Remove python 3.8 support and add python 3.13 support (#2007)

* update min requirements

* update environment files

* update installation documentation

* update workflows

* update importlib in init

* update min requirements file

* update workflows

* update changelog

* readd test file generation versions

* replace missed 3.8 versions

* update ros3 environment for py313

* update minimum requirements

* update runners for minimum python

* switch to macos-13 runner for min requirements

* simplify tox configuration

* readd version condition

* update tox workflow command

* add new tox env names to workflows

* upgrade numpy minimum

* update requirements

* add macos latest to tests workflow

* update position test

* update minimum requirements

* update pyproject.toml requirements

* add hdmf-zarr minimum

* update requirements

Author: stephprince

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -61,10 +61,11 @@ body:
       label: Python Version
       options:
         - "lower version (unsupported)"
-        - "3.8"
         - "3.9"
         - "3.10"
         - "3.11"
+        - "3.12"
+        - "3.13"
     validations:
       required: true
   - type: textarea

.github/workflows/deploy_release.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Install build dependencies
         run: |

.github/workflows/run_all_tests.yml

@@ -22,31 +22,30 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: linux-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
-          - { name: linux-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-python3.11             , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
-          - { name: linux-python3.11-opt         , test-tox-env: py311-optional  , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
-          - { name: linux-python3.12             , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: ubuntu-latest }
-          - { name: linux-python3.12-upgraded    , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: ubuntu-latest }
-          - { name: linux-python3.12-prerelease  , test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: ubuntu-latest }
-          - { name: windows-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: windows-latest }
-          - { name: windows-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: windows-latest }
-          - { name: windows-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: windows-latest }
-          - { name: windows-python3.11           , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: windows-latest }
-          - { name: windows-python3.11-opt       , test-tox-env: py311-optional  , build-tox-env: build-py311           , python-ver: "3.11", os: windows-latest }
-          - { name: windows-python3.12           , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: windows-latest }
-          - { name: windows-python3.12-upgraded  , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: windows-latest }
-          - { name: windows-python3.12-prerelease, test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.11", os: windows-latest }
-          # minimum versions of dependencies do not have wheels or cannot be built on macos-arm64
-          - { name: macos-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: macos-13 }
-          - { name: macos-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: macos-latest }
-          - { name: macos-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: macos-latest }
-          - { name: macos-python3.11             , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: macos-latest }
-          - { name: macos-python3.11-opt         , test-tox-env: py311-optional  , build-tox-env: build-py311           , python-ver: "3.11", os: macos-latest }
-          - { name: macos-python3.12             , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: macos-latest }
-          - { name: macos-python3.12-upgraded    , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: macos-latest }
-          - { name: macos-python3.12-prerelease  , test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: macos-latest }
+          - { name: linux-python3.9-minimum      , test-tox-env: test-py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-python3.10             , test-tox-env: test-py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-python3.11             , test-tox-env: test-py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
+          - { name: linux-python3.11-opt         , test-tox-env: test-py311-optional  , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
+          - { name: linux-python3.12             , test-tox-env: test-py312           , build-tox-env: build-py312           , python-ver: "3.12", os: ubuntu-latest }
+          - { name: linux-python3.13             , test-tox-env: test-py313           , build-tox-env: build-py313           , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-upgraded    , test-tox-env: test-py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-prerelease  , test-tox-env: test-py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
+          - { name: windows-python3.9-minimum    , test-tox-env: test-py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-python3.10           , test-tox-env: test-py310           , build-tox-env: build-py310           , python-ver: "3.10", os: windows-latest }
+          - { name: windows-python3.11           , test-tox-env: test-py311           , build-tox-env: build-py311           , python-ver: "3.11", os: windows-latest }
+          - { name: windows-python3.11-opt       , test-tox-env: test-py311-optional  , build-tox-env: build-py311           , python-ver: "3.11", os: windows-latest }
+          - { name: windows-python3.12           , test-tox-env: test-py312           , build-tox-env: build-py312           , python-ver: "3.12", os: windows-latest }
+          - { name: windows-python3.13           , test-tox-env: test-py313           , build-tox-env: build-py313           , python-ver: "3.13", os: windows-latest }
+          - { name: windows-python3.13-upgraded  , test-tox-env: test-py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: windows-latest }
+          - { name: windows-python3.13-prerelease, test-tox-env: test-py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: windows-latest }
+          - { name: macos-python3.9-minimum      , test-tox-env: test-py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: macos-13 }
+          - { name: macos-python3.10             , test-tox-env: test-py310           , build-tox-env: build-py310           , python-ver: "3.10", os: macos-latest }
