Remove Python 3.8 Support and Add 3.13 Support

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -60,11 +60,11 @@ body:
     attributes:
       label: Python Version
       options:
+        - "3.13"
         - "3.12"
         - "3.11"
         - "3.10"
         - "3.9"
-        - "3.8"
     validations:
       required: true
   - type: textarea

.github/workflows/run_all_tests.yml

@@ -25,30 +25,30 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.8-minimum       , test-tox-env: pytest-py38-minimum          , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: linux-python3.9               , test-tox-env: pytest-py39-pinned           , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-python3.9-minimum       , test-tox-env: pytest-py39-minimum          , python-ver: "3.9" , os: ubuntu-latest }
           - { name: linux-python3.10              , test-tox-env: pytest-py310-pinned          , python-ver: "3.10", os: ubuntu-latest }
           - { name: linux-python3.11              , test-tox-env: pytest-py311-pinned          , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-python3.11-optional     , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-python3.12              , test-tox-env: pytest-py312-pinned          , python-ver: "3.12", os: ubuntu-latest }
-          - { name: linux-python3.12-upgraded     , test-tox-env: pytest-py312-upgraded        , python-ver: "3.12", os: ubuntu-latest }
-          - { name: linux-python3.12-prerelease   , test-tox-env: pytest-py312-prerelease      , python-ver: "3.12", os: ubuntu-latest }
-          - { name: windows-python3.8-minimum     , test-tox-env: pytest-py38-minimum          , python-ver: "3.8" , os: windows-latest }
-          - { name: windows-python3.9             , test-tox-env: pytest-py39-pinned           , python-ver: "3.9" , os: windows-latest }
+          - { name: linux-python3.13              , test-tox-env: pytest-py313-pinned          , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-upgraded     , test-tox-env: pytest-py313-upgraded        , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-prerelease   , test-tox-env: pytest-py313-prerelease      , python-ver: "3.13", os: ubuntu-latest }
+          - { name: windows-python3.9-minimum     , test-tox-env: pytest-py39-minimum          , python-ver: "3.9" , os: windows-latest }
           - { name: windows-python3.10            , test-tox-env: pytest-py310-pinned          , python-ver: "3.10", os: windows-latest }
           - { name: windows-python3.11            , test-tox-env: pytest-py311-pinned          , python-ver: "3.11", os: windows-latest }
           - { name: windows-python3.11-optional   , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: windows-latest }
           - { name: windows-python3.12            , test-tox-env: pytest-py312-pinned          , python-ver: "3.12", os: windows-latest }
-          - { name: windows-python3.12-upgraded   , test-tox-env: pytest-py312-upgraded        , python-ver: "3.12", os: windows-latest }
-          - { name: windows-python3.12-prerelease , test-tox-env: pytest-py312-prerelease      , python-ver: "3.12", os: windows-latest }
-          - { name: macos-python3.8-minimum       , test-tox-env: pytest-py38-minimum          , python-ver: "3.8" , os: macos-13 }
-          - { name: macos-python3.9               , test-tox-env: pytest-py39-pinned           , python-ver: "3.9" , os: macos-13 }
+          - { name: windows-python3.13            , test-tox-env: pytest-py313-pinned          , python-ver: "3.13", os: windows-latest }
+          - { name: windows-python3.13-upgraded   , test-tox-env: pytest-py313-upgraded        , python-ver: "3.13", os: windows-latest }
+          - { name: windows-python3.13-prerelease , test-tox-env: pytest-py313-prerelease      , python-ver: "3.13", os: windows-latest }
+          - { name: macos-python3.9-minimum       , test-tox-env: pytest-py39-minimum          , python-ver: "3.9" , os: macos-13 }
           - { name: macos-python3.10              , test-tox-env: pytest-py310-pinned          , python-ver: "3.10", os: macos-latest }
           - { name: macos-python3.11              , test-tox-env: pytest-py311-pinned          , python-ver: "3.11", os: macos-latest }
           - { name: macos-python3.11-optional     , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: macos-latest }
           - { name: macos-python3.12              , test-tox-env: pytest-py312-pinned          , python-ver: "3.12", os: macos-latest }
-          - { name: macos-python3.12-upgraded     , test-tox-env: pytest-py312-upgraded        , python-ver: "3.12", os: macos-latest }
-          - { name: macos-python3.12-prerelease   , test-tox-env: pytest-py312-prerelease      , python-ver: "3.12", os: macos-latest }
+          - { name: macos-python3.13              , test-tox-env: pytest-py313-pinned          , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-upgraded     , test-tox-env: pytest-py313-upgraded        , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-prerelease   , test-tox-env: pytest-py313-prerelease      , python-ver: "3.13", os: macos-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4
@@ -97,18 +97,18 @@ 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-python3.9-minimum      , test-tox-env: gallery-py39-minimum          , python-ver: "3.9" , os: ubuntu-latest }
           - { name: linux-gallery-python3.11-optional    , test-tox-env: gallery-py311-optional-pinned , python-ver: "3.11", 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: 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-python3.11-optional  , test-tox-env: gallery-py311-optional-pinned , python-ver: "3.11", 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 }
-          - { name: macos-gallery-python3.8-minimum      , test-tox-env: gallery-py38-minimum          , python-ver: "3.8" , os: macos-13 }
+          - { 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-python3.11-optional    , test-tox-env: gallery-py311-optional-pinned , python-ver: "3.11", os: macos-latest }
-          - { 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: 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: Checkout repo with submodules
         uses: actions/checkout@v4
@@ -144,14 +144,13 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: conda-linux-python3.8-minimum     , test-tox-env: pytest-py38-minimum          , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: conda-linux-python3.9             , test-tox-env: pytest-py39-pinned           , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.9-minimum     , test-tox-env: pytest-py39-minimum          , python-ver: "3.9" , os: ubuntu-latest }
           - { name: conda-linux-python3.10            , test-tox-env: pytest-py310-pinned          , python-ver: "3.10", os: ubuntu-latest }
           - { name: conda-linux-python3.11            , test-tox-env: pytest-py311-pinned          , python-ver: "3.11", os: ubuntu-latest }
           - { name: conda-linux-python3.11-optional   , test-tox-env: pytest-py311-optional-pinned , python-ver: "3.11", os: ubuntu-latest }
-          - { name: conda-linux-python3.12            , test-tox-env: pytest-py312-pinned          , python-ver: "3.12", os: ubuntu-latest }
-          - { name: conda-linux-python3.12-upgraded   , test-tox-env: pytest-py312-upgraded        , python-ver: "3.12", os: ubuntu-latest }
-          - { name: conda-linux-python3.12-prerelease , test-tox-env: pytest-py312-prerelease      , python-ver: "3.12", os: ubuntu-latest }
+          - { name: conda-linux-python3.13            , test-tox-env: pytest-py313-pinned          , python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-linux-python3.13-upgraded   , test-tox-env: pytest-py313-upgraded        , python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-linux-python3.13-prerelease , test-tox-env: pytest-py313-prerelease      , python-ver: "3.13", os: ubuntu-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4
@@ -209,9 +208,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.12-ros3   , python-ver: "3.12", os: ubuntu-latest }
-          - { name: windows-python3.12-ros3 , python-ver: "3.12", os: windows-latest }
-          - { name: macos-python3.12-ros3   , python-ver: "3.12", os: macos-latest }
+          - { name: linux-python3.13-ros3   , python-ver: "3.13", os: ubuntu-latest }
+          - { name: windows-python3.13-ros3 , python-ver: "3.13", os: windows-latest }
+          - { name: macos-python3.13-ros3   , python-ver: "3.13", os: macos-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4

