[med-svn] [Git][med-team/seqan-raptor][master] 6 commits: salsa-ci: skip i386
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Jul 12 19:34:52 BST 2023
Michael R. Crusoe pushed to branch master at Debian Med / seqan-raptor
Commits:
9c8d932a by Michael R. Crusoe at 2023-07-12T13:49:01+02:00
salsa-ci: skip i386
- - - - -
3ad03072 by Michael R. Crusoe at 2023-07-12T19:25:16+02:00
update patch to use the included copy of chopper
- - - - -
e38ce3cb by Michael R. Crusoe at 2023-07-12T19:34:04+02:00
d/rules: Update list of subcommands for exporting man pages.
- - - - -
03de0ed2 by Michael R. Crusoe at 2023-07-12T19:59:26+02:00
cppreference-doc-en-html fixes
- - - - -
00230cd6 by Michael R. Crusoe at 2023-07-12T20:24:36+02:00
d/patches/doxygen_update: adjust options for older Doxygen 1.9.4
- - - - -
ccbbcdc7 by Michael R. Crusoe at 2023-07-12T20:31:22+02:00
d/not-installed: acknowledge that chopper is not installed
- - - - -
10 changed files:
- debian/changelog
- debian/control
- + debian/not-installed
- + debian/patches/debian_cppreference
- debian/patches/debian_seqan3
- + debian/patches/doxygen_update
- debian/patches/series
- debian/rules
- debian/salsa-ci.yml
- debian/seqan-raptor-doc.docs
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-seqan-raptor (3.0.0+ds-1) unstable; urgency=medium
+seqan-raptor (3.0.0+ds-1) UNRELEASED; urgency=medium
* d/watch: find complete source archives.
* New upstream version
@@ -7,6 +7,12 @@ seqan-raptor (3.0.0+ds-1) unstable; urgency=medium
* d/control: bump minimum Seqan3 build-dep to 3.2.0+ds-7 to grab GCC
12.3+ fix.
* d/patches/fix_missing_lambda_capture.patch: Cherry-pick patch from upstream.
+ * d/rules: Update list of subcommands for exporting man pages.
+ * d/control: build-dep on cppreference-doc-en-html
+ * d/patches/debian_cppreference: use cppreference-doc-en-html to build
+ docs instead of downloading.
+ * d/patches/doxygen_update: adjust options for older Doxygen 1.9.4
+ * d/not-installed: acknowledge that chopper is not installed
-- Michael R. Crusoe <crusoe at debian.org> Tue, 11 Jul 2023 16:24:53 +0200
=====================================
debian/control
=====================================
@@ -12,6 +12,7 @@ Build-Depends: debhelper-compat (= 13),
libsimde-dev,
pkg-config,
doxygen <!nodoc>,
+ cppreference-doc-en-html <!nodoc>,
texlive-font-utils <!nodoc>,
texlive-latex-base <!nodoc>,
texlive-latex-recommended <!nodoc>,
@@ -42,7 +43,7 @@ Architecture: all
Depends: ${misc:Depends}
Section: doc
Multi-Arch: foreign
-Description: HTML & PDF documentation for seqan-raptor and its APIs
+Description: HTML documentation for seqan-raptor and its APIs
Raptor is a system for approximately searching many queries such as
next-generation sequencing reads or transcripts in large collections of
nucleotide sequences. Raptor uses winnowing minimizers to define a set of
@@ -51,4 +52,4 @@ Description: HTML & PDF documentation for seqan-raptor and its APIs
This approach allows compression and partitioning of the IBF to enable the
effective use of secondary memory.
.
- This package contains Raptor's docs (HTML & PDF).
+ This package contains Raptor's docs as HTML.
