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[WIP] Drop support for Python 3.9, add support for 3.14 #298

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[WIP] Drop support for Python 3.9, add support for 3.14 #298

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5 changes: 3 additions & 2 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -53,11 +53,12 @@ body:
attributes:
label: Python Version
options:
- "3.14"
- "3.13"
- "3.12"
- "3.11"
- "3.10"
- "3.9"
- older (please specify in "Package Versions" below)
validations:
required: true
- type: textarea
Expand All @@ -78,4 +79,4 @@ body:

Before submitting this issue, please review the [Contributing Guide](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/docs/CONTRIBUTING.rst).

Please also ensure that this issue has not already been [reported](https://github.com/hdmf-dev/hdmf-zarr/issues). Thank you!
Please also ensure that this issue has not already been [reported](https://github.com/hdmf-dev/hdmf-zarr/issues). Thank you!
6 changes: 3 additions & 3 deletions .github/workflows/HDMF_dev.yaml
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Expand Up @@ -13,16 +13,16 @@ jobs:
uses: actions/checkout@v5
with:
fetch-depth: 0 # tags are required to determine the version

- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.13"
python-version: "3.14"

- name: Install HDMF_Zarr Requirements
run: |
python -m pip install ".[test]"

- name: Clone and Install HDMF Dev Branch
run: |
git clone https://github.com/hdmf-dev/hdmf.git --recurse-submodules
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/check_external_links.yml
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Expand Up @@ -18,7 +18,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.13'
python-version: '3.14'

- name: Install Sphinx dependencies and package
run: |
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/deploy_release.yml
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Expand Up @@ -17,7 +17,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.13'
python-version: '3.14'

- name: Install build dependencies
run: |
Expand Down
58 changes: 31 additions & 27 deletions .github/workflows/run_all_tests.yml
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Expand Up @@ -25,27 +25,30 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-python3.10-minimum , test-tox-env: py310-minimum , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.10 , test-tox-env: py310 , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.11 , test-tox-env: py311 , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-python3.12 , test-tox-env: py312 , python-ver: "3.12", os: ubuntu-latest }
- { name: linux-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-optional , test-tox-env: py313-optional , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-prerelease , test-tox-env: py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
- { name: windows-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: windows-latest }
- { name: linux-python3.14 , test-tox-env: py314 , python-ver: "3.14", os: ubuntu-latest }
- { name: linux-python3.14-optional , test-tox-env: py314-optional , python-ver: "3.14", os: ubuntu-latest }
- { name: linux-python3.14-prerelease , test-tox-env: py314-prerelease, python-ver: "3.14", os: ubuntu-latest }
- { name: windows-python3.10-minimum , test-tox-env: py310-minimum , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.10 , test-tox-env: py310 , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.11 , test-tox-env: py311 , python-ver: "3.11", os: windows-latest }
- { name: windows-python3.12 , test-tox-env: py312 , python-ver: "3.12", os: windows-latest }
- { name: windows-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-optional , test-tox-env: py313-optional , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-prerelease, test-tox-env: py313-prerelease, python-ver: "3.13", os: windows-latest }
- { name: macos-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: macos-latest }
- { name: windows-python3.12 , test-tox-env: py312 , python-ver: "3.12", os: windows-latest }
- { name: windows-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.14 , test-tox-env: py314 , python-ver: "3.14", os: windows-latest }
- { name: windows-python3.14-optional , test-tox-env: py314-optional , python-ver: "3.14", os: windows-latest }
- { name: windows-python3.14-prerelease, test-tox-env: py314-prerelease, python-ver: "3.14", os: windows-latest }
- { name: macos-python3.10-minimum , test-tox-env: py310-minimum , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.10 , test-tox-env: py310 , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.11 , test-tox-env: py311 , python-ver: "3.11", os: macos-latest }
- { name: macos-python3.12 , test-tox-env: py312 , python-ver: "3.12", os: macos-latest }
- { name: macos-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-optional , test-tox-env: py313-optional , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-prerelease , test-tox-env: py313-prerelease, python-ver: "3.13", os: macos-latest }
- { name: macos-python3.14 , test-tox-env: py314 , python-ver: "3.14", os: macos-latest }
- { name: macos-python3.14-optional , test-tox-env: py314-optional , python-ver: "3.14", os: macos-latest }
- { name: macos-python3.14-prerelease , test-tox-env: py314-prerelease, python-ver: "3.14", os: macos-latest }
steps:
- name: Checkout repo
uses: actions/checkout@v5
Expand Down Expand Up @@ -79,7 +82,7 @@ jobs:
- name: Test installation from a source distribution
run: |
tox -e wheelinstall --recreate --installpkg dist/*.tar.gz

