From 361b0b7ecc98c963c705fd0cd4e73a12bd4d6867 Mon Sep 17 00:00:00 2001
From: Romain Dorgueil <romain@dorgueil.net>
Date: Thu, 16 May 2019 10:19:47 +0100
Subject: [PATCH 1/3] Fixes unused return variable, restore stdout/stderr even
 if there is an error.

---
 bonobo/contrib/django/commands.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/bonobo/contrib/django/commands.py b/bonobo/contrib/django/commands.py
index f2a8a15..4974540 100644
--- a/bonobo/contrib/django/commands.py
+++ b/bonobo/contrib/django/commands.py
@@ -77,6 +77,7 @@ class ETLCommand(BaseCommand):
         self.stderr = OutputWrapper(ConsoleOutputPlugin._stderr, ending=CLEAR_EOL + "\n")
         self.stderr.style_func = lambda x: Fore.LIGHTRED_EX + Back.RED + "!" + Style.RESET_ALL + " " + x
 
-        results = self.run(*args, **options)
-
-        self.stdout, self.stderr = _stdout_backup, _stderr_backup
+        try:
+            return self.run(*args, **options)
+        finally:
+            self.stdout, self.stderr = _stdout_backup, _stderr_backup

From e17dbc7134c4d4ea8561b10dca91ad53a03ebce3 Mon Sep 17 00:00:00 2001
From: Romain Dorgueil <romain@dorgueil.net>
Date: Thu, 16 May 2019 11:50:38 +0200
Subject: [PATCH 2/3] Fixes code smell and ignore some useless (in context)
 lgtm rules.

---
 bonobo/__init__.py                |  4 ++--
 bonobo/_api.py                    |  7 +++----
 bonobo/execution/contexts/base.py |  2 +-
 bonobo/execution/contexts/node.py |  4 +++-
 bonobo/util/collections.py        | 13 ++++++++++---
 bonobo/util/statistics.py         |  2 +-
 6 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/bonobo/__init__.py b/bonobo/__init__.py
index 2487780..829aa6e 100644
--- a/bonobo/__init__.py
+++ b/bonobo/__init__.py
@@ -56,8 +56,8 @@ from bonobo._version import __version__
 __all__ = ["__version__"] + __all__
 with (Path(__file__).parent / "bonobo.svg").open() as f:
     __logo__ = f.read()
-__doc__ = __doc__
-__version__ = __version__
+__doc__ = __doc__  # lgtm [py/redundant-assignment]
+__version__ = __version__  # lgtm [py/redundant-assignment]
 
 
 def _repr_html_():
diff --git a/bonobo/_api.py b/bonobo/_api.py
index 78ed72f..8432eee 100644
--- a/bonobo/_api.py
+++ b/bonobo/_api.py
@@ -125,14 +125,13 @@ def open_fs(fs_url=None, *args, **kwargs):
     :param str default_protocol: The protocol to use if one is not supplied in the FS URL (defaults to ``"osfs"``).
     :returns: :class:`fs.base.FS` object
     """
+    import os
     from fs.opener import open_fs as _open_fs
-    from os.path import expanduser
-    from os import getcwd
 
     if fs_url is None:
-        fs_url = getcwd()
+        fs_url = os.getcwd()
 
-    return _open_fs(expanduser(str(fs_url)), *args, **kwargs)
+    return _open_fs(os.path.expanduser(str(fs_url)), *args, **kwargs)
 
 
 # standard transformations
diff --git a/bonobo/execution/contexts/base.py b/bonobo/execution/contexts/base.py
index 9399d3f..6f3fa71 100644
--- a/bonobo/execution/contexts/base.py
+++ b/bonobo/execution/contexts/base.py
@@ -74,7 +74,7 @@ class Lifecycle:
         self.start()
         return self
 
