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feat: remove python 3.8 and add support for 3.12 and 3.13
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.github/workflows/pythonpackage.yml

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@@ -10,7 +10,7 @@ jobs:
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environment: github-action-ci
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strategy:
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matrix:
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PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11"]
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PYTHON_VERSION: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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steps:
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- uses: actions/checkout@v2
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with:

.github/workflows/wheels.yml

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@@ -11,7 +11,7 @@ jobs:
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runs-on: ${{ matrix.platform.os }}
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strategy:
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matrix:
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python: [cp38, cp39, cp310, cp311]
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python: [cp38, cp39, cp310, cp311, cp312, cp313]
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platform:
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- os: ubuntu-24.04
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target: manylinux
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# Used to host cibuildwheel
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- uses: actions/setup-python@v4
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with:
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python-version: 3.8
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python-version: 3.9
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- name: Install cibuildwheel
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run: python -m pip install cibuildwheel==2.15.0

.readthedocs.yml

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build:
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os: ubuntu-22.04
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tools:
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python: "3.8"
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python: "3.9"
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version: 2
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submodules:
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include: all

README.md

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@@ -52,7 +52,7 @@ conda activate pybedlite
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[rtd-link]: http://pybedlite.readthedocs.org/en/stable
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**Requires python 3.8+** (for python < 3.8, please use pybedlite <= 0.0.3)
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**Requires python 3.9+**
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# Getting Setup for Development Work
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@@ -66,7 +66,7 @@ git clone --recurse-submodules https://github.com/fulcrumgenomics/pybedlite.git
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A simple way to create an environment with the desired version of python and poetry is to use [conda][conda-link]. E.g.:
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```bash
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conda create -n pybedlite python=3.8 poetry
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conda create -n pybedlite python=3.9 poetry
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conda activate pybedlite
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poetry install
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```

poetry.lock

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pybedlite/tests/test_overlap_detector.py

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@@ -213,7 +213,7 @@ def test_construction_from_ucsc_with_strand(strand: str) -> None:
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`Interval.from_ucsc()` should correctly parse UCSC position-formatted strings with strands.
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"""
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expected_interval = Interval("chr1", 100, 200, negative=(strand == "-"))
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assert Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval
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assert Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval # noqa: E231
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@pytest.mark.parametrize(
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"""
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`Interval.from_ucsc()` should accommodate non-human, decoy, custom, and other contig names.
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"""
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assert Interval.from_ucsc(f"{contig}:101-200") == Interval(contig, 100, 200)
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assert Interval.from_ucsc(f"{contig}:101-200") == Interval(contig, 100, 200) # noqa: E231
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def test_that_overlap_detector_allows_generic_parameterization() -> None:

pyproject.toml

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@@ -28,7 +28,7 @@ include = ["LICENSE"]
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packages = [{ include = "pybedlite" }, { include = "cgranges" }]
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[tool.poetry.dependencies]
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python = "^3.8.0"
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python = "^3.9.0"
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attrs = "^23.0.0"
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sphinx = { version = "^7.0.0", optional = true }
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