debian/changelog

+python-csb (1.2.5+dfsg-4) unstable; urgency=medium
+
+  * Remove Python2 support
+  * Remove API doc since it is created by deprecated epydoc
+    Closes: #881555
+  * Move to source section science and leace python3-csb to section python
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Secure URI in copyright format
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Remove trailing whitespace in debian/copyright
+  * Remove trailing whitespace in debian/rules
+  * rename debian/tests/control.autodep8 to debian/tests/control
+
+ -- Andreas Tille <tille@debian.org>  Thu, 01 Aug 2019 08:28:22 +0200
+
 python-csb (1.2.5+dfsg-3) unstable; urgency=medium
 
   * Standards-Version: 4.1.4

debian/compat

-11

debian/control

@@ -2,51 +2,28 @@ Source: python-csb
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Tomas Di Domenico <tdido@tdido.com.ar>,
            Andreas Tille <tille@debian.org>
-Section: python
+Section: science
 Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python-all,
                python3-all,
-               python-epydoc,
-               python-numpy,
-               python-scipy,
-               python-matplotlib,
-               python-setuptools,
                python3-numpy,
                python3-scipy,
                python3-matplotlib,
                python3-setuptools
-Standards-Version: 4.1.4
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/python-csb
 Vcs-Git: https://salsa.debian.org/med-team/python-csb.git
 Homepage: https://github.com/csb-toolbox/CSB
-X-Python-Version: >= 2.6
-X-Python3-Version: >= 3.1
-
-Package: python-csb
-Architecture: all
-Depends: ${misc:Depends},
-         ${python:Depends},
-         python-numpy,
-         python-scipy
-Suggests: python-csb-doc
-Description: Python framework for structural bioinformatics
- Computational Structural Biology Toolbox (CSB) is a Python class
- library for reading, storing and analyzing biomolecular structures
- in a variety of formats with rich support for statistical analyses.
- .
- CSB is designed for reusability and extensibility and comes with a clean,
- well-documented API following good object-oriented engineering practice.
 
 Package: python3-csb
 Architecture: all
+Section: python
 Depends: ${misc:Depends},
          ${python3:Depends},
          python3-numpy,
          python3-scipy
-Suggests: python-csb-doc
 Description: Python framework for structural bioinformatics (Python3 version)
  Computational Structural Biology Toolbox (CSB) is a Python class
  library for reading, storing and analyzing biomolecular structures
@@ -71,18 +48,3 @@ Description: Computational Structural Biology Toolbox (CSB)
  well-documented API following good object-oriented engineering practice.
  .
  This package contains some user executable tools.
-
-Package: python-csb-doc
-Architecture: all
-Section: doc
-Depends: ${misc:Depends},
-         ${python:Depends}
-Description: Python framework for structural bioinformatics (documentation)
- Computational Structural Biology Toolbox (CSB) is a Python class
- library for reading, storing and analyzing biomolecular structures
- in a variety of formats with rich support for statistical analyses.
- .
- CSB is designed for reusability and extensibility and comes with a clean,
- well-documented API following good object-oriented engineering practice.
- .
- This package contains the HTML documentation of the framework's API.

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: csb
 Upstream-Contact: Ivan Kalev <ivan.kalev@gmail.com>
 Source: http://csb.codeplex.com

debian/python-csb-doc.doc-base

-Document: csb
-Title: API Documentation for CSB (Computational Structural Biology Toolbox)
-Author: Michael Habeck <michael.habeck@tuebingen.mpg.de>
-Abstract: This is the API documentation for CSB.
- Computational Structural Biology Toolbox (CSB) is a Python class
- library for reading, storing and analyzing biomolecular structures
- in a variety of formats with rich support for statistical analyses.
-Section: Science/Biology
-
-Format: HTML
-Index: /usr/share/doc/python-csb-doc/api/index.html
-Files: /usr/share/doc/python-csb-doc/api/*

debian/python-csb-doc.install

-docs/api usr/share/doc/python-csb-doc/

debian/rules

@@ -3,34 +3,21 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
-PYVERS = $(shell pyversions -r)
 PY3VERS = $(shell py3versions -r)
-BUILDHOME = $(CURDIR)/debian/buildhome
 export PYBUILD_NAME=csb
 
 %:
-	dh $@ --with python2,python3 --buildsystem=pybuild
-	
-override_dh_auto_build:
-	dh_auto_build
-	mkdir -p $(CURDIR)/docs/api
-	mkdir -p $(BUILDHOME)
-	HOME=$(BUILDHOME) epydoc --html -o $(CURDIR)/docs/api --name CSB --no-private --introspect-only --exclude csb.test.cases --fail-on-error --fail-on-warning --fail-on-docstring-warning $(CURDIR)/csb
-
-override_dh_auto_clean:
-	dh_auto_clean
-	rm -rf $(BUILDHOME)
-	find . -name "*.pyc" -delete
-	rm -rf docs
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \
 		--test-args='set -e; \
                              cd {build_dir}; \
                              PYTHONPATH={build_dir} PYTHONWARNINGS=d {interpreter} csb/test/app.py --generated-resources /tmp --verbosity 2'
+endif
 
 override_dh_install:
 	dh_install
 	mkdir -p debian/$(PYBUILD_NAME)/usr
 	mv debian/python3-$(PYBUILD_NAME)/usr/bin debian/$(PYBUILD_NAME)/usr
-	rm -rf debian/python-$(PYBUILD_NAME)/usr/bin