=====================================
debian/not-installed
=====================================
@@ -0,0 +1,2 @@
+build/seqan-raptor-3.0.0+ds/obj-*/bin/chopper
+usr/lib/*/libchopper_layout_lib.a
=====================================
debian/patches/debian_cppreference
=====================================
@@ -0,0 +1,26 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Use the packaged version of cppreference
+Forwarded: not-needed
+--- seqan-raptor.orig/test/documentation/raptor-doxygen.cmake
++++ seqan-raptor/test/documentation/raptor-doxygen.cmake
+@@ -55,16 +55,11 @@
+ set (RAPTOR_DOXYGEN_STD_TAGFILE "${PROJECT_BINARY_DIR}/cppreference-doxygen-web.tag.xml")
+ include (ExternalProject)
+ ExternalProject_Add (download-cppreference-doxygen-web-tag
+- URL "https://github.com/PeterFeicht/cppreference-doc/releases/download/v20220730/html-book-20220730.tar.xz"
+- URL_HASH SHA256=71f15003c168b8dc5a00cbaf19b6480a9b3e87ab7e462aa39edb63d7511c028b
+- TLS_VERIFY ON
+- DOWNLOAD_DIR "${PROJECT_BINARY_DIR}"
+- DOWNLOAD_NAME "html-book.tar.xz"
+- DOWNLOAD_NO_EXTRACT YES
++ DOWNLOAD_COMMAND ""
+ BINARY_DIR "${PROJECT_BINARY_DIR}"
+- CONFIGURE_COMMAND /bin/sh -c "xzcat html-book.tar.xz | tar -xf - cppreference-doxygen-web.tag.xml"
+- BUILD_COMMAND rm "html-book.tar.xz"
+- INSTALL_COMMAND ""
++ CONFIGURE_COMMAND ""
++ BUILD_COMMAND ""
++ INSTALL_COMMAND ln -s /usr/share/devhelp/books/cppreference-doxygen-web.tag.xml "${PROJECT_BINARY_DIR}/"
+ )
+
+ ### TEST HELPER
=====================================
debian/patches/debian_seqan3
=====================================
@@ -21,9 +21,12 @@ Forwarded: not-needed
# Define cmake configuration flags to configure and build external projects with the same flags as specified for
--- seqan-raptor.orig/src/CMakeLists.txt
+++ seqan-raptor/src/CMakeLists.txt
-@@ -15,7 +15,6 @@
+@@ -13,9 +13,8 @@
+ # Dependency: Chopper
+ include (FetchContent)
- FetchContent_Declare (raptor_chopper_project URL "${RAPTOR_SUBMODULES_DIR}/chopper")
+-FetchContent_Declare (raptor_chopper_project URL "${RAPTOR_SUBMODULES_DIR}/chopper")
++FetchContent_Declare (raptor_chopper_project SOURCE_DIR "${RAPTOR_SUBMODULES_DIR}/chopper")
-set (SEQAN3_SUBMODULES_DIR "${RAPTOR_SUBMODULES_DIR}")
set (CHOPPER_SUBMODULES_DIR
=====================================
debian/patches/doxygen_update
=====================================
@@ -0,0 +1,56 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Adjust doxygen options for older Doxygen 1.9.4
+Forwarded: not-needed
+--- seqan-raptor.orig/test/documentation/raptor_doxygen_cfg.in
++++ seqan-raptor/test/documentation/raptor_doxygen_cfg.in
+@@ -91,7 +91,7 @@
+ HIDE_FRIEND_COMPOUNDS = NO
+ HIDE_IN_BODY_DOCS = NO
+ INTERNAL_DOCS = NO
+-CASE_SENSE_NAMES = SYSTEM
++CASE_SENSE_NAMES = YES
+ HIDE_SCOPE_NAMES = NO
+ HIDE_COMPOUND_REFERENCE= NO
+ SHOW_HEADERFILE = YES
+@@ -126,7 +126,6 @@
+ WARN_IF_DOC_ERROR = YES
+ WARN_IF_INCOMPLETE_DOC = YES
+ WARN_NO_PARAMDOC = NO
+-WARN_IF_UNDOC_ENUM_VAL = NO
+ WARN_AS_ERROR = NO
+ WARN_FORMAT = "$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 =
+@@ -157,7 +155,6 @@
+ FILTER_SOURCE_FILES = NO
+ FILTER_SOURCE_PATTERNS =
+ USE_MDFILE_AS_MAINPAGE =
+-FORTRAN_COMMENT_AFTER = 72
