From 6243656478ca662cce659360f528a17ab728770c Mon Sep 17 00:00:00 2001
From: John Marshall <jmarshall@hey.com>
Date: Tue, 21 Jan 2025 00:57:19 +1300
Subject: [PATCH] Update ci.yaml now that ubuntu-latest is Ubuntu 24.04

Python 3.7 is not available via setup-python on 24.04, so omit it
and add the semi-recently released 3.13 instead.

Ensure that libbz2 and liblzma development files are installed.
---
 .github/workflows/ci.yaml     | 10 +++++-----
 devtools/environment-dev.yaml |  2 ++
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 829a78dc..7ccc0f5c 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -8,15 +8,15 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu, macos]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
         exclude:
           # Run only the latest few 3.x versions on macOS
-          - os: macos
-            python-version: 3.7
           - os: macos
             python-version: 3.8
           - os: macos
             python-version: 3.9
+          - os: macos
+            python-version: 3.10
 
     steps:
       - name: Checkout pysam
@@ -34,7 +34,7 @@ jobs:
         if:   runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -q --no-install-recommends --no-install-suggests libcurl4-openssl-dev
+          sudo apt-get install -q --no-install-recommends --no-install-suggests libbz2-dev libcurl4-openssl-dev liblzma-dev
 
       - name: Update macOS build prerequisites
         if:   runner.os == 'macOS'
@@ -85,7 +85,7 @@ jobs:
         if:   runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -q --no-install-recommends --no-install-suggests libcurl4-openssl-dev
+          sudo apt-get install -q --no-install-recommends --no-install-suggests libbz2-dev libcurl4-openssl-dev liblzma-dev
 
       - name: Create source distribution
         run:  python setup.py sdist --owner=root --group=root
diff --git a/devtools/environment-dev.yaml b/devtools/environment-dev.yaml
index c98cc473..224ed084 100644
--- a/devtools/environment-dev.yaml
+++ b/devtools/environment-dev.yaml
@@ -2,5 +2,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - bzip2
   - cython
   - setuptools
+  - xz