[med-svn] [Git][med-team/centrifuge][master] 4 commits: d/salsa-ci.yml: disable i386 builds due to missing dependencies.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Aug 25 16:22:29 BST 2024
Étienne Mollier pushed to branch master at Debian Med / centrifuge
Commits:
fbd66d92 by Étienne Mollier at 2024-08-25T17:15:08+02:00
d/salsa-ci.yml: disable i386 builds due to missing dependencies.
- - - - -
859108fd by Étienne Mollier at 2024-08-25T17:18:45+02:00
hardening.patch: also propagate CPPFLAGS.
- - - - -
0d9a74c7 by Étienne Mollier at 2024-08-25T17:19:01+02:00
2to3.patch: unfuzz.
Gbp-Dch: ignore
- - - - -
f93a6615 by Étienne Mollier at 2024-08-25T17:19:41+02:00
Update changelog after fixing CI errors.
- - - - -
4 changed files:
- debian/changelog
- debian/patches/2to3.patch
- debian/patches/hardening.patch
- debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -8,8 +8,10 @@ centrifuge (1.0.4.1-1) unstable; urgency=medium
* fix_auto_ptr_usage_in_gcc-7.patch: delete: applied upstream.
* 0002-Fix-build-with-rank.patch: apparently not needed anymore.
* d/copyright: refer to the versioned GPL-3 file.
+ * d/salsa-ci.yml: disable i386 builds due to missing dependencies.
+ * hardening.patch: also propagate CPPFLAGS.
- -- Étienne Mollier <emollier at debian.org> Sun, 25 Aug 2024 17:03:48 +0200
+ -- Étienne Mollier <emollier at debian.org> Sun, 25 Aug 2024 17:19:30 +0200
centrifuge (1.0.3-12) unstable; urgency=medium
=====================================
debian/patches/2to3.patch
=====================================
@@ -3,9 +3,9 @@ Bug-Debian: https://bugs.debian.org/936281
Author: Andreas Tille <tille at debian.org>
Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
---- a/Makefile
-+++ b/Makefile
-@@ -364,11 +364,11 @@ centrifuge.bat:
+--- centrifuge.orig/Makefile
++++ centrifuge/Makefile
+@@ -365,11 +365,11 @@
centrifuge-build.bat:
echo "@echo off" > centrifuge-build.bat
@@ -19,31 +19,31 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
.PHONY: centrifuge-src
---- a/centrifuge-build
-+++ b/centrifuge-build
+--- centrifuge.orig/centrifuge-build
++++ centrifuge/centrifuge-build
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Copyright 2014, Daehwan Kim <infphilo at gmail.com>
---- a/centrifuge-inspect
-+++ b/centrifuge-inspect
+--- centrifuge.orig/centrifuge-inspect
++++ centrifuge/centrifuge-inspect
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Copyright 2014, Daehwan Kim <infphilo at gmail.com>
---- a/evaluation/centrifuge_evaluate.py
-+++ b/evaluation/centrifuge_evaluate.py
+--- centrifuge.orig/evaluation/centrifuge_evaluate.py
++++ centrifuge/evaluation/centrifuge_evaluate.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
import sys, os, subprocess, inspect
import platform, multiprocessing
-@@ -25,7 +25,7 @@ def read_taxonomy_tree(tax_file):
+@@ -25,7 +25,7 @@
"""
def compare_scm(centrifuge_out, true_out, taxonomy_tree, rank):
ancestors = set()
@@ -52,7 +52,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
if tax_id in ancestors:
continue
while True:
-@@ -106,7 +106,7 @@ def compare_scm(centrifuge_out, true_out
