[med-svn] [Git][med-team/seqan-raptor][master] 3 commits: build PDF again
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Thu Jul 13 13:36:19 BST 2023
Michael R. Crusoe pushed to branch master at Debian Med / seqan-raptor
Commits:
47764f0e by Michael R. Crusoe at 2023-07-13T14:35:53+02:00
build PDF again
- - - - -
253fe63b by Michael R. Crusoe at 2023-07-13T14:35:54+02:00
Fix auto_install for the docs package.
- - - - -
ef65ce16 by Michael R. Crusoe at 2023-07-13T14:35:54+02:00
remove unused path from the copyright
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/debian_cppreference
- debian/patches/doxygen_update
- debian/rules
- debian/seqan-raptor-doc.docs
Changes:
=====================================
debian/changelog
=====================================
@@ -14,6 +14,7 @@ seqan-raptor (3.0.0+ds-1) UNRELEASED; urgency=medium
* d/patches/doxygen_update: adjust options for older Doxygen 1.9.4
* d/not-installed: acknowledge that chopper is not installed
* d/rules: only list missing files; don't error
+ * Fix auto_install for the docs package.
-- Michael R. Crusoe <crusoe at debian.org> Tue, 11 Jul 2023 16:24:53 +0200
=====================================
debian/control
=====================================
@@ -17,6 +17,7 @@ Build-Depends: debhelper-compat (= 13),
texlive-latex-base <!nodoc>,
texlive-latex-recommended <!nodoc>,
texlive-latex-extra <!nodoc>,
+ texlive-xetex <!nodoc>,
texlive-plain-generic <!nodoc>,
texlive-fonts-recommended <!nodoc>,
ghostscript <!nodoc>
@@ -43,7 +44,7 @@ Architecture: all
Depends: ${misc:Depends}
Section: doc
Multi-Arch: foreign
-Description: HTML documentation for seqan-raptor and its APIs
+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
@@ -52,4 +53,4 @@ Description: HTML documentation for seqan-raptor and its APIs
This approach allows compression and partitioning of the IBF to enable the
effective use of secondary memory.
.
- This package contains Raptor's docs as HTML.
+ This package contains Raptor's docs (HTML & PDF).
=====================================
debian/copyright
=====================================
@@ -27,8 +27,7 @@ Files: lib/submodules/lemon/include/lemon/random.h
Copyright: 1997 - 2002, Makoto Matsumoto and Takuji Nishimura
License: BSD-3-clause
-Files: lib/chopper/lib/robin-hood-hashing/*
- lib/robin-hood-hashing/*
+Files: lib/robin-hood-hashing/*
Copyright: 2018-2021, Martin Ankerl <martin.ankerl at gmail.com> <http://martin.ankerl.com>
2016-2021, Viktor Kirilov
License: Expat
=====================================
debian/patches/debian_cppreference
=====================================
@@ -24,3 +24,14 @@ Forwarded: not-needed
)
### TEST HELPER
+--- seqan-raptor.orig/test/documentation/raptor_doxygen_cfg.in
++++ seqan-raptor/test/documentation/raptor_doxygen_cfg.in
+@@ -246,7 +246,7 @@
+ # Configuration options related to the LaTeX output
+ #---------------------------------------------------------------------------
+ ## MISC OPTIONS
+-GENERATE_LATEX = NO
++GENERATE_LATEX = YES
+ LATEX_OUTPUT = latex
+ LATEX_CMD_NAME =
+ MAKEINDEX_CMD_NAME = makeindex
=====================================
debian/patches/doxygen_update
=====================================
@@ -44,6 +44,29 @@ Forwarded: not-needed
HTML_COLORSTYLE_HUE = 220
HTML_COLORSTYLE_SAT = 100
HTML_COLORSTYLE_GAMMA = 80
+@@ -248,19 +244,19 @@
+ ## MISC OPTIONS
+ GENERATE_LATEX = YES
+ LATEX_OUTPUT = latex
+-LATEX_CMD_NAME =
++LATEX_CMD_NAME = xelatex
+ MAKEINDEX_CMD_NAME = makeindex
+ LATEX_MAKEINDEX_CMD = makeindex
+ COMPACT_LATEX = NO
+ PAPER_TYPE = a4
+-EXTRA_PACKAGES = {amsfonts}
++EXTRA_PACKAGES = {lstfiracode}
+ LATEX_HEADER =
+ LATEX_FOOTER =
+ LATEX_EXTRA_STYLESHEET =
+ LATEX_EXTRA_FILES =
+ PDF_HYPERLINKS = YES
+ USE_PDFLATEX = YES
+-LATEX_BATCHMODE = NO
++LATEX_BATCHMODE = YES
+ LATEX_HIDE_INDICES = NO
+ LATEX_BIB_STYLE = plain
+ LATEX_TIMESTAMP = NO
@@ -340,9 +336,6 @@
## DOT SUPPORT
HAVE_DOT = ${RAPTOR_DOXYGEN_HAVE_DOT}
=====================================
debian/rules
=====================================
@@ -10,7 +10,7 @@ include /usr/share/dpkg/buildflags.mk
%:
dh $@
-override_dh_auto_configure:
+override_dh_auto_configure-arch:
dh_auto_configure -- -DRAPTOR_NATIVE_BUILD=OFF -DRAPTOR_SUBMODULES_DIR=$(CURDIR)/lib
override_dh_auto_build-arch:
@@ -24,7 +24,12 @@ override_dh_auto_build-arch:
override_dh_auto_build-indep:
ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS) $(DEB_BUILD_PROFILES)))
- mkdir doc_build && cd doc_build && cmake ../test/documentation && $(MAKE) && ctest . --output-on-failure
+ mkdir doc_build && cd doc_build && cmake ../test/documentation && $(MAKE) && ctest . --output-on-failure && cd latex && $(MAKE)
+endif
+
+override_dh_auto_install-indep:
+ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS) $(DEB_BUILD_PROFILES)))
+ dh_auto_install --indep --builddir doc_build
endif
override_dh_missing:
=====================================
debian/seqan-raptor-doc.docs
=====================================
@@ -1 +1,2 @@
doc_build/html
+doc_build/latex/refman.pdf
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/c66eaa9a61b6d7dc8ac35e012c220153616cd42e...ef65ce16ef5eedc505ca42759df4799b8a141df8
--
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/c66eaa9a61b6d7dc8ac35e012c220153616cd42e...ef65ce16ef5eedc505ca42759df4799b8a141df8
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