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deprecate Python 3.9 #2141

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a0c0f53
deprecate Python 3.9
bendichter Nov 3, 2025
c1f4649
Update CHANGELOG to include deprecated Python 3.9
bendichter Nov 3, 2025
33a7355
Remove Python 3.9 specific numpy version constraints from requirements
bendichter Nov 3, 2025
f1a9f9b
Update minimum package versions in requirements-min.txt
bendichter Nov 3, 2025
f67d012
Update numpy and pandas versions in requirements-min.txt
bendichter Nov 3, 2025
413d93f
Apply suggestion from @stephprince
bendichter Nov 3, 2025
7c5b15e
Update package dependencies to latest compatible versions
bendichter Nov 3, 2025
0dc429c
Update .github/workflows/generate_test_files.yml
bendichter Nov 3, 2025
925f944
Merge branch 'dev' into dep-py39
bendichter Nov 13, 2025
e777f26
Merge branch 'dev' into dep-py39
rly Nov 13, 2025
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1 change: 0 additions & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -61,7 +61,6 @@ body:
label: Python Version
options:
- "lower version (unsupported)"
- "3.9"
- "3.10"
- "3.11"
- "3.12"
Expand Down
18 changes: 7 additions & 11 deletions .github/workflows/run_all_tests.yml
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Expand Up @@ -22,24 +22,21 @@ jobs:
fail-fast: false
matrix:
include:
- { 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-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.10-minimum , test-tox-env: test-py310-minimum , build-tox-env: build-py310-minimum , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-python3.11-opt , test-tox-env: test-py311-optional-pinned, build-tox-env: build-py311-pinned , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: ubuntu-latest }
- { name: linux-python3.13 , test-tox-env: test-py313-pinned , build-tox-env: build-py313-pinned , 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-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.10-minimum , test-tox-env: test-py310-minimum , build-tox-env: build-py310-minimum , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: windows-latest }
- { name: windows-python3.11-opt , test-tox-env: test-py311-optional-pinned, build-tox-env: build-py311-pinned , python-ver: "3.11", os: windows-latest }
- { name: windows-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: windows-latest }
- { name: windows-python3.13 , test-tox-env: test-py313-pinned , build-tox-env: build-py313-pinned , 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-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.10-minimum , test-tox-env: test-py310-minimum , build-tox-env: build-py310-minimum , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: macos-latest }
- { name: macos-python3.11-opt , test-tox-env: test-py311-optional-pinned, build-tox-env: build-py311-pinned , python-ver: "3.11", os: macos-latest }
- { name: macos-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: macos-latest }
Expand Down Expand Up @@ -92,13 +89,13 @@ 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-python3.10-minimum , test-tox-env: gallery-py310-minimum , python-ver: "3.10", 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-python3.10-minimum , test-tox-env: gallery-py310-minimum , python-ver: "3.10", 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-python3.10-minimum , test-tox-env: gallery-py310-minimum , python-ver: "3.10", 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:
Expand Down Expand Up @@ -138,8 +135,7 @@ jobs:
fail-fast: false
matrix:
include:
- { 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-pinned , build-tox-env: build-py310-pinned , python-ver: "3.10", os: ubuntu-latest }
- { name: conda-linux-python3.10-minimum , test-tox-env: test-py310-minimum , build-tox-env: build-py310-minimum , python-ver: "3.10", os: ubuntu-latest }
- { name: conda-linux-python3.11 , test-tox-env: test-py311-pinned , build-tox-env: build-py311-pinned , python-ver: "3.11", os: ubuntu-latest }
- { name: conda-linux-python3.12 , test-tox-env: test-py312-pinned , build-tox-env: build-py312-pinned , python-ver: "3.12", os: ubuntu-latest }
- { name: conda-linux-python3.13 , test-tox-env: test-py313-pinned , build-tox-env: build-py313-pinned , python-ver: "3.13", os: ubuntu-latest }
Expand Down
12 changes: 6 additions & 6 deletions .github/workflows/run_tests.yml
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Expand Up @@ -19,12 +19,12 @@ jobs:
fail-fast: false
matrix:
include:
- { 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-minimum , test-tox-env: test-py310-minimum , build-tox-env: build-py310-minimum , python-ver: "3.10" , os: ubuntu-latest }
# NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
- { name: linux-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: ubuntu-latest , upload-wheels: true }
- { 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-minimum , test-tox-env: test-py310-minimum , build-tox-env: build-py310-minimum , python-ver: "3.10" , 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: 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-minimum , test-tox-env: test-py310-minimum , build-tox-env: build-py310-minimum , python-ver: "3.10" , os: macos-13 }
- { name: macos-python3.13-upgraded , test-tox-env: test-py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13" , os: macos-latest }
steps:
- name: Cancel non-latest runs
Expand Down Expand Up @@ -79,9 +79,9 @@ 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-python3.10-minimum , test-tox-env: gallery-py310-minimum , python-ver: "3.10" , 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-python3.10-minimum , test-tox-env: gallery-py310-minimum , python-ver: "3.10" , os: windows-latest }
- { name: windows-gallery-python3.13-upgraded, test-tox-env: gallery-py313-upgraded, python-ver: "3.13", os: windows-latest }
steps:
- name: Cancel non-latest runs
Expand Down Expand Up @@ -120,7 +120,7 @@ jobs:
fail-fast: false
matrix:
include:
- { 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-minimum , test-tox-env: test-py310-minimum , build-tox-env: build-py310-minimum , python-ver: "3.10" , 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 }
steps:
- name: Cancel non-latest runs
Expand Down
4 changes: 2 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -12,8 +12,8 @@
- Fixed import structure test. @rly [#2136](https://github.com/NeurodataWithoutBorders/pynwb/pull/2136)