run-all-gallery-tests:
name: ${{ matrix.name }}
runs-on: ${{ matrix.os }}
Expand All @@ -93,15 +96,15 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-gallery-python3.9-minimum , test-tox-env: gallery-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-gallery-python3.13-optional , test-tox-env: gallery-py313-optional , 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-optional , test-tox-env: gallery-py313-optional , 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-latest }
- { name: macos-gallery-python3.13-optional , test-tox-env: gallery-py313-optional , 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 }
- { name: linux-gallery-python3.10-minimum , test-tox-env: gallery-py310-minimum , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-gallery-python3.14-optional , test-tox-env: gallery-py314-optional , python-ver: "3.14", os: ubuntu-latest }
- { name: linux-gallery-python3.14-prerelease , test-tox-env: gallery-py314-prerelease, python-ver: "3.14", os: ubuntu-latest }
- { name: windows-gallery-python3.10-minimum , test-tox-env: gallery-py310-minimum , python-ver: "3.10", os: windows-latest }
- { name: windows-gallery-python3.14-optional , test-tox-env: gallery-py314-optional , python-ver: "3.14", os: windows-latest }
- { name: windows-gallery-python3.14-prerelease, test-tox-env: gallery-py314-prerelease, python-ver: "3.14", os: windows-latest }
- { name: macos-gallery-python3.10-minimum , test-tox-env: gallery-py310-minimum , python-ver: "3.10", os: macos-latest }
- { name: macos-gallery-python3.14-optional , test-tox-env: gallery-py314-optional , python-ver: "3.14", os: macos-latest }
- { name: macos-gallery-python3.14-prerelease , test-tox-env: gallery-py314-prerelease, python-ver: "3.14", os: macos-latest }
steps:
- name: Checkout repo
uses: actions/checkout@v5
Expand Down Expand Up @@ -136,13 +139,14 @@ jobs:
fail-fast: false
matrix:
include:
- { name: conda-linux-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: conda-linux-python3.10-minimum , test-tox-env: py310-minimum , python-ver: "3.10", os: ubuntu-latest }
- { name: conda-linux-python3.10 , test-tox-env: py310 , python-ver: "3.10", os: ubuntu-latest }
- { name: conda-linux-python3.11 , test-tox-env: py311 , python-ver: "3.11", os: ubuntu-latest }
- { name: conda-linux-python3.12 , test-tox-env: py312 , python-ver: "3.12", os: ubuntu-latest }
- { name: conda-linux-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.13-optional , test-tox-env: py313-optional , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.13-prerelease, test-tox-env: py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.12 , test-tox-env: py312 , python-ver: "3.12", os: ubuntu-latest }
- { name: conda-linux-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.14 , test-tox-env: py314 , python-ver: "3.14", os: ubuntu-latest }
- { name: conda-linux-python3.14-optional , test-tox-env: py314-optional , python-ver: "3.14", os: ubuntu-latest }
- { name: conda-linux-python3.14-prerelease, test-tox-env: py314-prerelease, python-ver: "3.14", os: ubuntu-latest }
steps:
- name: Checkout repo
uses: actions/checkout@v5
Expand Down Expand Up @@ -182,7 +186,7 @@ jobs:
- name: Test installation from a wheel
run: |
tox -e wheelinstall --recreate --installpkg dist/*-none-any.whl

