Merge pull request #83 from Clinical-Genomics/version_0.9.3

Version 0.9.3

CHANGELOG.md

@@ -2,9 +2,10 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## [unreleased]
+## [0.9.3]
 ### Fixed
 - Switch build system to uv-hatchling
+- Version from importlib metadata
 
 ## [0.9.2]
 ### Fixed

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stranger"
-version = "0.9.2"
+version = "0.9.3"
 description = "Annotate VCF files with STR variants with pathogenicity implications"
 authors = [{name="Daniel Nilsson", email="[email protected]"}, {name="Mans Magnuson", email="[email protected]"}]
 license = {text = "MIT License"}
@@ -36,7 +36,6 @@ Repository = "https://github.com/Clinical-Genomics/stranger"
 Changelog = "https://github.com/Clinical-Genomics/stranger/blob/main/CHANGELOG.md"
 "Bug Tracker" = "https://github.com/Clinical-Genomics/stranger/issues"
 
-
 [project.scripts]
 stranger = "stranger.cli:cli"
 

stranger/cli.py

@@ -2,10 +2,15 @@
 import logging
 from codecs import getreader, open
 
+try:
+    from importlib.metadata import version
+except ImportError:
+    # Try backported to piPY<37 `importlib_resources`.
+    from importlib_resources import version
+
 import click
 import coloredlogs
 
-from stranger.__version__ import __version__
 from stranger.constants import ANNOTATE_REPEAT_KEYS, ANNOTATE_REPEAT_KEYS_TRGT
 from stranger.resources import repeats_json_path
 from stranger.utils import (
@@ -23,13 +28,6 @@
 LOG_LEVELS = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
 
 
-def print_version(ctx, param, value):
-    if not value or ctx.resilient_parsing:
-        return
-    click.echo(__version__)
-    ctx.exit()
-
-
 @click.command()
 @click.argument("vcf")
 @click.option(
@@ -45,19 +43,19 @@ def print_version(ctx, param, value):
 )
 @click.option("-i", "--family_id", default="1")
 @click.option("-t", "--trgt", is_flag=True, help="File was produced with TRGT")
-@click.option("--version", is_flag=True, callback=print_version, expose_value=False, is_eager=True)
 @click.option(
     "--loglevel",
     default="INFO",
     type=click.Choice(LOG_LEVELS),
     help="Set the level of log output.",
     show_default=True,
 )
+@click.version_option(version("stranger"))
 @click.pass_context
 def cli(context, vcf, family_id, repeats_file, loglevel, trgt):
     """Annotate str variants with str status"""
     coloredlogs.install(level=loglevel)
-    LOG.info("Running stranger version %s", __version__)
+    LOG.info("Running stranger version %s", version("stranger"))
 
     repeat_information = None
     repeats_file_type = "tsv"