintainer/conda/environment.yml b/maintainer/conda/environment.yml
index a3dbb3400ed..ea3e2b50028 100644
--- a/maintainer/conda/environment.yml
+++ b/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
diff --git a/package/CHANGELOG b/package/CHANGELOG
index c65ce91703a..3c5522cacd9 100644
--- a/package/CHANGELOG
+++ b/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
 
diff --git a/package/pyproject.toml b/package/pyproject.toml
index 4b1ed86317c..1b21650a5cf 100644
--- a/package/pyproject.toml
+++ b/package/pyproject.toml
@@ -11,8 +11,8 @@ requires = [
     # 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=='3.9' and platform_python_implementation != 'PyPy'",
+    "numpy==1.23.2; python_version=='3.10' and platform_python_implementation != 'PyPy'",
     "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
@@ -35,7 +35,7 @@ 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',
diff --git a/package/requirements.txt b/package/requirements.txt
index 0a95277bf2a..accac1b49fd 100644
--- a/package/requirements.txt
+++ b/package/requirements.txt
@@ -10,7 +10,7 @@ matplotlib
 mmtf-python
 netcdf4
 networkx
-numpy>=1.22.3
+numpy>=1.23.2
 packaging
 parmed
 pytest
diff --git a/package/setup.py b/package/setup.py
index ccc846b38ad..bef7ae75c47 100755
--- a/package/setup.py
+++ b/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,