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Return breaking changes removing deprecated classes & functions #1227

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merged 2 commits into from
Jan 9, 2025
Merged

Return breaking changes removing deprecated classes & functions #1227

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0dc44d4
Revert "Temporarily revert breaking changes for bugfix release (#1224)"
rly Jan 6, 2025
44e1ab1
Merge branch 'dev' into breaking
rly Jan 9, 2025
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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: 28 additions & 29 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-python3.8-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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
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-python3.12-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
Expand Down
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-python3.8-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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
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-20.04
os: ubuntu-22.04
tools:
python: '3.9'
python: '3.12'

# Build documentation in the docs/ directory with Sphinx
sphinx:
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7 changes: 7 additions & 0 deletions CHANGELOG.md
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@@ -1,5 +1,12 @@
# HDMF Changelog

## HDMF 4.0.0 (Upcoming)

### Breaking changes
- 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 reached end of life. Drop support for Python 3.8 and add support for Python 3.13. @mavaylon1 [#1209](https://github.com/hdmf-dev/hdmf/pull/1209)

## HDMF 3.14.6 (December 20, 2024)

### Enhancements
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1 change: 0 additions & 1 deletion docs/source/conf.py
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Expand Up @@ -87,7 +87,6 @@

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
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Expand Up @@ -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.

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2 changes: 1 addition & 1 deletion docs/source/overview_software_architecture.rst
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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.RegionBuilder` - represents a slice into data (Subclass of :py:class:`~hdmf.build.builders.DatasetBuilder`)
* :py:class:`~hdmf.build.builders.ReferenceBuilder` - represents a reference to another group or dataset

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

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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==3.12
- 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
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