[med-svn] [Git][med-team/pyqi][master] Remove redundant cgi import line
Nilesh Patra
gitlab at salsa.debian.org
Mon Mar 30 13:34:16 BST 2020
Nilesh Patra pushed to branch master at Debian Med / pyqi
Commits:
dc11ad21 by Nilesh Patra at 2020-03-30T17:59:38+05:30
Remove redundant cgi import line
- - - - -
1 changed file:
- debian/patches/2to3.patch
Changes:
=====================================
debian/patches/2to3.patch
=====================================
@@ -5,7 +5,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
--- a/doc/conf.py
+++ b/doc/conf.py
-@@ -40,8 +40,8 @@ source_suffix = '.rst'
+@@ -40,8 +40,8 @@
master_doc = 'index'
# General information about the project.
@@ -16,7 +16,7 @@ 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 +27,7 @@ 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 +38,7 @@ 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 = [
@@ -51,7 +51,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
--- a/doc/tutorials/defining_new_commands.rst
+++ b/doc/tutorials/defining_new_commands.rst
-@@ -20,7 +20,7 @@ To create our sequence collection summar
+@@ -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 +60,7 @@ 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 +69,7 @@ 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.
@@ -86,7 +86,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
# 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
+@@ -24,7 +24,7 @@
The resulting file will look something like this::
@@ -95,7 +95,7 @@ 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::
@@ -130,7 +130,7 @@ 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'])
@@ -187,7 +187,7 @@ 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 +196,7 @@ 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 = []
@@ -215,7 +215,7 @@ 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:
@@ -266,7 +266,7 @@ 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 +275,7 @@ 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 +284,7 @@ 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"""
@@ -341,7 +341,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
-@@ -18,7 +18,7 @@ import sys
+@@ -18,11 +18,10 @@
from pyqi.util import is_py2
if is_py2():
@@ -350,7 +350,11 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
else:
from http.server import BaseHTTPRequestHandler, HTTPServer
-@@ -125,7 +125,7 @@ class HTMLInputOption(InterfaceInputOpti
+-from cgi import parse_header, parse_multipart, parse_qs, FieldStorage
+ from copy import copy
+ from glob import glob
+ from os.path import abspath, exists, isdir, isfile, split
+@@ -125,7 +124,7 @@
if self.Choices is None:
raise IncompetentDeveloperError(
"must supply a list of Choices for type '%s'" % self.type, self)
@@ -359,7 +363,7 @@ 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 +513,7 @@ 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))
@@ -433,7 +437,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
"""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.
"""
@@ -442,7 +446,7 @@ 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:
@@ -451,7 +455,7 @@ 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':
@@ -460,7 +464,7 @@ 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':
@@ -469,7 +473,7 @@ 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):
@@ -486,7 +490,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
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
@@ -494,7 +498,7 @@ 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)
@@ -661,7 +665,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
#-----------------------------------------------------------------------------
# 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):
@@ -742,7 +746,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
-@@ -32,8 +32,8 @@ classes = """
+@@ -32,8 +32,8 @@
Topic :: Software Development :: Libraries :: Application Frameworks
Topic :: Software Development :: User Interfaces
Programming Language :: Python
@@ -753,7 +757,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200
Programming Language :: Python :: Implementation :: CPython
Operating System :: OS Independent
Operating System :: POSIX
-@@ -43,8 +43,8 @@ classifiers = [s.strip() for s in classe
+@@ -43,8 +43,8 @@
# Verify Python version
ver = '.'.join(map(str, [sys.version_info.major, sys.version_info.minor]))
View it on GitLab: https://salsa.debian.org/med-team/pyqi/-/commit/dc11ad21408d1eb4b0d7ec935f2d4dda3448a1af
--
View it on GitLab: https://salsa.debian.org/med-team/pyqi/-/commit/dc11ad21408d1eb4b0d7ec935f2d4dda3448a1af
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