[med-svn] [Git][med-team/seqsero][master] 4 commits: Update 2to3 patch

[Shruti Sridhar]

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 <shruti.sridhar99 at gmail.com>  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
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