From 8c0ddf104b26f988e047913b15f4848b1d285c11 Mon Sep 17 00:00:00 2001
From: Branwen Snelling <branwen.snelling@crick.ac.uk>
Date: Tue, 9 Jun 2026 10:12:16 +0100
Subject: [PATCH 1/4] allow python 3.11 and add to workflow

---
 .github/workflows/ci.yml | 8 +++++---
 pyproject.toml           | 2 +-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8298978..c204c12 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -17,6 +17,9 @@ jobs:
           - ubuntu-latest
           - macos-latest
           - windows-latest
+        python-version:
+          - "3.11"
+          - "3.13"
 
     steps:
       - name: Check out repository
@@ -25,7 +28,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: "3.13"
+          python-version: ${{ matrix.python-version }}
           cache: "pip"
           cache-dependency-path: pyproject.toml
 
@@ -43,5 +46,4 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml
-        if: matrix.os == 'ubuntu-latest'
-      
\ No newline at end of file
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.13'
diff --git a/pyproject.toml b/pyproject.toml
index 522d0e3..e243cce 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ dependencies = [
   "python-libsbml",
   "ruamel.yaml",
 ]
-requires-python = ">=3.13"
+requires-python = ">=3.11"
 description = "Specify parameter estimation problems and hybrid models."
 readme = "README.md"
 license = {file = "LICENSE"}

From 3b69b7255db7512a556a97a796a1b7a75aeb16f5 Mon Sep 17 00:00:00 2001
From: Branwen Snelling <branwen.snelling@crick.ac.uk>
Date: Tue, 9 Jun 2026 10:22:23 +0100
Subject: [PATCH 2/4] fix for py 3.11

---
 petab_sciml/standard/array_data.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/petab_sciml/standard/array_data.py b/petab_sciml/standard/array_data.py
index ddd5bc8..bcc2926 100644
--- a/petab_sciml/standard/array_data.py
+++ b/petab_sciml/standard/array_data.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import os
 from pathlib import Path
 from typing import TYPE_CHECKING, Iterable
 
@@ -228,7 +229,7 @@ def add_array_files_to_yaml(
                 )
             continue
 
-        array_file_relative = array_file.relative_to(yaml_dir, walk_up=True).as_posix()
+        array_file_relative = Path(os.path.relpath(array_file, yaml_dir)).as_posix()
         existing_array_files.append(array_file_relative)
 
     with open(yaml_file, "w") as f:

From 1af8bd459a4ee48afc62f93ff8359a89f56a03df Mon Sep 17 00:00:00 2001
From: Branwen Snelling <branwen.snelling@crick.ac.uk>
Date: Tue, 9 Jun 2026 10:37:00 +0100
Subject: [PATCH 3/4] Revert "fix for py 3.11"

This reverts commit 3b69b7255db7512a556a97a796a1b7a75aeb16f5.
---
 petab_sciml/standard/array_data.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/petab_sciml/standard/array_data.py b/petab_sciml/standard/array_data.py
index bcc2926..ddd5bc8 100644
--- a/petab_sciml/standard/array_data.py
+++ b/petab_sciml/standard/array_data.py
@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import os
 from pathlib import Path
 from typing import TYPE_CHECKING, Iterable
 
@@ -229,7 +228,7 @@ def add_array_files_to_yaml(
                 )
             continue
 
-        array_file_relative = Path(os.path.relpath(array_file, yaml_dir)).as_posix()
+        array_file_relative = array_file.relative_to(yaml_dir, walk_up=True).as_posix()
         existing_array_files.append(array_file_relative)
 
     with open(yaml_file, "w") as f:

From 93afb05bd27d5126b6547385967b6c0ff478aa9f Mon Sep 17 00:00:00 2001
From: Branwen Snelling <branwen.snelling@crick.ac.uk>
Date: Tue, 9 Jun 2026 10:39:29 +0100
Subject: [PATCH 4/4] 3.12 and latest

---
 .github/workflows/ci.yml | 6 +++---
 pyproject.toml           | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c204c12..03e1fbb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -18,8 +18,8 @@ jobs:
           - macos-latest
           - windows-latest
         python-version:
-          - "3.11"
-          - "3.13"
+          - "3.12"
+          - "3.x"
 
     steps:
       - name: Check out repository
@@ -46,4 +46,4 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.13'
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.x'
diff --git a/pyproject.toml b/pyproject.toml
index e243cce..88b3da7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ dependencies = [
   "python-libsbml",
   "ruamel.yaml",
 ]
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 description = "Specify parameter estimation problems and hybrid models."
 readme = "README.md"
 license = {file = "LICENSE"}