Andreas Tille pushed to branch master at Debian Med / salmon
Commits: fd2cee9e by Andreas Tille at 2021-10-11T09:36:19+02:00 Use sphinx theme that is packaged for Debian - - - - - 557b0c20 by Andreas Tille at 2021-10-11T09:37:40+02:00 I do not see any reason to remove license.rst from doc/source - - - - - e6d1717a by Andreas Tille at 2021-10-11T09:38:34+02:00 Cleanup changelog - - - - - bf67a606 by Andreas Tille at 2021-10-11T09:47:15+02:00 Upload to unstable - - - - - 7 changed files: - debian/changelog - debian/control - debian/copyright - debian/patches/disable-version-check.patch - debian/patches/series - + debian/patches/sphinx.patch - debian/patches/use_debian_packaged_libs.patch Changes: ===================================== debian/changelog ===================================== @@ -1,26 +1,16 @@ -salmon (1.5.2+ds1-1) UNRELEASED; urgency=medium +salmon (1.5.2+ds1-1) unstable; urgency=medium + [ Steffen Moeller ] * Team upload. + * Fix watchfile to detect new versions on github (routine-update) * New upstream version * Standards-Version: 4.6.0 (routine-update) * d/u/metadata: Added ref to SciCrunch (SCR_017036) - * source: Added deleted-during-build doc/source/license.rst - to files-excluded - * TODO - - missing indep-buildep https://github.com/pradyunsg/furo - ./doc/requirements.txt:furo - ./doc/source/conf.py:html_theme = 'furo' - Theme error: - no theme named 'furo' found (missing theme.conf?) - - -- Steffen Moeller <[email protected]> Fri, 03 Sep 2021 15:35:41 +0200 - -salmon (1.4.0+ds1-1.1) UNRELEASED; urgency=medium - * Non-maintainer upload. - * Fix watchfile to detect new versions on github (routine-update) + [ Andreas Tille ] + * Build-Depends: python3-docs-theme and use this instead of furo - -- Steffen Moeller <[email protected]> Fri, 03 Sep 2021 15:34:51 +0200 + -- Andreas Tille <[email protected]> Mon, 11 Oct 2021 09:38:42 +0200 salmon (1.4.0+ds1-1) unstable; urgency=medium ===================================== debian/control ===================================== @@ -29,6 +29,7 @@ Build-Depends: debhelper-compat (= 13), sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, + python3-docs-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, ===================================== debian/copyright ===================================== @@ -6,7 +6,6 @@ Files-Excluded: include/eigen3 src/posix.cc cmake/Modules/FindTBB.cmake scripts/cpld.bash - doc/source/license.rst Files: * Copyright: © 2015 The Salmon Authors ===================================== debian/patches/disable-version-check.patch ===================================== @@ -1,9 +1,9 @@ Author: Michael R. Crusoe <[email protected]> Description: Disable the newer version check Forwarded: not-needed ---- salmon.orig/src/Salmon.cpp -+++ salmon/src/Salmon.cpp -@@ -214,13 +214,6 @@ +--- a/src/Salmon.cpp ++++ b/src/Salmon.cpp +@@ -215,13 +215,6 @@ int main(int argc, char* argv[]) { std::transform(no_version_env.begin(), no_version_env.end(), no_version_env.begin(), [](unsigned char c){ return std::toupper(c); } // correct ); ===================================== debian/patches/series ===================================== @@ -5,3 +5,4 @@ disable-version-check.patch # use-system-pkg-config-tbb.patch # 0008-Remove-salmon_core-lib.patch # add_MEM_F_SELF_OVLP.patch +sphinx.patch ===================================== debian/patches/sphinx.patch ===================================== @@ -0,0 +1,23 @@ +Author: Andreas Tille +Last-Update: Mon, 11 Oct 2021 09:34:54 +0200 +Description: Use sphinx theme that is packaged for Debian + +--- a/doc/source/conf.py ++++ b/doc/source/conf.py +@@ -32,6 +32,7 @@ extensions = [ + 'sphinx.ext.autodoc', + 'sphinx.ext.todo', + 'sphinx.ext.ifconfig', ++ 'python_docs_theme' + ] + + # Add any paths that contain templates here, relative to this directory.. +@@ -107,7 +108,7 @@ pygments_style = 'sphinx' + #html_theme = "sphinx_rtd_theme" + #html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] + +-html_theme = 'furo' ++html_theme = 'python_docs_theme' + html_logo = '../logo.png' + + #html_theme = 'classic' ===================================== debian/patches/use_debian_packaged_libs.patch ===================================== @@ -2,8 +2,8 @@ Author: Andreas Tille <[email protected]> Last-Update: Tue, 11 Dec 2018 19:29:39 +0100 Description: Use Debian packaged libraries and make sure these are linked dynamically Forwarded: not-needed ---- salmon.orig/src/CMakeLists.txt -+++ salmon/src/CMakeLists.txt +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt @@ -1,6 +1,6 @@ include_directories( ${GAT_SOURCE_DIR}/include @@ -12,7 +12,7 @@ Forwarded: not-needed ${GAT_SOURCE_DIR}/external ${GAT_SOURCE_DIR}/external/cereal/include ${GAT_SOURCE_DIR}/external/install/include -@@ -209,15 +209,15 @@ +@@ -212,15 +212,15 @@ target_link_libraries(salmon graphdump ntcard gff @@ -31,7 +31,7 @@ Forwarded: not-needed ${BZIP2_LIBRARIES} ${LIBSALMON_LINKER_FLAGS} ${NON_APPLECLANG_LIBS} -@@ -225,8 +225,8 @@ +@@ -228,8 +228,8 @@ target_link_libraries(salmon ## PUFF_INTEGRATION alevin_core ${ASAN_LIB} @@ -42,7 +42,7 @@ Forwarded: not-needed ${LIBRT} ${CMAKE_DL_LIBS} #ubsan -@@ -240,14 +240,14 @@ +@@ -243,14 +243,14 @@ target_link_libraries(unitTests salmon_core gff ${STADEN_LIBRARIES} View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/d009c20a5b2d33d680ba03c60c4262228311b5e1...bf67a606acd3cf2440116d1959a85805f5160060 -- View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/d009c20a5b2d33d680ba03c60c4262228311b5e1...bf67a606acd3cf2440116d1959a85805f5160060 You're receiving this email because of your account on salsa.debian.org.
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