[med-svn] [Git][med-team/simka][master] Refresh patches
Shayan Doust
gitlab at salsa.debian.org
Tue Jul 28 12:18:11 BST 2020
Shayan Doust pushed to branch master at Debian Med / simka
Commits:
bc06b122 by Shayan Doust at 2020-07-28T12:17:59+01:00
Refresh patches
- - - - -
3 changed files:
- debian/patches/fix_binary_path.patch
- debian/patches/fix_temp_arrays.patch
- debian/patches/fix_test_path.patch
Changes:
=====================================
debian/patches/fix_binary_path.patch
=====================================
@@ -4,10 +4,8 @@ Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-09-13
---
-Index: simka/src/SimkaPotara.cpp
-===================================================================
---- simka.orig/src/SimkaPotara.cpp 2019-09-13 08:44:18.831548830 +0100
-+++ simka/src/SimkaPotara.cpp 2019-09-13 08:44:18.831548830 +0100
+--- simka.orig/src/SimkaPotara.cpp
++++ simka/src/SimkaPotara.cpp
@@ -28,7 +28,7 @@
*/
SimkaPotara::SimkaPotara(const string& execFilename) : Tool ("Simka")
=====================================
debian/patches/fix_temp_arrays.patch
=====================================
@@ -3,24 +3,8 @@ Description: separate out array as a defined struct
Last-Update: 2019-09-16
---
-Index: simka/src/SimkaPotara.hpp
-===================================================================
---- simka.orig/src/SimkaPotara.hpp 2019-09-16 15:21:36.549855248 +0100
-+++ simka/src/SimkaPotara.hpp 2019-09-16 15:21:36.545855212 +0100
-@@ -902,7 +902,8 @@
- }
- else{
- //sleep(1);
-- nanosleep((const struct timespec[]){{0, 100000000L}}, NULL);
-+ struct timespec ts = {0, 100000000L};
-+ nanosleep(&ts, NULL);
- }
-
- if(i >= this->_bankNames.size()) break;
-Index: simka/src/minikc/SimkaCountProcess.cpp
-===================================================================
---- simka.orig/src/minikc/SimkaCountProcess.cpp 2019-09-16 15:21:36.549855248 +0100
-+++ simka/src/minikc/SimkaCountProcess.cpp 2019-09-16 15:21:36.545855212 +0100
+--- simka.orig/src/minikc/SimkaCountProcess.cpp
++++ simka/src/minikc/SimkaCountProcess.cpp
@@ -22,7 +22,8 @@
int nbTries = 0;
while(ret != 0){
=====================================
debian/patches/fix_test_path.patch
=====================================
@@ -3,16 +3,14 @@ Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-09-13
---
-Index: simka/tests/simkaMin/test_simkaMin.py
-===================================================================
---- simka.orig/tests/simkaMin/test_simkaMin.py 2019-09-16 15:35:57.745165516 +0100
-+++ simka/tests/simkaMin/test_simkaMin.py 2019-09-16 15:35:57.741165482 +0100
+--- simka.orig/tests/simkaMin/test_simkaMin.py
++++ simka/tests/simkaMin/test_simkaMin.py
@@ -16,28 +16,28 @@
def create_command(scriptFilename, outputPrefix, k, filter, nb_reads, nb_kmers, nb_cores, input_filename):
outputDir = "k" + str(k) + "_" + filter.replace("-", "") + "_" + str(nb_reads) + "-" + str(nb_kmers) + "_n" + str(nb_cores)
- command = "python " + scriptFilename
-+ command =scriptFilename
++ command = "python3 " + scriptFilename
command += " -in " + input_filename
command += " -out " + outputPrefix + "/" + outputDir
command += " -nb-cores " + str(nb_cores)
@@ -28,9 +26,9 @@ Index: simka/tests/simkaMin/test_simkaMin.py
def create_command_update(scriptFilename, outputPrefix, k, filter, nb_reads, nb_kmers, nb_cores, input_filename):
outputDir = "k" + str(k) + "_" + filter.replace("-", "") + "_" + str(nb_reads) + "-" + str(nb_kmers) + "_n" + str(nb_cores)
- command = "python " + scriptFilename
-+ command = scriptFilename
++ command = "python3 " + scriptFilename
command += " -in " + input_filename
- command += " -in-to-update " + outputPrefix + "/" + outputDir
+ command += " -in-to-update " + outputPrefix + "/" + outputDir + "/simkamin"
command += " -nb-cores " + str(nb_cores)
command += " -max-memory 100 "
#command += " -kmer-size " + str(k)
@@ -44,8 +42,8 @@ Index: simka/tests/simkaMin/test_simkaMin.py
for nb_reads in NB_READS:
for nb_kmers in NB_KMERS:
for nb_cores in NB_CORES:
-- command, outputDir = create_command("../../simkaMin/simkaMin.py", "truth_simkaMin", k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")
-+ command, outputDir = create_command("simkaMin", "truth_simkaMin", k, filter, nb_reads, nb_kmers, nb_cores, " ../simka_input.txt ")
