[med-svn] [Git][med-team/seqan2][master] 7 commits: Retry mips*; patch adapted from Adrian Bunk <bunk at debian.org>
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Feb 17 15:12:14 UTC 2018
Michael R. Crusoe pushed to branch master at Debian Med / seqan2
Commits:
0b161e58 by Michael R. Crusoe at 2018-02-16T04:27:47-08:00
Retry mips*; patch adapted from Adrian Bunk <bunk at debian.org>
- - - - -
3441043b by Michael R. Crusoe at 2018-02-16T04:32:57-08:00
Document CWL generation. Mark all CWL files as executable
- - - - -
777353ec by Michael R. Crusoe at 2018-02-16T05:08:12-08:00
add AutoPackageTests for seqan-apps
- - - - -
a4b568f0 by Michael R. Crusoe at 2018-02-16T05:12:20-08:00
patch from upstream: add mandatory ctdVersion element.
- - - - -
a6dab878 by Michael R. Crusoe at 2018-02-16T05:19:10-08:00
Suggest cwltool | cwl-runner
- - - - -
faf937c1 by Michael R. Crusoe at 2018-02-16T05:35:43-08:00
Fix errors in manpage output
- - - - -
553e776b by Michael R. Crusoe at 2018-02-17T07:10:14-08:00
release 2.4.0+dfsg-6
- - - - -
10 changed files:
- + debian/README.source
- debian/changelog
- debian/control
- + debian/patches/ctdVersion.patch
- + debian/patches/fix_manpage_formatting.patch
- + debian/patches/install_fiona_illumina
- debian/patches/series
- debian/rules
- + debian/tests/control
- + debian/tests/run-tests
Changes:
=====================================
debian/README.source
=====================================
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,4 @@
+The cwl/ directory was generated thusly:
+
+All binaries were called with --write-ctd and those CTDs were converted to CWL
+using https://github.com/WorkflowConversion/CTDConverter
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,16 @@
+seqan2 (2.4.0+dfsg-6) unstable; urgency=medium
+
+ * Retry building on mips*; patch adapted from Adrian Bunk <bunk at debian.org>
+ Closes: #890385. Thanks!
+ * Document CWL generation via README.source. Mark all CWL files as
+ executable
+ * Enable AutoPackageTests for seqan-apps
+ * Applied 2 patches from upstream: add mandatory ctdVersion element,
+ fix errors in manpage output
+ * Suggest cwltool | cwl-runner.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 17 Feb 2018 07:09:41 -0800
+
seqan2 (2.4.0+dfsg-5) unstable; urgency=medium
* Ship CWL descriptions for a subset of seqan-apps
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -27,10 +27,10 @@ Homepage: http://www.seqan.de/
Rules-Requires-Root: no
Package: seqan-apps
-Architecture: any-amd64 arm64 armel armhf any-i386 mips64el ppc64el s390x alpha hppa ia64 m68k powerpc powerpcspe ppc64 sh4 sparc64 x32
-# Skipping mips & mipsel due to lack of memory
+Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
+Suggests: cwltool | cwl-runner
Description: C++ library for the analysis of biological sequences
SeqAn is a C++ template library of efficient algorithms and data
structures for the analysis of sequences with the focus on
=====================================
debian/patches/ctdVersion.patch
=====================================
--- /dev/null
+++ b/debian/patches/ctdVersion.patch
@@ -0,0 +1,34 @@
+From 59dd3a7450a57a8cf9f4d298df664348a9ef1af8 Mon Sep 17 00:00:00 2001
+From: smehringer <svenja.mehringer at fu-berlin.de>
+Date: Mon, 12 Feb 2018 16:46:04 +0000
+Subject: [PATCH] [INTERNAL] Fix ctd output: add ctdVersion tag in header.
