[med-svn] [Git][med-team/seqan-raptor][master] 3 commits: Update doxygen patch with upstream's help for better doxygen 1.9.8 compat.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Sep 6 14:08:49 BST 2023
Michael R. Crusoe pushed to branch master at Debian Med / seqan-raptor
Commits:
868ff949 by Michael R. Crusoe at 2023-09-05T13:57:19+02:00
Update doxygen patch with upstream's help for better doxygen 1.9.8 compat.
Closes: #1051156
- - - - -
48fac76e by Michael R. Crusoe at 2023-09-05T13:59:30+02:00
routine-update: Ready to upload to unstable
- - - - -
742a995b by Michael R. Crusoe at 2023-09-06T15:04:49+02:00
d/tests/run-unit-test: also use -DRAPTOR_NATIVE_BUILD=OFF here
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/doxygen_update
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,19 @@
-seqan-raptor (3.0.1+ds-4) UNRELEASED; urgency=medium
+seqan-raptor (3.0.1+ds-5) unstable; urgency=medium
+
+ * d/tests/run-unit-test: also use -DRAPTOR_NATIVE_BUILD=OFF here
+
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 06 Sep 2023 15:04:40 +0200
+
+seqan-raptor (3.0.1+ds-4) unstable; urgency=medium
* d/tests/*: added post-install running of the CLI tests againsted the
installed binary.
* d/rules: better clean up after ourselves.
+ * Update doxygen patch with upstream's help for better doxygen 1.9.8
+ compat. Closes: #1051156
+ * d/control: therefore xelatex is no longer needed to build the docs.
- -- Michael R. Crusoe <crusoe at debian.org> Fri, 25 Aug 2023 13:59:55 +0200
+ -- Michael R. Crusoe <crusoe at debian.org> Tue, 05 Sep 2023 13:59:30 +0200
seqan-raptor (3.0.1+ds-3) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -18,7 +18,6 @@ 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>
=====================================
debian/patches/doxygen_update
=====================================
@@ -1,9 +1,46 @@
-Author: Michael R. Crusoe <crusoe at debian.org>
-Description: Adjust doxygen options for older Doxygen 1.9.4
-Forwarded: not-needed
+From 033d61af4b12a358cade74bf21fc2cdc1957232b Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <enrico.seiler at hotmail.de>
+Date: Mon, 4 Sep 2023 20:00:22 +0200
+Subject: [PATCH] [DOC] Support UTF8 in doxygen latex output
+
+---
+ test/documentation/raptor-latex.sty | 4 +++
+ test/documentation/raptor_doxygen_cfg.in | 37 +++++++++++++++---------
+ 2 files changed, 27 insertions(+), 14 deletions(-)
+ create mode 100644 test/documentation/raptor-latex.sty
+
+--- /dev/null
++++ seqan-raptor/test/documentation/raptor-latex.sty
+@@ -0,0 +1,4 @@
++\NeedsTeXFormat{LaTeX2e}
++\RequirePackage{pmboxdraw}
++\RequirePackage{newunicodechar}
++\newunicodechar{≤}{\ensuremath{\leq}}
--- seqan-raptor.orig/test/documentation/raptor_doxygen_cfg.in
+++ seqan-raptor/test/documentation/raptor_doxygen_cfg.in
-@@ -91,7 +91,7 @@
+@@ -1,4 +1,4 @@
+-# Doxyfile 1.9.6
++# Doxyfile 1.9.8
+
+ #---------------------------------------------------------------------------
+ # Project related configuration options
