[med-svn] [Git][med-team/pyqi][master] 5 commits: fix_sphinx_htmlhelp.patch: normalize last-update timestamp.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Jan 8 21:12:05 GMT 2025
Étienne Mollier pushed to branch master at Debian Med / pyqi
Commits:
741cf1b4 by Étienne Mollier at 2025-01-08T22:04:22+01:00
fix_sphinx_htmlhelp.patch: normalize last-update timestamp.
- - - - -
8a30b8ab by Étienne Mollier at 2025-01-08T22:05:59+01:00
2to3.patch: bump support gating to Python 3.13.
This gating in setup.py does not achieve much and probably ought to be
removed, but that will suffice for now.
Closes: #1092521
- - - - -
71b23c8e by Étienne Mollier at 2025-01-08T22:08:03+01:00
fix-syntax-warning.patch: fix typo caught by lintian.
- - - - -
7300d191 by Étienne Mollier at 2025-01-08T22:09:02+01:00
d/control: add myself to uploaders.
- - - - -
76fdc7f3 by Étienne Mollier at 2025-01-08T22:11:24+01:00
d/changelog: ready for upload to unstable.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/2to3.patch
- debian/patches/fix-syntax-warning.patch
- debian/patches/fix_sphinx_htmlhelp.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+pyqi (0.3.2+dfsg-13) unstable; urgency=medium
+
+ * fix_sphinx_htmlhelp.patch: normalize last-update timestamp.
+ * 2to3.patch: bump support gating to Python 3.13.
+ This gating in setup.py does not achieve much and probably ought to be
+ removed, but that will suffice for now. (Closes: #1092521)
+ * fix-syntax-warning.patch: fix typo caught by lintian.
+ * d/control: add myself to uploaders.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 08 Jan 2025 22:09:16 +0100
+
pyqi (0.3.2+dfsg-12) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
Source: pyqi
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: python
Priority: optional
Build-Depends: debhelper-compat (= 13),
=====================================
debian/patches/2to3.patch
=====================================
@@ -1,11 +1,12 @@
Description: Use 2to3 to port to Python3
Bug-Debian: https://bugs.debian.org/937512
Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
+Last-Update: 2025-01-08
+Reviewed-By: Étienne Mollier <emollier at debian.org>
---- a/doc/conf.py
-+++ b/doc/conf.py
-@@ -40,8 +40,8 @@ source_suffix = '.rst'
+--- pyqi.orig/doc/conf.py
++++ pyqi/doc/conf.py
+@@ -40,8 +40,8 @@
master_doc = 'index'
# General information about the project.
@@ -16,7 +17,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
-@@ -181,8 +181,8 @@ latex_elements = {
+@@ -181,8 +181,8 @@
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
@@ -27,7 +28,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
]
# The name of an image file (relative to this directory) to place at the top of
-@@ -211,8 +211,8 @@ latex_documents = [
+@@ -211,8 +211,8 @@
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
@@ -38,7 +39,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
]
# If true, show URL addresses after external links.
-@@ -225,8 +225,8 @@ man_pages = [
+@@ -225,8 +225,8 @@
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
@@ -49,9 +50,9 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
'Miscellaneous'),
]
---- a/doc/tutorials/defining_new_commands.rst
-+++ b/doc/tutorials/defining_new_commands.rst
-@@ -20,7 +20,7 @@ To create our sequence collection summar
+--- pyqi.orig/doc/tutorials/defining_new_commands.rst
++++ pyqi/doc/tutorials/defining_new_commands.rst
+@@ -20,7 +20,7 @@
If you run this command locally, substituting your own name where applicable, you'll have a new file called ``sequence_collection_summarizer.py``, which will look roughly like the following::
@@ -60,7 +61,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
from __future__ import division
__credits__ = ["Greg Caporaso"]
-@@ -117,7 +117,7 @@ A complete example Command
+@@ -117,7 +117,7 @@
The following illustrates a complete python file defining a new pyqi ``Command``::