- name: Test installation from a source distribution
run: |
tox -e wheelinstall --recreate --installpkg dist/*.tar.gz
2 changes: 1 addition & 1 deletion .github/workflows/run_coverage.yml
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Expand Up @@ -28,7 +28,7 @@ jobs:
- { os: macos-latest , opt_req: false }
env: # used by codecov-action
OS: ${{ matrix.os }}
PYTHON: '3.13'
PYTHON: '3.14'
steps:
- name: Checkout repo
uses: actions/checkout@v5
Expand Down
32 changes: 16 additions & 16 deletions .github/workflows/run_tests.yml
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Expand Up @@ -19,15 +19,15 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-optional , test-tox-env: py313-optional, python-ver: "3.13", os: ubuntu-latest }
- { name: windows-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: windows-latest }
- { name: windows-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-optional, test-tox-env: py313-optional, python-ver: "3.13", os: windows-latest }
- { name: macos-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: macos-latest }
- { name: macos-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-optional , test-tox-env: py313-optional, python-ver: "3.13", os: macos-latest }
- { name: linux-python3.10-minimum , test-tox-env: py310-minimum , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.14 , test-tox-env: py314 , python-ver: "3.14", os: ubuntu-latest }
- { name: linux-python3.14-optional , test-tox-env: py314-optional, python-ver: "3.14", os: ubuntu-latest }
- { name: windows-python3.10-minimum , test-tox-env: py310-minimum , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.14 , test-tox-env: py314 , python-ver: "3.14", os: windows-latest }
- { name: windows-python3.14-optional, test-tox-env: py314-optional, python-ver: "3.14", os: windows-latest }
- { name: macos-python3.10-minimum , test-tox-env: py310-minimum , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.14 , test-tox-env: py314 , python-ver: "3.14", os: macos-latest }
- { name: macos-python3.14-optional , test-tox-env: py314-optional, python-ver: "3.14", os: macos-latest }
steps:
- name: Checkout repo
uses: actions/checkout@v5
Expand Down Expand Up @@ -75,10 +75,10 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-gallery-python3.9-minimum , test-tox-env: gallery-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-gallery-python3.13-optional , test-tox-env: gallery-py313-optional, 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-optional, test-tox-env: gallery-py313-optional, python-ver: "3.13", os: windows-latest }
- { name: linux-gallery-python3.10-minimum , test-tox-env: gallery-py310-minimum , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-gallery-python3.14-optional , test-tox-env: gallery-py314-optional, python-ver: "3.14", os: ubuntu-latest }
- { name: windows-gallery-python3.10-minimum , test-tox-env: gallery-py310-minimum , python-ver: "3.10", os: windows-latest }
- { name: windows-gallery-python3.14-optional, test-tox-env: gallery-py314-optional, python-ver: "3.14", os: windows-latest }
steps:
- name: Checkout repo
uses: actions/checkout@v5
Expand Down Expand Up @@ -113,9 +113,9 @@ jobs:
fail-fast: false
matrix:
include:
- { name: conda-linux-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: conda-linux-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.13-optional, test-tox-env: py313-optional, python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.10-minimum , test-tox-env: py310-minimum , python-ver: "3.10", os: ubuntu-latest }
- { name: conda-linux-python3.14 , test-tox-env: py314 , python-ver: "3.14", os: ubuntu-latest }
- { name: conda-linux-python3.14-optional, test-tox-env: py314-optional, python-ver: "3.14", os: ubuntu-latest }
steps:
- name: Checkout repo
uses: actions/checkout@v5
Expand Down
2 changes: 1 addition & 1 deletion .readthedocs.yaml
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Expand Up @@ -8,7 +8,7 @@ version: 2
build:
os: ubuntu-24.04
tools:
python: '3.13'
python: '3.14'

# Build documentation in the docs/ directory with Sphinx
sphinx:
Expand Down
2 changes: 1 addition & 1 deletion docs/source/installation.rst
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Expand Up @@ -31,7 +31,7 @@ often useful to use the ``dev`` branch of the ``hdmf`` GitHub repository.

