[med-svn] [Git][med-team/seqan-raptor][master] 5 commits: Generate and package the man pages.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Mon Oct 31 13:26:24 GMT 2022
Michael R. Crusoe pushed to branch master at Debian Med / seqan-raptor
Commits:
ca11679e by Michael R. Crusoe at 2022-10-20T17:45:46+02:00
Generate and package the man pages.
- - - - -
2317fd65 by Michael R. Crusoe at 2022-10-31T14:24:33+01:00
Upstream says doxygen docs aren't ready yet, so skip that for now.
- - - - -
a7d3e904 by Michael R. Crusoe at 2022-10-31T14:24:33+01:00
d/patched/privacy: don't phone home to check for a new version
- - - - -
728e33cb by Michael R. Crusoe at 2022-10-31T14:24:33+01:00
d/patches/debian_xxhash: get the libdir using pkg-config
- - - - -
b56fd9e0 by Michael R. Crusoe at 2022-10-31T14:24:33+01:00
release 2.0.0.0.git.fecfbca+ds-2 to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/patches/debian_xxhash
- + debian/patches/privacy
- debian/patches/series
- debian/rules
- − debian/seqan-raptor.install
- + debian/seqan-raptor.manpages
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+seqan-raptor (2.0.0.0.git.fecfbca+ds-2) unstable; urgency=medium
+
+ * Generate and package the man pages.
+ * Upstream says doxygen docs aren't ready yet, so skip that for now.
+ * d/patches/privacy: don't phone home to check for a new version
+ * d/patches/debian_xxhash: get the libdir using pkg-config (Closes:
+ #1023176)
+
+ -- Michael R. Crusoe <crusoe at debian.org> Mon, 31 Oct 2022 11:43:26 +0100
+
seqan-raptor (2.0.0.0.git.fecfbca+ds-1) unstable; urgency=medium
* Initial release (Closes: #1022057)
=====================================
debian/control
=====================================
@@ -10,14 +10,16 @@ Build-Depends: debhelper-compat (= 13),
libxxhash-dev,
libcereal-dev,
libsimde-dev,
- doxygen <!nodoc>,
- texlive-font-utils <!nodoc>,
- texlive-latex-base <!nodoc>,
- texlive-latex-recommended <!nodoc>,
- texlive-latex-extra <!nodoc>,
- texlive-plain-generic <!nodoc>,
- texlive-fonts-recommended <!nodoc>,
- ghostscript <!nodoc>
+ pkg-config
+# # https://github.com/seqan/raptor/issues/170#issuecomment-1285818250
+# doxygen <!nodoc>,
+# texlive-font-utils <!nodoc>,
+# texlive-latex-base <!nodoc>,
+# texlive-latex-recommended <!nodoc>,
+# texlive-latex-extra <!nodoc>,
+# texlive-plain-generic <!nodoc>,
+# texlive-fonts-recommended <!nodoc>,
+# ghostscript <!nodoc>
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/seqan-raptor
Vcs-Git: https://salsa.debian.org/med-team/seqan-raptor.git
@@ -38,18 +40,19 @@ Description: pre-filter for querying very large collections of nucleotide sequen
limitations of the new features using simulated and real datasets. Our data
structure can be used to accelerate various core bioinformatics applications.
-Package: seqan-raptor-doc
-Architecture: all
-Depends: ${misc:Depends}
-Description: HTML & PDF documentation for seqan-raptor and its APIs
- Raptor is a system for approximately searching many queries such as
- next-generation sequencing reads or transcripts in large collections of
- nucleotide sequences. Raptor uses winnowing minimizers to define a set of
- representative k-mers, an extension of the interleaved Bloom filters (IBFs) as
- a set membership data structure and probabilistic thresholding for minimizers.
- Our approach allows compression and partitioning of the IBF to enable the
- effective use of secondary memory. We test and show the performance and
- limitations of the new features using simulated and real datasets. Our data
- structure can be used to accelerate various core bioinformatics applications.
- .
- This package contains Raptor's docs (HTML & PDF).
