From 949fff3d9d3142f3c4ae68c0f527afc8b11e66bb Mon Sep 17 00:00:00 2001
From: Ziv Yaniv <zivyaniv@nih.gov>
Date: Tue, 10 Feb 2026 10:13:53 -0500
Subject: [PATCH] Update Python versions in CI, remove macos-intel.

Python 3.9 reached its end of life on October 31 2025.
Changing tested versions from 3.9 and 3.12 to 3.10 and 3.13.

Also, there is an issue with the llvmlite package on macos-15-intel.
It is no longer available from PyPI for Python 3.10 and above. As a
consequence we are removing testing on this platform as the minimal
tested Python version is now 3.10.
---
 .circleci/config.yml                      |  4 ++--
 .github/workflows/main.yml                | 16 +++++-----------
 .github/workflows/scheduled_or_manual.yml | 16 +++++-----------
 3 files changed, 12 insertions(+), 24 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 6a861b02..7ff76c05 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -28,7 +28,7 @@ executors:
 jobs:
   lint:
     docker:
-      - image: cimg/python:3.12
+      - image: cimg/python:3.13
     steps:
       - checkout
       - run:
@@ -111,7 +111,7 @@ workflows:
       - test:
           matrix:
             parameters:
-              python-version: ['3.9', '3.12']
+              python-version: ['3.10', '3.13']
               os: ["linux"]
           requires:
             - lint
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d857f78c..66638a9e 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -21,10 +21,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v6
-    - name: Set up Python 3.12
+    - name: Set up Python 3.13
       uses: actions/setup-python@v6
       with:
-        python-version: '3.12'
+        python-version: '3.13'
     - name: Install and run black for notebooks
       run: |
         python -m pip install --upgrade pip
@@ -33,15 +33,9 @@ jobs:
   test:
     needs: lint
     strategy:
-      matrix: #using macos-15-intel, last available intel architecture. macos-latest is arm64 architecture.
-        os: [macos-15-intel, windows-latest, ubuntu-latest, macos-latest]
-        python-version: ['3.9', '3.12']
-        # Combination of old architecture, macos-intel, and new python, 3.12, causes issues:
-        # llvmlite is not available for this combination from PyPI so skip that testing.
-        # It is available from conda-forge so not completely unsupported.
-        exclude:
-          - os: macos-15-intel
-            python-version: '3.12'
+      matrix:
+        os: [windows-latest, ubuntu-latest, macos-latest]
+        python-version: ['3.10', '3.13']
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v6
diff --git a/.github/workflows/scheduled_or_manual.yml b/.github/workflows/scheduled_or_manual.yml
index b429a09d..4b40a7b8 100644
--- a/.github/workflows/scheduled_or_manual.yml
+++ b/.github/workflows/scheduled_or_manual.yml
@@ -22,10 +22,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v6
-    - name: Set up Python 3.12
+    - name: Set up Python 3.13
       uses: actions/setup-python@v6
       with:
-        python-version: '3.12'
+        python-version: '3.13'
     - name: Install and run black for notebooks
       run: |
         python -m pip install --upgrade pip
@@ -34,15 +34,9 @@ jobs:
   test:
     needs: lint
     strategy:
-      matrix: #using macos-15-intel, last available intel architecture. macos-latest is arm64 architecture.
-        os: [macos-15-intel, windows-latest, macos-latest]
-        python-version: ['3.9', '3.12']
-        # Combination of old architecture, macos-intel, and new python, 3.12, causes issues:
-        # llvmlite is not available for this combination from PyPI so skip that testing.
-        # It is available from conda-forge so not completely unsupported.
-        exclude:
-          - os: macos-15-intel
-            python-version: '3.12'
+      matrix:
+        os: [windows-latest, macos-latest]
+        python-version: ['3.10', '3.13']
         inputs: ["00_ or 01_ or 02_ or 03_ or 04_ or 05_ or 10_ or 20_ or 21_ or 22_ or 300_ or 30_ or 31_ or 32_ or 33_ or 34_ or 35_ or 36_", "51_ or 55_ or 56_ or 60_ or 61_ or 62_ or 63_ or 64_", "65_ or 66_ or 67_ or 68_ or 69_ or 70_ or 71_"]
     runs-on: ${{ matrix.os }}
     steps: