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Remove requirements files, update tox and workflows
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@rly
rly committed Dec 18, 2024
1 parent 81db7ef commit 9117094
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Showing 10 changed files with 124 additions and 236 deletions.
4 changes: 2 additions & 2 deletions .github/workflows/deploy_release.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,11 @@ jobs:
- name: Run tox tests
run: |
tox -e py313-upgraded
tox -e py313
- name: Build wheel and source distribution
run: |
tox -e build-py313-upgraded
tox -e build
ls -1 dist
- name: Test installation from a wheel
Expand Down
70 changes: 33 additions & 37 deletions .github/workflows/run_all_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,30 +25,27 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-python3.9-minimum , test-tox-env: py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-python3.12 , test-tox-env: py312 , build-tox-env: build-py312 , python-ver: "3.12", os: ubuntu-latest }
- { name: linux-python3.13 , test-tox-env: py313 , build-tox-env: build-py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-optional , test-tox-env: py313-optional , build-tox-env: build-py313-optional , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-upgraded , test-tox-env: py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-prerelease , test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
- { name: windows-python3.9-minimum , test-tox-env: py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: windows-latest }
- { name: windows-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: windows-latest }
- { name: windows-python3.12 , test-tox-env: py312 , build-tox-env: build-py312 , python-ver: "3.12", os: windows-latest }
- { name: windows-python3.13 , test-tox-env: py313 , build-tox-env: build-py313 , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-optional , test-tox-env: py313-optional , build-tox-env: build-py313-optional , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-upgraded , test-tox-env: py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-prerelease, test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: windows-latest }
- { name: macos-python3.9-minimum , test-tox-env: py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: macos-latest }
- { name: macos-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: macos-latest }
- { name: macos-python3.12 , test-tox-env: py312 , build-tox-env: build-py312 , python-ver: "3.12", os: macos-latest }
- { name: macos-python3.13 , test-tox-env: py313 , build-tox-env: build-py313 , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-optional , test-tox-env: py313-optional , build-tox-env: build-py313-optional , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-upgraded , test-tox-env: py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-prerelease , test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: macos-latest }
- { name: linux-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-python3.10 , test-tox-env: py310 , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.11 , test-tox-env: py311 , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-python3.12 , test-tox-env: py312 , python-ver: "3.12", os: ubuntu-latest }
- { name: linux-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-optional , test-tox-env: py313-optional , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.13-prerelease , test-tox-env: py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
- { name: windows-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: windows-latest }
- { name: windows-python3.10 , test-tox-env: py310 , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.11 , test-tox-env: py311 , python-ver: "3.11", os: windows-latest }
- { name: windows-python3.12 , test-tox-env: py312 , python-ver: "3.12", os: windows-latest }
- { name: windows-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-optional , test-tox-env: py313-optional , python-ver: "3.13", os: windows-latest }
- { name: windows-python3.13-prerelease, test-tox-env: py313-prerelease, python-ver: "3.13", os: windows-latest }
- { name: macos-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: macos-latest }
- { name: macos-python3.10 , test-tox-env: py310 , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.11 , test-tox-env: py311 , python-ver: "3.11", os: macos-latest }
- { name: macos-python3.12 , test-tox-env: py312 , python-ver: "3.12", os: macos-latest }
- { name: macos-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-optional , test-tox-env: py313-optional , python-ver: "3.13", os: macos-latest }
- { name: macos-python3.13-prerelease , test-tox-env: py313-prerelease, python-ver: "3.13", os: macos-latest }
steps:
- name: Checkout repo
uses: actions/checkout@v4
Expand All @@ -70,7 +67,7 @@ jobs:
- name: Build wheel and source distribution
run: |
tox -e ${{ matrix.build-tox-env }}
tox -e build
ls -1 dist
- name: Test installation from a wheel
Expand All @@ -95,13 +92,13 @@ jobs:
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: linux-gallery-python3.13-optional , test-tox-env: gallery-py313-optional , 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-python3.13-upgraded , test-tox-env: gallery-py313-upgraded , python-ver: "3.13", os: windows-latest }
- { name: windows-gallery-python3.13-optional , test-tox-env: gallery-py313-optional , 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-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-optional , test-tox-env: gallery-py313-optional , 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
Expand Down Expand Up @@ -135,14 +132,13 @@ jobs:
fail-fast: false
matrix:
include:
- { name: conda-linux-python3.9-minimum , test-tox-env: py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.8" , os: ubuntu-latest }
- { name: conda-linux-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: ubuntu-latest }
- { name: conda-linux-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest }
- { name: conda-linux-python3.12 , test-tox-env: py312 , build-tox-env: build-py312 , python-ver: "3.12", os: ubuntu-latest }
- { name: conda-linux-python3.13 , test-tox-env: py313 , build-tox-env: build-py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.13-optional , test-tox-env: py313-optional , build-tox-env: build-py313-optional , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.13-upgraded , test-tox-env: py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.13-prerelease, test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.9-minimum , test-tox-env: py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: conda-linux-python3.10 , test-tox-env: py310 , python-ver: "3.10", os: ubuntu-latest }
- { name: conda-linux-python3.11 , test-tox-env: py311 , python-ver: "3.11", os: ubuntu-latest }
- { name: conda-linux-python3.12 , test-tox-env: py312 , python-ver: "3.12", os: ubuntu-latest }
- { name: conda-linux-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.13-optional , test-tox-env: py313-optional , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.13-prerelease, test-tox-env: py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
steps:
- name: Checkout repo
uses: actions/checkout@v4
Expand Down Expand Up @@ -173,7 +169,7 @@ jobs:
- name: Build wheel and source distribution
run: |
tox -e ${{ matrix.build-tox-env }}
tox -e build
ls -1 dist
- name: Test installation from a wheel
Expand Down
29 changes: 14 additions & 15 deletions .github/workflows/run_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,14 +22,13 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-python3.9-minimum , test-tox-env: py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-python3.13 , test-tox-env: py313 , build-tox-env: build-py313 , python-ver: "3.13", os: ubuntu-latest }
- { name: linux-python3.9-minimum , test-tox-env: py39-minimum, python-ver: "3.9" , 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: 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: py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: windows-latest }
- { name: windows-python3.13-upgraded , test-tox-env: py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: windows-latest }
- { name: macos-python3.9-minimum , test-tox-env: py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: macos-latest }
- { name: macos-python3.13-upgraded , test-tox-env: py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: macos-latest }
- { name: linux-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: ubuntu-latest , upload-wheels: true }
- { name: windows-python3.9-minimum, test-tox-env: py39-minimum, python-ver: "3.9" , os: windows-latest }
- { name: windows-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: windows-latest }
- { name: macos-python3.9-minimum , test-tox-env: py39-minimum, python-ver: "3.9" , os: macos-latest }
- { name: macos-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: macos-latest }
steps:
- name: Checkout repo
uses: actions/checkout@v4
Expand All @@ -51,7 +50,7 @@ jobs:
- name: Build wheel and source distribution
run: |
tox -e ${{ matrix.build-tox-env }}
tox -e build
ls -1 dist
- name: Test installation from a wheel
Expand Down Expand Up @@ -82,10 +81,10 @@ 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-python3.9-minimum , test-tox-env: gallery-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-gallery-python3.13-optional , test-tox-env: gallery-py313-optional, 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-optional, test-tox-env: gallery-py313-optional, python-ver: "3.13", os: windows-latest }
steps:
- name: Checkout repo
uses: actions/checkout@v4
Expand Down Expand Up @@ -118,8 +117,8 @@ jobs:
fail-fast: false
matrix:
include:
- { name: conda-linux-python3.9-minimum , test-tox-env: py39-minimum , build-tox-env: build-py39-minimum , python-ver: "3.9" , os: ubuntu-latest }
- { name: conda-linux-python3.13-upgraded , test-tox-env: py313-upgraded , build-tox-env: build-py313-upgraded , python-ver: "3.13", os: ubuntu-latest }
- { name: conda-linux-python3.9-minimum, test-tox-env: py39-minimum, python-ver: "3.9" , os: ubuntu-latest }
- { name: conda-linux-python3.13 , test-tox-env: py313 , python-ver: "3.13", os: ubuntu-latest }
steps:
- name: Checkout repo
uses: actions/checkout@v4
Expand Down Expand Up @@ -150,7 +149,7 @@ jobs:
- name: Build wheel and source distribution
run: |
tox -e ${{ matrix.build-tox-env }}
tox -e build
ls -1 dist
- name: Test installation from a wheel
Expand Down
32 changes: 26 additions & 6 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,12 +28,12 @@ classifiers = [
"Topic :: Scientific/Engineering :: Medical Science Apps."
]
dependencies = [
'hdmf>=3.14.5',
'zarr>=2.18.0, <3.0', # pin below 3.0 until HDMF-zarr supports zarr 3.0
'numpy>=1.24',
'numcodecs>=0.10.0',
'pynwb>=2.8.3',
'threadpoolctl>=3.1.0',
"hdmf>=3.14.5",
"zarr>=2.18.0, <3.0", # pin below 3.0 until HDMF-zarr supports zarr 3.0
"numpy>=1.24.0",
"numcodecs>=0.10.0",
"pynwb>=2.8.3",
"threadpoolctl>=3.1.0",
]
dynamic = ["version"]