@@ -69,7 +70,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
from __future__ import division
__credits__ = ["Greg Caporaso"]
-@@ -180,11 +180,11 @@ At this stage you have defined a new com
+@@ -180,11 +180,11 @@
>>> r
{'max_length': 12, 'min_length': 6, 'num_seqs': 2}
# Alternatively, you can access each value independently, as with any dictionary.
@@ -84,9 +85,9 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
12
# You can call this command again with different input.
# For example, we can call the command again passing the
---- a/doc/tutorials/defining_new_interfaces.rst
-+++ b/doc/tutorials/defining_new_interfaces.rst
-@@ -24,7 +24,7 @@ To create your interface, you'll need to
+--- pyqi.orig/doc/tutorials/defining_new_interfaces.rst
++++ pyqi/doc/tutorials/defining_new_interfaces.rst
+@@ -24,7 +24,7 @@
The resulting file will look something like this::
@@ -95,7 +96,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
from __future__ import division
__credits__ = ["Greg Caporaso"]
-@@ -281,7 +281,7 @@ Complete OptparseInterface configuration
+@@ -281,7 +281,7 @@
At this stage we've fully configured our interface. The final interface configuration file should look like this::
@@ -104,24 +105,24 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
from __future__ import division
__credits__ = ["Greg Caporaso"]
---- a/pyqi/__init__.py
-+++ b/pyqi/__init__.py
+--- pyqi.orig/pyqi/__init__.py
++++ pyqi/pyqi/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/commands/__init__.py
-+++ b/pyqi/commands/__init__.py
+--- pyqi.orig/pyqi/commands/__init__.py
++++ pyqi/pyqi/commands/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/commands/code_header_generator.py
-+++ b/pyqi/commands/code_header_generator.py
+--- pyqi.orig/pyqi/commands/code_header_generator.py
++++ pyqi/pyqi/commands/code_header_generator.py
@@ -1,5 +1,5 @@
-#!/usr/bin/env python
-from __future__ import division
@@ -130,7 +131,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
-@@ -61,12 +61,12 @@ class CodeHeaderGenerator(Command):
+@@ -61,12 +61,12 @@
credits = [head['author']]
if kwargs['credits'] is not None:
credits.extend(kwargs['credits'])
@@ -145,8 +146,8 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
header_lines.append("from __future__ import division")
header_lines.append("")
---- a/pyqi/commands/make_bash_completion.py
-+++ b/pyqi/commands/make_bash_completion.py
+--- pyqi.orig/pyqi/commands/make_bash_completion.py
++++ pyqi/pyqi/commands/make_bash_completion.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -162,16 +163,16 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
__credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Doug Wendel",
"Greg Caporaso"]
---- a/pyqi/commands/make_command.py
-+++ b/pyqi/commands/make_command.py
+--- pyqi.orig/pyqi/commands/make_command.py
++++ pyqi/pyqi/commands/make_command.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/commands/make_optparse.py
-+++ b/pyqi/commands/make_optparse.py
+--- pyqi.orig/pyqi/commands/make_optparse.py
++++ pyqi/pyqi/commands/make_optparse.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -187,7 +188,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
from operator import attrgetter
from pyqi.core.command import (Command, CommandIn, CommandOut,
ParameterCollection)
-@@ -137,7 +137,7 @@ class MakeOptparse(CodeHeaderGenerator):
+@@ -137,7 +137,7 @@
# construct inputs based off of CommandIns
cmdin_formatted = []
@@ -196,7 +197,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
key=attrgetter('Name')):
if cmdin.Required:
default_block = ''
-@@ -162,7 +162,7 @@ class MakeOptparse(CodeHeaderGenerator):
+@@ -162,7 +162,7 @@
cmdin_formatted.append(input_format % fmt)
cmdout_formatted = []
@@ -205,8 +206,8 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
key=attrgetter('Name')):
fmt = {'name':cmdin.Name}
cmdout_formatted.append(output_format % fmt)
---- a/pyqi/commands/make_release.py
-+++ b/pyqi/commands/make_release.py
+--- pyqi.orig/pyqi/commands/make_release.py
++++ pyqi/pyqi/commands/make_release.py
@@ -1,5 +1,5 @@
-#!/usr/bin/env python
-from __future__ import division
@@ -215,7 +216,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
