[med-svn] [python-bx] 06/09: Lintian-error free version ready to upload
Steffen Möller
moeller at moszumanska.debian.org
Sat Jan 14 11:13:03 UTC 2017
This is an automated email from the git hooks/post-receive script.
moeller pushed a commit to branch master
in repository python-bx.
commit 9aa1429c450fd4b0f56028dc0df24bd329456849
Author: Steffen Moeller <moeller at debian.org>
Date: Sat Jan 14 11:42:10 2017 +0100
Lintian-error free version ready to upload
---
debian/README.Debian | 9 +++++++++
debian/README.source | 6 ++++++
debian/changelog | 3 +++
debian/control | 19 ++++++++++++++++++-
debian/copyright | 3 +++
debian/python-bx-tools.dirs | 1 +
debian/python-bx.dirs | 1 +
debian/python-bx.install | 1 +
debian/python3-bx-tools.dirs | 1 +
debian/python3-bx.dirs | 1 +
debian/python3-bx.install | 1 +
debian/rules | 21 +++++++++++++++++++--
debian/watch | 2 +-
13 files changed, 65 insertions(+), 4 deletions(-)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..5561958
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,9 @@
+python-bx for Debian
+--------------------
+
+The situation is somewhat unfortunate in that both python2 and python3 occupy the same location in /usr/bin. The -tools packages separate those binaries from the modules.
+
+The language suffix ".py" was left for the time being, uncertain about reverse dependencies.
+
+--
+ Steffen Moeller <moeller at debian.org> Sat, 14 Jan 2017 10:43:03 +0100
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..9b39cbe
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,6 @@
+python-bx for Debian
+--------------------
+
+Generated files are removed from upstream as with
+grep -rli "Generated by Cython" lib/ | xargs -r rm
+
diff --git a/debian/changelog b/debian/changelog
index 1a4d49e..3d92f2d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,9 @@ python-bx (0.7.4-1) unstable; urgency=low
* Initial release (Closes: #851242)
* Added Michael and Steffen as uploaders
+ * Removing generated files from source tree in debian/copyright
+ * Added -tools packages to separate command line interface
+ from parallel-installable Python 2 and Python 3 modules.
-- Steffen Moeller <moeller at debian.org> Fri, 13 Jan 2017 13:25:31 +0100
diff --git a/debian/control b/debian/control
index b092108..cb68f2e 100644
--- a/debian/control
+++ b/debian/control
@@ -18,7 +18,7 @@ Build-Depends:
python3-all-dev,
python3-nose,
python3-numpy,
- cython3,
+ cython3
Standards-Version: 3.9.8
Homepage: https://github.com/bxlab/bx-python
Vcs-Git: https://anonscm.debian.org/git/debian-med/python-bx.git
@@ -55,6 +55,7 @@ Depends:
${shlibs:Depends},
${misc:Depends},
${python3:Depends},
+Recommends: python-bx-tools
Description: library to manage genomic data and its alignment
The bx-python project is a python library and associated set of scripts to
allow for rapid implementation of genome scale analyses. The library contains
@@ -73,3 +74,19 @@ Description: library to manage genomic data and its alignment
query and target intervals and associated annotation
.
This package provides the Python 3 library.
+
+Package: python-bx-tools
+Architecture: all
+Conflicts: python3-bx-tools
+Depends: python-bx, ${misc:Depends}, ${python:Depends}
+Description: command line interface to python3-bx
+ This package collects all command line tools to access the functionality
+ of the python-bx library. All scripts have python3 in their shebang line.
+
+Package: python3-bx-tools
+Architecture: all
+Conflicts: python-bx-tools
+Depends: python3-bx, ${misc:Depends}, ${python3:Depends}
+Description: command line interface to python3-bx
+ This package collects all command line tools to access the functionality
+ of the python-bx library. All scripts have python3 in their shebang line.
