[med-svn] [Git][med-team/hmmer2][master] 4 commits: Use NOTES as upstream changelog and install 00README

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / hmmer2


Commits:
77461522 by Andreas Tille at 2020-09-09T13:05:02+02:00
Use NOTES as upstream changelog and install 00README

- - - - -
004063d9 by Andreas Tille at 2020-09-09T13:05:02+02:00
Fix Debian revision number

- - - - -
6b6a3757 by Andreas Tille at 2020-09-09T13:05:02+02:00
Cleanup after running build time test

- - - - -
510936e9 by Andreas Tille at 2020-09-09T13:05:02+02:00
Remove some unused patches

- - - - -


7 changed files:

- debian/changelog
- + debian/hmmer2.docs
- − debian/patches/fix_install.patch
- − debian/patches/fix_install_man.patch
- − debian/patches/fix_typo.patch
- − debian/patches/static_lib.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-hmmer2 (2.3.2+dfsg-1) UNRELEASED; urgency=medium
+hmmer2 (2.3.2+dfsg-7) UNRELEASED; urgency=medium
 
   * Drop hmmer2-pvm package
   * Standards-Version: 4.5.0 (routine-update)
@@ -9,6 +9,8 @@ hmmer2 (2.3.2+dfsg-1) UNRELEASED; urgency=medium
   * Set upstream metadata fields: Repository, Repository-Browse.
   * Remove obsolete field Name from debian/upstream/metadata (already present in
     machine-readable debian/copyright).
+  * Use NOTES as upstream changelog and install 00README
+  * Cleanup after running build time test
 
  -- Andreas Tille <tille at debian.org>  Wed, 12 Aug 2020 11:44:30 +0200
 


=====================================
debian/hmmer2.docs
=====================================
@@ -0,0 +1 @@
+00README


=====================================
debian/patches/fix_install.patch deleted
=====================================
@@ -1,23 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 11 Jan 2019 15:43:07 +0100
-Description: Do not duplicate prefix
-
---- a/Makefile
-+++ b/Makefile
-@@ -55,13 +55,13 @@ src/libhmmer.a:
- #          Prefix those paths with ${DESTDIR} (rarely used, usually null;
- #          may be set on a make command line when building contrib RPMs).
- install:
--	mkdir -p ${DESTDIR}/$(BINDIR)/
-+	mkdir -p $(BINDIR)
- 
- 	for file in $(PROGS) ; do\
--		cp src/$$file "${DESTDIR}/$(BINDIR)/$$file""$(PROGSUFFIX)" ;\
-+		cp src/$$file "$(BINDIR)/$$file""$(PROGSUFFIX)" ;\
- 	done
- 	for file in hmmer2 $(ls documentation/man/); do\
--	   install -D documentation/man/$$file.man ${DESTDIR}/$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
-+	   install -D documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
- 	done
- 
- # Reverses the steps of "make install".  However, this should be handled


=====================================
debian/patches/fix_install_man.patch deleted
=====================================
@@ -1,17 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 11 Jan 2019 15:43:07 +0100
-Description: Fix installation of manpages
-
---- a/Makefile
-+++ b/Makefile
-@@ -60,8 +60,8 @@ install:
- 	for file in $(PROGS) ; do\
- 		cp src/$$file "$(BINDIR)/$$file""$(PROGSUFFIX)" ;\
- 	done
--	for file in hmmer2 $(ls documentation/man/); do\
--	   install -D documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
-+	for file in documentation/man/*.man ; do\
-+	   install -D $$file $(MANDIR)/man$(MANSUFFIX)/`basename $$file .man`.$(MANSUFFIX);\
- 	done
- 
- # Reverses the steps of "make install".  However, this should be handled


=====================================
debian/patches/fix_typo.patch deleted
=====================================
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 11 Jan 2019 15:43:07 +0100
-Description: Typo in referencing biosquid function
-
---- a/src/histogram.c
-+++ b/src/histogram.c
-@@ -470,7 +470,7 @@ EVDBasicFit(struct histogram_s *h) {
-     d[sc - h->lowscore] = log(-1. * log(d[sc - h->lowscore]));
- 
-   // do the linear regression
--  FLinefit(x, d, hsize-1, &intercept, &slope, &corr);
-+  Linefit(x, d, hsize-1, &intercept, &slope, &corr);
-   // calc mu, lambda
-   lambda = -1. * slope;
-   mu     = intercept / lambda;


=====================================
debian/patches/static_lib.patch deleted
=====================================
@@ -1,20 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 11 Jan 2019 15:43:07 +0100
-Description: Try to create static library
- Unfortunately this does not work - thus the patch is deactivated
-
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -54,9 +54,9 @@ ${PROGS}: %: %.o ${OBJS}
- module: $(HMMLIB)
- 
- $(HMMLIB): $(OBJS)
--#	$(AR) libhmmer.a $(OBJS)
--#	$(RANLIB) libhmmer.a
--#	chmod 644 libhmmer.a
-+	$(AR) libhmmer.a $(OBJS)
-+	$(RANLIB) libhmmer.a
-+	chmod 644 libhmmer.a
- 	gcc -shared $(OBJS) -o $@
- 
- 


=====================================
debian/rules
=====================================
@@ -42,11 +42,16 @@ override_dh_auto_install:
 	sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' $(CURDIR)/debian/tmp/share/man/man1/*
 
 override_dh_installchangelogs:
-	dh_installchangelogs -k 00README
+	dh_installchangelogs -k NOTES
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	dh_auto_test
+	cd testsuite && make clean
+endif
 
 override_dh_installexamples:
 	dh_installexamples
-	# cd testsuite && make clean
 	mkdir -p $(sampledir);
 	sed -i "s#hmm#hmm2#g" testsuite/exercises.sqc
 	rm -f testsuite/*.ssi;



View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/compare/47c6a33656873ec3990108398f99315a1a01ca35...510936e97c9f0aad27af2265a53458dc80e7ae64

-- 
View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/compare/47c6a33656873ec3990108398f99315a1a01ca35...510936e97c9f0aad27af2265a53458dc80e7ae64
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