+
+---
+ include/seqan/arg_parse/arg_parse_ctd_support.h | 2 +-
+ tests/arg_parse/test_app.ctd | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/include/seqan/arg_parse/arg_parse_ctd_support.h b/include/seqan/arg_parse/arg_parse_ctd_support.h
+index 9125fd78b..a2164604f 100644
+--- a/include/seqan/arg_parse/arg_parse_ctd_support.h
++++ b/include/seqan/arg_parse/arg_parse_ctd_support.h
+@@ -377,7 +377,7 @@ writeCTD(ArgumentParser const & me, std::ostream & ctdfile)
+ }
+
+ ctdfile << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
+- ctdfile << "<tool name=\"" << class_name << "\" version=\"" << xmlEscape(getVersion(me)) << "\" docurl=\"http://www.seqan.de\" category=\"" << xmlEscape(getCategory(me)) << "\" >\n";
++ ctdfile << "<tool name=\"" << class_name << "\" version=\"" << xmlEscape(getVersion(me)) << "\" docurl=\"http://www.seqan.de\" category=\"" << xmlEscape(getCategory(me)) << "\" ctdVersion=\"1.7\">\n";
+ ctdfile << _indent(currentIndent) << "<executableName>" << toolname << "</executableName>\n";
+ ctdfile << _indent(currentIndent) << "<description>" << xmlEscape(getShortDescription(me)) << "</description>\n";
+ ctdfile << _indent(currentIndent) << "<manual>" << xmlEscape(_getManual(me)) << "</manual>\n"; // TODO(aiche): as soon as we have a more sophisticated documentation embedded into the CmdParser, we should at this here
+diff --git a/tests/arg_parse/test_app.ctd b/tests/arg_parse/test_app.ctd
+index f4346e23e..55313b0e7 100644
+--- a/tests/arg_parse/test_app.ctd
++++ b/tests/arg_parse/test_app.ctd
+@@ -1,5 +1,5 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+-<tool name="TestApp" version="0.1.0" docurl="http://www.seqan.de" category="SeqAn/Testing" >
++<tool name="TestApp" version="0.1.0" docurl="http://www.seqan.de" category="SeqAn/Testing" ctdVersion="1.7">
+ <executableName>test_app</executableName>
+ <description>This is a test-app.</description>
+ <manual>This is the first line of our test description.
=====================================
debian/patches/fix_manpage_formatting.patch
=====================================
--- /dev/null
+++ b/debian/patches/fix_manpage_formatting.patch
@@ -0,0 +1,60 @@
+From 8c7c3ef5a20529366322297bbdb4b53868cb62e4 Mon Sep 17 00:00:00 2001
+From: smehringer <svenja.mehringer at fu-berlin.de>
+Date: Mon, 12 Feb 2018 16:22:54 +0000
+Subject: [PATCH] [INTERNAL] Fixes man page output: Escape special characters
+ '.' or ''' at the beginning of a line.
+
+---
+ include/seqan/arg_parse/tool_doc.h | 25 +++++++++++++++++++++----
+ 1 file changed, 21 insertions(+), 4 deletions(-)
+
+diff --git a/include/seqan/arg_parse/tool_doc.h b/include/seqan/arg_parse/tool_doc.h
+index 78f7db717..c31460287 100644
+--- a/include/seqan/arg_parse/tool_doc.h
++++ b/include/seqan/arg_parse/tool_doc.h
+@@ -1531,6 +1531,20 @@ void TextToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
+ }
+ }
+
++// --------------------------------------------------------------------------
++// Function ManToolDocPrinter_::print()
++// --------------------------------------------------------------------------
++
++//brief: "." or "'" indicate man page macros that need to be escaped with "\\&"
++template <typename TString>
++void print_first_in_line(std::ostream & stream, TString const & str)
++{
++ if (length(str) > 0 &&
++ (str[0] == '.' || str[0] == '\''))
++ stream << "\\&";
++ stream << str;
++}
++
+ inline
+ void ManToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
+ {
+@@ -1580,7 +1594,8 @@ void ManToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
+ stream << ".sp\n";
+ else if (!isFirstInSection && !line->isParagraph())
+ stream << ".br\n";
+- stream << line->_text << "\n";
++ print_first_in_line(stream, line->_text);
++ stream << "\n";
+ isFirstInSection = false;
+ }
+ break;
+@@ -1588,9 +1603,11 @@ void ManToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
+ case ToolDocEntry_::LIST_ITEM:
+ {
+ ToolDocListItem_ const * item = static_cast<ToolDocListItem_ const *>(entry);
+- stream << ".TP\n"
+- << item->_term << "\n"
+- << item->_description << "\n";
++ stream << ".TP\n";
++ print_first_in_line(stream, item->_term);
++ stream << "\n";
++ print_first_in_line(stream, item->_description);
++ stream << "\n";
+ isFirstInSection = false;
+ }
+ break;
=====================================
debian/patches/install_fiona_illumina
=====================================
--- /dev/null
+++ b/debian/patches/install_fiona_illumina
@@ -0,0 +1,13 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: Install the Illumina version of Fiona as well
+--- seqan2.orig/apps/fiona/CMakeLists.txt
++++ seqan2/apps/fiona/CMakeLists.txt
+@@ -83,7 +83,7 @@
+ endif (NOT SEQAN_PREFIX_SHARE_DOC)
+
+ # Install fiona in ${PREFIX}/bin directory
+-install (TARGETS fiona compute_gain DESTINATION ${CMAKE_INSTALL_BINDIR})
++install (TARGETS fiona fiona_illumina compute_gain DESTINATION ${CMAKE_INSTALL_BINDIR})
+
+ # Install non-binary files for the package to "." for app builds and
+ # ${PREFIX}/share/doc/fiona for SeqAn release builds.