.github/workflows/run_coverage.yml

@@ -84,7 +84,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.12-ros3  , python-ver: "3.12", os: ubuntu-latest }
+          - { name: linux-python3.13-ros3  , python-ver: "3.13", os: ubuntu-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4

.github/workflows/run_tests.yml

@@ -23,13 +23,13 @@ jobs:
       matrix:
         include:
           # NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
-          - { name: linux-python3.8-minimum      , test-tox-env: pytest-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: linux-python3.12             , test-tox-env: pytest-py312-pinned    , python-ver: "3.12", os: ubuntu-latest }
-          - { name: linux-python3.12-upgraded    , test-tox-env: pytest-py312-upgraded  , python-ver: "3.12", os: ubuntu-latest , upload-wheels: true }
-          - { name: windows-python3.8-minimum    , test-tox-env: pytest-py38-minimum    , python-ver: "3.8" , os: windows-latest }
-          - { name: windows-python3.12-upgraded  , test-tox-env: pytest-py312-upgraded  , python-ver: "3.12", os: windows-latest }
-          - { name: macos-python3.8-minimum      , test-tox-env: pytest-py38-minimum    , python-ver: "3.8" , os: macos-13 }
-          - { name: macos-python3.12-upgraded    , test-tox-env: pytest-py312-upgraded  , python-ver: "3.12", os: macos-latest }
+          - { name: linux-python3.9-minimum      , test-tox-env: pytest-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-python3.13             , test-tox-env: pytest-py313-pinned    , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-upgraded    , test-tox-env: pytest-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest , upload-wheels: true }
+          - { name: windows-python3.9-minimum    , test-tox-env: pytest-py39-minimum    , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-python3.13-upgraded  , test-tox-env: pytest-py313-upgraded  , python-ver: "3.13", os: windows-latest }
+          - { name: macos-python3.9-minimum      , test-tox-env: pytest-py39-minimum    , python-ver: "3.9" , os: macos-13 }
+          - { name: macos-python3.13-upgraded    , test-tox-env: pytest-py313-upgraded  , python-ver: "3.13", os: macos-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4
@@ -85,10 +85,10 @@ 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: 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: 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: 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 }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4
@@ -124,8 +124,8 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: conda-linux-python3.8-minimum    , test-tox-env: pytest-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: conda-linux-python3.12-upgraded  , test-tox-env: pytest-py312-upgraded  , python-ver: "3.12", os: ubuntu-latest }
+          - { name: conda-linux-python3.9-minimum    , test-tox-env: pytest-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.13-upgraded  , test-tox-env: pytest-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4
@@ -188,7 +188,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Download wheel and source distributions from artifact
         uses: actions/download-artifact@v4
@@ -221,7 +221,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.12-ros3  , python-ver: "3.12", os: ubuntu-latest }
+          - { name: linux-python3.13-ros3  , python-ver: "3.13", os: ubuntu-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4

