Andreas Tille pushed to branch master at Debian Med / jellyfish
Commits: 2d410647 by Andreas Tille at 2018-09-21T06:45:39Z Drop python3-dna-jellyfish package since the Python module had issues in build process - - - - - 6e084088 by Andreas Tille at 2018-09-21T06:58:28Z Upload to unstable - - - - - 4 changed files: - + debian/NEWS.Debian - debian/changelog - debian/control - debian/rules Changes: ===================================== debian/NEWS.Debian ===================================== @@ -0,0 +1,12 @@ +jellyfish (2.2.10-1) unstable; urgency=medium + + The the binary package python3-dna-jellyfish containing the Python module + was dropped due to issues in the build process which is documented in this + mail to the developers list + + https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-September/065549.html + + I'd happily re-introduce the Python module if anybody will provide a + patch for a successful build. + + -- Andreas Tille <[email protected]> Mon, 03 Sep 2018 11:57:00 +0200 ===================================== debian/changelog ===================================== @@ -1,4 +1,4 @@ -jellyfish (2.2.10-1) UNRELEASED; urgency=medium +jellyfish (2.2.10-1) unstable; urgency=medium * New upstream version * Point Vcs fields to salsa.debian.org @@ -8,8 +8,10 @@ jellyfish (2.2.10-1) UNRELEASED; urgency=medium * Catch exceptions by reference * Do not replace random '-L' strings in command line Closes: #907819 + * Drop python3-dna-jellyfish package since the Python module had issues in + build process and nobody seemed to be interested to help solving theses - -- Andreas Tille <[email protected]> Mon, 03 Sep 2018 08:34:22 +0200 + -- Andreas Tille <[email protected]> Fri, 21 Sep 2018 08:45:53 +0200 jellyfish (2.2.8-3) unstable; urgency=medium ===================================== debian/control ===================================== @@ -92,28 +92,28 @@ Description: count k-mers in DNA sequences (development files of jellyfish) This package contains the development files (static library and header files) -Package: python3-dna-jellyfish -Architecture: any -Section: python -Depends: ${python3:Depends}, - ${misc:Depends}, - ${shlibs:Depends} -Description: count k-mers in DNA sequences (Python bindings of jellyfish) - JELLYFISH is a tool for fast, memory-efficient counting of k-mers in - DNA. A k-mer is a substring of length k, and counting the occurrences - of all such substrings is a central step in many analyses of DNA - sequence. JELLYFISH can count k-mers using an order of magnitude less - memory and an order of magnitude faster than other k-mer counting - packages by using an efficient encoding of a hash table and by - exploiting the "compare-and-swap" CPU instruction to increase - parallelism. - . - JELLYFISH is a command-line program that reads FASTA and multi-FASTA - files containing DNA sequences. It outputs its k-mer counts in an - binary format, which can be translated into a human-readable text - format using the "jellyfish dump" command. - . - This package contains the Python bindings of jellyfish. +#Package: python3-dna-jellyfish +#Architecture: any +#Section: python +#Depends: ${python3:Depends}, +# ${misc:Depends}, +# ${shlibs:Depends} +#Description: count k-mers in DNA sequences (Python bindings of jellyfish) +# JELLYFISH is a tool for fast, memory-efficient counting of k-mers in +# DNA. A k-mer is a substring of length k, and counting the occurrences +# of all such substrings is a central step in many analyses of DNA +# sequence. JELLYFISH can count k-mers using an order of magnitude less +# memory and an order of magnitude faster than other k-mer counting +# packages by using an efficient encoding of a hash table and by +# exploiting the "compare-and-swap" CPU instruction to increase +# parallelism. +# . +# JELLYFISH is a command-line program that reads FASTA and multi-FASTA +# files containing DNA sequences. It outputs its k-mer counts in an +# binary format, which can be translated into a human-readable text +# format using the "jellyfish dump" command. +# . +# This package contains the Python bindings of jellyfish. Package: libjellyfish-perl Architecture: any ===================================== debian/rules ===================================== @@ -14,22 +14,22 @@ export PERL_MM_OPT=INSTALLDIRS=vendor export PYBUILD_BUILD_ARGS=build_ext --rpath "${CURDIR}/debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}" %: - dh $@ --with python3 + dh $@ # --with python3 override_dh_auto_install: dh_auto_install -- install-data override_dh_install: # dh_install -X*.a -X*.la -Xpkgconfig - dh_install -ppython3-dna-jellyfish - pybuild -d swig/python --name dna-jellyfish -# pybuild -d swig/python --name dna-jellyfish --disable test/python3 -# pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_string_mers.py" -# pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_hash_counter.py" - chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so +# dh_install -ppython3-dna-jellyfish +# pybuild -d swig/python --name dna-jellyfish +## pybuild -d swig/python --name dna-jellyfish --disable test/python3 +## pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_string_mers.py" +## pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_hash_counter.py" +# chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so dh_auto_configure --sourcedirectory=swig/perl5 -# dh_auto_configure --sourcedirectory=swig/python +## dh_auto_configure --sourcedirectory=swig/python dh_auto_build --sourcedirectory=swig/perl5 dh_auto_install --sourcedirectory=swig/perl5 chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/69f40959442997142e115c4634999724d71f3963...6e0840884bea5d162b9dfd75812d66c99820976b -- View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/69f40959442997142e115c4634999724d71f3963...6e0840884bea5d162b9dfd75812d66c99820976b You're receiving this email because of your account on salsa.debian.org.
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