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Temporarily revert breaking changes for bugfix release (#1224)
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rly authored Dec 20, 2024
1 parent 6396a81 commit 035d3ec
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2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/run_coverage.yml
Original file line number Diff line number Diff line change
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
Expand Down
30 changes: 15 additions & 15 deletions .github/workflows/run_tests.yml
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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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7 changes: 1 addition & 6 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,11 +1,6 @@
# HDMF Changelog

## HDMF 4.0.0 (Upcoming)

### Deprecations
- The following classes have been deprecated and removed: Array, AbstractSortedArray, SortedArray, LinSpace, Query, RegionSlicer, ListSlicer, H5RegionSlicer, DataRegion, RegionBuilder. 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 development for region references. @mavaylon1, @rly [#1998](https://github.com/hdmf-dev/hdmf/pull/1198), [#1212](https://github.com/hdmf-dev/hdmf/pull/1212)
- Importing from hdmf.build.map is no longer supported. Import from hdmf.build instead. @rly [#1221](https://github.com/hdmf-dev/hdmf/pull/1221)
- 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)
## HDMF 3.14.6 (Upcoming)

### 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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1 change: 1 addition & 0 deletions docs/source/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,7 @@

nitpicky = True
nitpick_ignore = [('py:class', 'Intracomm'),
('py:class', 'h5py.RegionReference'),
('py:class', 'h5py._hl.dataset.Dataset'),
('py:class', 'function'),
('py:class', 'unittest.case.TestCase'),
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2 changes: 1 addition & 1 deletion docs/source/install_users.rst
Original file line number Diff line number Diff line change
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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2 changes: 1 addition & 1 deletion docs/source/overview_software_architecture.rst
Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ Builder
* :py:class:`~hdmf.build.builders.GroupBuilder` - represents a collection of objects
* :py:class:`~hdmf.build.builders.DatasetBuilder` - represents data
* :py:class:`~hdmf.build.builders.LinkBuilder` - represents soft-links
* :py:class:`~hdmf.build.builders.ReferenceBuilder` - represents a reference to another group or dataset
* :py:class:`~hdmf.build.builders.RegionBuilder` - represents a slice into data (Subclass of :py:class:`~hdmf.build.builders.DatasetBuilder`)

* **Main Module:** :py:class:`hdmf.build.builders`

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10 changes: 5 additions & 5 deletions environment-ros3.yml
Original file line number Diff line number Diff line change
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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