Nilesh Patra pushed to branch master at Debian Med / uncalled
Commits: b7519758 by Nilesh Patra at 2023-07-13T21:47:58+05:30 Update patch to link to hdf5 lib on system The upstream way to summon extra_objects for it is not relevant to us - - - - - a325440d by Nilesh Patra at 2023-07-13T21:50:26+05:30 Add my work to d/ch - - - - - 3 changed files: - debian/changelog - debian/patches/debian_hdf5 - debian/patches/debian_toml11.patch Changes: ===================================== debian/changelog ===================================== @@ -1,11 +1,17 @@ uncalled (2.3+ds-1) UNRELEASED; urgency=medium + [ Andreas Tille ] * Team upload. - * New upstream version + * New upstream version (Refreshed patches) * Standards-Version: 4.6.2 (routine-update) * Set upstream metadata fields: Bug-Submit. - -- Andreas Tille <[email protected]> Thu, 13 Jul 2023 15:38:18 +0200 + [ Nilesh Patra ] + * Update patch to link to hdf5 lib on system + + The upstream way to summon extra_objects for it is + not relevant to us (downstream). + + -- Nilesh Patra <[email protected]> Thu, 13 Jul 2023 21:48:42 +0530 uncalled (2.2+ds1-1) unstable; urgency=medium ===================================== debian/patches/debian_hdf5 ===================================== @@ -18,7 +18,7 @@ Forwarded: not-needed BWA_LIB=-L./submods/bwa $(LIBBWA) --- a/setup.py +++ b/setup.py -@@ -55,7 +55,7 @@ class pre_build(build_ext): +@@ -55,7 +55,7 @@ "-f", "../../src/Makefile_bwa" ]) @@ -27,7 +27,7 @@ Forwarded: not-needed sys.stderr.write("Found libhdf5.a\n") else: -@@ -101,7 +101,7 @@ uncalled = Extension( +@@ -101,7 +101,7 @@ include_dirs = [ "./submods", @@ -36,15 +36,20 @@ Forwarded: not-needed "./submods/fast5/include", "./submods/pdqsort", "./submods/toml11", -@@ -109,11 +109,9 @@ uncalled = Extension( +@@ -109,14 +109,13 @@ ], library_dirs = [ - "./submods/bwa" ++ subprocess.check_output("pkg-config --libs-only-L hdf5-serial | sed 's/-L//'", shell=True, encoding='UTF-8').strip() ], extra_objects = [ - "./submods/hdf5/lib/libhdf5.a" ], - libraries = ["bwa", "z", "dl", "m"], +- libraries = ["bwa", "z", "dl", "m"], ++ libraries = ["bwa", "hdf5", "z", "dl", "m"], + + extra_compile_args = ["-std=c++11", "-O3"], + ===================================== debian/patches/debian_toml11.patch ===================================== @@ -4,7 +4,7 @@ Last-Update: Wed, 16 Feb 2022 15:39:15 +0100 --- a/Makefile +++ b/Makefile -@@ -10,7 +10,7 @@ BWA_LIB=$(LIBBWA) +@@ -10,7 +10,7 @@ BWA_INCLUDE=-I/usr/include/bwa LIBS=$(HDF5_LIB) $(BWA_LIB) -lstdc++ -lz -ldl -pthread -lm @@ -15,7 +15,7 @@ Last-Update: Wed, 16 Feb 2022 15:39:15 +0100 BUILD=build --- a/setup.py +++ b/setup.py -@@ -10,7 +10,6 @@ ROOT_DIR = os.getcwd() +@@ -10,7 +10,6 @@ SUBMOD_DIR = os.path.join(ROOT_DIR, "submods") SUBMODS = [ @@ -23,7 +23,7 @@ Last-Update: Wed, 16 Feb 2022 15:39:15 +0100 ] class get_pybind_include(object): -@@ -100,7 +99,6 @@ uncalled = Extension( +@@ -100,7 +99,6 @@ subprocess.check_output("pkg-config --cflags hdf5-serial | sed 's/-I//'", shell=True, encoding='UTF-8').strip(), "/usr/include/fast5/", "/usr/include/", View it on GitLab: https://salsa.debian.org/med-team/uncalled/-/compare/39d685081f465b189cb1a4df904353f494d3317b...a325440d0ac30bd967426ea5c312d9e95029e463 -- View it on GitLab: https://salsa.debian.org/med-team/uncalled/-/compare/39d685081f465b189cb1a4df904353f494d3317b...a325440d0ac30bd967426ea5c312d9e95029e463 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
