Drop Python 3.9; focus tests on 3.10 and 3.13 (#4912)

Note the last 32bit Windows MiniConda was for Python 3.9, this means
we will be dropping testing on 32bit Windows with these changes.

.appveyor.yml

@@ -5,9 +5,8 @@ os: Visual Studio 2015
 
 environment:
   matrix:
-    - PY_MAJOR_VER: 3
-      PYTHON_ARCH: "x86"
-    - PY_MAJOR_VER: 3
+  # String fragments for URLs at https://repo.anaconda.com/miniconda/
+    - PY_MAJOR_VER: "3"
       PYTHON_ARCH: "x86_64"
 
 matrix:

.circleci/config.yml

@@ -12,7 +12,7 @@ orbs:
 jobs:
   build:
     docker:
-      - image: cimg/python:3.9
+      - image: cimg/python:3.10
     steps:
       - checkout
       - run:

.github/workflows/ci.yml

@@ -40,7 +40,7 @@ jobs:
     - name: Setup Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.10"
 
     - name: Installing pre-commit
       run: |
@@ -63,7 +63,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.11", "3.13"]
+        python-version: ["3.10", "3.13"]
 
     steps:
     - uses: actions/checkout@v4
@@ -101,7 +101,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.10"
 
     - name: Install Python packaging tools
       run: |
@@ -116,7 +116,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-2019]
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     runs-on: ${{ matrix.os }}
 
@@ -166,7 +166,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.11", "3.13"]
+        python-version: ["3.10", "3.13"]
 
     steps:
 
@@ -223,7 +223,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.13"]
+        python-version: ["3.10", "3.13"]
 
     steps:
     - uses: actions/checkout@v4
@@ -269,9 +269,7 @@ jobs:
     runs-on: windows-2019
     strategy:
       matrix:
-        # TODO - Try Python 3.11 again, was Python 3.11.0 was
-        # failing when trying to delete SQlite databases.
-        python-version: ["3.9", "3.10", "3.13"]
+        python-version: ["3.10", "3.13"]
 
     steps:
     - uses: actions/checkout@v4
@@ -317,7 +315,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [pypy-3.9]
+        python-version: [pypy-3.10]
 
     steps:
     - uses: actions/checkout@v4
@@ -365,7 +363,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.10"
 
     - uses: actions/cache@v4
       id: cache-pip

DEPRECATED.rst

@@ -8,8 +8,9 @@ Python
 
 Python 3.9
 ----------
-First supported in release 1.79, although it was mostly working in 1.78.
-Support deprecated as of Release 1.84.
+No longer supported as of Release 1.86, having triggered a deprecation
+warning as of Release 1.84. First supported in release 1.79, although
+it was mostly working in 1.78.
 
 Python 3.8
 ----------

setup.py

@@ -56,15 +56,13 @@ if setuptools_version_tuple < (70, 1) and "bdist_wheel" in sys.argv:
 
 
 # Make sure we have the right Python version.
-MIN_PY_VER = (3, 9)
+MIN_PY_VER = (3, 10)
 if sys.version_info[:2] < MIN_PY_VER:
     sys.stderr.write(
         ("ERROR: Biopython requires Python %i.%i or later. " % MIN_PY_VER)
         + ("Python %d.%d detected.\n" % sys.version_info[:2])
     )
     sys.exit(1)
-elif sys.version_info[:2] == (3, 9):
-    sys.stderr.write("WARNING: Biopython support for Python 3.9 is now deprecated.\n")
 
 
 class test_biopython(Command):
@@ -255,7 +253,6 @@ setup(
         "Operating System :: OS Independent",
         "Programming Language :: Python",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",