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Description: remove setuptools from runtime dependencies.
This allows dh-python to cease filling python3:Dependencies substvar
with the deprecated python3-pkg-resources. The patch may be beneficial
upstream since other automated tools may pull setuptools unnecessarily
due to its presence in requirements files.
Author: Étienne Mollier <emollier@debian.org>
Bug-Debian: https://bugs.debian.org/1083334
Forwarded: no
Last-Update: 2024-10-09
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/changeo.egg-info/requires.txt
+++ b/changeo.egg-info/requires.txt
@@ -3,6 +3,5 @@
pandas>=0.24
biopython>=1.77
PyYAML>=5.1
-setuptools>=2.0
presto>=0.7.0
airr>=1.3.1
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,6 +3,5 @@
pandas>=0.24
biopython>=1.77
PyYAML>=5.1
-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}
|