-    def __exit__(self, exc_type=None, exc_val=None, exc_tb=None):
+    def __exit__(self, exc_type=None, exc_val=None, exc_tb=None):  # lgtm [py/special-method-wrong-signature]
         self.stop()
 
     def get_flags_as_string(self):
diff --git a/bonobo/execution/contexts/node.py b/bonobo/execution/contexts/node.py
index 30b0d5b..2a4294c 100644
--- a/bonobo/execution/contexts/node.py
+++ b/bonobo/execution/contexts/node.py
@@ -259,7 +259,9 @@ class NodeExecutionContext(BaseContext, WithStatistics):
         """
         for message in messages:
             if not isinstance(message, Token):
-                message = ensure_tuple(message, cls=self._input_type, length=self._input_length)
+                message = ensure_tuple(
+                    message, cls=self._input_type, length=self._input_length
+                )  # lgtm [py/call/wrong-named-argument]
                 if self._input_length is None:
                     self._input_length = len(message)
             self.input.put(message)
diff --git a/bonobo/util/collections.py b/bonobo/util/collections.py
index 9e903ec..bd00954 100644
--- a/bonobo/util/collections.py
+++ b/bonobo/util/collections.py
@@ -34,6 +34,10 @@ def _with_length_check(f):
 
 
 def tuple_or_const(tuple_or_mixed, *, consts=(None, False), **kwargs):
+    """
+    Like ensure_tuple, but also accept as valid outputs a list of constants.
+    """
+
     if tuple_or_mixed in consts:
         return tuple_or_mixed
     if isinstance(tuple_or_mixed, str):
@@ -49,10 +53,13 @@ def ensure_tuple(tuple_or_mixed, *, cls=None):
     If it's not a tuple, let's make a tuple of one item.
     Otherwise, not changed.
 
-    :param tuple_or_mixed:
-    :return: tuple
-
+    :param tuple_or_mixed: material to work on.
+    :param cls: type of the resulting tuple, or `tuple` if not provided.
+    :param length: provided by `_with_length_check` decorator, if specified, make sure that the tuple is of this
+                   length (and raise a `TypeError` if not), otherwise, do nothing.
+    :return: tuple (or something of type `cls`, if provided)
     """
+
     if cls is None:
         cls = tuple
 
diff --git a/bonobo/util/statistics.py b/bonobo/util/statistics.py
index 62a5075..23c7ccd 100644
--- a/bonobo/util/statistics.py
+++ b/bonobo/util/statistics.py
@@ -26,7 +26,7 @@ class Timer:
         self.__start = time.time()
         return self
 
-    def __exit__(self, type=None, value=None, traceback=None):
+    def __exit__(self, type=None, value=None, traceback=None):  # lgtm [py/special-method-wrong-signature]
         # Error handling here
         self.__finish = time.time()
 

From 3bc28aa0c22750f51836b4660adac8c632155183 Mon Sep 17 00:00:00 2001
From: Romain Dorgueil <romain@dorgueil.net>
Date: Thu, 16 May 2019 11:53:21 +0200
Subject: [PATCH 3/3] Update requirements, fixes packaging version problem.

---
 Makefile                                |  2 +-
 Projectfile                             |  2 +-
 bonobo/__init__.py                      | 49 ++++---------------------
 bonobo/commands/__init__.py             |  1 +
 bonobo/config/__init__.py               |  6 +--
 bonobo/contrib/django/__init__.py       |  2 +-
 bonobo/contrib/django/commands.py       |  4 +-
 bonobo/contrib/google/__init__.py       |  7 ++--
 bonobo/contrib/opendatasoft/__init__.py |  2 +-
 bonobo/examples/__init__.py             |  2 +-
 bonobo/execution/strategies/__init__.py |  4 +-
 bonobo/util/__init__.py                 | 12 +-----
 requirements-dev.txt                    |  3 +-
 requirements-docker.txt                 |  1 -
 requirements-jupyter.txt                |  6 +--
 requirements-sqlalchemy.txt             |  1 -
 requirements.txt                        |  3 +-
 setup.py                                |  4 +-
 18 files changed, 33 insertions(+), 78 deletions(-)

diff --git a/Makefile b/Makefile
index 0cb2978..841d9a2 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-# Generated by Medikit 0.7.1 on 2019-05-08.
+# Generated by Medikit 0.7.1 on 2019-05-16.
 # All changes will be overriden.
 # Edit Projectfile and run “make update” (or “medikit update”) to regenerate.
 