+@@ -106,7 +106,7 @@
unclassified += 1
raw_unique_classified = 0
@@ -61,7 +61,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
if len(value) == 1:
raw_unique_classified += 1
return classified, unique_classified, unclassified, len(db_dic), raw_unique_classified
-@@ -152,7 +152,7 @@ def compare_abundance(centrifuge_out, tr
+@@ -152,7 +152,7 @@
if tax_id in db_dic:
SSR += (abundance - db_dic[tax_id]) ** 2;
if debug:
@@ -70,7 +70,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
else:
SSR += (abundance) ** 2
-@@ -179,7 +179,7 @@ def sql_execute(sql_db, sql_query):
+@@ -179,7 +179,7 @@
"""
def create_sql_db(sql_db):
if os.path.exists(sql_db):
@@ -79,7 +79,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
return
columns = [
-@@ -316,7 +316,7 @@ def evaluate(index_base,
+@@ -316,7 +316,7 @@
os.mkdir(index_path)
index_fnames = ["%s/%s.%d.cf" % (index_path, index_base, i+1) for i in range(3)]
if not check_files(index_fnames):
@@ -88,7 +88,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
os.system("cd %s; wget ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/%s.tar.gz; tar xvzf %s.tar.gz; rm %s.tar.gz; ln -s %s/%s* .; cd -" % \
(index_path, index_base, index_base, index_base, index_base, index_base))
assert check_files(index_fnames)
-@@ -356,7 +356,7 @@ def evaluate(index_base,
+@@ -356,7 +356,7 @@
scm_fname = "%s/%s.scm" % (read_path, read_base)
read_fnames = [read1_fname, read2_fname, truth_fname, scm_fname]
if not check_files(read_fnames):
@@ -97,7 +97,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
centrifuge_simulate = os.path.join(path_base, "centrifuge_simulate_reads.py")
simulate_cmd = [centrifuge_simulate,
"--num-fragment", str(num_fragment)]
-@@ -377,11 +377,11 @@ def evaluate(index_base,
+@@ -377,11 +377,11 @@
else:
base_fname = read_base + "_single"
@@ -112,7 +112,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
program_bin_base = "%s/.." % path_base
def get_program_version(program, version):
-@@ -428,7 +428,7 @@ def evaluate(index_base,
+@@ -428,7 +428,7 @@
if version:
program_name += ("_%s" % version)
@@ -121,7 +121,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
if paired:
program_dir = program_name + "_paired"
else:
-@@ -449,7 +449,7 @@ def evaluate(index_base,
+@@ -449,7 +449,7 @@
program_cmd = get_program_cmd(program, version, read1_fname, read2_fname, out_fname)
start_time = datetime.now()
if verbose:
@@ -130,7 +130,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
if program in ["centrifuge"]:
proc = subprocess.Popen(program_cmd, stdout=open(out_fname, "w"), stderr=subprocess.PIPE)
else:
-@@ -462,7 +462,7 @@ def evaluate(index_base,
+@@ -462,7 +462,7 @@
if duration < 0.1:
duration = 0.1
if verbose:
@@ -139,7 +139,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
results = {"strain" : [0, 0, 0],
"species" : [0, 0, 0],
-@@ -484,21 +484,21 @@ def evaluate(index_base,
+@@ -484,21 +484,21 @@
# if rank == "strain":
# assert num_cases == num_fragment
@@ -170,15 +170,15 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
if runtime_only:
os.chdir("..")