diff --git a/debian/copyright b/debian/copyright
index d1d0739..bff374f 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,6 +1,9 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: bx-python
Source: https://github.com/bxlab/bx-python
+# Update the list of files to exclude by
+# grep -rl "Generated by Cython"
+Files-Excluded: lib/bx/bbi/bbi_file.h lib/bx/_seqmapping.c lib/bx/bitset.c lib/bx/pwm/_position_weight_matrix.c lib/bx/motif/_pwm.c lib/bx/bbi/cirtree_file.c lib/bx/bbi/bbi_file.c lib/bx/bbi/bpt_file.c lib/bx/bbi/bigwig_file.c lib/bx/bbi/bigbed_file.c lib/bx/intseq/ngramcount.c lib/bx/seq/_twobit.c lib/bx/seq/_nib.c lib/bx/intervals/cluster.c lib/bx/intervals/intersection.c lib/bx/misc/_seekbzip2.c lib/bx/misc/bgzf.c lib/bx/arrays/wiggle.c lib/bx/arrays/bed.c lib/bx/arrays/array_tree.c l [...]
Files: *
Copyright: 2005-2015 The Pennsylvania State University
diff --git a/debian/python-bx-tools.dirs b/debian/python-bx-tools.dirs
new file mode 100644
index 0000000..73752c9
--- /dev/null
+++ b/debian/python-bx-tools.dirs
@@ -0,0 +1 @@
+usr
diff --git a/debian/python-bx.dirs b/debian/python-bx.dirs
new file mode 100644
index 0000000..e772481
--- /dev/null
+++ b/debian/python-bx.dirs
@@ -0,0 +1 @@
+usr/bin
diff --git a/debian/python-bx.install b/debian/python-bx.install
new file mode 100644
index 0000000..9e84839
--- /dev/null
+++ b/debian/python-bx.install
@@ -0,0 +1 @@
+#usr/bin
diff --git a/debian/python3-bx-tools.dirs b/debian/python3-bx-tools.dirs
new file mode 100644
index 0000000..73752c9
--- /dev/null
+++ b/debian/python3-bx-tools.dirs
@@ -0,0 +1 @@
+usr
diff --git a/debian/python3-bx.dirs b/debian/python3-bx.dirs
new file mode 100644
index 0000000..e772481
--- /dev/null
+++ b/debian/python3-bx.dirs
@@ -0,0 +1 @@
+usr/bin
diff --git a/debian/python3-bx.install b/debian/python3-bx.install
new file mode 100644
index 0000000..9e84839
--- /dev/null
+++ b/debian/python3-bx.install
@@ -0,0 +1 @@
+#usr/bin
diff --git a/debian/rules b/debian/rules
index a749ec2..2782b78 100755
--- a/debian/rules
+++ b/debian/rules
@@ -7,13 +7,30 @@ export LC_ALL=C.UTF-8
export NOSE_VERBOSE=2
+export PYBUILD_DESTDIR_python2=debian/python-bx/
+#export PYBUILD_DESTDIR_python2-dbg=debian/python-foo-dbg/
+export PYBUILD_DESTDIR_python3=debian/python3-bx/
+#export PYBUILD_DESTDIR_python3-dbg=debian/python3-foo-dbg/
+
+
%:
- dh $@ --with python2,python3
+ dh $@ --with python2,python3 --buildsystem=pybuild
override_dh_auto_clean:
dh_auto_clean
# C files are generated by Cython
- #find -name "*.pyx" | sed 's/pyx$$/c/' | xargs $(RM)
+ find -name "*.pyx" | sed 's/pyx$$/c/' | xargs $(RM)
+ grep -rli "Generated by Cython" lib/ | xargs -r rm
+# Changes perpetually redone
+ rm -rf lib/bx_python.egg-info
+
+override_dh_install:
+ dh_install --autodest
+ dh_install
+ mkdir -p $(CURDIR)/debian/python-bx-tools/usr
+ mv $(CURDIR)/debian/python-bx/usr/bin $(CURDIR)/debian/python-bx-tools/usr/
+ mkdir -p $(CURDIR)/debian/python3-bx-tools/usr
+ mv $(CURDIR)/debian/python3-bx/usr/bin $(CURDIR)/debian/python3-bx-tools/usr/
override_dh_auto_test:
# skipped
diff --git a/debian/watch b/debian/watch
index 89336b9..79f1dea 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,7 +1,7 @@
# Compulsory line, this is a version 4 file
version=4
# GitHub hosted projects
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%<project>-$1.tar.gz%" \
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%python-bx-$1.tar.gz%" \
https://github.com/bxlab/bx-python/tags \
(?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate
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