-@@ -74,7 +74,7 @@ class MakeRelease(Command):
+@@ -74,7 +74,7 @@
def _bump_version(self, version):
try:
@@ -224,8 +225,8 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
except ValueError:
self._fail('Current version is not numeric')
parts[-1] += 1
---- a/pyqi/commands/serve_html_interface.py
-+++ b/pyqi/commands/serve_html_interface.py
+--- pyqi.orig/pyqi/commands/serve_html_interface.py
++++ pyqi/pyqi/commands/serve_html_interface.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -241,16 +242,16 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
__credits__ = ["Evan Bolyen"]
---- a/pyqi/core/__init__.py
-+++ b/pyqi/core/__init__.py
+--- pyqi.orig/pyqi/core/__init__.py
++++ pyqi/pyqi/core/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/core/command.py
-+++ b/pyqi/core/command.py
+--- pyqi.orig/pyqi/core/command.py
++++ pyqi/pyqi/core/command.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -266,7 +267,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
__credits__ = ["Greg Caporaso", "Daniel McDonald", "Doug Wendel",
"Jai Ram Rideout"]
-@@ -162,7 +162,7 @@ class Command(object):
+@@ -162,7 +162,7 @@
self_str = str(self.__class__)
# check required parameters
@@ -275,7 +276,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
if p.Required and p.Name not in kwargs:
err_msg = 'Missing required CommandIn %s in %s' % (p.Name,
self_str)
-@@ -187,7 +187,7 @@ class Command(object):
+@@ -187,7 +187,7 @@
"""Validate the result from a ``Command.run``"""
self_str = str(self.__class__)
@@ -284,7 +285,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
if p.Name not in result:
err_msg = "CommandOut %s not in %s" % (p.Name, self_str)
self._logger.fatal(err_msg)
-@@ -200,7 +200,7 @@ class Command(object):
+@@ -200,7 +200,7 @@
def _set_defaults(self, kwargs):
"""Set defaults for optional parameters"""
@@ -293,55 +294,55 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
if not p.Required and p.Name not in kwargs:
kwargs[p.Name] = p.Default
---- a/pyqi/core/container.py
-+++ b/pyqi/core/container.py
+--- pyqi.orig/pyqi/core/container.py
++++ pyqi/pyqi/core/container.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/core/exception.py
-+++ b/pyqi/core/exception.py
+--- pyqi.orig/pyqi/core/exception.py
++++ pyqi/pyqi/core/exception.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/core/factory.py
-+++ b/pyqi/core/factory.py
+--- pyqi.orig/pyqi/core/factory.py
++++ pyqi/pyqi/core/factory.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/core/interface.py
-+++ b/pyqi/core/interface.py
+--- pyqi.orig/pyqi/core/interface.py
++++ pyqi/pyqi/core/interface.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/core/interfaces/__init__.py
-+++ b/pyqi/core/interfaces/__init__.py
+--- pyqi.orig/pyqi/core/interfaces/__init__.py
++++ pyqi/pyqi/core/interfaces/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/core/interfaces/html/__init__.py
-+++ b/pyqi/core/interfaces/html/__init__.py
+--- pyqi.orig/pyqi/core/interfaces/html/__init__.py
++++ pyqi/pyqi/core/interfaces/html/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
-@@ -18,11 +18,10 @@ import sys
+@@ -18,11 +18,10 @@
from pyqi.util import is_py2
if is_py2():
@@ -354,7 +355,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
from copy import copy
from glob import glob
from os.path import abspath, exists, isdir, isfile, split
-@@ -125,7 +124,7 @@ class HTMLInputOption(InterfaceInputOpti
+@@ -125,7 +124,7 @@
if self.Choices is None:
raise IncompetentDeveloperError(
"must supply a list of Choices for type '%s'" % self.type, self)
@@ -363,7 +364,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
raise IncompetentDeveloperError(
"choices must be a list of strings ('%s' supplied)"
% str(type(self.Choices)).split("'")[1], self)
-@@ -513,7 +512,7 @@ def get_http_handler(module):
+@@ -513,7 +512,7 @@
def start_server(port, module):
"""Start a server for the HTMLInterface on the specified port"""
interface_server = HTTPServer(("", port), get_http_handler(module))
@@ -372,48 +373,48 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
print("To close the server, type 'ctrl-c' into this window.")