diff --git a/Projectfile b/Projectfile
index 590f670..d6ab52b 100644
--- a/Projectfile
+++ b/Projectfile
@@ -47,7 +47,7 @@ python.add_requirements(
     'graphviz >=0.8,<0.9',
     'jinja2 ~=2.9',
     'mondrian ~=0.8',
-    'packaging ~=17.0',
+    'packaging ~=19.0',
     'psutil ~=5.4',
     'python-slugify ~=1.2.0',
     'requests ~=2.0',
diff --git a/bonobo/__init__.py b/bonobo/__init__.py
index 829aa6e..ee146fd 100644
--- a/bonobo/__init__.py
+++ b/bonobo/__init__.py
@@ -8,50 +8,17 @@
 import sys
 from pathlib import Path
 
+from bonobo._api import (
+    CsvReader, CsvWriter, FileReader, FileWriter, Filter, FixedWindow, Format, Graph, JsonReader, JsonWriter,
+    LdjsonReader, LdjsonWriter, Limit, MapFields, OrderFields, PickleReader, PickleWriter, PrettyPrinter, RateLimited,
+    Rename, SetFields, Tee, UnpackItems, __all__, __doc__, count, create_reader, create_strategy, create_writer,
+    get_argument_parser, get_examples_path, identity, inspect, noop, open_examples_fs, open_fs, parse_args, run
+)
+from bonobo._version import __version__
+
 if sys.version_info < (3, 5):
     raise RuntimeError("Python 3.5+ is required to use Bonobo.")
 
-from bonobo._api import (
-    run,
-    inspect,
-    Graph,
-    create_strategy,
-    open_fs,
-    CsvReader,
-    CsvWriter,
-    FileReader,
-    FileWriter,
-    Filter,
-    FixedWindow,
-    Format,
-    JsonReader,
-    JsonWriter,
-    LdjsonReader,
-    LdjsonWriter,
-    Limit,
-    MapFields,
-    OrderFields,
-    PickleReader,
-    PickleWriter,
-    PrettyPrinter,
-    RateLimited,
-    Rename,
-    SetFields,
-    Tee,
-    UnpackItems,
-    count,
-    identity,
-    noop,
-    create_reader,
-    create_writer,
-    get_examples_path,
-    open_examples_fs,
-    get_argument_parser,
-    parse_args,
-    __all__,
-    __doc__,
-)
-from bonobo._version import __version__
 
 __all__ = ["__version__"] + __all__
 with (Path(__file__).parent / "bonobo.svg").open() as f:
diff --git a/bonobo/commands/__init__.py b/bonobo/commands/__init__.py
index 7568ae3..e66c85f 100644
--- a/bonobo/commands/__init__.py
+++ b/bonobo/commands/__init__.py
@@ -2,6 +2,7 @@ import argparse
 import logging
 
 import mondrian
+
 from bonobo import settings
 from bonobo.commands.base import BaseCommand, BaseGraphCommand
 
diff --git a/bonobo/config/__init__.py b/bonobo/config/__init__.py
index 3e2f3bf..243dc99 100644
--- a/bonobo/config/__init__.py
+++ b/bonobo/config/__init__.py
@@ -5,10 +5,10 @@ configurable transformations, either class-based or function-based.
 """
 
 from bonobo.config.configurables import Configurable
-from bonobo.config.functools import transformation_factory, partial
+from bonobo.config.functools import partial, transformation_factory
 from bonobo.config.options import Method, Option
-from bonobo.config.processors import ContextProcessor, use_context, use_context_processor, use_raw_input, use_no_input
-from bonobo.config.services import Container, Exclusive, Service, use, create_container
+from bonobo.config.processors import ContextProcessor, use_context, use_context_processor, use_no_input, use_raw_input
+from bonobo.config.services import Container, Exclusive, Service, create_container, use
 from bonobo.util import deprecated_alias
 
 requires = deprecated_alias("requires", use)
diff --git a/bonobo/contrib/django/__init__.py b/bonobo/contrib/django/__init__.py
index 24fe68d..459a6c8 100644
--- a/bonobo/contrib/django/__init__.py
+++ b/bonobo/contrib/django/__init__.py
@@ -6,7 +6,7 @@ This module contains all tools for Bonobo and Django to interract nicely.
 
