Python 3.12 support (#193)

Author: standage

.github/workflows/cibuild.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python ${{ matrix.python-version }}

CHANGELOG.md

@@ -8,6 +8,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Changed
 - Intermediate FASTQ files are now bgzip compressed to reduce storage requirements (#189).
 - Colons are now used instead of commas to separate SNP alleles in microhap alleles (#192).
+- Implemented Python 3.12 support by integrating happer package and increasing minimum version of MicroHapDB dependency (#193).
 - Updated working directory organization to provide additional structure (#194).
 
 ### Fixed

Makefile

@@ -35,10 +35,10 @@ clean:
 
 ## style:     check code style vs Black
 style:
-	black --line-length=99 --check microhapulator/*.py microhapulator/*/*.py setup.py
+	black --line-length=99 --check microhapulator/*.py microhapulator/*/*.py microhapulator/*/*/*.py setup.py
 	snakefmt --line-length=99 --check microhapulator/workflows/*.smk
 
 ## format:    autoformat Python code
 format:
-	black --line-length=99 microhapulator/*.py microhapulator/*/*.py setup.py
+	black --line-length=99 microhapulator/*.py microhapulator/*/*.py microhapulator/*/*/*.py setup.py
 	snakefmt --line-length=99 microhapulator/workflows/*.smk

microhapulator/__init__.py

@@ -21,3 +21,4 @@
 from . import profile
 from . import api
 from . import cli
+from . import happer