From 9c690805fbb9cba842210111a079f932fccca159 Mon Sep 17 00:00:00 2001 From: Daniel Nilsson <daniel.k.nilsson@gmail.com> Date: Thu, 24 Oct 2024 13:01:30 +0200 Subject: [PATCH] latest major in docker, actions. releasing most requirement constraints. pkg_resources deprecated - move version. --- .github/workflows/build_and_publish.yml | 4 ++-- Dockerfile.pytest | 2 +- genmod/__init__.py | 18 +++++------------- genmod/__version__.py | 1 + requirements.txt | 16 ++++++++-------- setup.py | 5 ++++- 6 files changed, 21 insertions(+), 25 deletions(-) create mode 100644 genmod/__version__.py diff --git a/.github/workflows/build_and_publish.yml b/.github/workflows/build_and_publish.yml index 95331bb..c4e62f1 100644 --- a/.github/workflows/build_and_publish.yml +++ b/.github/workflows/build_and_publish.yml @@ -15,10 +15,10 @@ jobs: - name: Check out git repository uses: actions/checkout@v4 - - name: Set up Python 3.12 + - name: Set up Python 3.13 uses: actions/setup-python@v5 with: - python-version: 3.12 + python-version: 3.13 - name: Install build tools run: >- diff --git a/Dockerfile.pytest b/Dockerfile.pytest index 6935d10..5043d01 100644 --- a/Dockerfile.pytest +++ b/Dockerfile.pytest @@ -1,5 +1,5 @@ # Dockerfile to run genmod pytest suite -FROM python:3.12 +FROM python:3.13 RUN mkdir -p /genmod diff --git a/genmod/__init__.py b/genmod/__init__.py index 9a5e744..e30b8ca 100644 --- a/genmod/__init__.py +++ b/genmod/__init__.py @@ -1,14 +1,6 @@ -from __future__ import (print_function, absolute_import) -from logging import getLogger -from pkg_resources import get_distribution, DistributionNotFound -from os import environ - -logger = getLogger(__name__) - try: - __version__ = get_distribution("genmod").version -except DistributionNotFound as error: - # Genmod is not installed (as the case for docker test suite) - if 'GENMOD_DOCKER_TEST' not in environ.keys(): - raise error - __version__ = '-1.-1.-1' + from importlib.metadata import version +except ImportError: # Backport support for importlib metadata on Python 3.7 + from importlib_metadata import version + +__version__ = version("genmod") diff --git a/genmod/__version__.py b/genmod/__version__.py new file mode 100644 index 0000000..bbb7fa0 --- /dev/null +++ b/genmod/__version__.py @@ -0,0 +1 @@ +__version__ = "3.9" \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index 6028fc9..24cea6e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,10 +1,10 @@ -ped_parser == 1.6.6 -pytabix == 0.1 -pytest == 7.3.1 +ped_parser +pytabix +pytest interval_tree == 0.3.4 -click == 8.1.3 -configobj == 5.0.8 +click +configobj intervaltree == 3.1.0 -extract_vcf == 0.5 -vcftoolbox == 1.5.1 -six == 1.16.0 +extract_vcf +vcftoolbox +six diff --git a/setup.py b/setup.py index 4140e42..1528a45 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,10 @@ from setuptools import setup, find_packages except ImportError: from distutils.core import setup -import pkg_resources + +about = {} +with open(os.path.join(os.path.abspath(os.path.dirname(__file__)), "genmod", "__version__.py")) as f: + exec(f.read(), about) # Shortcut for building/publishing to Pypi if sys.argv[-1] == 'publish':