[med-svn] [Git][med-team/nim-hts][master] 8 commits: Add watch file

Nilesh Patra gitlab at salsa.debian.org
Sun Nov 1 06:12:42 GMT 2020 


Nilesh Patra pushed to branch master at Debian Med / nim-hts


Commits:
d7cd93e4 by Nilesh Patra at 2020-11-01T10:44:57+05:30
Add watch file

- - - - -
f8c670f8 by Nilesh Patra at 2020-11-01T10:47:21+05:30
Repack to remove binary files

- - - - -
fdcfe021 by Nilesh Patra at 2020-11-01T10:47:32+05:30
New upstream version 0.3.12+ds
- - - - -
311cd0f2 by Nilesh Patra at 2020-11-01T10:47:34+05:30
Update upstream source from tag 'upstream/0.3.12+ds'

Update to upstream version '0.3.12+ds'
with Debian dir 43521ed649d0b5afcbe771e46b17b834ee3057f0
- - - - -
fde41403 by Nilesh Patra at 2020-11-01T11:37:34+05:30
Add missing sources for sourceless binaries

- - - - -
79c57baf by Nilesh Patra at 2020-11-01T11:37:56+05:30
Regenerate repacked files

- - - - -
141a330a by Nilesh Patra at 2020-11-01T11:38:29+05:30
Disable tests for binaries which cannot be generated

- - - - -
428af928 by Nilesh Patra at 2020-11-01T11:40:30+05:30
Add upstream/metadata

- - - - -


18 changed files:

- + debian/README.source
- debian/changelog
- debian/control
- debian/copyright
- + debian/missing-sources/HG02002.sam
- + debian/patches/disable-test-with-sourceless-file.patch
- debian/patches/series
- debian/rules
- + debian/upstream/metadata
- + debian/watch
- − tests/HG02002.bam
- − tests/HG02002.bam.bai
- − tests/other-for-test.bcf.csi
- − tests/sa.bam
- − tests/sa.bam.bai
- − tests/test.bcf.csi
- − tests/test.vcf.gz.tbi
- − tests/test_files/simple.tsv.gz.csi


Changes:

=====================================
debian/README.source
=====================================
@@ -0,0 +1,19 @@
+Upstream provides binary files without sources for:
+
+* tests/HG02002.bam.bai
+* tests/HG02002.bam
+
+These have been converted to corresponding text (.sam) files with command:
+* samtools view -h -o <out>.sam <in>.bam 
+
+And the corresponding *.sam files are added to: debian/missing-sources
+
+They can be generated back with the following commands:
+*	cat debian/missing-sources/HG02002.sam | samtools view -Sb - > tests/HG02002.bam
+*	samtools index tests/HG02002.bam tests/HG02002.bam.bai
+
+
+These commands are also being run in debian/rules since these binaries are needed for autopkgtests.
+
+ -- Nilesh Patra <npatra974 at gmail.com>  Sun, 01 Nov 2020 11:14:35 +0530
+


=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-nim-hts (0.3.12-1) UNRELEASED; urgency=medium
+nim-hts (0.3.12+ds-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #973510)
 


=====================================
debian/control
=====================================
@@ -6,7 +6,10 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
            Debian Nim Team <team+nim at tracker.debian.org>
 Build-Depends: debhelper-compat (= 13),
                nim,
-               libhts-dev
+               libhts-dev,
+               samtools,
+               tabix,
+               bcftools
 Standards-Version: 4.5.0
 Homepage: https://github.com/brentp/hts-nim
 Vcs-Browser: https://salsa.debian.org/med-team/nim-hts


=====================================
debian/copyright
=====================================
@@ -1,6 +1,10 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: nim-hts
 Source: https://github.com/brentp/hts-nim
+Files-Excluded: tests/*.bam*
+                tests/*.tbi
+                tests/test_files/*.csi
+                tests/*.csi
 