---- a/evaluation/centrifuge_simulate_reads.py
-+++ b/evaluation/centrifuge_simulate_reads.py
+--- centrifuge.orig/evaluation/centrifuge_simulate_reads.py
++++ centrifuge/evaluation/centrifuge_simulate_reads.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#
# Copyright 2015, Daehwan Kim <infphilo at gmail.com>
-@@ -156,7 +156,7 @@ def read_transcript(genomes_seq, gtf_fil
+@@ -156,7 +156,7 @@
transcripts[transcript_id][2].append([left, right])
# Sort exons and merge where separating introns are <=5 bps
@@ -187,7 +187,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
exons.sort()
tmp_exons = [exons[0]]
for i in range(1, len(exons)):
-@@ -167,7 +167,7 @@ def read_transcript(genomes_seq, gtf_fil
+@@ -167,7 +167,7 @@
transcripts[tran] = [chr, strand, tmp_exons]
tmp_transcripts = {}
@@ -196,7 +196,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
exon_lens = [e[1] - e[0] + 1 for e in exons]
transcript_len = sum(exon_lens)
if transcript_len >= frag_len:
-@@ -444,8 +444,8 @@ def getSamAlignment(dna, exons, genome_s
+@@ -444,8 +444,8 @@
MD += ("{}".format(MD_match_len))
if len(read_seq) != read_len:
@@ -207,7 +207,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
assert False
return pos, cigars, cigar_descs, MD, XM, NM, Zs, read_seq
-@@ -575,8 +575,8 @@ def samRepOk(genome_seq, read_seq, chr,
+@@ -575,8 +575,8 @@
tMD += ("{}".format(match_len))
if tMD != MD or tXM != XM or tNM != NM or XM > max_mismatch or XM != NM:
@@ -218,7 +218,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
assert False
-@@ -631,7 +631,7 @@ def simulate_reads(index_fname, base_fna
+@@ -631,7 +631,7 @@
# Read genome sequences into memory
genomes_fname = index_fname + ".fa"
if not os.path.exists(genomes_fname):
@@ -227,7 +227,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
extract_cmd = [centrifuge_inspect,
index_fname]
extract_proc = subprocess.Popen(extract_cmd, stdout=open(genomes_fname, 'w'))
-@@ -660,15 +660,15 @@ def simulate_reads(index_fname, base_fna
+@@ -660,15 +660,15 @@
assert num_frag == sum(expr_profile)
if dna:
@@ -246,7 +246,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
truth_list = []
normalized_sum = 0.0
debug_num_frag = 0
-@@ -695,19 +695,19 @@ def simulate_reads(index_fname, base_fna
+@@ -695,19 +695,19 @@
if can_tax_id in names:
name = names[can_tax_id]
abundance = raw_abundance / genome_len / normalized_sum
@@ -270,7 +270,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
read_file = open(base_fname + "_1.fa", "w")
if paired_end:
-@@ -718,11 +718,11 @@ def simulate_reads(index_fname, base_fna
+@@ -718,11 +718,11 @@
t_num_frags = expr_profile[t]
if dna:
tax_id = genome_ids[t]
@@ -284,7 +284,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
genome_seq = genome_seqs[tax_id]
genome_len = len(genome_seq)
-@@ -763,14 +763,14 @@ def simulate_reads(index_fname, base_fna
+@@ -763,14 +763,14 @@
XS = "\tXS:A:{}".format(strand)
TI = "\tTI:Z:{}".format(transcript_id)
@@ -304,7 +304,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
cur_read_id += 1
-@@ -865,7 +865,7 @@ if __name__ == '__main__':
+@@ -865,7 +865,7 @@
parser.print_help()
exit(1)
if not args.dna:
@@ -313,15 +313,15 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
exit(1)
# if args.dna:
# args.expr_profile = "constant"
---- a/evaluation/test/centrifuge_evaluate_mason.py
-+++ b/evaluation/test/centrifuge_evaluate_mason.py
+--- centrifuge.orig/evaluation/test/centrifuge_evaluate_mason.py
++++ centrifuge/evaluation/test/centrifuge_evaluate_mason.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
import sys, os, subprocess, inspect
import platform, multiprocessing
-@@ -27,7 +27,7 @@ def compare_scm(centrifuge_out, true_out
+@@ -27,7 +27,7 @@
higher_ranked = {}
ancestors = set()
@@ -330,7 +330,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
