debian/changelog

+obitools (1.2.13+dfsg-2) unstable; urgency=medium
+
+  * Apply patch by Olivier Sallou to work around bug at cleanup
+    This also prevents creating sphinx documentation.
+    Closes: #935287
+  * Standards-Version: 4.4.1
+  * Use secure URI in debian/watch.
+  * Remove src/OBITools.egg-info in clean target to build twice in a row
+
+ -- Andreas Tille <tille@debian.org>  Mon, 02 Dec 2019 12:17:04 +0100
+
 obitools (1.2.13+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 12),
                ipython,
                python-wheel,
                python-virtualenv
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/obitools
 Vcs-Git: https://salsa.debian.org/med-team/obitools.git
 Homepage: https://pypi.python.org/pypi/OBITools

debian/obitools.doc-base

-Document: obitools
-Title: OBITools manual
-Author: Eric coissac
-Abstract: This manual describes OBITools and its tools
-Section: Science/Biology
-
-Format: HTML
-Index: /usr/share/doc/obitools/html/index.html
-Files: /usr/share/doc/obitools/html/*.html

debian/obitools.install

-build/sphinx/html  usr/share/doc/obitools
+#build/sphinx/html  usr/share/doc/obitools

debian/obitools.manpages

-build/sphinx/man/*.1
+#build/sphinx/man/*.1

debian/patches/series

 use_debian_libs
 fix_path_interpreter
+# 2to3.patch

debian/patches/use_debian_libs

@@ -7,7 +7,7 @@ Last-Updated: 2015-04-30
 Forwarded: no
 --- a/distutils.ext/obidistutils/serenity/__init__.py
 +++ b/distutils.ext/obidistutils/serenity/__init__.py
-@@ -63,7 +63,7 @@ def serenity_snake(envname,package,versi
+@@ -63,7 +63,7 @@
          
      log.info("%s will be installed with python : %s" % (package,virtualpython))
          
@@ -18,7 +18,7 @@ Forwarded: no
      
 --- a/distutils.ext/obidistutils/serenity/checkpackage.py
 +++ b/distutils.ext/obidistutils/serenity/checkpackage.py
-@@ -15,48 +15,7 @@ from distutils import log
+@@ -15,48 +15,7 @@
  from obidistutils.serenity.checkpip import get_a_pip_module
  
  def is_installed(requirement,pip=None):
@@ -68,9 +68,83 @@ Forwarded: no
  
  
  def get_requirements(pip=None):
+@@ -77,52 +36,13 @@
+     
+ def install_requirements(skip_virtualenv=True,pip=None):
+     
+-    if pip is None:
+-        pip = get_a_pip_module()
+-    
+     install_something=False
+-    try:
+-        requirements = open('requirements.txt').readlines()
+-        requirements = [x.strip() for x in requirements]
+-        requirements = [x for x in requirements if x[0]!='-']
+-    
+-        log.info("Required packages for the installation :")
+-        for x in requirements:
+-            if not skip_virtualenv or x[0:10]!='virtualenv':
+-                ok = is_installed(x,pip)
+-                if not ok:
+-                    log.info("  Installing requirement : %s" % x)
+-                    pip_install_package(x,pip=pip)
+-                    install_something=True
+-                
+-    except IOError:
+-        pass
+     
+     return install_something
+  
+ 
+ def check_requirements(skip_virtualenv=True,pip=None):
+-    
+-    if pip is None:
+-        pip = get_a_pip_module()
+-    
+-    
+-    try:
+-        requirements = open('requirements.txt').readlines()
+-        requirements = [x.strip() for x in requirements]
+-        requirements = [x for x in requirements if x[0]!='-']
+-    
+-        log.info("Required packages for the installation :")
+-        for x in requirements:
+-            if not skip_virtualenv or x[0:10]!='virtualenv':
+-                ok = is_installed(x,pip)
+-                if not ok:
+-                    log.error("  Missing requirement : %s -- Package installation stopped" % x)
+-                    sys.exit(0)
+-                
+-    except IOError:
+-        pass
+- 
++    pass 
+ 
+ 
+ def parse_package_requirement(requirement):
+@@ -146,18 +66,7 @@
+     
+ 
+ def get_package_requirement(package,pip=None):            
+-    if pip is None:
+-        pip = get_a_pip_module()
+-        
+-    requirements = get_requirements(pip)
+-    req = [x for x in requirements
+-             if x[0:len(package)]==package
+-          ]
+-    
+-    if len(req)==1:
+-        return req[0]
+-    else:
+-        return None
++    return None
+         
+         
+ def pip_install_package(package,directory=None,pip=None):
 --- a/setup.py
 +++ b/setup.py
-@@ -66,5 +66,5 @@ if __name__=="__main__":
+@@ -66,5 +66,5 @@
            license=LICENSE,
            url=URL,
            python_src=SRC,
@@ -78,3 +152,41 @@ Forwarded: no
 -          serenity=serenity)
 +          sse='sse2')
 +          #serenity=serenity)
+--- a/distutils.ext/obidistutils/core.py
++++ b/distutils.ext/obidistutils/core.py
+@@ -24,13 +24,11 @@
+ from obidistutils.command.build import build
+ from obidistutils.command.littlebigman import littlebigman
+ from obidistutils.command.build_cexe import build_cexe
+-from obidistutils.command.build_sphinx import build_sphinx
+ from obidistutils.command import build_ext
+ from obidistutils.command.build_ctools import build_ctools
+ from obidistutils.command.build_files import build_files
+ from obidistutils.command.build_scripts import build_scripts
+ from obidistutils.command.install_scripts import install_scripts
+-from obidistutils.command.install_sphinx import install_sphinx
+ from obidistutils.command.install import install
+ from obidistutils.command.pidname import pidname
+ 
+@@ -125,9 +123,7 @@
+             'build_cexe':build_cexe, 
+             'build_ext': build_ext,
+             'build_scripts':build_scripts, 
+-            'build_sphinx':build_sphinx, 
+             'install_scripts':install_scripts,
+-            'install_sphinx':install_sphinx,
+             'install':install,
+             'sdist':sdist}
+ 
+--- a/distutils.ext/obidistutils/command/build.py
++++ b/distutils.ext/obidistutils/command/build.py
+@@ -38,8 +38,7 @@
+                     ('build_ctools', has_ctools),
+                     ('build_files', has_files),
+                     ('build_cexe', has_executables)] \
+-                   + ori_build.sub_commands + \
+-                   [('build_sphinx',has_doc)]
++                   + ori_build.sub_commands
+                    
+     def run(self):
+         log.info('\n\nRunning obidistutils build process\n\n')

debian/rules

@@ -12,12 +12,13 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 export PYBUILD_NAME=obitools
 
 %:
-	dh $@  --with python2,sphinxdoc --buildsystem=pybuild
+	dh $@  --with python2 --buildsystem=pybuild
 
 override_dh_clean:
 	dh_clean
 	rm -rf build
 	rm -f doc/sphinx/build_dir.txt
+	rm -rf src/OBITools.egg-info
 
 override_dh_auto_install:
 	PYTHONPATH=$(shell pybuild --print build_dir --interpreter python) \

debian/watch

 version=3
 opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//,uversionmangle=s/(rc|a|b|c)/~$1/,repack,compression=xz" \
-http://pypi.debian.net/OBITools/OBITools-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
+https://pypi.debian.net/OBITools/OBITools-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))