From 01d82003855625886355a80b3f3ec3d982c9bea4 Mon Sep 17 00:00:00 2001
From: dbouget <bougetd@gmail.com>
Date: Wed, 9 Jul 2025 17:34:19 +0200
Subject: [PATCH 1/2] Trying the unified onnxruntime [skip ci]

---
 .github/workflows/build.yml | 24 ++++++++++++++++--------
 pyproject.toml              |  9 ++++-----
 2 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index a9fd4e0..699a420 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -66,8 +66,6 @@ jobs:
     strategy:
       matrix:
         include:
-          - os: ubuntu-22.04
-            python-version: "3.8"
           - os: ubuntu-22.04
             python-version: "3.9"
           - os: ubuntu-22.04
@@ -76,8 +74,8 @@ jobs:
             python-version: "3.11"
           - os: ubuntu-22.04
             python-version: "3.12"
-          - os: ubuntu-24.04
-            python-version: "3.8"
+          - os: ubuntu-22.04
+            python-version: "3.13"
           - os: ubuntu-24.04
             python-version: "3.9"
           - os: ubuntu-24.04
@@ -86,8 +84,8 @@ jobs:
             python-version: "3.11"
           - os: ubuntu-24.04
             python-version: "3.12"
-          - os: windows-2022
-            python-version: "3.8"
+          - os: ubuntu-24.04
+            python-version: "3.13"
           - os: windows-2022
             python-version: "3.9"
           - os: windows-2022
@@ -96,6 +94,8 @@ jobs:
             python-version: "3.11"
           - os: windows-2022
             python-version: "3.12"
+          - os: windows-2022
+            python-version: "3.13"
           - os: windows-2025
             python-version: "3.9"
           - os: windows-2025
@@ -104,8 +104,8 @@ jobs:
             python-version: "3.11"
           - os: windows-2025
             python-version: "3.12"
-          - os: macos-13
-            python-version: "3.8"
+          - os: windows-2025
+            python-version: "3.13"
           - os: macos-13
             python-version: "3.9"
           - os: macos-13
@@ -118,10 +118,18 @@ jobs:
             python-version: "3.10"
           - os: macos-14
             python-version: "3.11"
+          - os: macos-14
+            python-version: "3.12"
+          - os: macos-14
+            python-version: "3.13"
           - os: macos-15
             python-version: "3.10"
           - os: macos-15
             python-version: "3.11"
+          - os: macos-15
+            python-version: "3.12"
+          - os: macos-15
+            python-version: "3.13"
 
     steps:
         - name: Set up Python ${{ matrix.python-version }}
diff --git a/pyproject.toml b/pyproject.toml
index da0b418..a956854 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,11 +4,11 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "raidionicsseg"
-version = "1.4.1"
+version = "1.4.2"
 description = "Raidionics segmentation and classification back-end with ONNX runtime"
 readme = "README.md"
 license = { text = "BSD-2-Clause" }
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 authors = [{ name = "David Bouget", email = "david.bouget@sintef.no" }]
 
 dependencies = [
@@ -20,9 +20,8 @@ dependencies = [
   "scikit-image",
   "tqdm",
   "numpy",
-  "onnxruntime; platform_machine!='arm64'",
-  "numpy>=1.21.6,<2.0; platform_system=='Darwin' and platform_machine=='arm64'",
-  "onnxruntime-silicon; platform_system=='Darwin' and platform_machine=='arm64'",]
+  "onnxruntime",
+  "numpy>=1.21.6,<2.0; platform_system=='Darwin' and platform_machine=='arm64'",]
 
 [project.scripts]
 raidionicsseg = "raidionicsseg.__main__:main"

From b7876ee8d54d3729df13292e155dd86c6a5ede8b Mon Sep 17 00:00:00 2001
From: dbouget <bougetd@gmail.com>
Date: Wed, 9 Jul 2025 18:15:45 +0200
Subject: [PATCH 2/2] Loosening numpy versioning [skip ci]

---
 .github/workflows/build.yml | 2 +-
 pyproject.toml              | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 699a420..0f68886 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -163,7 +163,7 @@ jobs:
         - name: Integration tests
           run: |
               pip install pytest pytest-cov pytest-timeout requests
-              pytest -vvv --cov=raidionicsseg ${{github.workspace}}/tests/generic_tests --cov-report=xml --timeout=1000 --log-cli-level=DEBUG
+              pytest -vvv --cov=raidionicsseg ${{github.workspace}}/tests/generic_tests --cov-report=xml --timeout=1500 --log-cli-level=DEBUG
 
         - name: Upload coverage to Codecov
           if: ${{ matrix.os == 'ubuntu-22.04' && matrix.python-version == '3.9' }}
diff --git a/pyproject.toml b/pyproject.toml
index a956854..79e9a4e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,8 +20,7 @@ dependencies = [
   "scikit-image",
   "tqdm",
   "numpy",
-  "onnxruntime",
-  "numpy>=1.21.6,<2.0; platform_system=='Darwin' and platform_machine=='arm64'",]
+  "onnxruntime",]
 
 [project.scripts]
 raidionicsseg = "raidionicsseg.__main__:main"