.readthedocs.yaml

@@ -6,9 +6,9 @@
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: '3.9'
+    python: '3.12'
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

CHANGELOG.md

@@ -4,6 +4,7 @@
 
 ### Deprecations
 - The following classes have been deprecated and removed: Array, AbstractSortedArray, SortedArray, LinSpace, Query, RegionSlicer, ListSlicer, H5RegionSlicer, DataRegion. The following methods have been deprecated and removed: fmt_docval_args, call_docval_func, get_container_cls, add_child, set_dataio (now refactored as set_data_io). We have also removed all early evelopment for region references. @mavaylon1 [#1998](https://github.com/hdmf-dev/hdmf/pull/1198)
+- Python 3.8 has been deprecated. Python 3.9 is the new minimum with support for Python 3.13. @mavaylon1 [#1209](https://github.com/hdmf-dev/hdmf/pull/1209)
 
 ### Enhancements
 - Added support for expandable datasets of references for untyped and compound data types. @stephprince [#1188](https://github.com/hdmf-dev/hdmf/pull/1188)

docs/source/install_users.rst

@@ -4,7 +4,7 @@
 Installing HDMF
 ---------------
 
-HDMF requires having Python 3.8, 3.9, 3.10, 3.11, or 3.12 installed. If you don't have Python installed and want the simplest way to
+HDMF requires having Python 3.9-3.13 installed. If you don't have Python installed and want the simplest way to
 get started, we recommend you install and use the `Anaconda Distribution`_. It includes Python, NumPy, and many other
 commonly used packages for scientific computing and data science.
 

environment-ros3.yml

@@ -4,11 +4,11 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python==3.12
-  - h5py==3.11.0
-  - matplotlib==3.8.4
-  - numpy==2.0.0
-  - pandas==2.2.2
+  - python==3.13
+  - h5py==3.12.1
+  - matplotlib==3.9.2
+  - numpy==2.1.3
+  - pandas==2.2.3
   - python-dateutil==2.8.2
   - pytest==8.1.2  # regression introduced in pytest 8.2.*, will be fixed in 8.3.0
   - pytest-cov==5.0.0

pyproject.toml

@@ -13,15 +13,15 @@ authors = [
 ]
 description = "A hierarchical data modeling framework for modern science data standards"
 readme = "README.rst"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = {text = "BSD-3-Clause"}
 classifiers = [
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "License :: OSI Approved :: BSD License",
     "Development Status :: 5 - Production/Stable",
     "Operating System :: OS Independent",
@@ -30,22 +30,22 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Medical Science Apps.",
 ]
 dependencies = [
-    "h5py>=2.10",
-    "jsonschema>=2.6.0",
-    'numpy>=1.18',
-    "pandas>=1.0.5",
+    "h5py>=3.1.0",
+    "jsonschema>=3.2.0",
+    'numpy>=1.19.3',
+    "pandas>=1.2.0",
     "ruamel.yaml>=0.16",
-    "scipy>=1.4",
-    "importlib-resources; python_version < '3.9'",  # TODO: remove when minimum python version is 3.9
+    "scipy>=1.7",
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
 tqdm = ["tqdm>=4.41.0"]
-termset = ["linkml-runtime>=1.5.5; python_version >= '3.9'",
-           "schemasheets>=0.1.23; python_version >= '3.9'",
-           "oaklib>=0.5.12; python_version >= '3.9'",
-           "pyyaml>=6.0.1; python_version >= '3.9'"]
+zarr = ["zarr>=2.12.0"]
+termset = ["linkml-runtime>=1.5.5",
+           "schemasheets>=0.1.23",
+           "oaklib>=0.5.12",
+           "pyyaml>=6.0.1"]
 
 [project.urls]
 "Homepage" = "https://github.com/hdmf-dev/hdmf"