From fbb8276b32a9aafe3d0b58e7bbb55b2a37cf2ea6 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Sun, 17 Nov 2019 17:34:03 +0100
Subject: [PATCH] Revert "drop python2"

This reverts commit feea4660e2dfdd2702594e1eee0bae3c53c6d3cb.
---
 debian/control                        | 17 +++++++++++++++++
 debian/python-pysam.links             |  4 ++++
 debian/python-pysam.lintian-overrides |  4 ++++
 debian/rules                          |  2 +-
 4 files changed, 26 insertions(+), 1 deletion(-)
 create mode 100755 debian/python-pysam.links
 create mode 100644 debian/python-pysam.lintian-overrides

diff --git a/debian/control b/debian/control
index 8627369..ca1f9b8 100644
--- a/debian/control
+++ b/debian/control
@@ -10,18 +10,35 @@ Build-Depends: debhelper (>= 11~),
                dh-python,
                libhts-dev (>= 1.9),
                zlib1g-dev,
+               python-all-dev,
+               python-setuptools,
+               cython (>= 0.23),
                python3-all-dev,
                python3-setuptools,
                cython3 (>= 0.23),
                tabix <!nocheck>,
                samtools (>= 1.9) <!nocheck>,
                bcftools (>= 1.9) <!nocheck>,
+               python-pytest <!nocheck>,
                python3-pytest <!nocheck>
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/python-pysam
 Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git
 Homepage: http://pysam.readthedocs.org/en/latest
 
+Package: python-pysam
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         ${python:Depends}
+Provides: ${python:Provides}
+Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2)
+ Pysam is a Python module for reading and manipulating Samfiles. It's a
+ lightweight wrapper of the samtools C-API. Pysam also includes an interface
+ for tabix.
+ .
+ This package installs the module for Python 2.
+
 Package: python3-pysam
 Architecture: any
 Depends: ${shlibs:Depends},
diff --git a/debian/python-pysam.links b/debian/python-pysam.links
new file mode 100755
index 0000000..8cc3b2c
--- /dev/null
+++ b/debian/python-pysam.links
@@ -0,0 +1,4 @@
+#!/usr/bin/dh-exec
+/usr/lib/python2.7/dist-packages/pysam/libcsamtools.${DEB_HOST_GNU_TYPE}.so /usr/lib/python2.7/dist-packages/pysam/libcsamtools.so
+/usr/lib/python2.7/dist-packages/pysam/libcbcftools.${DEB_HOST_GNU_TYPE}.so /usr/lib/python2.7/dist-packages/pysam/libcbcftools.so
+/usr/lib/python2.7/dist-packages/pysam/libchtslib.${DEB_HOST_GNU_TYPE}.so /usr/lib/python2.7/dist-packages/pysam/libchtslib.so
diff --git a/debian/python-pysam.lintian-overrides b/debian/python-pysam.lintian-overrides
new file mode 100644
index 0000000..785680d
--- /dev/null
+++ b/debian/python-pysam.lintian-overrides
@@ -0,0 +1,4 @@
+# These are apparently false-positives
+# Inspection of the build logs shows that these are indeed compiled with
+# -D_FORTIFY_SOURCE=2
+hardening-no-fortify-functions usr/lib/python2.7/dist-packages/pysam/lib*.so
diff --git a/debian/rules b/debian/rules
index 38b8c72..091888f 100755
--- a/debian/rules
+++ b/debian/rules
@@ -21,7 +21,7 @@ export HTSLIB_INCLUDE_DIR=/usr/include
 
 clean: clean-tests
 %:
-	dh $@ --with python3 --buildsystem=pybuild
+	dh $@ --with python2,python3 --buildsystem=pybuild
 
 override_dh_install: clean-tests
 	dh_install -Xtest.gtf.gz
-- 
2.30.2