Test hictkpy against Python 3.13 (#99)

* Bump Python version used by CI
* Test hictkpy with Python 3.13

.github/workflows/build-conan-deps.yml

@@ -261,7 +261,7 @@ jobs:
       - uses: actions/setup-python@v5
         if: steps.cache-conan.outputs.cache-hit != 'true'
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Update build deps
         if: steps.cache-conan.outputs.cache-hit != 'true'
@@ -366,7 +366,7 @@ jobs:
       - uses: actions/setup-python@v5
         if: steps.cache-conan.outputs.cache-hit != 'true'
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Update build deps
         if: steps.cache-conan.outputs.cache-hit != 'true'

.github/workflows/pip.yml

@@ -47,7 +47,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-2019, macos-latest, ubuntu-latest]
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.9", "3.12", "3.13"]
 
     runs-on: ${{ matrix.os }}
 
@@ -83,6 +83,11 @@ jobs:
           echo 'CXX=clang++' >> $GITHUB_ENV
 
       - name: Build and install
+        if: matrix.python-version == '3.13'
+        run: pip install --verbose '.[numpy,scipy,test]'
+
+      - name: Build and install
+        if: matrix.python-version != '3.13'
         run: pip install --verbose '.[all,test]'
 
       - name: Save Conan cache

.github/workflows/wheels.yml

@@ -60,7 +60,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install cibuildwheel
         run: pip install 'cibuildwheel>=2.21'
@@ -232,6 +232,7 @@ jobs:
         with:
           only: ${{ matrix.wheel-config }}
         env:
+          CIBW_BUILD_VERBOSITY: 1
           CIBW_ENVIRONMENT_LINUX: >
             PIP_VERBOSE=1
             HICTK_CI=1

pyproject.toml

@@ -24,6 +24,10 @@ authors = [
 requires-python = ">=3.9"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
   "Topic :: Scientific/Engineering :: Bio-Informatics",
   "License :: OSI Approved :: MIT License"
 ]
@@ -52,7 +56,6 @@ optional-dependencies.all = [
 ]
 
 optional-dependencies.test = [
-  "hictkpy[all]",
   "pytest>=8.0",
 ]
 
@@ -104,16 +107,15 @@ testpaths = [
 ]
 
 [tool.cibuildwheel]
-skip = ["cp313*", "*musllinux*", "pp*"]
+skip = ["cp313*", "cp314*", "*musllinux*", "pp*"]
 test-command = "python -m pytest {project}/test"
-test-extras = ["test"]
-test-skip = ["cp313*", "*universal2", "pp*"]
+test-extras = ["test", "numpy", "pandas", "pyarrow", "scipy"]
+test-skip = ["cp313*", "cp314*", "*universal2", "pp*"]
 
 # Setuptools bug causes collision between pypy and cpython artifacts
 before-build = [
   "rm -rf '{project}/build'",
 ]
-environment = { PIP_VERBOSE=1 }
 
 # We are using static linking, thus repairing wheels is not necessary.
 repair-wheel-command = ""

test/test_bin_table.py

@@ -56,7 +56,10 @@ def test_getters(self):
         with pytest.raises(Exception):
             bins.get_id("abc", 100)
 
-    @pytest.mark.skipif(not numpy_avail(), reason="numpy is not available")
+    @pytest.mark.skipif(
+        not numpy_avail() or not pandas_avail() or not pyarrow_avail(),
+        reason="numpy, pandas, or pyarrow are not available",
+    )
     def test_vectorized_getters(self):
         import numpy as np