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,6 @@ skip-seqan-revision
fix-version_check-test
skip-some-apps-on-some-archs
tweak_readmes
+install_fiona_illumina
+ctdVersion.patch
+fix_manpage_formatting.patch
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -16,19 +16,16 @@ DEB_HOST_ARCH ?= $(shell dpkg-architecture -qDEB_HOST_ARCH)
DEB_BUILD_ARCH ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH)
-ifneq (,$(filter sparc64,$(DEB_HOST_ARCH)))
- DEB_CXXFLAGS_MAINT_APPEND+=-D__arch64__=1 -DSEQAN_BIG_ENDIAN=1
-endif
-
ifneq (,$(filter mips mipsel mips64el,$(DEB_BUILD_ARCH)))
- DEB_CXXFLAGS_MAINT_APPEND+=-mxgot -O2
- export DEB_CFLAGS_MAINT_APPEND+=-O2
-else
- DEB_CXXFLAGS_MAINT_APPEND+=-O3
- export DEB_CFLAGS_MAINT_APPEND+=-O3
+ DEB_CXXFLAGS_MAINT_APPEND+=-mxgot
+endif
+ifneq (,$(filter mips mipsel,$(DEB_BUILD_ARCH)))
+ DEB_CXXFLAGS_MAINT_APPEND+=-g1
+ DEB_CFLAGS_MAINT_APPEND+=-g1
endif
# As per upstream's instructions
-DEB_CXXFLAGS_MAINT_APPEND+=-DNDEBUG
+export DEB_CFLAGS_MAINT_APPEND+=-O3
+export DEB_CXXFLAGS_MAINT_APPEND+=-DNDEBUG -O3
MAX_PARALLEL=""
# Disable or limit parallel building on some build archs to save memory
@@ -38,13 +35,6 @@ else ifneq (,$(filter amd64,$(DEB_BUILD_ARCH)))
MAX_PARALLEL=--max-parallel=2
endif
-# ifneq (,$(filter mips64el ppc64el s390x alpha hppa powerpc ppc64 sparc64,$(DEB_HOST_ARCH)))
-# # Disable async io on certain target archs, as per upstream
-# # https://github.com/seqan/seqan/issues/1861#issuecomment-336484553
-# DEB_CXXFLAGS_MAINT_APPEND+=-DSEQAN_ASYNC_IO=0
-# endif
-
-export DEB_CXXFLAGS_MAINT_APPEND
pkgapps=seqan-apps
pkgdev=libseqan2-dev
@@ -85,6 +75,8 @@ override_dh_install:
fi
find $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin -type f \
-name "*.sh" | xargs chmod a+x
+ find $(CURDIR)/debian/$(pkgapps)/usr/share/commonwl -type f \
+ -name "*.cwl" | xargs chmod a+x
override_dh_auto_clean:
dh_auto_clean
=====================================
debian/tests/control
=====================================
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-tests
+Depends: seqan-apps
+Restrictions: allow-stderr
=====================================
debian/tests/run-tests
=====================================
--- /dev/null
+++ b/debian/tests/run-tests
@@ -0,0 +1,9 @@
+#!/bin/sh -e
+
+mkdir build
+cd build
+cmake ../
+rmdir bin
+ln -s /usr/lib/seqan/bin bin
+ctest --tests-regex 'app_.*' --parallel $(nproc)
+
View it on GitLab: https://salsa.debian.org/med-team/seqan2/compare/7a2518abf88971ff57f583c8a2ce2c4a79b0b229...553e776b97c0429536036b684694064c4597b3c3
---
View it on GitLab: https://salsa.debian.org/med-team/seqan2/compare/7a2518abf88971ff57f583c8a2ce2c4a79b0b229...553e776b97c0429536036b684694064c4597b3c3
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