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Revert "Remove Python 3.8 Support and Add 3.13 Support (#1209)"
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This reverts commit 26d584c.
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@rly
rly committed Dec 20, 2024
1 parent d928c18 commit 89f1f8b
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Showing 14 changed files with 99 additions and 88 deletions.
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -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
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57 changes: 29 additions & 28 deletions .github/workflows/run_all_tests.yml
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Expand Up @@ -25,30 +25,30 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-python3.9-minimum , test-tox-env: pytest-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { 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-python3.10 , 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-python3.13 , 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: 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: 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-python3.13 , 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: 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: 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-python3.13 , 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 }
- { 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 }
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
Expand Down Expand Up @@ -97,18 +97,18 @@ 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-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , 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-python3.13-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: 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-python3.11-optional , test-tox-env: gallery-py311-optional-pinned , python-ver: "3.11", 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: 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: macos-gallery-python3.11-optional , test-tox-env: gallery-py311-optional-pinned , python-ver: "3.11", 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 }
- { 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 }
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
Expand Down Expand Up @@ -144,13 +144,14 @@ jobs:
fail-fast: false
matrix:
include:
- { name: conda-linux-python3.9-minimum , test-tox-env: pytest-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { 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-python3.10 , 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-python3.13 , 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 }
- { 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 }
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
Expand Down Expand Up @@ -208,9 +209,9 @@ jobs:
fail-fast: false
matrix:
include:
- { 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 }
- { 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 }
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
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2 changes: 1 addition & 1 deletion .github/workflows/run_coverage.yml
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Expand Up @@ -84,7 +84,7 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-python3.13-ros3 , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.12-ros3 , python-ver: "3.12", os: ubuntu-latest }
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
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30 changes: 15 additions & 15 deletions .github/workflows/run_tests.yml
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Expand Up @@ -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-python3.9-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 }
- { 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 }
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
Expand Down Expand Up @@ -85,10 +85,10 @@ 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-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 }
- { 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 }
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
Expand Down Expand Up @@ -124,8 +124,8 @@ jobs:
fail-fast: false
matrix:
include:
- { 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 }
- { 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 }
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
Expand Down Expand Up @@ -188,7 +188,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.13'
python-version: '3.12'

- name: Download wheel and source distributions from artifact
uses: actions/download-artifact@v4
Expand Down Expand Up @@ -221,7 +221,7 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-python3.13-ros3 , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.12-ros3 , python-ver: "3.12", os: ubuntu-latest }
steps:
- name: Checkout repo with submodules
uses: actions/checkout@v4
Expand Down
4 changes: 2 additions & 2 deletions .readthedocs.yaml
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Expand Up @@ -6,9 +6,9 @@
version: 2

build:
os: ubuntu-22.04
os: ubuntu-20.04
tools:
python: '3.12'
python: '3.9'

# Build documentation in the docs/ directory with Sphinx
sphinx:
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1 change: 0 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -4,7 +4,6 @@

### 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)
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2 changes: 1 addition & 1 deletion docs/source/install_users.rst
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Expand Up @@ -4,7 +4,7 @@
Installing HDMF
---------------

HDMF requires having Python 3.9-3.13 installed. If you don't have Python installed and want the simplest way to
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
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.

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10 changes: 5 additions & 5 deletions environment-ros3.yml
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Expand Up @@ -4,11 +4,11 @@ channels:
- conda-forge
- defaults
dependencies:
- python==3.13
- h5py==3.12.1
- matplotlib==3.9.2
- numpy==2.1.3
- pandas==2.2.3
- python==3.12
- h5py==3.11.0
- matplotlib==3.8.4
- numpy==2.0.0
- pandas==2.2.2
- 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
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24 changes: 12 additions & 12 deletions pyproject.toml
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Expand Up @@ -13,15 +13,15 @@ authors = [
]
description = "A hierarchical data modeling framework for modern science data standards"
readme = "README.rst"
requires-python = ">=3.9"
requires-python = ">=3.8"
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",
Expand All @@ -30,22 +30,22 @@ classifiers = [
"Topic :: Scientific/Engineering :: Medical Science Apps.",
]
dependencies = [
"h5py>=3.1.0",
"jsonschema>=3.2.0",
'numpy>=1.19.3',
"pandas>=1.2.0",
"h5py>=2.10",
"jsonschema>=2.6.0",
'numpy>=1.18',
"pandas>=1.0.5",
"ruamel.yaml>=0.16",
"scipy>=1.7",
"scipy>=1.4",
"importlib-resources; python_version < '3.9'", # TODO: remove when minimum python version is 3.9
]
dynamic = ["version"]

[project.optional-dependencies]
tqdm = ["tqdm>=4.41.0"]
zarr = ["zarr>=2.12.0"]
termset = ["linkml-runtime>=1.5.5",
"schemasheets>=0.1.23",
"oaklib>=0.5.12",
"pyyaml>=6.0.1"]
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'"]

[project.urls]
"Homepage" = "https://github.com/hdmf-dev/hdmf"
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