try:
interface_server.serve_forever()
---- a/pyqi/core/interfaces/html/input_handler.py
-+++ b/pyqi/core/interfaces/html/input_handler.py
+--- pyqi.orig/pyqi/core/interfaces/html/input_handler.py
++++ pyqi/pyqi/core/interfaces/html/input_handler.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
---- a/pyqi/core/interfaces/html/output_handler.py
-+++ b/pyqi/core/interfaces/html/output_handler.py
+--- pyqi.orig/pyqi/core/interfaces/html/output_handler.py
++++ pyqi/pyqi/core/interfaces/html/output_handler.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
---- a/pyqi/core/interfaces/optparse/__init__.py
-+++ b/pyqi/core/interfaces/optparse/__init__.py
+--- pyqi.orig/pyqi/core/interfaces/optparse/__init__.py
++++ pyqi/pyqi/core/interfaces/optparse/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/core/interfaces/optparse/input_handler.py
-+++ b/pyqi/core/interfaces/optparse/input_handler.py
+--- pyqi.orig/pyqi/core/interfaces/optparse/input_handler.py
++++ pyqi/pyqi/core/interfaces/optparse/input_handler.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Command line interface input handlers
---- a/pyqi/core/interfaces/optparse/output_handler.py
-+++ b/pyqi/core/interfaces/optparse/output_handler.py
+--- pyqi.orig/pyqi/core/interfaces/optparse/output_handler.py
++++ pyqi/pyqi/core/interfaces/optparse/output_handler.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Command line interface output handlers
---- a/pyqi/core/log.py
-+++ b/pyqi/core/log.py
+--- pyqi.orig/pyqi/core/log.py
++++ pyqi/pyqi/core/log.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -429,15 +430,15 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
from sys import stderr
from datetime import datetime
---- a/pyqi/core/parallel.py
-+++ b/pyqi/core/parallel.py
+--- pyqi.orig/pyqi/core/parallel.py
++++ pyqi/pyqi/core/parallel.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Manage IPython.parallel clusters in the notebook.
-@@ -73,7 +73,7 @@ class ClusterManager(LoggingConfigurable
+@@ -73,7 +73,7 @@
def update_profiles(self):
"""List all profiles in the ipython_dir and cwd.
"""
@@ -446,7 +447,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
for profile in list_profiles_in(path):
pd = self.get_profile_dir(profile, path)
if profile not in self.profiles:
-@@ -94,7 +94,7 @@ class ClusterManager(LoggingConfigurable
+@@ -94,7 +94,7 @@
def check_profile(self, profile):
if profile not in self.profiles:
@@ -455,7 +456,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
def profile_info(self, profile):
self.check_profile(profile)
-@@ -112,7 +112,7 @@ class ClusterManager(LoggingConfigurable
+@@ -112,7 +112,7 @@
self.check_profile(profile)
data = self.profiles[profile]
if data['status'] == 'running':
@@ -464,7 +465,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
cl, esl, default_n = self.build_launchers(data['profile_dir'])
n = n if n is not None else default_n
-@@ -154,7 +154,7 @@ class ClusterManager(LoggingConfigurable
+@@ -154,7 +154,7 @@
self.check_profile(profile)
data = self.profiles[profile]
if data['status'] == 'stopped':
@@ -473,7 +474,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
data = self.profiles[profile]
cl = data['controller_launcher']
esl = data['engine_set_launcher']
-@@ -172,7 +172,7 @@ class ClusterManager(LoggingConfigurable
+@@ -172,7 +172,7 @@
return result
def stop_all_clusters(self):
@@ -482,15 +483,15 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
self.stop_cluster(p)
---- a/pyqi/functional.py
-+++ b/pyqi/functional.py
+--- pyqi.orig/pyqi/functional.py
++++ pyqi/pyqi/functional.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
from pyqi.core.interface import Interface, InterfaceOption
from testing import FilterSamples, FilterObservations
-@@ -7,6 +7,7 @@ from types import NoneType
+@@ -7,6 +7,7 @@
from pyqi.core.factory import general_factory
from biom.table import Table as BIOMTable
from biom.parse import parse_biom_table
@@ -498,7 +499,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
class Functional(Interface):
-@@ -67,11 +68,11 @@ t3 = parse_biom_table(
+@@ -67,11 +68,11 @@
open('/Users/mcdonadt/ResearchWork/software/biom-format/examples/rich_sparse_otu_table.biom'))
res = g(f("asdasdasd", seqs_per_sample=3), seqs_per_observation=1)