+ #---------------------------------------------------------------------------
+ # Configuration options related to source browsing
+ #---------------------------------------------------------------------------
+@@ -188,7 +185,6 @@
+ ${RAPTOR_DOXYGEN_SOURCE_DIR}/test/documentation/raptor_dark.css
+ ### Extra files that we can link to
+ HTML_EXTRA_FILES =
+-HTML_COLORSTYLE = AUTO_LIGHT
+ HTML_COLORSTYLE_HUE = 220
+ HTML_COLORSTYLE_SAT = 100
+ HTML_COLORSTYLE_GAMMA = 80
+@@ -340,9 +336,6 @@
+ ## DOT SUPPORT
+ HAVE_DOT = ${RAPTOR_DOXYGEN_HAVE_DOT}
+ DOT_NUM_THREADS = ${RAPTOR_DOXYGEN_DOT_NUM_THREADS}
+-DOT_COMMON_ATTR = "fontname=Helvetica,fontsize=10"
+-DOT_EDGE_ATTR = "labelfontname=Helvetica,labelfontsize=10"
+-DOT_NODE_ATTR = "shape=box,height=0.2,width=0.4"
+ DOT_FONTPATH =
+ CLASS_GRAPH = YES
+ COLLABORATION_GRAPH = YES
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,5 @@ privacy
chopper_no_test
debian_seqan3
debian_xxhash
+debian_cppreference
+doxygen_update
=====================================
debian/rules
=====================================
@@ -18,14 +18,13 @@ override_dh_auto_build-arch:
obj-*/bin/raptor --export-help man > debian/raptor.1
obj-*/bin/raptor build --export-help man > debian/raptor-build.1
obj-*/bin/raptor search --export-help man > debian/raptor-search.1
- obj-*/bin/raptor socks --export-help man > debian/raptor-socks.1
- obj-*/bin/raptor socks build --export-help man > debian/raptor-socks-build.1
- obj-*/bin/raptor socks lookup-kmer --export-help man > debian/raptor-socks-lookup-kmer.1
+ obj-*/bin/raptor layout --export-help man > debian/raptor-layout.1
+ obj-*/bin/raptor prepare --export-help man > debian/raptor-prepare.1
obj-*/bin/raptor upgrade --export-help man > debian/raptor-upgrade.1
override_dh_auto_build-indep:
ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS) $(DEB_BUILD_PROFILES)))
- cd obj-* && $(MAKE) doc && cd doc/latex && $(MAKE)
+ mkdir doc_build && cd doc_build && cmake ../test/documentation && $(MAKE) && ctest . --output-on-failure
endif
### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
=====================================
debian/salsa-ci.yml
=====================================
@@ -4,7 +4,8 @@ include:
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
# To exclude single tests you can use
-#variables:
+variables:
+ SALSA_CI_DISABLE_BUILD_PACKAGE_I386: 1
# SALSA_CI_DISABLE_APTLY: 1
# SALSA_CI_DISABLE_AUTOPKGTEST: 1
# SALSA_CI_DISABLE_BLHC: 1
@@ -13,5 +14,3 @@ include:
# SALSA_CI_DISABLE_REPROTEST: 1
# SALSA_CI_DISABLE_BUILD_PACKAGE_ALL: 1
# SALSA_CI_DISABLE_BUILD_PACKAGE_ANY: 1
-# In case for instance i386 is explicitly excluded by Build-Depends
-# SALSA_CI_DISABLE_BUILD_PACKAGE_I386: 1
=====================================
debian/seqan-raptor-doc.docs
=====================================
@@ -1,2 +1 @@
-obj-*/doc/html
-obj-*/doc/latex/refman.pdf
+doc_build/html
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/e941def4cdd680ae8e5d0b6c0f8693d78a7eaf65...ccbbcdc7d867e3f74bf6d1a1117dcb45f1907773
--
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/e941def4cdd680ae8e5d0b6c0f8693d78a7eaf65...ccbbcdc7d867e3f74bf6d1a1117dcb45f1907773
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