[med-svn] [Git][med-team/tiddit][master] 9 commits: Update test acc to updated binary
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Tue Jul 26 19:53:39 BST 2022
Nilesh Patra pushed to branch master at Debian Med / tiddit
Commits:
b9e19d20 by Nilesh Patra at 2022-07-26T23:56:31+05:30
Update test acc to updated binary
- - - - -
dbf9a832 by Nilesh Patra at 2022-07-26T23:57:09+05:30
B-D on python3-all-dev to build bindings for all supported py versions
- - - - -
efe65a6c by Nilesh Patra at 2022-07-26T23:59:11+05:30
Remove use_debian_packaged_libs.patch as well since cmakelists.txt is redundant now
- - - - -
f7501fc9 by Nilesh Patra at 2022-07-27T00:00:42+05:30
Remove B-D on libbamtools-dev and zlib1g, instead B-D on python3-pysam
- - - - -
ca2156b7 by Nilesh Patra at 2022-07-27T00:18:36+05:30
Drop python3-numpy from test deps
- - - - -
feef1c2a by Nilesh Patra at 2022-07-27T00:18:36+05:30
Remove unused override
- - - - -
7eed4c64 by Nilesh Patra at 2022-07-27T00:18:36+05:30
Add 2022 to copyr year
- - - - -
f2963e2c by Nilesh Patra at 2022-07-27T00:18:36+05:30
d/rules: Add "export PYBUILD_NAME=tiddit"
- - - - -
d7369a1b by Nilesh Patra at 2022-07-27T00:22:18+05:30
Interim d/ch
- - - - -
9 changed files:
- debian/changelog
- debian/control
- debian/copyright
- − debian/lintian-overrides
- − debian/patches/series
- − debian/patches/use_debian_packaged_libs.patch
- debian/rules
- debian/tests/control
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,7 @@
-tiddit (3.1.0+dfsg-1) UNRELEASED; urgency=medium
+tiddit (3.1.0+dfsg-1) unstable; urgency=medium
+ * Team Upload.
+ [ Andreas Tille ]
* Fix watchfile to detect new versions on github
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
@@ -7,8 +9,22 @@ tiddit (3.1.0+dfsg-1) UNRELEASED; urgency=medium
* Drop cmake drom Build-Depends, add python3-setuptools,
python3-numpy to Build-Depends
* Use pybuild build system
+ * Fix manpages
- -- Andreas Tille <tille at debian.org> Tue, 26 Jul 2022 09:44:27 +0200
+ [ Nilesh Patra ]
+ * Update test acc to updated binary
+ * B-D on python3-all-dev to build bindings for all
+ supported py versions
+ * Remove use_debian_packaged_libs.patch as well since
+ cmakelists.txt is redundant now
+ * Remove B-D on libbamtools-dev and zlib1g, instead
+ B-D on python3-pysam
+ * Drop python3-numpy from test deps
+ * Remove unused override
+ * Add 2022 to copyr year
+ * d/rules: Add "export PYBUILD_NAME=tiddit"
+
+ -- Nilesh Patra <nilesh at debian.org> Wed, 27 Jul 2022 00:22:07 +0530
tiddit (2.12.2+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -6,11 +6,10 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-python,
cython3,
- python3-dev,
+ python3-all-dev,
python3-setuptools,
python3-numpy,
- libbamtools-dev (>= 2.5.1+dfsg-6),
- zlib1g-dev
+ python3-pysam
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/tiddit
Vcs-Git: https://salsa.debian.org/med-team/tiddit.git
=====================================
debian/copyright
=====================================
@@ -13,7 +13,7 @@ Copyright: 2016-2020 Francesco Vezzi <francesco.vezzi at scilifelab.se>,
License: GPL-3
Files: debian/*
-Copyright: 2020 Andreas Tille <tille at debian.org>
+Copyright: 2020-2022 Andreas Tille <tille at debian.org>
License: GPL-3
License: GPL-3
=====================================
debian/lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-tiddit: script-with-language-extension usr/bin/*.*
=====================================
debian/patches/series deleted
=====================================
@@ -1 +0,0 @@
-use_debian_packaged_libs.patch
=====================================
debian/patches/use_debian_packaged_libs.patch deleted
=====================================
@@ -1,41 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 25 May 2020 11:58:02 +0200
-Description: Use Debian packaged bamtools
- Note: Tiddit source came with a patched BamTools. The Debian packaged bamtools
- has taken it over in
- https://salsa.debian.org/med-team/bamtools/-/blob/master/debian/patches/tiddit.patch
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -14,8 +14,8 @@ set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOU
- set( CMAKE_BUILD_TYPE Release )
-
- include_directories("${PROJECT_SOURCE_DIR}/src")
--include_directories("${PROJECT_SOURCE_DIR}/lib/")
--include_directories("${PROJECT_SOURCE_DIR}/lib/bamtools/src")
-+#include_directories("${PROJECT_SOURCE_DIR}/lib/")
-+#include_directories("${PROJECT_SOURCE_DIR}/lib/bamtools/src")
-
-
- # source code
-@@ -28,10 +28,17 @@ file(GLOB TIDDIT_FILES
- )
-
-
--add_subdirectory(lib)
--
-+# add_subdirectory(lib)
-+find_path(bamtools_INCLUDE_DIR api/BamReader.h
-+ HINTS ENV BAMTOOLS_INC
-+ PATH_SUFFIXES bamtools
-+ )
-+set(bamtools_INCLUDE_DIRS ${bamtools_INCLUDE_DIR})
-+# the code above does not seem to have the wanted effect
-+include_directories(/usr/include/bamtools)
-+find_library(BAMTOOLS_LIBRARIES libbamtools.a)
-
- # TIDDIT executable
- add_executable(TIDDIT ${TIDDIT_FILES})
- target_link_libraries(TIDDIT ${ZLIB_LIBRARIES})
--target_link_libraries(TIDDIT BamTools)
-+target_link_libraries(TIDDIT bamtools)
=====================================
debian/rules
=====================================
@@ -5,6 +5,7 @@ export LC_ALL=C.UTF-8
# for hardening you might like to uncomment this:
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export PYBUILD_NAME=tiddit
%:
dh $@ --with python3 --buildsystem=pybuild
=====================================
debian/tests/control
=====================================
@@ -1,4 +1,3 @@
Tests: run-unit-test
-Depends: @, samtools, python3-numpy
+Depends: @, samtools
Restrictions: allow-stderr
-
=====================================
debian/tests/run-unit-test
=====================================
@@ -18,8 +18,8 @@ cat tumor.sam | samtools view -Sb - > tumor.bam
set -x
echo 'Test 1'
-tiddit --cov -bam normal.bam -o test1
-tiddit --cov -w -bam normal.bam -o test1
+tiddit --cov --bam normal.bam -o test1
+tiddit --cov -w --bam normal.bam -o test1
for f in test1.*
do
[ -s $f ] || exit 1
@@ -29,8 +29,8 @@ rm -f ./test1*
echo 'PASS'
echo 'Test 2'
-tiddit --cov -b normal.bam -o test2
-tiddit --cov -w -b tumor.bam -o test2
+tiddit --cov --bam normal.bam -o test2
+tiddit --cov -w --bam tumor.bam -o test2
for f in test2.*
do
[ -s $f ] || exit 1
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/a8ad2868ffde3b7b7f3e17f63bcf6b6c225e2591...d7369a1b546f2936f637eea87c696a61370f3450
--
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/a8ad2868ffde3b7b7f3e17f63bcf6b6c225e2591...d7369a1b546f2936f637eea87c696a61370f3450
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