@@ -515,8 +516,8 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
+ print(i)
+print("***")
+print(res3)
---- a/pyqi/interfaces/__init__.py
-+++ b/pyqi/interfaces/__init__.py
+--- pyqi.orig/pyqi/interfaces/__init__.py
++++ pyqi/pyqi/interfaces/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -532,32 +533,32 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
__credits__ = ["Greg Caporaso", "Daniel McDonald", "Doug Wendel",
"Jai Ram Rideout"]
---- a/pyqi/interfaces/html/config/make_bash_completion.py
-+++ b/pyqi/interfaces/html/config/make_bash_completion.py
+--- pyqi.orig/pyqi/interfaces/html/config/make_bash_completion.py
++++ pyqi/pyqi/interfaces/html/config/make_bash_completion.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/interfaces/html/config/make_command.py
-+++ b/pyqi/interfaces/html/config/make_command.py
+--- pyqi.orig/pyqi/interfaces/html/config/make_command.py
++++ pyqi/pyqi/interfaces/html/config/make_command.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/interfaces/html/config/make_optparse.py
-+++ b/pyqi/interfaces/html/config/make_optparse.py
+--- pyqi.orig/pyqi/interfaces/html/config/make_optparse.py
++++ pyqi/pyqi/interfaces/html/config/make_optparse.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/interfaces/optparse/__init__.py
-+++ b/pyqi/interfaces/optparse/__init__.py
+--- pyqi.orig/pyqi/interfaces/optparse/__init__.py
++++ pyqi/pyqi/interfaces/optparse/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -573,40 +574,40 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
__credits__ = ["Greg Caporaso", "Daniel McDonald", "Doug Wendel",
"Jai Ram Rideout"]
---- a/pyqi/interfaces/optparse/config/__init__.py
-+++ b/pyqi/interfaces/optparse/config/__init__.py
+--- pyqi.orig/pyqi/interfaces/optparse/config/__init__.py
++++ pyqi/pyqi/interfaces/optparse/config/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/interfaces/optparse/config/make_bash_completion.py
-+++ b/pyqi/interfaces/optparse/config/make_bash_completion.py
+--- pyqi.orig/pyqi/interfaces/optparse/config/make_bash_completion.py
++++ pyqi/pyqi/interfaces/optparse/config/make_bash_completion.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/interfaces/optparse/config/make_command.py
-+++ b/pyqi/interfaces/optparse/config/make_command.py
+--- pyqi.orig/pyqi/interfaces/optparse/config/make_command.py
++++ pyqi/pyqi/interfaces/optparse/config/make_command.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/interfaces/optparse/config/make_optparse.py
-+++ b/pyqi/interfaces/optparse/config/make_optparse.py
+--- pyqi.orig/pyqi/interfaces/optparse/config/make_optparse.py
++++ pyqi/pyqi/interfaces/optparse/config/make_optparse.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/interfaces/optparse/config/make_release.py
-+++ b/pyqi/interfaces/optparse/config/make_release.py
+--- pyqi.orig/pyqi/interfaces/optparse/config/make_release.py
++++ pyqi/pyqi/interfaces/optparse/config/make_release.py
@@ -1,5 +1,5 @@
-#!/usr/bin/env python
-from __future__ import division
@@ -615,16 +616,16 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
__credits__ = ["Daniel McDonald"]
---- a/pyqi/interfaces/optparse/config/serve_html_interface.py
-+++ b/pyqi/interfaces/optparse/config/serve_html_interface.py
+--- pyqi.orig/pyqi/interfaces/optparse/config/serve_html_interface.py
++++ pyqi/pyqi/interfaces/optparse/config/serve_html_interface.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/pyqi/interfaces/optparse/input_handler.py
-+++ b/pyqi/interfaces/optparse/input_handler.py
+--- pyqi.orig/pyqi/interfaces/optparse/input_handler.py
++++ pyqi/pyqi/interfaces/optparse/input_handler.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -640,8 +641,8 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
__credits__ = ["Greg Caporaso", "Daniel McDonald", "Doug Wendel",
"Jai Ram Rideout"]
---- a/pyqi/interfaces/optparse/output_handler.py
-+++ b/pyqi/interfaces/optparse/output_handler.py
+--- pyqi.orig/pyqi/interfaces/optparse/output_handler.py
++++ pyqi/pyqi/interfaces/optparse/output_handler.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -657,15 +658,15 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
__credits__ = ["Greg Caporaso", "Daniel McDonald", "Doug Wendel",
"Jai Ram Rideout"]
---- a/pyqi/util.py
-+++ b/pyqi/util.py
