debian/changelog

-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@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@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

+test
+data

debian/patches/python3compat.patch

 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

 no-py-ext
 python3compat.patch
+spelling

debian/patches/spelling

+From: Michael R. Crusoe <michael.crusoe@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

+Tests: run-unit-test
+Depends: @, poppler-utils
+Restrictions: allow-stderr

debian/tests/run-unit-test

+#!/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"