 """
 
-from .utils import create_or_update
 from .commands import ETLCommand
+from .utils import create_or_update
 
 __all__ = ["ETLCommand", "create_or_update"]
diff --git a/bonobo/contrib/django/commands.py b/bonobo/contrib/django/commands.py
index 4974540..e96eac4 100644
--- a/bonobo/contrib/django/commands.py
+++ b/bonobo/contrib/django/commands.py
@@ -2,13 +2,13 @@ from logging import getLogger
 from types import GeneratorType
 
 from colorama import Back, Fore, Style
-from django.core.management import BaseCommand
-from django.core.management.base import OutputWrapper
 from mondrian import term
 
 import bonobo
 from bonobo.plugins.console import ConsoleOutputPlugin
 from bonobo.util.term import CLEAR_EOL
+from django.core.management import BaseCommand
+from django.core.management.base import OutputWrapper
 
 from .utils import create_or_update
 
diff --git a/bonobo/contrib/google/__init__.py b/bonobo/contrib/google/__init__.py
index 126a468..449b58f 100644
--- a/bonobo/contrib/google/__init__.py
+++ b/bonobo/contrib/google/__init__.py
@@ -1,14 +1,15 @@
 import os
 
-# https://developers.google.com/api-client-library/python/guide/aaa_oauth
-# pip install google-api-python-client (1.6.4)
-
 import httplib2
 from apiclient import discovery
 from oauth2client import client, tools
 from oauth2client.file import Storage
 from oauth2client.tools import argparser
 
+# https://developers.google.com/api-client-library/python/guide/aaa_oauth
+# pip install google-api-python-client (1.6.4)
+
+
 HOME_DIR = os.path.expanduser("~")
 GOOGLE_SECRETS = os.path.join(HOME_DIR, ".cache/secrets/client_secrets.json")
 
diff --git a/bonobo/contrib/opendatasoft/__init__.py b/bonobo/contrib/opendatasoft/__init__.py
index 0d00a57..d7377e2 100644
--- a/bonobo/contrib/opendatasoft/__init__.py
+++ b/bonobo/contrib/opendatasoft/__init__.py
@@ -3,8 +3,8 @@ from urllib.parse import urlencode
 import requests  # todo: make this a service so we can substitute it ?
 
 from bonobo.config import Option
-from bonobo.config.processors import ContextProcessor
 from bonobo.config.configurables import Configurable
+from bonobo.config.processors import ContextProcessor
 from bonobo.util.objects import ValueHolder
 
 
diff --git a/bonobo/examples/__init__.py b/bonobo/examples/__init__.py
index ed8a873..3d5cc05 100644
--- a/bonobo/examples/__init__.py
+++ b/bonobo/examples/__init__.py
@@ -1,7 +1,7 @@
 import os
 
 import bonobo
-from bonobo.execution.strategies import STRATEGIES, DEFAULT_STRATEGY
+from bonobo.execution.strategies import DEFAULT_STRATEGY, STRATEGIES
 from bonobo.util.statistics import Timer
 
 
diff --git a/bonobo/execution/strategies/__init__.py b/bonobo/execution/strategies/__init__.py
index 1d66554..5995bf0 100644
--- a/bonobo/execution/strategies/__init__.py
+++ b/bonobo/execution/strategies/__init__.py
@@ -7,9 +7,7 @@ at home if you want to give it a shot.
 
 """
 from bonobo.execution.strategies.executor import (
-    ProcessPoolExecutorStrategy,
-    ThreadPoolExecutorStrategy,
-    AsyncThreadPoolExecutorStrategy,
+    AsyncThreadPoolExecutorStrategy, ProcessPoolExecutorStrategy, ThreadPoolExecutorStrategy
 )
 from bonobo.execution.strategies.naive import NaiveStrategy
 
diff --git a/bonobo/util/__init__.py b/bonobo/util/__init__.py
index 881fada..c3c33e2 100644
--- a/bonobo/util/__init__.py
+++ b/bonobo/util/__init__.py
@@ -6,17 +6,9 @@ and inspect transformations, graphs, and nodes.
 from bonobo.util.collections import cast, ensure_tuple, sortedlist, tuplize
 from bonobo.util.compat import deprecated, deprecated_alias
 from bonobo.util.inspect import (
-    inspect_node,
-    isconfigurable,
-    isconfigurabletype,
-    iscontextprocessor,
-    isdict,
-    ismethod,
-    isoption,
-    istuple,
-    istype,
+    inspect_node, isconfigurable, isconfigurabletype, iscontextprocessor, isdict, ismethod, isoption, istuple, istype
 )
-from bonobo.util.objects import get_name, get_attribute_or_create, ValueHolder
+from bonobo.util.objects import ValueHolder, get_attribute_or_create, get_name
 
