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Temporarily revert breaking changes for bugfix release #1224

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merged 5 commits into from
Dec 20, 2024
Merged

Temporarily revert breaking changes for bugfix release #1224

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a814b44
Revert "Delete src/hdmf/build/map.py (#1221)"
rly Dec 20, 2024
7eeee7a
Revert "Delete SortedQueryTest.h5 (#1220)"
rly Dec 20, 2024
d928c18
Revert "Remove RegionBuilder and remaining references to region refer…
rly Dec 20, 2024
89f1f8b
Revert "Remove Python 3.8 Support and Add 3.13 Support (#1209)"
rly Dec 20, 2024
5f708f2
Revert "Coverage to 90% (#1198)"
rly Dec 20, 2024
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2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
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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
Expand Down
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
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-python3.13-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
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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:
Expand Down
7 changes: 1 addition & 6 deletions CHANGELOG.md
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@@ -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)
Expand Down
1 change: 1 addition & 0 deletions docs/source/conf.py
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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'),
Expand Down
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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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.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
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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
Expand Down
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