+# https://github.com/seqan/raptor/issues/170#issuecomment-1285818250
+# Package: seqan-raptor-doc
+# Architecture: all
+# Depends: ${misc:Depends}
+# Description: HTML & PDF documentation for seqan-raptor and its APIs
+# Raptor is a system for approximately searching many queries such as
+# next-generation sequencing reads or transcripts in large collections of
+# nucleotide sequences. Raptor uses winnowing minimizers to define a set of
+# representative k-mers, an extension of the interleaved Bloom filters (IBFs) as
+# a set membership data structure and probabilistic thresholding for minimizers.
+# Our approach allows compression and partitioning of the IBF to enable the
+# effective use of secondary memory. We test and show the performance and
+# limitations of the new features using simulated and real datasets. Our data
+# structure can be used to accelerate various core bioinformatics applications.
+# .
+# This package contains Raptor's docs (HTML & PDF).
=====================================
debian/patches/debian_xxhash
=====================================
@@ -3,12 +3,13 @@ Description: Use the packaged version of libxxhash
Forwarded: not-needed
--- seqan-raptor.orig/lib/chopper/CMakeLists.txt
+++ seqan-raptor/lib/chopper/CMakeLists.txt
-@@ -65,7 +65,7 @@
+@@ -65,7 +65,8 @@
list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_VERBOSE_MAKEFILE=${CMAKE_VERBOSE_MAKEFILE}")
# Dependency: xxHash
-set (CHOPPER_XXHASH_PATH "${PROJECT_BINARY_DIR}/lib/libxxhash.a")
-+set (CHOPPER_XXHASH_PATH "/usr/lib/x86_64-linux-gnu/libxxhash.a")
++execute_process(COMMAND pkg-config --variable libdir libxxhash OUTPUT_VARIABLE XXHASH_LIBDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
++set (CHOPPER_XXHASH_PATH "${XXHASH_LIBDIR}/libxxhash.a")
if (EXISTS "${CHOPPER_XXHASH_PATH}")
add_custom_target (xxhash_project)
=====================================
debian/patches/privacy
=====================================
@@ -0,0 +1,16 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Don't automatically check for a new version
+Forwarded: not-needed
+
+As per Debian privacy perserving policy
+--- seqan-raptor.orig/src/raptor.cpp
++++ seqan-raptor/src/raptor.cpp
+@@ -18,7 +18,7 @@
+ sharg::parser top_level_parser{"raptor",
+ argc,
+ argv,
+- sharg::update_notifications::on,
++ sharg::update_notifications::off,
+ {"build", "search", "socks", "upgrade"}};
+ raptor::init_shared_meta(top_level_parser);
+ top_level_parser.info.description.emplace_back(
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+privacy
chopper_no_test
chopper_no_ccache
debian_seqan3
=====================================
debian/rules
=====================================
@@ -21,10 +21,21 @@ export CPPFLAGS=-I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/inclu
%:
dh $@
-override_dh_auto_build-indep:
-ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS) $(DEB_BUILD_PROFILES)))
- cd obj-* && $(MAKE) doc && cd doc/latex && $(MAKE)
-endif
+override_dh_auto_build:
+ dh_auto_build
+ obj-*/bin/raptor --export-help man > debian/raptor.1
+ obj-*/bin/raptor search --export-help man > debian/raptor-search.1
+ obj-*/bin/raptor socks --export-help man > debian/raptor-socks.1
+ obj-*/bin/raptor socks build --export-help man > debian/raptor-socks-build.1
+ obj-*/bin/raptor socks lookup-kmer --export-help man > debian/raptor-socks-lookup-kmer.1
+ obj-*/bin/raptor upgrade --export-help man > debian/raptor-upgrade.1
+
+# # https://github.com/seqan/raptor/issues/170#issuecomment-1285818250
+# # see also d/control
+# override_dh_auto_build-indep:
+# ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS) $(DEB_BUILD_PROFILES)))
+# cd obj-* && $(MAKE) doc && cd doc/latex && $(MAKE)
+# endif
### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
#override_dh_auto_test:
=====================================
debian/seqan-raptor.install deleted
=====================================
@@ -1 +0,0 @@
-usr/bin/*
=====================================
debian/seqan-raptor.manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/c38741a14469bea0b3001b0a9cbafceb075f32ff...b56fd9e0cb6b0ab863e618bbc2b3b465083349a4
--
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/c38741a14469bea0b3001b0a9cbafceb075f32ff...b56fd9e0cb6b0ab863e618bbc2b3b465083349a4
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