[med-svn] [Git][med-team/changeo][master] extend pkg_resources.patch to actually remove pkg_resources

[Alexandre Detiste (@detiste-guest)]

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
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