+@@ -60,6 +60,7 @@
+ EXTENSION_MAPPING = .no_extension=C++
+ MARKDOWN_SUPPORT = YES
+ TOC_INCLUDE_HEADINGS = 2
++MARKDOWN_ID_STYLE = DOXYGEN
+ AUTOLINK_SUPPORT = YES
+ BUILTIN_STL_SUPPORT = NO
+ CPP_CLI_SUPPORT = NO
+@@ -73,6 +74,7 @@
+ TYPEDEF_HIDES_STRUCT = NO
+ LOOKUP_CACHE_SIZE = 0
+ NUM_PROC_THREADS = 1
++TIMESTAMP = NO
+ #---------------------------------------------------------------------------
+ # Build related configuration options
+ #---------------------------------------------------------------------------
+@@ -91,7 +93,7 @@
HIDE_FRIEND_COMPOUNDS = NO
HIDE_IN_BODY_DOCS = NO
INTERNAL_DOCS = NO
@@ -12,45 +49,26 @@ Forwarded: not-needed
HIDE_SCOPE_NAMES = NO
HIDE_COMPOUND_REFERENCE= NO
SHOW_HEADERFILE = YES
-@@ -126,7 +126,6 @@
- WARN_IF_DOC_ERROR = YES
- WARN_IF_INCOMPLETE_DOC = YES
- WARN_NO_PARAMDOC = NO
--WARN_IF_UNDOC_ENUM_VAL = NO
- WARN_AS_ERROR = NO
- WARN_FORMAT = "$file:$line: $text"
- WARN_LINE_FORMAT = "at line $line of file $file"
-@@ -140,7 +139,6 @@
- ${RAPTOR_DOXYGEN_SOURCE_DIR}/LICENSE.md \
- ${RAPTOR_DOXYGEN_SOURCE_DIR}/CHANGELOG.md
- INPUT_ENCODING = UTF-8
--INPUT_FILE_ENCODING =
- FILE_PATTERNS = *
- RECURSIVE = YES
- EXCLUDE =
-@@ -158,7 +156,6 @@
- FILTER_SOURCE_FILES = NO
- FILTER_SOURCE_PATTERNS =
- USE_MDFILE_AS_MAINPAGE =
--FORTRAN_COMMENT_AFTER = 72
- #---------------------------------------------------------------------------
- # Configuration options related to source browsing
- #---------------------------------------------------------------------------
-@@ -189,7 +186,6 @@
- ${RAPTOR_DOXYGEN_SOURCE_DIR}/test/documentation/raptor_dark.css
- ### Extra files that we can link to
- HTML_EXTRA_FILES =
--HTML_COLORSTYLE = AUTO_LIGHT
+@@ -193,9 +195,9 @@
HTML_COLORSTYLE_HUE = 220
HTML_COLORSTYLE_SAT = 100
HTML_COLORSTYLE_GAMMA = 80
-@@ -249,19 +245,19 @@
- ## MISC OPTIONS
- GENERATE_LATEX = YES
- LATEX_OUTPUT = latex
--LATEX_CMD_NAME =
-+LATEX_CMD_NAME = xelatex
- MAKEINDEX_CMD_NAME = makeindex
+-HTML_TIMESTAMP = YES
+ HTML_DYNAMIC_MENUS = YES
+ HTML_DYNAMIC_SECTIONS = YES
++HTML_CODE_FOLDING = YES
+ HTML_INDEX_NUM_ENTRIES = 100
+ GENERATE_DOCSET = NO
+ DOCSET_FEEDNAME = "Doxygen generated docs"
+@@ -210,6 +212,7 @@
+ CHM_INDEX_ENCODING =
+ BINARY_TOC = NO
+ TOC_EXPAND = NO
++SITEMAP_URL =
+ GENERATE_QHP = NO
+ QCH_FILE =
+ QHP_NAMESPACE = org.doxygen.Project
+@@ -254,17 +257,16 @@
LATEX_MAKEINDEX_CMD = makeindex
COMPACT_LATEX = NO
PAPER_TYPE = a4
@@ -58,7 +76,8 @@ Forwarded: not-needed
+EXTRA_PACKAGES = {lstfiracode}
LATEX_HEADER =
LATEX_FOOTER =
- LATEX_EXTRA_STYLESHEET =
+-LATEX_EXTRA_STYLESHEET =
++LATEX_EXTRA_STYLESHEET = ${RAPTOR_DOXYGEN_SOURCE_DIR}/test/documentation/raptor-latex.sty
LATEX_EXTRA_FILES =
PDF_HYPERLINKS = YES
USE_PDFLATEX = YES
@@ -66,14 +85,59 @@ Forwarded: not-needed
+LATEX_BATCHMODE = YES
LATEX_HIDE_INDICES = NO
LATEX_BIB_STYLE = plain
- LATEX_TIMESTAMP = NO
-@@ -341,9 +337,6 @@
+-LATEX_TIMESTAMP = NO
+ LATEX_EMOJI_DIRECTORY =
