Shruti Sridhar pushed to branch master at Debian Med / seqsero
Commits: 6092d93d by Shruti Sridhar at 2021-03-07T23:45:06+05:30 Update 2to3 patch - - - - - 368095b1 by Shruti Sridhar at 2021-03-07T23:45:32+05:30 Add autopkgtest - - - - - f4411d9c by Shruti Sridhar at 2021-03-07T23:45:43+05:30 Add docs - - - - - c5585ac2 by Shruti Sridhar at 2021-03-07T23:50:19+05:30 Update changelog - - - - - 6 changed files: - + debian/README.test - debian/changelog - debian/docs - debian/patches/2to3.patch - + debian/tests/data/sra_data.fastq - debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,14 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +This package can be tested by running the provided test: + + sh run-unit-test + +in order to confirm its integrity. + +Notes on the files used for testing +──────────────────────────────────────── +Files: debian/tests/data/* +Source: https://www.ncbi.nlm.nih.gov/sra/SRX839168 + ===================================== debian/changelog ===================================== @@ -1,3 +1,15 @@ +seqsero (1.0.1+dfsg-2ubuntu1) UNRELEASED; urgency=medium + + [ Nilesh Patra ] + * Add test depends on current package, cleaup debug statements + + [ Shruti Sridhar ] + * Update 2to3 patch + * Add autopkgtest. Closes #970598 + * Add docs + + -- Shruti Sridhar <[email protected]> Sun, 07 Mar 2021 23:47:46 +0530 + seqsero (1.0.1+dfsg-2) unstable; urgency=medium * Use 2to3 to port from Python2 to Python3 ===================================== debian/docs ===================================== @@ -1,2 +1,4 @@ README.md User_manual.pdf +debian/README* +debian/tests/run-unit-test \ No newline at end of file ===================================== debian/patches/2to3.patch ===================================== @@ -20,8 +20,9 @@ Last-Update: Wed, 11 Dec 2019 16:37:38 +0100 + print(dataset[0]) os.system("cp "+dataset[0]+" "+make_dir) os.chdir(make_dir) - os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1") +- os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1") - print "\n\n\nResult:\n" ++ os.system("python3 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1") + print("\n\n\nResult:\n") os.system("cat Seqsero_result.txt") os.system("rm "+dataset[0].split("/")[-1]) @@ -31,23 +32,26 @@ Last-Update: Wed, 11 Dec 2019 16:37:38 +0100 fnameB=dataset[1].split("/")[-1] os.chdir(make_dir) - print "check fastq id and make them in accordance with each other...please wait..." -+ print("check fastq id and make them in accordance with each other...please wait...") - os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2") +- os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2") - print "\n\n\nResult:\n" ++ print("check fastq id and make them in accordance with each other...please wait...") ++ os.system("python3 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2") + print("\n\n\nResult:\n") os.system("cat Seqsero_result.txt") elif mode_choice=="3": os.system("cp "+dataset[0]+" "+make_dir) os.chdir(make_dir) - os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3") +- os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3") - print "\n\n\nResult:\n" ++ os.system("python3 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3") + print("\n\n\nResult:\n") os.system("cat Seqsero_result.txt") elif mode_choice=="4": os.system("cp "+dataset[0]+" "+make_dir) os.chdir(make_dir) - os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1]) +- os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1]) - print "\n\n\nResult:\n" ++ os.system("python3 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1]) + print("\n\n\nResult:\n") os.system("cat Seqsero_result.txt") ===================================== debian/tests/data/sra_data.fastq ===================================== ===================================== debian/tests/run-unit-test ===================================== @@ -12,3 +12,12 @@ fi cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" cd "${AUTOPKGTEST_TMP}" + +seqsero -m 3 -i sra_data.fastq +cat $(find -name "Seqsero_result.txt") > result +echo "d87480d5b8ed2cb5125583b02c8694ed result" > checksums +md5sum --check checksums + + + + View it on GitLab: https://salsa.debian.org/med-team/seqsero/-/compare/7471ca9cebf9cde0743773efc5ebf28680e69088...c5585ac2f573396a4b20d303980e2e44bbb4a83b -- View it on GitLab: https://salsa.debian.org/med-team/seqsero/-/compare/7471ca9cebf9cde0743773efc5ebf28680e69088...c5585ac2f573396a4b20d303980e2e44bbb4a83b You're receiving this email because of your account on salsa.debian.org.
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