feat: remove python 3.8 and add support for 3.12 and 3.13 (#44)

* feat: remove python 3.8 and add support for 3.12 and 3.13
* chore: update actions versions to make CI work

Author: nh13

.github/workflows/pythonpackage.yml

@@ -10,9 +10,9 @@ jobs:
     environment: github-action-ci
     strategy:
       matrix:
-        PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11"]
+        PYTHON_VERSION: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         submodules: 'true'
 
@@ -36,7 +36,7 @@ jobs:
       run: poetry config virtualenvs.in-project true
 
     - name: Set up cache
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache
       with:
         path: .venv

.github/workflows/wheels.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.platform.os }}
     strategy:
       matrix:
-        python: [cp38, cp39, cp310, cp311]
+        python: [cp39, cp310, cp311, cp312, cp313]
         platform:
           - os: ubuntu-24.04
             target: manylinux
@@ -43,7 +43,7 @@ jobs:
       # Used to host cibuildwheel
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel==2.15.0

.readthedocs.yml

@@ -1,7 +1,7 @@
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.9"
 version: 2
 submodules:
   include: all

README.md

@@ -63,7 +63,7 @@ conda activate pybedlite
 
 [rtd-link]:    http://pybedlite.readthedocs.org/en/stable
 
-**Requires python 3.8+** (for python < 3.8, please use pybedlite <= 0.0.3)
+**Requires python 3.9+** 
 
 # Getting Setup for Development Work
 
@@ -77,7 +77,7 @@ git clone --recurse-submodules https://github.com/fulcrumgenomics/pybedlite.git
 A simple way to create an environment with the desired version of python and poetry is to use [conda][conda-link].  E.g.:
 
 ```bash
-conda create -n pybedlite python=3.8 poetry
+conda create -n pybedlite python=3.9 poetry
 conda activate pybedlite
 poetry install
 ```

docs/conf.py

@@ -32,7 +32,7 @@
               'sphinx.ext.intersphinx',
               'sphinx.ext.napoleon']
 
-intersphinx_mapping = {'python': ('http://docs.python.org/3.8', None)}
+intersphinx_mapping = {'python': ('http://docs.python.org/3.9', None)}
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/installation.rst

@@ -2,7 +2,7 @@
 Installation
 ============
 
-**Requires python 3.8+**
+**Requires python 3.9+**
 
 Install with::
 
@@ -17,7 +17,7 @@ Getting Setup
 A simple way to create an environment with the desired version of python and poetry is to use `conda <https://docs.conda.io/en/latest/miniconda.html>`_.
 E.g.::
 
-    conda create -n pybedlite python=3.8 poetry
+    conda create -n pybedlite python=3.9 poetry
     conda activate pybedlite
     poetry install
 

poetry.lock

@@ -213,7 +213,7 @@ def test_construction_from_ucsc_with_strand(strand: str) -> None:
     `Interval.from_ucsc()` should correctly parse UCSC position-formatted strings with strands.
     """
     expected_interval = Interval("chr1", 100, 200, negative=(strand == "-"))
-    assert Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval
+    assert Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval  # noqa: E231
 
 
 @pytest.mark.parametrize(
@@ -223,7 +223,7 @@ def test_construction_from_ucsc_other_contigs(contig: str) -> None:
     """
     `Interval.from_ucsc()` should accommodate non-human, decoy, custom, and other contig names.
     """
-    assert Interval.from_ucsc(f"{contig}:101-200") == Interval(contig, 100, 200)
+    assert Interval.from_ucsc(f"{contig}:101-200") == Interval(contig, 100, 200)  # noqa: E231
 
 
 def test_that_overlap_detector_allows_generic_parameterization() -> None:

pybedlite/tests/test_overlap_detector.py

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