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Merged
rly merged 2 commits into from
Feb 27, 2026
+16 −23
Merged

Fix dependency problems #55

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27b9ef2
Use dependency groups and fix minimal requirements
h-mayorquin Jan 21, 2026
e7f498d
Ryan suggestion
h-mayorquin Feb 27, 2026
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16 changes: 5 additions & 11 deletions .github/workflows/run_all_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,23 +22,17 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-python3.8-minimum , requirements: minimum , python-ver: "3.8" , os: ubuntu-latest }
- { name: linux-python3.8 , requirements: upgraded , python-ver: "3.8" , os: ubuntu-latest }
- { name: linux-python3.9 , requirements: upgraded , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-python3.10-minimum , requirements: minimum , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.10 , requirements: upgraded , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.11 , requirements: upgraded , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-python3.12 , requirements: upgraded , python-ver: "3.12", os: ubuntu-latest }
- { name: linux-python3.13 , requirements: upgraded , python-ver: "3.13", os: ubuntu-latest }
- { name: windows-python3.8-minimum , requirements: minimum , python-ver: "3.8" , os: windows-latest }
- { name: windows-python3.8 , requirements: upgraded , python-ver: "3.8" , os: windows-latest }
- { name: windows-python3.9 , requirements: upgraded , python-ver: "3.9" , os: windows-latest }
- { name: windows-python3.10-minimum , requirements: minimum , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.10 , requirements: upgraded , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.11 , requirements: upgraded , python-ver: "3.11", os: windows-latest }
- { name: windows-python3.12 , requirements: upgraded , python-ver: "3.12", os: windows-latest }
- { name: windows-python3.13 , requirements: upgraded , python-ver: "3.13", os: windows-latest }
- { name: macos-python3.8-minimum , requirements: minimum , python-ver: "3.8" , os: macos-latest }
- { name: macos-python3.8 , requirements: upgraded , python-ver: "3.8" , os: macos-latest }
- { name: macos-python3.9 , requirements: upgraded , python-ver: "3.9" , os: macos-latest }
- { name: macos-python3.10-minimum , requirements: minimum , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.10 , requirements: upgraded , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.11 , requirements: upgraded , python-ver: "3.11", os: macos-latest }
- { name: macos-python3.12 , requirements: upgraded , python-ver: "3.12", os: macos-latest }
Expand All @@ -58,7 +52,7 @@ jobs:
if: ${{ matrix.requirements == 'minimum' }}
run: |
python -m pip install --upgrade pip
python -m pip install ".[min-reqs,test]"
python -m pip install . --group min-reqs --group test
python -m pip list
python -m pip check

Expand All @@ -67,7 +61,7 @@ jobs:
run: |
python -m pip install --upgrade pip
# force upgrade of all dependencies to latest versions within allowed range
python -m pip install -U ".[test]"
python -m pip install -U . --group test
python -m pip list
python -m pip check
- name: Run tests
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2 changes: 1 addition & 1 deletion .github/workflows/run_coverage.yml
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Expand Up @@ -40,7 +40,7 @@ jobs:
run: |
python -m pip install --upgrade pip
# force upgrade of all dependencies to latest versions within allowed range
python -m pip install -U ".[test]"
python -m pip install -U . --group test
python -m pip list
python -m pip check
- name: Run tests and generate coverage report
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -168,3 +168,4 @@ cython_debug/

# Mac finder
.DS_Store
uv.lock
20 changes: 9 additions & 11 deletions pyproject.toml
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Expand Up @@ -18,12 +18,10 @@ authors = [
]
description = "NWB extension to store pose estimation data"
readme = "README.md"
requires-python = ">=3.8"
requires-python = ">=3.10"
license = {text = "BSD-3"}
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",
Expand All @@ -44,31 +42,31 @@ dependencies = [
"hdmf>=3.13.0",
]

[project.optional-dependencies]
# Dependency groups (PEP 735) - for development, not published to PyPI
[dependency-groups]
test = [
"coverage>=7.5.4",
"pytest>=8.2.2",
"pytest-cov>=5.0.0",
"pytest-subtests>=0.12.1",
"python-dateutil>=2.8.2",
]

docs = [
"hdmf-docutils>=0.4.7",
]

dev = [
"black>=24.4.2",
"codespell>=2.3.0",
"pre-commit>=3.5.0",
"ruff>=0.4.10",
"ndx-pose[docs,test]",
{include-group = "docs"},
{include-group = "test"},
]

# minimum requirements of project dependencies for testing (see .github/workflows/run_all_tests.yml)
# minimum requirements of project dependencies for testing on Python 3.10 (see .github/workflows/run_all_tests.yml)
min-reqs = [
"pynwb==2.6.0",
"hdmf==3.13.0",
"pynwb==2.6.0; python_version == '3.10'",
"hdmf==3.13.0; python_version == '3.10'",
"numpy<2; python_version == '3.10'",
]

# TODO: add URLs before release
Expand Down