chore: Bump Python minimum to 3.10, update linkml-owl to 0.5.0 (#548)

## Changes

- **Python minimum**: `>=3.9` → `>=3.10` (3.9 is EOL since Oct 2025;
sssom already requires 3.10+)
- **linkml-owl**: `>=0.3.0` → `>=0.5.0` (migrated from funowl to
py-horned-owl in [linkml-owl
v0.5.0](https://github.com/linkml/linkml-owl/releases/tag/v0.5.0))
- Updated poetry.lock

Author: caufieldjh

.cruft.json

@@ -7,7 +7,7 @@
       "project_name": "ontogpt",
       "__project_slug": "ontogpt",
       "project_description": "ontogpt",
-      "min_python_version": "3.9",
+      "min_python_version": "3.10",
       "file_name": "OAK for Artifical Intelligence",
       "greeting_recipient": "World",
       "full_name": "Harshad Hegde",

.github/workflows/deploy-docs.yml

@@ -22,7 +22,7 @@ jobs:
     - name: Set up Python3
       uses: actions/setup-python@v3
       with:
-        python-version: 3.9
+        python-version: 3.10
 
     - name: Install uv
       run: pip install uv

.github/workflows/pypi-publish.yml

@@ -19,7 +19,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.10
           cache: pip
           cache-dependency-path: '**/pyproject.toml'
 

.github/workflows/qc.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
 
     steps:
       - uses: actions/checkout@v3.0.2

README.md

@@ -15,7 +15,7 @@ _OntoGPT_ is a Python package for extracting structured information from text wi
 
 OntoGPT runs on the command line, though there's also a minimal web app interface (see `Web Application` section below).
 
-1. Ensure you have Python 3.9 or greater installed.
+1. Ensure you have Python 3.10 or greater installed.
 2. Install with `pip`:
 
     ```bash

docs/index.md

@@ -17,7 +17,7 @@ Please see the Setup page on the left for more detailed instructions.
 
 OntoGPT runs on the command line, though there's also a minimal web app interface (see `Web Application` section below).
 
-1. Ensure you have Python (3.9 to 3.12) installed.
+1. Ensure you have Python (3.10 to 3.13) installed.
 2. Install with `pip`:
 
     ```bash

docs/setup.md

@@ -8,7 +8,7 @@ OntoGPT uses `litellm` to interface with LLM endpoints. Familiarity with this fr
 
 ### Additional requirements and options
 
-* Python 3.9 to 3.13.
+* Python 3.10 to 3.13.
 
 * OpenAI API key: necessary for using OpenAI's GPT models. This is a paid API and you will be charged based on usage. If you do not have an OpenAI account, [you may sign up here](https://platform.openai.com/signup).
 

pyproject.toml

@@ -1,14 +1,14 @@
 [project]
 name = "ontogpt"
-version = "1.0.19"
+version = "1.1.0"
 description = "OntoGPT is a Python package for extracting structured information from text with large language models (LLMs), instruction prompts, and ontology-based grounding."
 readme = "README.md"
 authors = [
     {name = "Chris Mungall", email = "cjmungall@lbl.gov"},
     {name = "J. Harry Caufield", email = "jhc@lbl.gov"},
 ]
 license = {text = "BSD-3"}
-requires-python = ">=3.9,!=3.9.7,<3.14"
+requires-python = ">=3.10,<3.14"
 dependencies = [
     "ruamel-yaml>=0.17.31",
     "aiohttp>=3.8.4",
@@ -19,7 +19,7 @@ dependencies = [
     "inflect>=6.0.2",
     "inflection>=0.5.1",
     "linkml>=1.9.3-rc1",
-    "linkml-owl<1.0.0,>=0.3.0",
+    "linkml-owl<1.0.0,>=0.5.0",
     "oaklib>=0.5.28",
     "pydantic>=2.4.0",
     "requests<3.0.0,>=2.31.0",
@@ -89,7 +89,7 @@ ontogpt = ["*.yaml"]
 
 [tool.black]
 line-length = 100
-target-version = ["py39", "py310", "py313"]
+target-version = ["py310", "py313"]
 
 [tool.isort]
 profile = "black"