[med-svn] [Git][med-team/ragout][master] 2 commits: patch-out usage of "six"
Alexandre Detiste (@detiste-guest)
gitlab at salsa.debian.org
Sat Mar 7 15:21:17 GMT 2026
Alexandre Detiste pushed to branch master at Debian Med / ragout
Commits:
f110f77a by Alexandre Detiste at 2026-03-07T16:17:35+01:00
patch-out usage of "six"
- - - - -
a5266d45 by Alexandre Detiste at 2026-03-07T16:18:05+01:00
rewrite d/rules with newer & shorter syntax
- - - - -
3 changed files:
- debian/control
- debian/patches/python3.12.patch
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -9,7 +9,6 @@ Build-Depends:
python3-dev,
python3-networkx,
python3-setuptools,
- python3-six,
Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/ragout
Vcs-Git: https://salsa.debian.org/med-team/ragout.git
@@ -19,7 +18,6 @@ Package: ragout
Architecture: any
Depends:
python3-networkx,
- python3-six,
${misc:Depends},
${python3:Depends},
${shlibs:Depends},
=====================================
debian/patches/python3.12.patch
=====================================
@@ -961,175 +961,249 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
-sys.meta_path.append(_importer)
--- a/ragout/breakpoint_graph/breakpoint_graph.py
+++ b/ragout/breakpoint_graph/breakpoint_graph.py
-@@ -18,8 +18,8 @@ from collections import namedtuple
+@@ -18,8 +18,6 @@
import networkx as nx
from ragout.shared.debug import DebugConfig
-from ragout.six.moves import map
-from ragout.six.moves import zip
-+from six.moves import map
-+from six.moves import zip
logger = logging.getLogger()
debugger = DebugConfig.get_instance()
--- a/ragout/breakpoint_graph/chimera_detector.py
+++ b/ragout/breakpoint_graph/chimera_detector.py
-@@ -13,7 +13,7 @@ from __future__ import division
+@@ -13,7 +13,6 @@
import logging
from collections import defaultdict, namedtuple
from copy import copy, deepcopy
-from ragout.six.moves import range
-+from six.moves import range
logger = logging.getLogger()
--- a/ragout/breakpoint_graph/permutation.py
+++ b/ragout/breakpoint_graph/permutation.py
-@@ -19,7 +19,7 @@ from ragout.shared.debug import DebugCon
+@@ -19,7 +19,6 @@
from ragout.shared import config
from ragout.shared.datatypes import Block, Permutation, output_permutations
import ragout.breakpoint_graph.repeat_resolver as rr
-from ragout.six.moves import filter
-+from six.moves import filter
logger = logging.getLogger()
debugger = DebugConfig.get_instance()
--- a/ragout/breakpoint_graph/repeat_resolver.py
+++ b/ragout/breakpoint_graph/repeat_resolver.py
-@@ -18,8 +18,8 @@ from copy import deepcopy, copy
+@@ -18,8 +18,6 @@
import logging
import networkx as nx
-from ragout.six.moves import filter
-from ragout.six.moves import range
-+from six.moves import filter
-+from six.moves import range
logger = logging.getLogger()
--- a/ragout/maf2synteny/maf2synteny.py
+++ b/ragout/maf2synteny/maf2synteny.py
-@@ -15,7 +15,7 @@ import os
+@@ -15,7 +15,6 @@
from ragout.shared.utils import which
from ragout.shared import config
-from ragout.six.moves import map
-+from six.moves import map
logger = logging.getLogger()
--- a/ragout/main.py
+++ b/ragout/main.py
-@@ -41,7 +41,7 @@ import ragout.synteny_backend.sibelia
+@@ -41,7 +41,6 @@
#import synteny_backend.cactus
import ragout.synteny_backend.maf
import ragout.synteny_backend.hal
-import ragout.six as six
-+import six
logger = logging.getLogger()
debugger = DebugConfig.get_instance()
+@@ -137,7 +136,7 @@
+
+ def _get_synteny_scale(recipe, synteny_backend):
+ if "blocks" in recipe:
+- if isinstance(recipe["blocks"], six.string_types):
++ if isinstance(recipe["blocks"], str):
+ scale = config.vals["blocks"][recipe["blocks"]]
+ else:
+ scale = recipe["blocks"]
--- a/ragout/parsers/fasta_parser.py
+++ b/ragout/parsers/fasta_parser.py
-@@ -19,7 +19,7 @@ else:
+@@ -19,7 +19,6 @@
_STR = bytes.decode
_BYTES = str.encode
-from ragout.six.moves import range
-+from six.moves import range
logger = logging.getLogger()
--- a/ragout/parsers/recipe_parser.py
+++ b/ragout/parsers/recipe_parser.py
-@@ -14,7 +14,7 @@ import logging
+@@ -14,7 +14,6 @@
from ragout.parsers.phylogeny_parser import get_leaves_names, PhyloException
import ragout.shared.config as config
-from ragout.six.moves import map
-+from six.moves import map
logger = logging.getLogger()
--- a/ragout/scaffolder/merge_iters.py
+++ b/ragout/scaffolder/merge_iters.py
-@@ -25,8 +25,8 @@ from ragout.scaffolder.output_generator
+@@ -25,8 +25,6 @@
from ragout.scaffolder.scaffolder import build_scaffolds
from ragout.breakpoint_graph.inferer import Adjacency
from ragout.breakpoint_graph.breakpoint_graph import GenChrPair
-from ragout.six.moves import range
-from ragout.six.moves import zip
-+from six.moves import range
-+from six.moves import zip
logger = logging.getLogger()
--- a/ragout/scaffolder/output_generator.py
+++ b/ragout/scaffolder/output_generator.py
-@@ -12,7 +12,7 @@ import os
+@@ -12,7 +12,6 @@
from ragout.parsers.fasta_parser import write_fasta_dict, reverse_complement
from ragout.__version__ import __version__
import ragout.shared.config as config
-from ragout.six.moves import map, range, zip
-+from six.moves import map, range, zip
logger = logging.getLogger()
--- a/ragout/scaffolder/scaffolder.py
+++ b/ragout/scaffolder/scaffolder.py
-@@ -20,7 +20,7 @@ from ragout.shared.datatypes import (Con
+@@ -20,7 +20,6 @@
output_permutations)
from ragout.scaffolder.output_generator import output_links
from ragout.breakpoint_graph.inferer import Adjacency
-from ragout.six.moves import range, zip
-+from six.moves import range, zip
logger = logging.getLogger()
--- a/ragout/assembly_graph/assembly_refine.py
+++ b/ragout/assembly_graph/assembly_refine.py
-@@ -11,9 +11,9 @@ from __future__ import division
+@@ -11,11 +11,7 @@
import networkx as nx
import re
import logging
-from ragout.six.moves import zip
-+from six.moves import zip
- try:
+-try:
- import ragout.six.moves.queue
-+ import six.moves.queue
- except ImportError:
- import queue as Queue
+-except ImportError:
+- import queue as Queue
++from queue import Queue
-@@ -231,7 +231,7 @@ def _shortest_path(graph, src, dst, rest
+ from ragout.shared import config
+ from ragout.shared.datatypes import Contig, Scaffold
+@@ -231,7 +227,7 @@
"""
Finds shortest path wrt to restricted nodes
"""
- queue = ragout.six.moves.queue.Queue()
-+ queue = six.moves.queue.Queue()
++ queue = Queue()
queue.put(src)
visited = set([src])
parent = {src : src}
--- a/ragout/phylogeny/inferer.py
+++ b/ragout/phylogeny/inferer.py
-@@ -15,8 +15,8 @@ from itertools import (combinations,
+@@ -15,8 +15,6 @@
combinations_with_replacement, chain)
from ragout.newick.tree import Leaf, Tree
-from ragout.six.moves import map
-from ragout.six.moves import zip
-+from six.moves import map
-+from six.moves import zip
class TreeInferer:
def __init__(self, perm_container):
--- a/ragout/shared/datatypes.py
+++ b/ragout/shared/datatypes.py
-@@ -9,7 +9,7 @@ This module provides some common data st
+@@ -9,7 +9,6 @@
from __future__ import absolute_import
from __future__ import division
from copy import copy
-from ragout.six.moves import zip
-+from six.moves import zip
class Block:
+--- a/scripts/compare-assemblies.py
++++ b/scripts/compare-assemblies.py
+@@ -20,8 +20,6 @@
+
+ from utils.lastz_parser import (parse_lastz_maf, run_lastz,
+ filter_intersecting, filter_by_length)
+-from six.moves import map
+-from six.moves import zip
+
+
+ def get_alignment(reference, target, overwrite):
+--- a/scripts/debug-report.py
++++ b/scripts/debug-report.py
+@@ -24,7 +24,6 @@
+ from utils.nucmer_parser import parse_nucmer_coords
+ from utils.common import (filter_by_coverage, join_collinear,
+ group_by_chr, get_order, aln_len)
+-from six.moves import map
+
+ Edge = namedtuple("Edge", ["start", "end"])
+ Adjacency = namedtuple("Adjacency", ["left", "right", "infinite"])
+--- a/scripts/simulate-rearrangements.py
++++ b/scripts/simulate-rearrangements.py
+@@ -18,7 +18,6 @@
+ from Bio.SeqRecord import SeqRecord
+
+ from utils.nucmer_parser import *
+-from six.moves import range
+
+
+ def get_unique_contigs(alignment):
+--- a/scripts/utils/common.py
++++ b/scripts/utils/common.py
+@@ -9,7 +9,6 @@
+
+ from __future__ import absolute_import
+ from collections import namedtuple, defaultdict
+-from six.moves import filter
+
+
+ AlignmentColumn = namedtuple("AlignmentColumn", ["ref", "qry"])
+--- a/scripts/utils/lastz_parser.py
++++ b/scripts/utils/lastz_parser.py
+@@ -14,7 +14,6 @@
+ from itertools import combinations
+
+ from .common import AlignmentColumn, AlignmentRow
+-from six.moves import filter
+
+ def parse_lastz_maf(filename):
+ alignments = []
+--- a/scripts/utils/nucmer_parser.py
++++ b/scripts/utils/nucmer_parser.py
+@@ -1,6 +1,5 @@
+
+ from .common import AlignmentRow, AlignmentColumn
+-from six.moves import map
+
+ #(c) 2013-2014 by Authors
+ #This file is a part of Ragout program.
+--- a/scripts/verify-minimap.py
++++ b/scripts/verify-minimap.py
+@@ -20,8 +20,6 @@
+ from utils.common import AlignmentRow, AlignmentColumn
+ from utils.common import (filter_by_coverage, join_collinear,
+ group_by_chr, get_order)
+-from six.moves import map
+-from six.moves import range
+
+ Scaffold = namedtuple("Scaffold", ["name", "contigs"])
+ Contig = namedtuple("Contig", ["name", "sign"])
+--- a/scripts/verify-order.py
++++ b/scripts/verify-order.py
+@@ -20,7 +20,6 @@
+ from utils.nucmer_parser import parse_nucmer_coords
+ from utils.common import (filter_by_coverage, join_collinear,
+ group_by_chr, get_order)
+-from six.moves import map
+
+ Scaffold = namedtuple("Scaffold", ["name", "contigs"])
+ Contig = namedtuple("Contig", ["name", "sign"])
=====================================
debian/rules
=====================================
@@ -10,8 +10,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
dh $@ --buildsystem=pybuild
-override_dh_install:
- dh_install
+execute_after_dh_install:
find debian -name LICENSE -delete
override_dh_auto_clean:
View it on GitLab: https://salsa.debian.org/med-team/ragout/-/compare/2b29d570752b6fd9028f65feaf756edc75034dff...a5266d45c49a3c58959c88379c0e7a78cdc853b4
--
View it on GitLab: https://salsa.debian.org/med-team/ragout/-/compare/2b29d570752b6fd9028f65feaf756edc75034dff...a5266d45c49a3c58959c88379c0e7a78cdc853b4
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20260307/f4afeef9/attachment-0001.htm>
More information about the debian-med-commit
mailing list