Update version to 3.12

.gitignore

@@ -52,6 +52,8 @@ profile_default/
 ipython_config.py
 
 .python-version
+!/.python-version
+!/scripts/population/.python-version
 
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow
 __pypackages__/
@@ -71,4 +73,4 @@ venv.bak/
 
 # mac os
 .DS_Store
-common/.DS_Store
+common/.DS_Store

Dockerfile.dev

@@ -1,4 +1,4 @@
-FROM python:3.10
+FROM python:3.12
 # Contains relevant basics for Python, like GCC and similar by default
 LABEL maintainer="ensembl-variation@ebi.ac.uk"
 

Dockerfile.prod

@@ -1,4 +1,4 @@
-FROM python:3.10
+FROM python:3.12
 # Contains relevant basics for Python, like GCC and similar by default
 LABEL maintainer="ensembl-variation@ebi.ac.uk"
 

README.md

@@ -18,6 +18,10 @@ The API can be queried against a single endpoint specifying the payload to be re
 ![alt text](assets/architecture.png)
 
 
+## Python version
+
+Use Python 3.12 for local development and Docker builds.
+
 
 ## Running the API using Docker
 
@@ -72,4 +76,4 @@ query variant_example {
     }
 }
 ```
-More example queries can be found in `examples/`
+More example queries can be found in `examples/`

common/base_file_client.py

@@ -5,10 +5,10 @@
 import io
 import os
 import subprocess
-from common.file_model.variant import Variant
-from common.file_model.structural_variant import StructuralVariant
 
-import vcfpy
+from common.file_model.structural_variant import StructuralVariant
+from common.file_model.variant import Variant
+from common.vcf_reader import read_vcf
 
 
 class BaseFileClient:
@@ -81,7 +81,7 @@ def get_record_from_file(
 
         reader = None
         try:
-            reader = vcfpy.Reader.from_path(datafile)
+            reader = read_vcf(datafile)
             try:
                 for rec in reader.fetch(contig, pos - 1, pos):
                     if self.record_matches(rec, contig, pos, id):
@@ -90,7 +90,7 @@ def get_record_from_file(
                 if not fallback_to_iteration:
                     return None
                 self.close_reader(reader)
-                reader = vcfpy.Reader.from_path(datafile)
+                reader = read_vcf(datafile)
                 for rec in reader:
                     if self.record_matches(rec, contig, pos, id):
                         return record_class(rec, reader.header, genome_uuid)
@@ -133,7 +133,7 @@ def get_record_with_bcftools(
         if result.returncode != 0:
             return None
 
-        reader = vcfpy.Reader(io.StringIO(result.stdout))
+        reader = read_vcf(stream=io.StringIO(result.stdout))
         for rec in reader:
             if self.record_matches(rec, contig, pos, id):
                 return record_class(rec, reader.header, genome_uuid)

mypy.ini

@@ -1,12 +1,9 @@
 [mypy]
-python_version = 3.8
+python_version = 3.12
 
 [mypy-requests.*]
 ignore_missing_imports = True
 
-[mypy-snapshottest.*]
-ignore_missing_imports = True
-
 [mypy-aiodataloader.*]
 ignore_missing_imports = True
 

requirements-dev.txt

@@ -1,8 +1,7 @@
 -r requirements.txt
-pytest==7.1.2
-pytest-asyncio==0.18.3
-snapshottest==0.6.0
-pylint==2.14.3
-mypy==0.961
-black==22.6.0
-ruff==0.12.7
+pytest==7.4.4
+pytest-asyncio==0.23.8
+pylint==3.0.4
+mypy==1.8.0
+black==24.3.0
+ruff==0.12.7

requirements.txt

@@ -1,11 +1,11 @@
 duckdb
-mongomock==4.0.0
+mongomock==4.3.0
 pymongo==4.1.1
 requests==2.28.0
 aiodataloader==0.2.1
 ariadne==0.19.1
 python-dotenv==0.20.0
 uvicorn==0.18.1
-pysam==0.21.0
-vcfpy @ git+https://github.com/likhitha-surapaneni/vcfpy@header-fix
+pysam==0.22.1
+vcfpy==0.13.8
 

ruff.toml

@@ -3,7 +3,7 @@
 
 # --- Linting rules ---
 line-length = 88 # Black style
-target-version = "py310"
+target-version = "py312"
 
 # --- Formatting ---
 [format]

setup.py

@@ -1,4 +1,5 @@
-"""
+"""Configure packaging for the Ensembl Variation GraphQL API.
+
 .. See the NOTICE file distributed with this work for additional information
    regarding copyright ownership.
    Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,8 +14,8 @@
 """
 
 from pathlib import Path
-from setuptools import setup, find_packages
 
+from setuptools import find_packages, setup
 
 with open(Path(__file__).parent / "LICENSE") as f:
     LICENSE_CT = f.read()
@@ -26,7 +27,7 @@
     version="0.1.0",
     packages=find_packages(),
     license=LICENSE_CT,
-    python_requires=">=3.8",
+    python_requires=">=3.12",
     package_data={
         # Make sure schema makes it to distro
         "common": ["*.graphql"]