+          - { name: macos-python3.11             , test-tox-env: test-py311           , build-tox-env: build-py311           , python-ver: "3.11", os: macos-latest }
+          - { name: macos-python3.11-opt         , test-tox-env: test-py311-optional  , build-tox-env: build-py311           , python-ver: "3.11", os: macos-latest }
+          - { name: macos-python3.12             , test-tox-env: test-py312           , build-tox-env: build-py312           , python-ver: "3.12", os: macos-latest }
+          - { name: macos-python3.13             , test-tox-env: test-py313           , build-tox-env: build-py313           , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-upgraded    , test-tox-env: test-py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-prerelease  , test-tox-env: test-py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -93,16 +92,15 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.8-minimum      , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: linux-gallery-python3.12-upgraded    , test-tox-env: gallery-py312-upgraded  , python-ver: "3.12", os: ubuntu-latest }
-          - { name: linux-gallery-python3.12-prerelease  , test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: ubuntu-latest }
-          - { name: windows-gallery-python3.8-minimum    , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: windows-latest }
-          - { name: windows-gallery-python3.12-upgraded  , test-tox-env: gallery-py312-upgraded  , python-ver: "3.12", os: windows-latest }
-          - { name: windows-gallery-python3.12-prerelease, test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: windows-latest }
-          # minimum versions of dependencies do not have wheels or cannot be built on macos-arm64
-          - { name: macos-gallery-python3.8-minimum      , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: macos-13 }
-          - { name: macos-gallery-python3.12-upgraded    , test-tox-env: gallery-py312-upgraded  , python-ver: "3.12", os: macos-latest }
-          - { name: macos-gallery-python3.12-prerelease  , test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: macos-latest }
+          - { name: linux-gallery-python3.9-minimum      , test-tox-env: gallery-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-gallery-python3.13-upgraded    , test-tox-env: gallery-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-gallery-python3.13-prerelease  , test-tox-env: gallery-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
+          - { name: windows-gallery-python3.9-minimum    , test-tox-env: gallery-py39-minimum    , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-gallery-python3.13-upgraded  , test-tox-env: gallery-py313-upgraded  , python-ver: "3.13", os: windows-latest }
+          - { name: windows-gallery-python3.13-prerelease, test-tox-env: gallery-py313-prerelease, python-ver: "3.13", os: windows-latest }
+          - { name: macos-gallery-python3.9-minimum      , test-tox-env: gallery-py39-minimum    , python-ver: "3.9" , os: macos-13 }
+          - { name: macos-gallery-python3.13-upgraded    , test-tox-env: gallery-py313-upgraded  , python-ver: "3.13", os: macos-latest }
+          - { name: macos-gallery-python3.13-prerelease  , test-tox-env: gallery-py313-prerelease, python-ver: "3.13", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -140,13 +138,13 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: conda-linux-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: conda-linux-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
-          - { name: conda-linux-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
-          - { name: conda-linux-python3.11           , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
-          - { name: conda-linux-python3.12           , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: ubuntu-latest }
-          - { name: conda-linux-python3.12-upgraded  , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: ubuntu-latest }
-          - { name: conda-linux-python3.12-prerelease, test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: ubuntu-latest }
+          - { name: conda-linux-python3.9-minimum    , test-tox-env: test-py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.10           , test-tox-env: test-py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.11           , test-tox-env: test-py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-linux-python3.12           , test-tox-env: test-py312           , build-tox-env: build-py312           , python-ver: "3.12", os: ubuntu-latest }
+          - { name: conda-linux-python3.13           , test-tox-env: test-py313           , build-tox-env: build-py313           , python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-linux-python3.13-upgraded  , test-tox-env: test-py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-linux-python3.13-prerelease, test-tox-env: test-py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -201,9 +199,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: conda-linux-python3.12-ros3  , python-ver: "3.12", os: ubuntu-latest }
-          - { name: conda-windows-python3.12-ros3, python-ver: "3.12", os: windows-latest }
-          - { name: conda-macos-python3.12-ros3  , python-ver: "3.12", os: macos-latest }
+          - { name: conda-linux-python3.13-ros3  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-windows-python3.13-ros3, python-ver: "3.13", os: windows-latest }
+          - { name: conda-macos-python3.13-ros3  , python-ver: "3.13", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -248,9 +246,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: conda-linux-gallery-python3.12-ros3  , python-ver: "3.12", os: ubuntu-latest }
-          - { name: conda-windows-gallery-python3.12-ros3, python-ver: "3.12", os: windows-latest }
-          - { name: conda-macos-gallery-python3.12-ros3  , python-ver: "3.12", os: macos-latest }
+          - { name: conda-linux-gallery-python3.13-ros3  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-windows-gallery-python3.13-ros3, python-ver: "3.13", os: windows-latest }
+          - { name: conda-macos-gallery-python3.13-ros3  , python-ver: "3.13", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]

.github/workflows/run_coverage.yml

@@ -28,7 +28,7 @@ jobs:
           - { os: macos-latest  , opt_req: false }
     env:
       OS: ${{ matrix.os }}
-      PYTHON: '3.12'
+      PYTHON: '3.13'
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]

.github/workflows/run_dandi_read_tests.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Install run dependencies
         run: |