Expand All @@ -42,6 +42,26 @@ tqdm = ["tqdm>=4.41.0"]
fsspec = ["fsspec"]
s3fs = ["s3fs"]

# development dependencies
test = [
"codespell",
"hdf5plugin", # hdf5plugin is used to test conversion of plugin filters
"pre-commit",
"pytest",
"pytest-cov",
"python-dateutil",
"ruff",
"tox",
]

docs = [
"matplotlib",
"sphinx>=4", # improved support for docutils>=0.17
"sphinx_rtd_theme>=1", # <1 does not work with docutils>=0.17
"sphinx-gallery",
"sphinx-copybutton",
]

[project.urls]
"Homepage" = "https://github.com/hdmf-dev/hdmf-zarr"
"Bug Tracker" = "https://github.com/hdmf-dev/hdmf-zarr/issues"
Expand Down
15 changes: 0 additions & 15 deletions requirements-dev.txt
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6 changes: 0 additions & 6 deletions requirements-doc.txt
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6 changes: 4 additions & 2 deletions requirements-min.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
# minimum versions of package dependencies for installing HDMF
# NOTE: these should match the minimum bound for dependencies in pyproject.toml
hdmf==3.14.5
zarr==2.13.0
zarr==2.18.0
numpy==1.24.0
numcodecs==0.10.0
pynwb==2.8.3
setuptools
threadpoolctl==3.1.0
3 changes: 0 additions & 3 deletions requirements-opt.txt
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9 changes: 0 additions & 9 deletions requirements.txt
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