+- command, outputDir = create_command("../../simkaMin/simkaMin.py", "truth_simkaMin_symetrical", k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")
++ command, outputDir = create_command("simkaMin.py", "truth_simkaMin_symetrical", k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")
print (command)
ret = os.system(command)
if ret != 0: exit(1)
@@ -58,7 +56,7 @@ Index: simka/tests/simkaMin/test_simkaMin.py
print (command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
-@@ -168,25 +168,25 @@
+@@ -166,25 +166,25 @@
os.mkdir(out_dir)
merged_sketch_filename = os.path.join(out_dir, "merged_sketch.bin")
@@ -88,7 +86,7 @@ Index: simka/tests/simkaMin/test_simkaMin.py
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
-@@ -196,12 +196,12 @@
+@@ -194,12 +194,12 @@
os.remove(filename_temp)
@@ -103,38 +101,38 @@ Index: simka/tests/simkaMin/test_simkaMin.py
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
-@@ -226,23 +226,23 @@
+@@ -223,10 +223,10 @@
+ clear(out_dir)
os.mkdir(out_dir)
- init = False
- filename = "../../example/simka_input.txt"
+- filename_temp1 = os.path.join("../../example/test_simkaMin_input_temp1.txt")
+ filename = "../simka_input.txt"
- for line in open(filename):
- line = line.strip()
- if len(line) == 0: continue
-
-- filename_temp = os.path.join("../../example/test_simkaMin_input_temp.txt")
-+ filename_temp = os.path.join("../test_simkaMin_input_temp.txt")
- f = open(filename_temp, "w")
- f.write(line)
- f.close()
++ filename_temp1 = os.path.join("../test_simkaiMin_input_temp1.txt")
+ f1 = open(filename_temp1, "w")
+- filename_temp2 = os.path.join("../../example/test_simkaMin_input_temp2.txt")
++ filename_temp2 = os.path.join("../test_simkaMin_input_temp2.txt")
+ f2 = open(filename_temp2, "w")
+ N=2 #where to split the file
+ i=0
+@@ -241,13 +241,13 @@
+ f2.close()
+
+ # init
+- command, outputDir = create_command("../../simkaMin/simkaMin.py", out_dir, 21, "", 0, 100, 4, filename_temp1)
++ command, outputDir = create_command("simkaMin.py", out_dir, 21, "", 0, 100, 4, filename_temp1)
+ print(command)
+ ret = os.system(command + suffix)
+ if ret != 0: exit(1)
- if init:
-- command, outputDir = create_command_update("../../simkaMin/simkaMin_update.py", out_dir, 21, "", 0, 100, 4, filename_temp)
-+ command, outputDir = create_command_update("simkaMin_update", out_dir, 21, "", 0, 100, 4, filename_temp)
- print(command)
- ret = os.system(command + suffix)
- if ret != 0: exit(1)
- else:
-- command, outputDir = create_command("../../simkaMin/simkaMin.py", out_dir, 21, "", 0, 100, 4, filename_temp)
-+ command, outputDir = create_command("simkaMin", out_dir, 21, "", 0, 100, 4, filename_temp)
- print(command)
- ret = os.system(command + suffix)
- if ret != 0: exit(1)
-Index: simka/tests/simple_test.py
-===================================================================
---- simka.orig/tests/simple_test.py 2019-09-16 15:35:57.745165516 +0100
-+++ simka/tests/simple_test.py 2019-09-16 15:35:57.741165482 +0100
+ # update
+- command, outputDir = create_command_update("../../simkaMin/simkaMin_update.py", out_dir, 21, "", 0, 100, 4, filename_temp2)
++ command, outputDir = create_command_update("simkaMin_update.py", out_dir, 21, "", 0, 100, 4, filename_temp2)
+ print(command)
+ ret = os.system(command + suffix)
+ if ret != 0: exit(1)
+--- simka.orig/tests/simple_test.py
++++ simka/tests/simple_test.py
@@ -91,7 +91,7 @@
#test k=31 t=0
clear()
@@ -183,10 +181,8 @@ Index: simka/tests/simple_test.py
os.system(command + suffix)
test_parallelization()
-Index: simka/example/simple_test.sh
-===================================================================
---- simka.orig/example/simple_test.sh 2019-09-16 15:35:57.745165516 +0100
-+++ simka/example/simple_test.sh 2019-09-16 15:36:47.117582577 +0100
+--- simka.orig/example/simple_test.sh
++++ simka/example/simple_test.sh
@@ -3,23 +3,23 @@
# look for simka binary. In devel mode, it's in ../build/bin directory.
View it on GitLab: https://salsa.debian.org/med-team/simka/-/commit/bc06b1228af1ce5853eddfbcdd9773e3eab2e10a
--
View it on GitLab: https://salsa.debian.org/med-team/simka/-/commit/bc06b1228af1ce5853eddfbcdd9773e3eab2e10a
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