From fe382395ceecbc7fdc9b90e5a179d249f2dbc382 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sat, 7 Dec 2024 16:46:24 +0000
Subject: [PATCH] Build py3.13 wheel for pysam 0.22.1

Also:
- Drop Python 3.8 support
- Add Python 3.13 support
---
 .github/workflows/ci.yaml   | 6 +++---
 .github/workflows/lint.yaml | 2 +-
 pyproject.toml              | 4 ++--
 recipes/pysam/meta.yaml     | 1 +
 wheel_builder.py            | 1 +
 5 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 784e71e..50026c8 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -1,7 +1,7 @@
 name: Build and upload wheels
 on: [push, pull_request]
 env:
-  CIBW_BUILD: 'cp38-* cp39-* cp310-* cp311-* cp312-*'
+  CIBW_BUILD: 'cp38-* cp39-* cp310-* cp311-* cp312-* cp313-*'
   CIBW_SKIP: '*-musllinux_*'
 concurrency:
   # Group runs by PR, but keep runs on the default branch separate
@@ -74,7 +74,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
       - uses: actions/download-artifact@v4
         with:
           name: recipe_list
@@ -107,7 +107,7 @@ jobs:
           path: wheelhouse/
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
       - name: Setup deploy environment
         run: python3 -m pip install s3pypi
       - name: Deploy wheels
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 3145c20..b14ba83 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.9', '3.13']
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
diff --git a/pyproject.toml b/pyproject.toml
index 2124f3c..f6477fd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,13 +1,13 @@
 [tool.black]
 line-length = 120
-target-version = ['py38']
+target-version = ['py39']
 include = '\.pyi?$'
 
 [tool.darker]
 isort = true
 
 [tool.ruff]
-target-version = "py38"
+target-version = "py39"
 
 [tool.ruff.lint]
 select = ["E", "F", "B", "UP"]
diff --git a/recipes/pysam/meta.yaml b/recipes/pysam/meta.yaml
index 4807960..c1877cc 100644
--- a/recipes/pysam/meta.yaml
+++ b/recipes/pysam/meta.yaml
@@ -1,4 +1,5 @@
 ---
+
 name: pysam
 version: 0.22.1
 # as of 0.22.0 {project} in pyproject.toml [tool.cibuildwheel] expects to be the package dir
diff --git a/wheel_builder.py b/wheel_builder.py
index af2d629..9ed3f1b 100644
--- a/wheel_builder.py
+++ b/wheel_builder.py
@@ -69,6 +69,7 @@
         if is_package_pure or run_in_sdist:
             tar_temp_dir = Path(tempfile.mkdtemp(dir=temp_dir))
             with tarfile.open(sdist_filepath) as tar:
+                tar.extraction_filter = getattr(tarfile, "data_filter", (lambda member, path: member))
                 tar.extractall(path=tar_temp_dir)
 
             try: