[med-svn] [Git][med-team/iva][master] Python module was renamed from fastaq to pyfastaq
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Jul 7 22:11:50 BST 2026
Andreas Tille pushed to branch master at Debian Med / iva
Commits:
2615b1f3 by Andreas Tille at 2026-07-07T23:10:28+02:00
Python module was renamed from fastaq to pyfastaq
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/fix-pyfastaq-rename.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -11,7 +11,6 @@ iva (1.5.0+ds-1) UNRELEASED; urgency=medium
* Remove Priority field (cme)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* Set upstream metadata fields: Repository.
- TODO: package https://github.com/sanger-pathogens/Fastaq
-- Andreas Tille <tille at debian.org> Tue, 07 Jul 2026 21:53:13 +0200
=====================================
debian/patches/fix-pyfastaq-rename.patch
=====================================
@@ -0,0 +1,231 @@
+Description: Rename fastaq module to pyfastaq
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-07-07
+
+--- a/iva/assembly.py
++++ b/iva/assembly.py
+@@ -3,7 +3,7 @@ import pysam
+ import tempfile
+ import shutil
+ from iva import contig, mapping, seed, mummer, graph, edge
+-import fastaq
++import pyfastaq as fastaq
+
+ class Assembly:
+ def __init__(self, contigs_file=None, map_index_k=15, map_index_s=3, threads=1, max_insert=1000, map_minid=0.5, min_clip=3, ext_min_cov=5, ext_min_ratio=2, ext_bases=100, verbose=0, seed_min_cov=5, seed_min_ratio=10, seed_min_kmer_count=200, seed_max_kmer_count=1000000000, seed_start_length=None, seed_stop_length=500, seed_overlap_length=None, make_new_seeds=False, contig_iter_trim=10, seed_ext_max_bases=50, max_contigs=50, clean=True, strand_bias=0.2):
+--- a/iva/contig_trim.py
++++ b/iva/contig_trim.py
+@@ -2,7 +2,7 @@ import os
+ import sys
+ import shutil
+ import tempfile
+-import fastaq
++import pyfastaq as fastaq
+ import pysam
+ from iva import mapping, common
+
+--- a/iva/edge.py
++++ b/iva/edge.py
+@@ -1,5 +1,5 @@
+ import copy
+-from fastaq import intervals
++from pyfastaq import intervals
+
+ class Error (Exception): pass
+
+--- a/iva/external_progs.py
++++ b/iva/external_progs.py
+@@ -2,7 +2,7 @@ import shutil
+ import subprocess
+ import re
+ import sys
+-import fastaq
++import pyfastaq as fastaq
+ from iva import common
+
+ class Error (Exception): pass
+--- a/iva/graph.py
++++ b/iva/graph.py
+@@ -1,5 +1,5 @@
+ import networkx
+-from fastaq import intervals
++from pyfastaq import intervals
+ from iva import edge
+
+ class Error (Exception): pass
+--- a/iva/kcount.py
++++ b/iva/kcount.py
+@@ -2,7 +2,7 @@ import os
+ import sys
+ import tempfile
+ import shutil
+-import fastaq
++import pyfastaq as fastaq
+ import pysam
+ from iva import common, mapping
+
+--- a/iva/kraken.py
++++ b/iva/kraken.py
+@@ -7,7 +7,7 @@ import time
+ import re
+ import urllib.request
+ import iva
+-import fastaq
++import pyfastaq as fastaq
+
+
+ class Error (Exception): pass
+--- a/iva/mapping.py
++++ b/iva/mapping.py
+@@ -2,7 +2,7 @@ import os
+ import re
+ import subprocess
+ import collections
+-import fastaq
++import pyfastaq as fastaq
+ import pysam
+ from iva import common
+
+--- a/iva/mummer.py
++++ b/iva/mummer.py
+@@ -1,7 +1,7 @@
+ import os
+ import tempfile
+ import shutil
+-import fastaq
++import pyfastaq as fastaq
+ from iva import edge, common
+
+ class Error (Exception): pass
+--- a/iva/qc.py
++++ b/iva/qc.py
+@@ -2,7 +2,7 @@ import os
+ import inspect
+ import tempfile
+ import copy
+-import fastaq
++import pyfastaq as fastaq
+ import shutil
+ import multiprocessing
+ import collections
+--- a/iva/qc_external.py
++++ b/iva/qc_external.py
+@@ -4,7 +4,7 @@ import shutil
+ import os
+ import sys
+ import inspect
+-import fastaq
++import pyfastaq as fastaq
+ from iva import common
+
+ class Error (Exception): pass
+--- a/iva/seed.py
++++ b/iva/seed.py
+@@ -2,7 +2,7 @@ import copy
+ import os
+ import shutil
+ import tempfile
+-import fastaq
++import pyfastaq as fastaq
+ from iva import kcount, kmers, mapping
+
+ class Error (Exception): pass
+--- a/iva/seed_processor.py
++++ b/iva/seed_processor.py
+@@ -4,7 +4,7 @@ import sys
+ import shutil
+ import multiprocessing
+ from iva import mapping, seed
+-import fastaq
++import pyfastaq as fastaq
+
+ class Error (Exception): pass
+
+--- a/iva/tests/contig_test.py
++++ b/iva/tests/contig_test.py
+@@ -3,7 +3,7 @@
+ import unittest
+ import os
+ from iva import contig
+-from fastaq import sequences
++from pyfastaq import sequences
+
+ class TestContig(unittest.TestCase):
+ def test_init(self):
+--- a/iva/tests/edge_test.py
++++ b/iva/tests/edge_test.py
+@@ -1,7 +1,7 @@
+ import unittest
+ import copy
+ from iva import edge
+-from fastaq import intervals
++from pyfastaq import intervals
+
+ class TestEdge(unittest.TestCase):
+ def test_open_end(self):
+--- a/iva/tests/graph_test.py
++++ b/iva/tests/graph_test.py
+@@ -3,7 +3,7 @@ import os
+ import filecmp
+ import pysam
+ from iva import graph, assembly, edge
+-from fastaq import intervals
++from pyfastaq import intervals
+
+ modules_dir = os.path.dirname(os.path.abspath(graph.__file__))
+ data_dir = os.path.join(modules_dir, 'tests', 'data')
+--- a/iva/tests/mapping_test.py
++++ b/iva/tests/mapping_test.py
+@@ -4,7 +4,7 @@ import shutil
+ import os
+ import filecmp
+ import pysam
+-import fastaq
++import pyfastaq as fastaq
+ from iva import mapping
+
+ modules_dir = os.path.dirname(os.path.abspath(mapping.__file__))
+--- a/iva/tests/mummer_test.py
++++ b/iva/tests/mummer_test.py
+@@ -2,7 +2,7 @@ import unittest
+ import os
+ import filecmp
+ import pysam
+-import fastaq
++import pyfastaq as fastaq
+ from iva import mummer, edge
+
+ modules_dir = os.path.dirname(os.path.abspath(mummer.__file__))
+--- a/iva/tests/qc_test.py
++++ b/iva/tests/qc_test.py
+@@ -3,7 +3,7 @@ import os
+ import filecmp
+ import pysam
+ from iva import qc, mummer
+-import fastaq
++import pyfastaq as fastaq
+
+ modules_dir = os.path.dirname(os.path.abspath(qc.__file__))
+ data_dir = os.path.join(modules_dir, 'tests', 'data')
+--- a/iva/tests/seed_processor_test.py
++++ b/iva/tests/seed_processor_test.py
+@@ -1,7 +1,7 @@
+ import unittest
+ import os
+ import filecmp
+-import fastaq
++import pyfastaq as fastaq
+ from iva import seed_processor
+
+ modules_dir = os.path.dirname(os.path.abspath(seed_processor.__file__))
+--- a/iva/tests/seed_test.py
++++ b/iva/tests/seed_test.py
+@@ -2,7 +2,7 @@ import unittest
+ import os
+ import filecmp
+ import shutil
+-import fastaq
++import pyfastaq as fastaq
+ from iva import seed
+
+ modules_dir = os.path.dirname(os.path.abspath(seed.__file__))
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ perl-shebang.patch
samtools1.10
disable-ram-test.patch
syntax-warning.patch
+fix-pyfastaq-rename.patch
View it on GitLab: https://salsa.debian.org/med-team/iva/-/commit/2615b1f39677dd6cd57bdf4c1185fdbdb1f7c4a5
--
View it on GitLab: https://salsa.debian.org/med-team/iva/-/commit/2615b1f39677dd6cd57bdf4c1185fdbdb1f7c4a5
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