[med-svn] [Git][med-team/sra-sdk][master] 5 commits: Formally start work on sra-sdk 3.2.1+dfsg-2.

Thu Apr 10 01:44:05 BST 2025


Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk


Commits:
19cc740f by Aaron M. Ucko at 2025-04-09T20:34:03-04:00
Formally start work on sra-sdk 3.2.1+dfsg-2.

- - - - -
17477b4e by Aaron M. Ucko at 2025-04-09T20:35:09-04:00
.gitignore: Belatedly add .pc.

- - - - -
7588b2a6 by Aaron M. Ucko at 2025-04-09T20:39:32-04:00
Minimally modernize Python logistics.

* debian/control: Build-depend on python3-setuptools.
* debian/patches/setuptools.patch (new): Substitute setuptools for
  distutils (retired) in ngs/ngs-python/setup.py.
* debian/rules:
  - Set PIP_BREAK_SYSTEM_PACKAGES for upstream's test suite.
  - Substitute pybuild for direct setup.py invocation and clean up after
    it.
* .gitignore: Add .pybuild.

- - - - -
90c59658 by Aaron M. Ucko at 2025-04-09T20:40:48-04:00
debian/patches/fix_arm64_build.patch: Correct parenthesis placement.

- - - - -
58e2b6d8 by Aaron M. Ucko at 2025-04-09T20:41:32-04:00
Finalize sra-sdk 3.2.1+dfsg-2, still targeting experimental.

- - - - -


7 changed files:

- .gitignore
- debian/changelog
- debian/control
- debian/patches/fix_arm64_build.patch
- debian/patches/series
- + debian/patches/setuptools.patch
- debian/rules


Changes:

=====================================
.gitignore
=====================================
@@ -1,3 +1,5 @@
+/.pc
+/.pybuild
 /ngs/ngs-python/dist
 /ngs/ngs-python/ngs.egg-info
 /obj-*


=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+sra-sdk (3.2.1+dfsg-2) experimental; urgency=medium
+
+  * debian/control: Build-depend on python3-setuptools.
+  * debian/patches/fix_arm64_build.patch: Correct parenthesis placement.
+  * debian/patches/setuptools.patch (new): Substitute setuptools for
+    distutils (retired) in ngs/ngs-python/setup.py.
+  * debian/rules:
+    - Set PIP_BREAK_SYSTEM_PACKAGES for upstream's test suite.
+    - Substitute pybuild for direct setup.py invocation and clean up after
+      it.
+  * .gitignore: Add .pc (belatedly) and .pybuild.
+
+ -- Aaron M. Ucko <ucko at debian.org>  Wed, 09 Apr 2025 20:41:31 -0400
+
 sra-sdk (3.2.1+dfsg-1) experimental; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/control
=====================================
@@ -21,6 +21,7 @@ Build-Depends: debhelper-compat (= 13),
                libsam-extract-dev,
                maven-repo-helper,
                python3-all,
+               python3-setuptools,
                python3-vdb,
                default-jdk,
                flex,


=====================================
debian/patches/fix_arm64_build.patch
=====================================
@@ -1,5 +1,3 @@
-Index: b/libs/inc/bm/bmsse2.h
-===================================================================
 --- a/libs/inc/bm/bmsse2.h
 +++ b/libs/inc/bm/bmsse2.h
 @@ -22,7 +22,7 @@ For more information please visit:  http
@@ -11,8 +9,6 @@ Index: b/libs/inc/bm/bmsse2.h
  #ifndef BMWASMSIMDOPT
  #include<mmintrin.h>
  #endif
-Index: b/libs/inc/bm/bmutil.h
-===================================================================
 --- a/libs/inc/bm/bmutil.h
 +++ b/libs/inc/bm/bmutil.h
 @@ -26,7 +26,7 @@ For more information please visit:  http
@@ -33,8 +29,6 @@ Index: b/libs/inc/bm/bmutil.h
          return (unsigned)__builtin_popcountll(x);
      #else
          #if (defined(__arm__)) // 32-bit
-Index: b/libs/inc/bm/encoding.h
-===================================================================
 --- a/libs/inc/bm/encoding.h
 +++ b/libs/inc/bm/encoding.h
 @@ -1810,7 +1810,8 @@ unsigned bit_in<TDecoder>::gamma() BMNOE
@@ -43,7 +37,7 @@ Index: b/libs/inc/bm/encoding.h
          unsigned first_bit_idx =
 -            #if defined(BM_x86) && (defined(__GNUG__) || defined(_MSC_VER)) && !(defined(__arm64__) || defined(__arm__))
 +            #if defined(BM_x86) && (defined(__GNUG__) || defined(_MSC_VER)) && \
-+	      !defined(__aarch64__) || (defined(__arm64__) || defined(__arm__))
++	      !(defined(__aarch64__) || defined(__arm64__) || defined(__arm__))
                  bm::bsf_asm32(acc);
              #else
                  bm::bit_scan_fwd(acc);


=====================================
debian/patches/series
=====================================
@@ -41,3 +41,4 @@ no_sse4.2.patch
 fix_arm64_build.patch
 support_libre2-11.patch
 pyhon3.12-syntax.patch
+setuptools.patch


=====================================
debian/patches/setuptools.patch
=====================================
@@ -0,0 +1,8 @@
+--- a/ngs/ngs-python/setup.py
++++ b/ngs/ngs-python/setup.py
+@@ -1,4 +1,4 @@
+-from distutils.core import setup
++from setuptools import setup
+ import sys
+ #import version
+ 


=====================================
debian/rules
=====================================
@@ -12,14 +12,14 @@ export DEB_CPPFLAGS_MAINT_APPEND = -DH5_USE_110_API
 export DEB_CFLAGS_MAINT_APPEND   = -fsigned-char
 export DEB_CXXFLAGS_MAINT_APPEND = -fsigned-char
 
+export PIP_BREAK_SYSTEM_PACKAGES = 1
+
 pkg := sra-toolkit
 
 include /usr/share/dpkg/architecture.mk
 include /usr/share/dpkg/buildflags.mk
 include /usr/share/dpkg/pkg-info.mk
 
-build3vers := $(shell py3versions -sv)
-
 %:
 	dh $@ --buildsystem=cmake \
 	    --with python3,javahelper,jh_maven_repo_helper
@@ -51,6 +51,7 @@ override_dh_auto_clean:
 	rm -f ngs/ngs-sdk/examples/actual.txt
 
 	-rm -f debian/libngs-jni.links
+	rm -rf .pybuild
 
 override_dh_auto_configure:
 	dh_auto_configure -- -DVDB_LIBDIR=/usr/lib/${DEB_HOST_MULTIARCH} \
@@ -131,14 +132,7 @@ override_dh_install:
 	dh_install
 	# remove susipcious file which is not executable and conflicts with package magic
 	rm -f debian/*/usr/bin/magic
-	set -e && for i in $(build3vers); do \
-	    cd ngs/ngs-python; \
-	    python$$i ./setup.py install --install-layout=deb \
-	        --root $(CURDIR)/debian/python3-ngs; \
-	    cd ../..; \
-	done
-	find debian -name "*.pyc" -delete
-	find debian -type d -name __pycache__ | xargs rm -rf
+	pybuild --install --name ngs -d ngs/ngs-python
 
 override_dh_installexamples:
 	dh_installexamples



View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/021aa260410e23c92b978e1e016f3bf3ff76ad4b...58e2b6d8d50cc7fb37bbf20b441ebeece4140452

-- 
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/021aa260410e23c92b978e1e016f3bf3ff76ad4b...58e2b6d8d50cc7fb37bbf20b441ebeece4140452
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