[med-svn] [Git][med-team/cnvkit][master] 8 commits: Remove trailing whitespace in debian/rules
Michael R. Crusoe
gitlab at salsa.debian.org
Sun Jan 6 12:15:38 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / cnvkit
Commits:
1c9085ae by Michael R. Crusoe at 2019-01-06T07:50:36Z
Remove trailing whitespace in debian/rules
- - - - -
4bd77ec2 by Michael R. Crusoe at 2019-01-06T09:40:26Z
Run the included tests as autopkgtests.
- - - - -
798edaa8 by Michael R. Crusoe at 2019-01-06T09:52:28Z
fix spelling typo
- - - - -
683e1f49 by Michael R. Crusoe at 2019-01-06T10:13:21Z
Mark cnv_expression_correlate as a script
- - - - -
9f5e9589 by Michael R. Crusoe at 2019-01-06T10:36:57Z
remove old bits
- - - - -
a12b1996 by Michael R. Crusoe at 2019-01-06T11:57:21Z
remove duplicate snpfilter.sh
- - - - -
96ff8eed by Michael R. Crusoe at 2019-01-06T11:58:22Z
amd64 only, due to the realities of where python-pysam is available.
- - - - -
ce96ad92 by Michael R. Crusoe at 2019-01-06T12:14:33Z
upload to unstable
- - - - -
9 changed files:
- debian/changelog
- debian/control
- + debian/examples
- debian/patches/python3compat.patch
- debian/patches/series
- + debian/patches/spelling
- debian/rules
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,17 @@
-cnvkit (0.9.5-2) UNRELEASED; urgency=medium
+cnvkit (0.9.5-2) unstable; urgency=medium
+ [ Jelmer Vernooij ]
* Use secure copyright file specification URI.
* Trim trailing whitespace.
- -- Jelmer Vernooij <jelmer at debian.org> Sat, 20 Oct 2018 13:52:50 +0000
+ [ Michael R. Crusoe ]
+ * Remove trailing whitespace in debian/rules
+ * Standards-Version: 4.3.0
+ * Run the included tests as autopkgtests.
+ * Mark cnv_expression_correlate as a script
+ * amd64 only, due to the realities of where python-pysam is available.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sun, 06 Jan 2019 04:12:46 -0800
cnvkit (0.9.5-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -18,17 +18,20 @@ Build-Depends: debhelper (>= 11~),
python3-matplotlib,
python3-pyvcf,
python3-future,
- r-cran-pscbs
+ r-bioc-dnacopy,
+ poppler-utils
+# poppler-utils provides pdfunite, needed for the tests
# python-subprocess32 # required only for python2
-Standards-Version: 4.2.0
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/cnvkit
Vcs-Git: https://salsa.debian.org/med-team/cnvkit.git
Homepage: http://cnvkit.readthedocs.org
Package: cnvkit
-Architecture: all
+Architecture: amd64
Depends: ${python3:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ r-bioc-dnacopy
Description: Copy number variant detection from targeted DNA sequencing
A command-line toolkit and Python library for detecting copy number variants
and alterations genome-wide from targeted DNA sequencing. It is designed for
=====================================
debian/examples
=====================================
@@ -0,0 +1,2 @@
+test
+data
=====================================
debian/patches/python3compat.patch
=====================================
@@ -1,6 +1,6 @@
Description: enable building with Python3
---- a/test/Makefile
-+++ b/test/Makefile
+--- cnvkit.orig/test/Makefile
++++ cnvkit/test/Makefile
@@ -3,7 +3,9 @@
# Dependency: pdfunite (poppler-utils)
# (Otherwise, all-scatters.pdf and all-diagrams.pdf will be empty files.)
@@ -12,7 +12,7 @@ Description: enable building with Python3
# ------------------------------------------------------------------------------
# Samples pre-processed with Picard CalculateHsMetrics
-@@ -34,10 +36,10 @@ clean:
+@@ -34,10 +36,10 @@
.PHONY: test
test:
@@ -27,91 +27,98 @@ Description: enable building with Python3
# ------------------------------------------------------------------------------
---- a/test/test_cnvlib.py
-+++ b/test/test_cnvlib.py
+--- cnvkit.orig/test/test_cnvlib.py
++++ cnvkit/test/test_cnvlib.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Unit tests for the CNVkit library, cnvlib."""