if tax_id in ancestors:
continue
while True:
-@@ -82,7 +82,7 @@ def compare_scm(centrifuge_out, true_out
+@@ -82,7 +82,7 @@
fields = line.strip().split('\t')
if len(fields) != 3:
@@ -339,7 +339,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
continue
read_name, tax_id = fields[1:3]
# Traverse up taxonomy tree to match the given rank parameter
-@@ -117,7 +117,7 @@ def compare_scm(centrifuge_out, true_out
+@@ -117,7 +117,7 @@
# print read_name
raw_unique_classified = 0
@@ -348,7 +348,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
if len(maps) == 1 and read_name not in higher_ranked:
raw_unique_classified += 1
return classified, unique_classified, unclassified, len(db_dic), raw_unique_classified
-@@ -184,7 +184,7 @@ def evaluate(index_base,
+@@ -184,7 +184,7 @@
read_fname]
if verbose:
@@ -357,7 +357,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
out_fname = "centrifuge.output"
proc = subprocess.Popen(centrifuge_cmd, stdout=open(out_fname, "w"), stderr=subprocess.PIPE)
-@@ -208,12 +208,12 @@ def evaluate(index_base,
+@@ -208,12 +208,12 @@
# if rank == "strain":
# assert num_cases == num_fragment
@@ -376,7 +376,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
# Calculate sum of squared residuals in abundance
"""
-@@ -252,12 +252,12 @@ def evaluate(index_base,
+@@ -252,12 +252,12 @@
if rank_taxID not in true_abundance:
true_abundance[rank_taxID] = 0.0
true_abundance[rank_taxID] += (reads / float(genomeSize))
@@ -393,7 +393,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
read_fname = "centrifuge_data/bacteria_sim10M/bacteria_sim10M.fa"
summary_fname = "centrifuge.summary"
-@@ -271,14 +271,14 @@ def evaluate(index_base,
+@@ -271,14 +271,14 @@
read_fname]
if verbose:
@@ -410,7 +410,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
calc_abundance[taxID] = 0.0
first = True
for line in open(summary_fname):
-@@ -296,12 +296,12 @@ def evaluate(index_base,
+@@ -296,12 +296,12 @@
"""
abundance_file = open("abundance.cmp", 'w')
@@ -425,7 +425,7 @@ Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
assert taxID in calc_abundance
rank_taxID = taxID
while True:
-@@ -322,11 +322,11 @@ def evaluate(index_base,
+@@ -322,11 +322,11 @@
calc_abundance_rank[rank_taxID] += calc_abundance[taxID]
ssr = 0.0 # Sum of Squared Residuals
=====================================
debian/patches/hardening.patch
=====================================
@@ -2,19 +2,24 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Sat, 25 Nov 2017 21:24:23 +0100
Description: Propagate hardening options
---- a/Makefile
-+++ b/Makefile
-@@ -168,7 +168,7 @@ RELEASE_FLAGS = -O3 $(BITS_FLAG) $(SSE_
+--- centrifuge.orig/Makefile
++++ centrifuge/Makefile
+@@ -168,7 +168,7 @@
RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
-CFLAGS =
-+#CFLAGS =
++#CFLAGS =
#CFLAGS = -fdiagnostics-color=always
ifeq (1,$(USE_SRA))
-@@ -255,7 +255,8 @@ DEFS=-fno-strict-aliasing \
- $(CFLAGS) \
+@@ -252,10 +252,12 @@
+ -DBUILD_TIME="\"`date --utc --date=@$(SOURCE_DATE_EPOCH) +%F`\"" \
+ -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
+ $(FILE_FLAGS) \
+- $(CFLAGS) \
++ $(CPPFLAGS) \
++ $(CFLAGS) \
$(PREF_DEF) \
$(MM_DEF) \
- $(SHMEM_DEF)
=====================================
debian/salsa-ci.yml
=====================================
@@ -2,3 +2,6 @@
include:
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+
+variables:
+ SALSA_CI_DISABLE_BUILD_PACKAGE_I386: "true"
View it on GitLab: https://salsa.debian.org/med-team/centrifuge/-/compare/ae589c52d70d2f8a57870662183f0fa55aeebb38...f93a6615c45f56482accf7a8166a5fa4546e7af5
--
View it on GitLab: https://salsa.debian.org/med-team/centrifuge/-/compare/ae589c52d70d2f8a57870662183f0fa55aeebb38...f93a6615c45f56482accf7a8166a5fa4546e7af5
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