Alexandre Detiste pushed to branch master at Debian Med / changeo
Commits: 2f060c9e by Alexandre Detiste at 2026-02-04T20:17:14+01:00 extend pkg_resources.patch to actually remove pkg_resources - - - - - 1 changed file: - debian/patches/rm-setuptools.patch Changes: ===================================== debian/patches/rm-setuptools.patch ===================================== @@ -9,8 +9,8 @@ Forwarded: no Last-Update: 2024-10-09 --- This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ ---- changeo.orig/changeo.egg-info/requires.txt -+++ changeo/changeo.egg-info/requires.txt +--- a/changeo.egg-info/requires.txt ++++ b/changeo.egg-info/requires.txt @@ -3,6 +3,5 @@ pandas>=0.24 biopython>=1.77 @@ -18,8 +18,8 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ -setuptools>=2.0 presto>=0.7.0 airr>=1.3.1 ---- changeo.orig/requirements.txt -+++ changeo/requirements.txt +--- a/requirements.txt ++++ b/requirements.txt @@ -3,6 +3,5 @@ pandas>=0.24 biopython>=1.77 @@ -27,3 +27,61 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ -setuptools>=2.0 presto>=0.7.0 airr>=1.3.1 +--- a/bin/AssignGenes.py ++++ b/bin/AssignGenes.py +@@ -11,7 +11,7 @@ + import shutil + from argparse import ArgumentParser + from collections import OrderedDict +-from pkg_resources import parse_version ++from packaging.version import parse as parse_version + from textwrap import dedent + from time import time + import re +--- a/changeo/Distance.py ++++ b/changeo/Distance.py +@@ -9,7 +9,7 @@ + import numpy as np + import pandas as pd + from itertools import combinations, product, zip_longest +-from pkg_resources import resource_stream ++from importlib.resources import open_text + from scipy.cluster.hierarchy import fcluster, linkage + from scipy.spatial.distance import squareform + +@@ -220,22 +220,22 @@ + ham_model = getDNADistMatrix(mask_dist=0, gap_dist=0) + + # Load model data +-with resource_stream(__name__, 'data/hh_s1f_dist.tsv') as f: ++with open_text('changeo', 'data/hh_s1f_dist.tsv') as f: + hh_s1f_model = pd.read_csv(f, sep='\t', index_col=0) + +-with resource_stream(__name__, 'data/hh_s5f_dist.tsv') as f: ++with open_text('changeo', 'data/hh_s5f_dist.tsv') as f: + hh_s5f_model = pd.read_csv(f, sep='\t', index_col=0) + +-with resource_stream(__name__, 'data/mk_rs1nf_dist.tsv') as f: ++with open_text('changeo', 'data/mk_rs1nf_dist.tsv') as f: + mk_rs1nf_model = pd.read_csv(f, sep='\t', index_col=0) + +-with resource_stream(__name__, 'data/mk_rs5nf_dist.tsv') as f: ++with open_text('changeo', 'data/mk_rs5nf_dist.tsv') as f: + mk_rs5nf_model = pd.read_csv(f, sep='\t', index_col=0) + +-with resource_stream(__name__, 'data/m1n_compat_dist.tsv') as f: ++with open_text('changeo', 'data/m1n_compat_dist.tsv') as f: + m1n_compat_model = pd.read_csv(f, sep='\t', index_col=0) + +-with resource_stream(__name__, 'data/hs1f_compat_dist.tsv') as f: ++with open_text('changeo', 'data/hs1f_compat_dist.tsv') as f: + hs1f_compat_model = pd.read_csv(f, sep='\t', index_col=0) + + distance_models = {'ham': ham_model, +@@ -245,4 +245,4 @@ + 'mk_rs1nf': mk_rs1nf_model, + 'mk_rs5nf': mk_rs5nf_model, + 'm1n_compat': m1n_compat_model, +- 'hs1f_compat': hs1f_compat_model} +\ No newline at end of file ++ 'hs1f_compat': hs1f_compat_model} View it on GitLab: https://salsa.debian.org/med-team/changeo/-/commit/2f060c9e2c12c5bdd79e1cfa6cefe1658bb4189b -- View it on GitLab: https://salsa.debian.org/med-team/changeo/-/commit/2f060c9e2c12c5bdd79e1cfa6cefe1658bb4189b You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