from __future__ import absolute_import, division, print_function
import sys
---- a/test/test_genome.py
-+++ b/test/test_genome.py
+--- cnvkit.orig/test/test_genome.py
++++ cnvkit/test/test_genome.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Unit tests for the 'genome' sub-package."""
from __future__ import absolute_import, division, print_function
import random
---- a/test/test_io.py
-+++ b/test/test_io.py
+--- cnvkit.orig/test/test_io.py
++++ cnvkit/test/test_io.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Unit tests for the CNVkit library, cnvlib."""
from __future__ import absolute_import, division, print_function
---- a/test/test_r.py
-+++ b/test/test_r.py
+--- cnvkit.orig/test/test_r.py
++++ cnvkit/test/test_r.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Unit tests for CNVkit that require an R installation."""
from __future__ import absolute_import, division, print_function
---- a/cnvkit.py
-+++ b/cnvkit.py
+--- cnvkit.orig/cnvkit.py
++++ cnvkit/cnvkit.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Command-line interface for CNVkit, the Copy Number Variation toolkit."""
from future import standard_library
---- a/scripts/cnv_annotate.py
-+++ b/scripts/cnv_annotate.py
+--- cnvkit.orig/scripts/cnv_annotate.py
++++ cnvkit/scripts/cnv_annotate.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Update gene names in CNVkit .cnn/.cnr files.
"""
---- a/scripts/cnv_updater.py
-+++ b/scripts/cnv_updater.py
+--- cnvkit.orig/scripts/cnv_updater.py
++++ cnvkit/scripts/cnv_updater.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Update .cnn/.cnr files from older CNVkit versions to match current defaults.
CNVkit v0.8.0 and later uses a 'depth' column in the *.targetcoverage.cnn and
---- a/scripts/cnv_ztest.py
-+++ b/scripts/cnv_ztest.py
+--- cnvkit.orig/scripts/cnv_ztest.py
++++ cnvkit/scripts/cnv_ztest.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Z-test for single-bin copy number alterations."""
from __future__ import division, print_function
---- a/scripts/guess_baits.py
-+++ b/scripts/guess_baits.py
+--- cnvkit.orig/scripts/guess_baits.py
++++ cnvkit/scripts/guess_baits.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Guess the coordinates of captured regions from sample read depths.
Two approaches available:
---- a/scripts/reference2targets.py
-+++ b/scripts/reference2targets.py
+--- cnvkit.orig/scripts/reference2targets.py
++++ cnvkit/scripts/reference2targets.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Extract target and antitarget BED files from a CNVkit reference file.
---- a/scripts/skg_convert.py
-+++ b/scripts/skg_convert.py
+--- cnvkit.orig/scripts/skg_convert.py
++++ cnvkit/scripts/skg_convert.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Convert between tabular formats using scikit-genome I/O."""
from __future__ import absolute_import, division, print_function
import argparse
+--- cnvkit.orig/scripts/cnv_expression_correlate.py
++++ cnvkit/scripts/cnv_expression_correlate.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/python3
+ """Calculate correlation coefficients for gene expression and copy number.
+
+ Data source for both inputs is TCGA via cBioPortal.
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
no-py-ext
python3compat.patch
+spelling
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,22 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Fix typos
+--- cnvkit.orig/cnvlib/commands.py
++++ cnvkit/cnvlib/commands.py
+@@ -165,7 +165,7 @@
+ P_batch.add_argument("--rlibpath", metavar="DIRECTORY",
+ help=argparse.SUPPRESS)
+ P_batch.add_argument("--rscript-path", metavar="PATH", default="Rscript",
+- help="""Path to the Rscript excecutable to use for running R code.
++ help="""Path to the Rscript executable to use for running R code.
+ Use this option to specify a non-default R installation.