 # Bonobo's util API
 __all__ = [
diff --git a/requirements-dev.txt b/requirements-dev.txt
index eb8e9c5..4cc73b8 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -20,11 +20,10 @@ jinja2==2.10.1
 markupsafe==1.1.1
 more-itertools==7.0.0
 packaging==19.0
-pathlib2==2.3.3
 pluggy==0.11.0
 poyo==0.4.2
 py==1.8.0
-pygments==2.3.1
+pygments==2.4.0
 pyparsing==2.4.0
 pytest-cov==2.7.1
 pytest-timeout==1.3.3
diff --git a/requirements-docker.txt b/requirements-docker.txt
index b29ec7f..223cc84 100644
--- a/requirements-docker.txt
+++ b/requirements-docker.txt
@@ -24,7 +24,6 @@ requests==2.21.0
 semantic-version==2.6.0
 six==1.12.0
 stevedore==1.30.1
-typing==3.6.6
 unidecode==1.0.23
 urllib3==1.24.3
 websocket-client==0.56.0
diff --git a/requirements-jupyter.txt b/requirements-jupyter.txt
index 59cf1bd..f8b23f3 100644
--- a/requirements-jupyter.txt
+++ b/requirements-jupyter.txt
@@ -7,7 +7,7 @@ bleach==3.1.0
 decorator==4.4.0
 defusedxml==0.6.0
 entrypoints==0.3
-ipykernel==5.1.0
+ipykernel==5.1.1
 ipython-genutils==0.2.0
 ipython==7.5.0
 ipywidgets==6.0.1
@@ -30,8 +30,8 @@ pickleshare==0.7.5
 prometheus-client==0.6.0
 prompt-toolkit==2.0.9
 ptyprocess==0.6.0
-pygments==2.3.1
-pyrsistent==0.15.1
+pygments==2.4.0
+pyrsistent==0.15.2
 python-dateutil==2.8.0
 pyzmq==18.0.1
 qtconsole==4.4.4
diff --git a/requirements-sqlalchemy.txt b/requirements-sqlalchemy.txt
index d297067..3e386b6 100644
--- a/requirements-sqlalchemy.txt
+++ b/requirements-sqlalchemy.txt
@@ -22,7 +22,6 @@ requests==2.21.0
 six==1.12.0
 sqlalchemy==1.3.3
 stevedore==1.30.1
-typing==3.6.6
 unidecode==1.0.23
 urllib3==1.24.3
 whistle==1.0.1
diff --git a/requirements.txt b/requirements.txt
index d4c6c9f..7ea6f18 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -10,7 +10,7 @@ idna==2.8
 jinja2==2.10.1
 markupsafe==1.1.1
 mondrian==0.8.0
-packaging==17.1
+packaging==19.0
 pbr==5.2.0
 psutil==5.6.2
 pyparsing==2.4.0
@@ -19,7 +19,6 @@ pytz==2019.1
 requests==2.21.0
 six==1.12.0
 stevedore==1.30.1
-typing==3.6.6
 unidecode==1.0.23
 urllib3==1.24.3
 whistle==1.0.1
diff --git a/setup.py b/setup.py
index a91d362..16fb16c 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,4 @@
-# Generated by Medikit 0.7.1 on 2019-05-08.
+# Generated by Medikit 0.7.1 on 2019-05-16.
 # All changes will be overriden.
 # Edit Projectfile and run “make update” (or “medikit update”) to regenerate.
 
@@ -70,7 +70,7 @@ setup(
         "graphviz (>= 0.8, < 0.9)",
         "jinja2 (~= 2.9)",
         "mondrian (~= 0.8)",
-        "packaging (~= 17.0)",
+        "packaging (~= 19.0)",
         "psutil (~= 5.4)",
         "python-slugify (~= 1.2.0)",
         "requests (~= 2.0)",