[med-svn] [mash] 01/02: split package into mash, libmash-dev and mash-doc

Tue Jul 19 12:51:46 UTC 2016

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satta pushed a commit to branch master
in repository mash.

commit 4feae97cedadf3102a91137bf04cff94e1f01a18
Author: Sascha Steinbiss <satta at debian.org>
Date:   Tue Jul 19 12:49:59 2016 +0000

    split package into mash, libmash-dev and mash-doc
---
 debian/control                          | 22 +++++++++++++++++++++-
 debian/libmash-dev.install              |  2 ++
 debian/mash-doc.doc-base                | 11 +++++++++++
 debian/mash-doc.docs                    |  1 +
 debian/mash.install                     |  1 +
 debian/patches/hardening.patch          | 14 ++++++++++++++
 debian/patches/series                   |  2 ++
 debian/patches/use_debian_mathjax.patch | 10 ++++++++++
 debian/rules                            | 12 ++++++++++--
 9 files changed, 72 insertions(+), 3 deletions(-)

diff --git a/debian/control b/debian/control
index ed8f550..6d3825e 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,9 @@ Build-Depends: debhelper (>= 9),
                libcapnp-dev,
                libgsl-dev,
                dh-autoreconf,
-               zlib1g-dev
+               zlib1g-dev,
+               python-sphinx,
+               libjs-mathjax
 Standards-Version: 3.9.8
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
@@ -26,3 +28,21 @@ Description: fast genome and metagenome distance estimation using MinHash
  Illumina, Pacific Biosciences, and Oxford Nanopore.
  For metagenomics, Mash scales to thousands of samples and can replicate Human
  Microbiome Project and Global Ocean Survey results in a fraction of the time.
+
+Package: libmash-dev
+Architecture: all
+Section: libdevel
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: development headers and static library for Mash
+ This package contains C++ development headers and a static library to
+ build custom programs utilizing Mash, a MinHash based genome distance
+ estimator.
+
+Package: mash-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}, libjs-mathjax
+Description: documentation for Mash
+ This package contains further documentation (tutorials, explanations,
+ etc.) for Mash, a MinHash based genome distance estimator.
diff --git a/debian/libmash-dev.install b/debian/libmash-dev.install
new file mode 100644
index 0000000..da07fdd
--- /dev/null
+++ b/debian/libmash-dev.install
@@ -0,0 +1,2 @@
+usr/include
+usr/lib
diff --git a/debian/mash-doc.doc-base b/debian/mash-doc.doc-base
new file mode 100644
index 0000000..dbca58a
--- /dev/null
+++ b/debian/mash-doc.doc-base
@@ -0,0 +1,11 @@
+Document: mash
+Title: mash documentation
+Author: Mash authors
+Abstract: Additional documentation for Mash
+ This contains tutorials and further, more detailed explanations of
+ Mash concepts.
+Section: Science/Biology
+
+Format: HTML
+Files: /usr/share/doc/mash-doc/*
+Index: /usr/share/doc/mash-doc/index.html
diff --git a/debian/mash-doc.docs b/debian/mash-doc.docs
new file mode 100644
index 0000000..acc9ca8
--- /dev/null
+++ b/debian/mash-doc.docs
@@ -0,0 +1 @@
+debian/sphinxdoc/*
diff --git a/debian/mash.install b/debian/mash.install
new file mode 100644
index 0000000..51a8a51
--- /dev/null
+++ b/debian/mash.install
@@ -0,0 +1 @@
+usr/bin/mash
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..5167c0b
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,14 @@
+Description: add hardening support
+ This patch adds the missing LDFLAGS for hardening support.
+Author: Sascha Steinbiss <satta at debian.org>
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -35,7 +35,7 @@
+ all : mash libmash.a
+ 
+ mash : libmash.a src/mash/memcpyWrap.o
+-	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o mash src/mash/memcpyWrap.o libmash.a @capnp@/lib/libcapnp.a @capnp@/lib/libkj.a @mathlib@ -lstdc++ -lz -lm -lpthread
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o mash src/mash/memcpyWrap.o libmash.a @capnp@/lib/libcapnp.a @capnp@/lib/libkj.a @mathlib@ -lstdc++ -lz -lm -lpthread $(LDFLAGS)
+ 
+ libmash.a : $(OBJECTS)
+ 	ar -cr libmash.a $(OBJECTS)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..47dce94
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+hardening.patch
+use_debian_mathjax.patch
diff --git a/debian/patches/use_debian_mathjax.patch b/debian/patches/use_debian_mathjax.patch
new file mode 100644
index 0000000..49cfeb4
--- /dev/null
+++ b/debian/patches/use_debian_mathjax.patch
@@ -0,0 +1,10 @@
+Description: use Debian's Mathjax
+Author: Sascha Steinbiss <satta at debian.org>
+--- a/doc/sphinx/conf.py
++++ b/doc/sphinx/conf.py
+@@ -256,3 +256,5 @@
+ 
+ # If true, do not generate a @detailmenu in the "Top" node's menu.
+ #texinfo_no_detailmenu = False
++
++mathjax_path = 'file:///usr/share/javascript/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
diff --git a/debian/rules b/debian/rules
index 0115680..106aa44 100755
--- a/debian/rules
+++ b/debian/rules
@@ -20,8 +20,16 @@ export LC_ALL=C.UTF-8
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
-	dh $@  --with autoreconf --parallel
+	dh $@  --with autoreconf,sphinxdoc --parallel
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -rf $(CURDIR)/debian/sphinxdoc
 
 override_dh_auto_configure:
-	dh_auto_configure --  --with-capnp=/usr --with-gsl=/usr --prefix=$(CURDIR)/debian/mash/usr
+	dh_auto_configure --  --with-capnp=/usr --with-gsl=/usr --prefix=$(CURDIR)/debian/tmp/usr
 
+override_dh_auto_build:
+	dh_auto_build
+	sphinx-build doc/sphinx $(CURDIR)/debian/sphinxdoc
+	#find debian/sphinxdoc -type f -name "*.html" -exec sed -i 's?https://cdn.mathjax.org/mathjax/latest/?/usr/share/javascript/mathjax?g' \{\} \;

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mash.git