### Changed
- Change UI of documentation assistant to be an accordion that is always visible. @bendichter [#2124](https://github.com/NeurodataWithoutBorders/pynwb/pull/2124)
- Updated minimum HDMF version to 4.1.2 and updated tests accordingly. @rly [#2144](https://github.com/NeurodataWithoutBorders/pynwb/pull/2144)
- Changed UI of documentation assistant to be an accordion that is always visible. @bendichter [#2124](https://github.com/NeurodataWithoutBorders/pynwb/pull/2124)
- Deprecated Python 3.9 support. (EOL was Oct 31, 2025) @bendichter [#2141](https://github.com/NeurodataWithoutBorders/pynwb/pull/2141)


## PyNWB 3.1.2 (August 13, 2025)
Expand Down
6 changes: 3 additions & 3 deletions docs/source/install_developers.rst
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Expand Up @@ -6,7 +6,7 @@ Installing PyNWB for Developers

PyNWB has the following minimum requirements, which must be installed before you can get started using PyNWB.

#. Python 3.9, 3.10, 3.11, 3.12, or 3.13
#. Python 3.10, 3.11, 3.12, or 3.13
#. pip


Expand Down Expand Up @@ -54,11 +54,11 @@ Option 2: Using conda
^^^^^^^^^^^^^^^^^^^^^

First, install Anaconda_ to install the ``conda`` tool. Then create and
activate a new virtual environment called "venv" with Python 3.9 installed.
activate a new virtual environment called "venv" with Python 3.10 installed.

.. code:: bash

conda create --name venv python=3.9
conda create --name venv python=3.10
conda activate venv

Similar to a virtual environment created with ``virtualenv``, a conda environment
Expand Down
4 changes: 1 addition & 3 deletions docs/source/install_users.rst
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Expand Up @@ -6,7 +6,7 @@ Installing PyNWB

PyNWB has the following minimum requirements, which must be installed before you can get started using PyNWB.

