CU-869aupp8v: Remove python 3.9 support (#172)

Author: mart-r

.github/workflows/medcat-den_main.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
+        python-version: [ '3.10', '3.11', '3.12' ]
       max-parallel: 4
     steps:
       - uses: actions/checkout@v5
@@ -57,7 +57,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       - name: Install dependencies
         run: |

.github/workflows/medcat-den_release.yml

@@ -26,7 +26,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       - name: Install dependencies
         run: |

.github/workflows/medcat-v1_main.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
+        python-version: [ '3.10', '3.11', '3.12' ]
       max-parallel: 4
 
     steps:
@@ -93,10 +93,10 @@ jobs:
           ref: 'main'
           fetch-depth: 0
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v6
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
       - name: Install pypa/build
         run: >-

.github/workflows/medcat-v1_production.yml

@@ -29,10 +29,10 @@ jobs:
           ref: ${{ github.event.release.target_commitish }}
           fetch-depth: 0
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v6
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
       - name: Run UATs
         run: |

.github/workflows/medcat-v2_main.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
+        python-version: [ '3.10', '3.11', '3.12' ]
       max-parallel: 4
     steps:
       - uses: actions/checkout@v5

.github/workflows/medcat-v2_release.yml

@@ -50,10 +50,10 @@ jobs:
           git pull origin $BRANCH_NAME
 
         # NOTE: building with the lowest python version supported by the package
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v6
         with:
-          python-version: "3.9"
+          python-version: "3.10"
 
       - name: Install build dependencies
         run: pip install --upgrade build
@@ -75,7 +75,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - name: Checkout repository
         uses: actions/checkout@v5
@@ -90,25 +90,10 @@ jobs:
 
       - name: Generate requirements and download (CPU)
         run: |
-          if [[ "${{ matrix.python-version }}" == "3.9" ]]; then
-            echo "Runnoing unsafe index strategy for Python 3.9 to avoid issues with torch / numpy compatibility"
-            # NOTE: for python 3.9 it will otherwise look for `numpy>2` in torch's index
-            #       but there's (as of writing on 2025-07-02) none there that support 3.9
-            #       (though there are ones that support 3.10+) and because of that this
-            #       step would fail wihtout the unsafe index match
-            #       for some documentation on dependency confusion attacks, can reference:
-            #       https://docs.astral.sh/uv/reference/settings/#pip_index-strategy
-            uv pip compile pyproject.toml --only-binary=:all: \
+          uv pip compile pyproject.toml --only-binary=:all: \
               --extra spacy --extra deid --extra meta-cat --extra rel-cat \
               --extra-index-url https://download.pytorch.org/whl/cpu \
-              --index-strategy unsafe-best-match \
               > req-cpu.txt
-          else
-            uv pip compile pyproject.toml --only-binary=:all: \
-              --extra spacy --extra deid --extra meta-cat --extra rel-cat \
-              --extra-index-url https://download.pytorch.org/whl/cpu \
-              > req-cpu.txt
-          fi
           uv venv .venv
           .venv/bin/python -m ensurepip
           .venv/bin/python -m pip download --only-binary=:all: --dest bundle-cpu -r req-cpu.txt --extra-index-url https://download.pytorch.org/whl/cpu

medcat-den/pyproject.toml

@@ -11,7 +11,7 @@ license = { text = "Apache-2.0" }
 authors = [
     { name="Mart Ratas", email="mart.ratas@kcl.ac.uk" }
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 
 keywords = ["NLP", "medical", "MedCAT", "model-registry"]
 
@@ -20,7 +20,6 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",

medcat-v2/docs/main.md

@@ -41,7 +41,7 @@ Some guides on how to use MedCAT v2 are available at [MedCAT Tutorials](https://
 - [MedCATtrainer](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-trainer/) - an interface for building, improving and customising a given Named Entity Recognition and Linking (NER+L) model (MedCAT) for biomedical domain text.
 - [MedCATservice](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-service/) - implements the MedCAT NLP application as a service behind a REST API.
 
-## Install using PIP (Requires Python 3.9+)
+## Install using PIP (Requires Python 3.10+)
 Installation instructions are to follow upon a release of this version on PyPI.
 Though installation is likely to be simply `pip install "medcat>=2.0"` at that time.
 Currently the installation for the 2.0 beta release is simply:

medcat-v2/pyproject.toml

@@ -7,7 +7,7 @@ description = "Medical Concept Annotation Toolkit (v2)"
 
 readme = "README.md"
 
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 
 license = "Apache-2.0"
 
@@ -42,7 +42,6 @@ classifiers = [
   # that you indicate you support Python 3. These classifiers are *not*
   # checked by "pip install". See instead "python_requires" below.
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
@@ -85,7 +84,6 @@ dev = [
 ]
 spacy = [
   "spacy",
-  "spacy<3.8.4; python_version == '3.9'"
 ]
 meta_cat = [
   "transformers>=4.41.0,<5.0", # avoid major bump