+ [Default: %(default)s]""")
+
+@@ -667,7 +667,7 @@
+ P_segment.add_argument("--rlibpath", metavar="DIRECTORY",
+ help=argparse.SUPPRESS)
+ P_segment.add_argument("--rscript-path", metavar="PATH", default="Rscript",
+- help="""Path to the Rscript excecutable to use for running R code.
++ help="""Path to the Rscript executable to use for running R code.
+ Use this option to specify a non-default R installation.
+ [Default: %(default)s]""")
+ P_segment.add_argument('-p', '--processes',
=====================================
debian/rules
=====================================
@@ -10,22 +10,19 @@ include /usr/share/dpkg/pkg-info.mk
override_dh_auto_build:
[ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted build
- #mv scripts/genome2access.py ./ # no longer distributed
if [ -f scripts/cnv_annotate.py ]; then \
cd scripts && for script in *.py; do \
mv $${script} cnvkit-$${script%%.py}; \
done; \
fi
dh_auto_build
- cd scripts && for script in *; do \
+ cd scripts && for script in cnvkit-*; do \
mv $${script} $${script##cnvkit-}.py; \
done
mv cnvkit cnvkit.py
- #mv genome2access.py scripts/ # no longer distributed
override_dh_auto_install:
[ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted install
- #mv scripts/genome2access.py ./ # no longer distributed
if [ -f scripts/cnv_annotate.py ]; then \
cd scripts && for script in *.py; do \
mv $${script} cnvkit-$${script%%.py}; \
@@ -36,24 +33,20 @@ override_dh_auto_install:
--name="a command-line toolkit for copy number analysis." \
./cnvkit > debian/cnvkit.1
PYTHONPATH=$$PYTHONPATH:. debian/genmanpages.py ${DEB_VERSION_UPSTREAM}
- # no longer distributed
- #cd scripts && PYTHONPATH=../ help2man --no-info \
- # --version-string=${DEB_VERSION_UPSTREAM} --help-option='-h' \
- # ./cnvkit-refFlat2bed --name='Generate a BED file of the genes or exons in the reference genome given in UCSC refFlat.txt format.' \
- # > ../debian/cnvkit-refFlat2bed.1;
cd scripts && PYTHONPATH=../ help2man --no-info \
--version-string=${DEB_VERSION_UPSTREAM} --help-option='-h' \
./cnvkit-reference2targets --name='Extract target and antitarget BED files from a CNVkit reference file.' \
> ../debian/cnvkit-reference2targets.1;
- cd scripts && for script in *; do \
+ cd scripts && for script in cnvkit-*; do \
mv $${script} $${script##cnvkit-}.py; \
done
mv cnvkit cnvkit.py
- #mv genome2access.py scripts/ # no longer distributed
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- cd test && ${MAKE}
+ cd test && ${MAKE} -j$(shell nproc)
+ cd test && ${MAKE} -j$(shell nproc) clean || /bin/true
+ rm -Rf test/build test/*.tsv
endif
override_dh_auto_clean:
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, poppler-utils
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,18 @@
+#!/bin/bash
+set -e
+
+pkg="cnvkit"
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+fi
+
+cp -arL /usr/share/doc/${pkg}/examples/test "${AUTOPKGTEST_TMP}/"
+cp -arL /usr/share/doc/${pkg}/examples/data "${AUTOPKGTEST_TMP}/"
+
+cd "${AUTOPKGTEST_TMP}"
+find . -name "*.gz" -exec gunzip \{\} \;
+cd test
+make "-j$(nproc)" cnvkit=/usr/bin/cnvkit
+
+echo "PASS"
View it on GitLab: https://salsa.debian.org/med-team/cnvkit/compare/6ffbe43f11ff869542f20d5c7378449c9eec43fd...ce96ad927d477babe416a8c20ac2f88ec794e106
--
View it on GitLab: https://salsa.debian.org/med-team/cnvkit/compare/6ffbe43f11ff869542f20d5c7378449c9eec43fd...ce96ad927d477babe416a8c20ac2f88ec794e106
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