From 7c88a7584b540b80deb897e99656c344dbe366d1 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Fri, 1 Nov 2024 16:15:34 +0100
Subject: [PATCH] Release v3.6.0

---
 .github/workflows/package.yml      | 10 +++++-----
 .github/workflows/requirements.txt |  1 +
 CHANGELOG.md                       | 19 ++++++++++++++++++-
 docs/_static/json/switcher.json    |  7 ++++++-
 pyproject.toml                     |  2 +-
 5 files changed, 31 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
index b3b0e3d..1707712 100644
--- a/.github/workflows/package.yml
+++ b/.github/workflows/package.yml
@@ -9,7 +9,7 @@ jobs:
 
   wheel-linux-aarch64:
     name: Build Linux wheels (Aarch64)
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v3
       with:
@@ -34,7 +34,7 @@ jobs:
 
   wheel-linux-x86_64:
     name: Build Linux wheels (x86-64)
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v4
       with:
@@ -131,7 +131,7 @@ jobs:
     - name: Install build requirements
       run: python -m pip install -r .github/workflows/requirements.txt
     - name: Build source distribution
-      run: python setup.py sdist
+      run: python -m build -s .
     - name: Store built source distribution
       uses: actions/upload-artifact@v4
       with:
@@ -154,7 +154,7 @@ jobs:
           name: sdist
           path: dist/
     - name: Update pip to latest version
-      run: python -m pip install -U pip setuptools wheel
+      run: python -m pip install -U pip
     - name: Install built wheel
       run: python -m pip install --no-binary pyrodigal --find-links=dist pyrodigal
     - name: Run tests without coverage
@@ -193,7 +193,7 @@ jobs:
     runs-on: ubuntu-latest
     permissions: 
       contents: write
-    if: "!contains(github.ref, 'rc')"
+    if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
     name: Release
     needs: upload
     steps:
diff --git a/.github/workflows/requirements.txt b/.github/workflows/requirements.txt
index 4b0ef84..d612970 100644
--- a/.github/workflows/requirements.txt
+++ b/.github/workflows/requirements.txt
@@ -1,2 +1,3 @@
 cython ~=3.0
 scikit-build-core
+build
diff --git a/CHANGELOG.md b/CHANGELOG.md
index cd3e952..2a9b809 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,7 +6,24 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pyrodigal/compare/v3.5.1...HEAD
+[Unreleased]: https://github.com/althonos/pyrodigal/compare/v3.6.0...HEAD
+
+
+## [v3.6.0] - 2024-11-02
+[v3.6.0]: https://github.com/althonos/pyrodigal/compare/v3.5.1...v3.6.0
+
+### Added
+- Support for Python 3.13.
+
+### Changed
+- Reorganize project to build with CMake and `scikit-build-core`.
+- Build separate Python modules for various SIMD implementations to avoid potential linking issues.
+
+### Fixed
+- Pointer dereference issue when calling `TrainingInfo.load` in PyPI or with objects missing a `readinto` method.
+
+### Removed
+- Support for Python 3.6.
 
 
 ## [v3.5.2] - 2024-09-04
diff --git a/docs/_static/json/switcher.json b/docs/_static/json/switcher.json
index 8745f42..e3e7606 100644
--- a/docs/_static/json/switcher.json
+++ b/docs/_static/json/switcher.json
@@ -1,6 +1,11 @@
 [
     {
-        "name": "v3.5 (stable)",
+        "name": "v3.6 (stable)",
+        "version": "3.6.0",
+        "url": "https://pyrodigal.readthedocs.io/en/v3.6.0/"
+    },
+    {
+        "name": "v3.5",
         "version": "3.5.2",
         "url": "https://pyrodigal.readthedocs.io/en/v3.5.2/"
     },
diff --git a/pyproject.toml b/pyproject.toml
index 801f0e1..d8dec58 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "pyrodigal"
-version = "3.5.1"
+version = "3.6.0"
 description = "Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes."
 readme = "README.md"
 requires-python = ">=3.7"