 Files: *
 Copyright: 2017-2020 Brent Pedersen


=====================================
debian/missing-sources/HG02002.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/patches/disable-test-with-sourceless-file.patch
=====================================
@@ -0,0 +1,39 @@
+Description: Two binaries:
+1. tests/other-for-test.bcf.csi - has undergone a lossy transformation and source can't be recovered
+2. tests/test_files/simple.tsv.gz.csi - cannot be indexed properly from the existing tsv
+Hence disabled tests involving these
+Author: Nilesh Patra <npatr974 at gmail.com>
+Forwarded: not-needed
+Last-Update: 2020-11-01
+--- a/tests/vcftest.nim
++++ b/tests/vcftest.nim
+@@ -246,10 +246,10 @@
+       check variant.info.set("myflag", val) == Status.OK
+       check "myflag" notin variant.tostring()
+ 
+-  test "load index":
++  #[test "load index":
+     var vcf:VCF
+     check open(vcf, "tests/test.bcf")
+-    vcf.load_index("tests/other-for-test.bcf.csi")
++    vcf.load_index("tests/other-for-test.bcf.csi")]#
+ 
+   test "remove info from header":
+     var vcf:VCF
+--- a/tests/bgzftest.nim
++++ b/tests/bgzftest.nim
+@@ -90,7 +90,7 @@
+       check reg == "aaa\t4\t10"
+     check found == 1
+ 
+-  test "bgzi-query from VCF rows":
++  #[test "bgzi-query from VCF rows":
+     ## There was a discrepancy between rec.POS (int32) and BGZI.query (int64)
+     var db:BGZI
+     check db.open("tests/test_files/simple.tsv.gz")
+@@ -102,4 +102,4 @@
+       for row in db.query($rec.CHROM, rec.POS - 1, rec.POS):
+         rows.add row
+     check rows.len == 1
+-    check rows[0] == "1\t10492\tC\tT"
++    check rows[0] == "1\t10492\tC\tT"]#


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 dontDoNestedTests.patch
+disable-test-with-sourceless-file.patch


=====================================
debian/rules
=====================================
@@ -6,6 +6,13 @@ DEB_BUILD_OPTIONS += nodoc
 	dh $@
 
 override_dh_auto_test:
+	# Regenerate repacked files
+	cat tests/sa.sam | samtools view -Sb - > tests/sa.bam
+	samtools index tests/sa.bam tests/sa.bam.bai
+	cat debian/missing-sources/HG02002.sam | samtools view -Sb - > tests/HG02002.bam
+	samtools index tests/HG02002.bam tests/HG02002.bam.bai
+	tabix tests/test.vcf.gz
+	bcftools index tests/test.bcf
 	#nim c -p=/usr/share/nimble/unicodedb/ -p=/usr/share/nimble/unicodeplus/ -p=/usr/share/nimble/regex/ test/test.nim
 	#nim c tests/run.nim
 	#./tests/run


=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,7 @@
+---
+Archive: GitHub
+Bug-Database: https://github.com/brentp/hts-nim/issues
+Bug-Submit: https://github.com/brentp/hts-nim/issues/new
+Changelog: https://github.com/brentp/hts-nim/tags
+Repository: https://github.com/brentp/hts-nim.git
+Repository-Browse: https://github.com/brentp/hts-nim


=====================================
debian/watch
=====================================
@@ -0,0 +1,4 @@
+version=4
+
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%,repacksuffix=+ds,dversionmangle=auto" \
+https://github.com/brentp/hts-nim/releases .*/archive/v?@ANY_VERSION@\.tar\.gz


=====================================
tests/HG02002.bam deleted
=====================================
Binary files a/tests/HG02002.bam and /dev/null differ


=====================================
tests/HG02002.bam.bai deleted
=====================================
Binary files a/tests/HG02002.bam.bai and /dev/null differ


=====================================
tests/other-for-test.bcf.csi deleted
=====================================
Binary files a/tests/other-for-test.bcf.csi and /dev/null differ


=====================================
tests/sa.bam deleted
=====================================
Binary files a/tests/sa.bam and /dev/null differ


=====================================
tests/sa.bam.bai deleted
=====================================
Binary files a/tests/sa.bam.bai and /dev/null differ


=====================================
tests/test.bcf.csi deleted
=====================================
Binary files a/tests/test.bcf.csi and /dev/null differ


=====================================
tests/test.vcf.gz.tbi deleted
=====================================
Binary files a/tests/test.vcf.gz.tbi and /dev/null differ


=====================================
tests/test_files/simple.tsv.gz.csi deleted
=====================================
Binary files a/tests/test_files/simple.tsv.gz.csi and /dev/null differ



View it on GitLab: https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666

-- 
View it on GitLab: https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666
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