+--- pyqi.orig/pyqi/util.py
++++ pyqi/pyqi/util.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
-@@ -88,7 +88,7 @@ def old_to_new_command(driver_name, proj
+@@ -88,7 +88,7 @@
Use like this (put in the script you want to deprecate):
@@ -674,79 +675,79 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
import sys
from pyqi.util import old_to_new_command
---- a/scripts/bar
-+++ b/scripts/bar
+--- pyqi.orig/scripts/bar
++++ pyqi/scripts/bar
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
__author__ = "b"
__copyright__ = "q"
---- a/scripts/direct_make_command.py
-+++ b/scripts/direct_make_command.py
+--- pyqi.orig/scripts/direct_make_command.py
++++ pyqi/scripts/direct_make_command.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/scripts/foo
-+++ b/scripts/foo
+--- pyqi.orig/scripts/foo
++++ pyqi/scripts/foo
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
from __future__ import division
__author__ = "b"
---- a/scripts/optparse
-+++ b/scripts/optparse
+--- pyqi.orig/scripts/optparse
++++ pyqi/scripts/optparse
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/scripts/pyqi
-+++ b/scripts/pyqi
+--- pyqi.orig/scripts/pyqi
++++ pyqi/scripts/pyqi
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/scripts/qiime
-+++ b/scripts/qiime
+--- pyqi.orig/scripts/qiime
++++ pyqi/scripts/qiime
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
---- a/scripts/test_bar
-+++ b/scripts/test_bar
+--- pyqi.orig/scripts/test_bar
++++ pyqi/scripts/test_bar
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
__author__ = "b"
__copyright__ = "q"
---- a/scripts/testing
-+++ b/scripts/testing
+--- pyqi.orig/scripts/testing
++++ pyqi/scripts/testing
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
from pyqi.core.interfaces.optparse import (OptparseOption,
OptparseUsageExample,
---- a/setup.py
-+++ b/setup.py
+--- pyqi.orig/setup.py
++++ pyqi/setup.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
-@@ -32,8 +32,10 @@ classes = """
+@@ -32,8 +32,11 @@
Topic :: Software Development :: Libraries :: Application Frameworks
Topic :: Software Development :: User Interfaces
Programming Language :: Python
@@ -756,17 +757,18 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
+ Programming Language :: Python :: 3.10
+ Programming Language :: Python :: 3.11
+ Programming Language :: Python :: 3.12
++ Programming Language :: Python :: 3.13
Programming Language :: Python :: Implementation :: CPython
Operating System :: OS Independent
Operating System :: POSIX
-@@ -43,8 +44,8 @@ classifiers = [s.strip() for s in classe
+@@ -43,8 +46,8 @@
# Verify Python version
ver = '.'.join(map(str, [sys.version_info.major, sys.version_info.minor]))
-if ver not in ['2.7', '3.3']:
- sys.stderr.write("Only Python 2.7 and 3.3 are supported.")
-+if ver not in ['3.9', '3.10', '3.11', '3.12']:
-+ sys.stderr.write("Only Python 3.9 to 3.12 are supported.")
++if ver not in ['3.9', '3.10', '3.11', '3.12', '3.13']:
++ sys.stderr.write("Only Python 3.9 to 3.13 are supported.")
sys.exit(1)
long_description = """pyqi (canonically pronounced pie chee) is a Python framework designed to support wrapping general commands in multiple types of interfaces, including at the command line, HTML, and API levels."""
=====================================
debian/patches/fix-syntax-warning.patch
=====================================
@@ -1,5 +1,5 @@
Description: Fix SyntaxWarning
- Fix SyntaxWarning emited during the build.
+ Fix SyntaxWarning emitted during the build.
Author: Emmanuel Arias <eamanu at debian.org>
Forwarded: no
Last-Update: 2024-12-09
=====================================
debian/patches/fix_sphinx_htmlhelp.patch
=====================================
@@ -1,7 +1,7 @@
Description: Fix htmlhelp in sphinx
Bug-Debian: https://bugs.debian.org/959598
Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 11 May 2020 09:35:05 +0200
+Last-Update: 2020-05-11
--- a/doc/Makefile
+++ b/doc/Makefile
View it on GitLab: https://salsa.debian.org/med-team/pyqi/-/compare/81519ac5661f7e1c4bb30f75bc73277722b3b9cf...76fdc7f35569351b1335212f0ab761510a3eb661
--
View it on GitLab: https://salsa.debian.org/med-team/pyqi/-/compare/81519ac5661f7e1c4bb30f75bc73277722b3b9cf...76fdc7f35569351b1335212f0ab761510a3eb661
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