[med-svn] [Git][med-team/uncalled][master] 2 commits: Update patch to link to hdf5 lib on system

[Nilesh Patra (@nilesh)]

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 <tille at debian.org>  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 <nilesh at debian.org>  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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230713/b364a237/attachment-0001.htm>