#. Python 3.9, 3.10, 3.11, 3.12, or 3.13
#. Python 3.10, 3.11, 3.12, or 3.13
#. pip

.. note:: If you are a developer then please see the :ref:`install_developers` installation instructions instead.
Expand Down Expand Up @@ -53,5 +53,3 @@ own project against the latest version of PyNWB.
.. code::

$ pip install -U pynwb --find-links https://github.com/NeurodataWithoutBorders/pynwb/releases/tag/latest --no-index


8 changes: 3 additions & 5 deletions pyproject.toml
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Expand Up @@ -14,11 +14,10 @@ authors = [
]
description= "Package for working with Neurodata stored in the NWB format."
readme = "README.rst"
requires-python = ">=3.9"
requires-python = ">=3.10"
license = {text = "BSD-3-Clause"}
classifiers = [
"Programming Language :: Python",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
Expand All @@ -33,10 +32,10 @@ classifiers = [
"Topic :: Scientific/Engineering :: Medical Science Apps."
]
dependencies = [
"h5py>=3.2.0",
"h5py>=3.6.0",
"hdmf>=4.1.2,<5",
"numpy>=1.24.0",
"pandas>=1.2.0",
"pandas>=1.3.5",
"python-dateutil>=2.8.2",
"platformdirs>=4.1.0"
]
Expand Down Expand Up @@ -122,4 +121,3 @@ line-length = 120

[tool.ruff.lint.mccabe]
max-complexity = 17

6 changes: 3 additions & 3 deletions requirements-min.txt
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@@ -1,7 +1,7 @@
# minimum versions of package dependencies for installing PyNWB
h5py==3.2.0
h5py==3.6.0
hdmf==4.1.2
numpy==1.24.0
pandas==1.2.0
pandas==1.3.5
python-dateutil==2.8.2
platformdirs==4.1.0
platformdirs==4.1.0
3 changes: 1 addition & 2 deletions requirements.txt
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@@ -1,8 +1,7 @@
# pinned dependencies to reproduce an entire development environment to use PyNWB
h5py==3.12.1
hdmf==4.1.2
numpy==2.1.1; python_version > "3.9" # numpy 2.1+ is not compatible with py3.9
numpy==2.0.2; python_version == "3.9"
numpy==2.1.1
pandas==2.2.3
python-dateutil==2.9.0.post0
platformdirs==4.3.6
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14 changes: 7 additions & 7 deletions tox.ini
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Expand Up @@ -4,7 +4,7 @@
# and then run "tox" from this directory.

[tox]
envlist = test-py{39,310,311,312,313}-pinned
envlist = test-py{310,311,312,313}-pinned
requires = pip >= 22.0

[testenv]
Expand Down Expand Up @@ -37,18 +37,18 @@ commands =
[testenv:test-py313-upgraded]
[testenv:test-py313-prerelease]
[testenv:test-py311-optional-pinned] # some optional reqs not compatible with py312 yet
[testenv:test-py{39,310,311,312,313}-pinned]
[testenv:test-py39-minimum]
[testenv:test-py{310,311,312,313}-pinned]
[testenv:test-py310-minimum]

[testenv:gallery-py313-upgraded]
[testenv:gallery-py313-prerelease]
[testenv:gallery-py311-optional-pinned]
[testenv:gallery-py{39,310,311,312,313}-pinned]
[testenv:gallery-py39-minimum]
[testenv:gallery-py{310,311,312,313}-pinned]
[testenv:gallery-py310-minimum]

[testenv:build-py313-upgraded]
[testenv:build-py313-prerelease]
[testenv:build-py{39,310,311,312,313}-pinned] # using tox for this so that we can have a clean build environment
[testenv:build-py39-minimum]
[testenv:build-py{310,311,312,313}-pinned] # using tox for this so that we can have a clean build environment
[testenv:build-py310-minimum]

[testenv:wheelinstall] # use with `--installpkg dist/*-none-any.whl`
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