debian/changelog

+deepnano (0.0+git20170813.e8a621e-3.1) unstable; urgency=medium
+
+  * Non-maintainer upload.
+  * Add py3-compat.patch.
+  * Switched package to Python 3 (Closes: #936381, #943005).
+
+ -- Thomas Goirand <zigo@debian.org>  Sun, 03 Nov 2019 17:22:33 +0100
+
 deepnano (0.0+git20170813.e8a621e-3) unstable; urgency=medium
 
   * Use less data for autopkgtest

debian/control

@@ -5,10 +5,10 @@ Uploaders: Çağrı ULAŞ <cagriulas@gmail.com>,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 12~),
-               python-all,
+               python3-all,
                dh-python,
-               python-markdown,
-               python-theano
+               python3-markdown,
+               python3-theano
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/deepnano
 Vcs-Git: https://salsa.debian.org/med-team/deepnano.git
@@ -16,15 +16,15 @@ Homepage: https://bitbucket.org/vboza/deepnano
 
 Package: deepnano
 Architecture: any
-Depends: ${python:Depends},
+Depends: ${python3:Depends},
          ${misc:Depends},
          ${shlibs:Depends},
-         python-h5py,
-         python-numpy,
-         python-dateutil,
-         python-theano,
+         python3-h5py,
+         python3-numpy,
+         python3-dateutil,
+         python3-theano,
          deepnano-data
-Recommends: python-watchdog
+Recommends: python3-watchdog
 Description: alternative basecaller for MinION reads of genomic sequences
  DeepNano is alternative basecaller for Oxford Nanopore MinION reads
  based on deep recurrent neural networks.

debian/patches/series

 she_bang.patch
 path_align_2d.patch
+py3-compat.patch

debian/patches/she_bang.patch

@@ -5,14 +5,14 @@ Description: Add missing #! line
 --- a/basecall.py
 +++ b/basecall.py
 @@ -1,3 +1,4 @@
-+#!/usr/bin/python
++#!/usr/bin/python3
  import argparse
  from rnn_fin import RnnPredictor
  import h5py
 --- a/basecall_no_metrichor.py
 +++ b/basecall_no_metrichor.py
 @@ -1,3 +1,4 @@
-+#!/usr/bin/python
++#!/usr/bin/python3
  import argparse
  from rnn_fin import RnnPredictor
  import h5py

debian/rules

@@ -5,11 +5,11 @@
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 %:
-	dh $@  --with python2
+	dh $@  --with python3
 
 override_dh_auto_build:
 	dh_auto_build
-	markdown_py -f README.html README.md
+	python3 -m markdown -f README.html README.md
 	g++ $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -std=gnu++0x align_2d.cc -o align_2d
 	g++ $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -std=gnu++0x training/realign.cc -o realign