[med-svn] [Git][med-team/jellyfish][master] 2 commits: Drop python3-dna-jellyfish package since the Python module had issues in build process
Andreas Tille
gitlab at salsa.debian.org
Fri Sep 21 08:03:16 BST 2018
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 <tille at debian.org> 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 <tille at debian.org> Mon, 03 Sep 2018 08:34:22 +0200
+ -- Andreas Tille <tille at debian.org> 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
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