+ #---------------------------------------------------------------------------
+ # Configuration options related to the RTF output
+@@ -300,6 +302,12 @@
+ #---------------------------------------------------------------------------
+ GENERATE_AUTOGEN_DEF = NO
+ #---------------------------------------------------------------------------
++# Configuration options related to Sqlite3 output
++#---------------------------------------------------------------------------
++GENERATE_SQLITE3 = NO
++SQLITE3_OUTPUT = sqlite3
++SQLITE3_RECREATE_DB = YES
++#---------------------------------------------------------------------------
+ # Configuration options related to the Perl module output
+ #---------------------------------------------------------------------------
+ GENERATE_PERLMOD = NO
+@@ -334,16 +342,15 @@
+ EXTERNAL_GROUPS = YES
+ EXTERNAL_PAGES = YES
+ #---------------------------------------------------------------------------
+-# Configuration options related to the dot tool
++# Configuration options related to diagram generator tools
+ #---------------------------------------------------------------------------
+-DIA_PATH =
+ HIDE_UNDOC_RELATIONS = YES
## DOT SUPPORT
HAVE_DOT = ${RAPTOR_DOXYGEN_HAVE_DOT}
DOT_NUM_THREADS = ${RAPTOR_DOXYGEN_DOT_NUM_THREADS}
-DOT_COMMON_ATTR = "fontname=Helvetica,fontsize=10"
-DOT_EDGE_ATTR = "labelfontname=Helvetica,labelfontsize=10"
-DOT_NODE_ATTR = "shape=box,height=0.2,width=0.4"
++DOT_COMMON_ATTR =
++DOT_EDGE_ATTR =
++DOT_NODE_ATTR =
DOT_FONTPATH =
CLASS_GRAPH = YES
COLLABORATION_GRAPH = YES
+@@ -364,7 +371,7 @@
+ INTERACTIVE_SVG = ${RAPTOR_DOXYGEN_HAVE_DOT}
+ DOT_PATH =
+ DOTFILE_DIRS =
+-MSCFILE_DIRS =
++DIA_PATH =
+ DIAFILE_DIRS =
+ PLANTUML_JAR_PATH =
+ PLANTUML_CFG_FILE =
+@@ -374,6 +381,8 @@
+ DOT_MULTI_TARGETS = NO
+ GENERATE_LEGEND = YES
+ DOT_CLEANUP = YES
++MSCGEN_TOOL =
++MSCFILE_DIRS =
+ #---------------------------------------------------------------------------
+ # Configuration options related to the deployment by Vercel
+ #---------------------------------------------------------------------------
=====================================
debian/tests/run-unit-test
=====================================
@@ -16,7 +16,7 @@ export CXXFLAGS="-I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/incl
cd "${AUTOPKGTEST_TMP}"
patch -p1 < debian/tests/use_installed_binaries.patch
cd "${AUTOPKGTEST_TMP}"/test/unit
-cmake -DRAPTOR_SUBMODULES_DIR=${PWD}/../../lib .
+cmake -DRAPTOR_SUBMODULES_DIR=${PWD}/../../lib -DRAPTOR_NATIVE_BUILD=OFF .
make
find . -name raptor -delete
ctest .
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/0e68cccb5f6a8b30553165c4c42aa110acb519ee...742a995b834bc014a5fb52490f960e85dabc2c3f
--
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/0e68cccb5f6a8b30553165c4c42aa110acb519ee...742a995b834bc014a5fb52490f960e85dabc2c3f
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230906/c87b95db/attachment-0001.htm>
More information about the debian-med-commit
mailing list