.. code-block::

conda create --name hdmf-zarr-dev python=3.13
conda create --name hdmf-zarr-dev python=3.14
conda activate hdmf-zarr-dev

git clone --recurse-submodules https://github.com/hdmf-dev/hdmf.git
Expand Down
4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -11,15 +11,15 @@ authors = [
]
description = "A package defining a Zarr I/O backend for HDMF"
readme = "README.rst"
requires-python = ">=3.9"
requires-python = ">=3.10"
license = {text = "BSD"}
classifiers = [
"Programming Language :: Python",
"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",
"Programming Language :: Python :: 3.14",
"License :: OSI Approved :: BSD License",
"Development Status :: 4 - Beta",
"Intended Audience :: Developers",
Expand Down
36 changes: 18 additions & 18 deletions tox.ini
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Expand Up @@ -5,9 +5,9 @@
# Tox is used by the GitHub Actions workflow to run tests on multiple environments.

[tox]
# NOTE: if the string "py39" is in the environment name, then the py39 interpreter is used,
# NOTE: if the string "py310" is in the environment name, then the py310 interpreter is used,
# so we can omit specifying the basepython version below.
envlist = py39, py310, py311, py312, py313
envlist = py310, py311, py312, py313, py314
requires = pip >= 24.3.1

[testenv]
Expand All @@ -24,31 +24,31 @@ commands =

# Env to create coverage report locally
[testenv:localcoverage]
basepython = python3.13
basepython = python3.14
commands =
python -m pip list
python -m pip check
pytest --cov=hdmf_zarr
coverage html -d tests/coverage/htmlcov

# Envs that run tests
[testenv:py{39,310,311,312,313}]
[testenv:py{310,311,312,313,314}]
commands = {[testenv]commands}

# Test with python 3.13 and all optional dependencies
[testenv:py313-optional]
# Test with python 3.14 and all optional dependencies
[testenv:py314-optional]
extras = {[testenv]extras}, full
commands = {[testenv]commands}

# Test with python 3.13 and all optional dependencies, using pre-release versions
[testenv:py313-prerelease]
# Test with python 3.14 and all optional dependencies, using pre-release versions
[testenv:py314-prerelease]
install_command =
python -m pip install -U --pre {opts} {packages}
extras = {[testenv]extras}, full
commands = {[testenv]commands}

# Test with python 3.9 and minimum dependencies
[testenv:py39-minimum]
# Test with python 3.10 and minimum dependencies
[testenv:py310-minimum]
install_command =
python -m pip install {opts} {packages}
deps =
Expand All @@ -63,7 +63,7 @@ commands =
python -m pip list
python -m pip check
python -m build


# Envs that will test installation from a wheel
[testenv:wheelinstall]
Expand All @@ -82,23 +82,23 @@ commands =
python -m pip check
python test_gallery.py

[testenv:gallery-{py39,py310,py311,py312,py313}]
[testenv:gallery-{py310,py311,py312,py313,py314}]
commands = {[testenv:gallery]commands}

# Test with python 3.13 and all optional dependencies
[testenv:gallery-py313-optional]
# Test with python 3.14 and all optional dependencies
[testenv:gallery-py314-optional]
extras = {[testenv:gallery]extras}, full
commands = {[testenv:gallery]commands}

# Test with python 3.13 and all optional dependencies, using pre-release versions
[testenv:gallery-py313-prerelease]
# Test with python 3.14 and all optional dependencies, using pre-release versions
[testenv:gallery-py314-prerelease]
install_command =
python -m pip install -U --pre {opts} {packages}
extras = {[testenv:gallery]extras}, full
commands = {[testenv:gallery]commands}

# Test with python 3.9 and minimum dependencies
[testenv:gallery-py39-minimum]
# Test with python 3.10 and minimum dependencies
[testenv:gallery-py310-minimum]
install_command =
python -m pip install {opts} {packages}
deps =
Expand Down
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