[OMIT ME] Temporarily avoid Cython 3.1.0 on the PR branch

Author: jmarshall

.github/workflows/ci.yaml

@@ -28,7 +28,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install prerequisite Python libraries
-        run:  pip install cython mypy pytest setuptools
+        run:  pip install 'cython<3.1' mypy pytest setuptools
 
       - name: Install Linux build prerequisites
         if:   runner.os == 'Linux'
@@ -79,7 +79,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install prerequisite Python libraries
-        run:  pip install cython pytest
+        run:  pip install 'cython<3.1' pytest
 
       - name: Install build prerequisites
         if:   runner.os == 'Linux'

devtools/environment-dev.yaml

@@ -3,6 +3,6 @@ channels:
   - bioconda
 dependencies:
   - bzip2
-  - cython
+  - cython<3.1
   - setuptools
   - xz

pyproject.toml

@@ -18,7 +18,7 @@ dynamic = [
 "Release notes" = "https://pysam.readthedocs.io/en/stable/release.html"
 
 [build-system]
-requires = ["setuptools>=59.0", "Cython>=0.29.12,<4"]
+requires = ["setuptools>=59.0", "Cython>=0.29.12,<3.1"]
 build-backend = "setuptools.build_meta:__legacy__"
 
 [tool.cibuildwheel]

requirements-dev.txt

@@ -1 +1 @@
-Cython>=0.29.12,<4
+Cython>=0.29.12,<3.1