From 6a1203602f7f7fe8ff5f16b48a8bfbb7191ed5f5 Mon Sep 17 00:00:00 2001
From: Romain Dorgueil <romain@dorgueil.net>
Date: Mon, 16 Jul 2018 10:00:28 +0200
Subject: [PATCH 1/3] Minor tweaks about code quality.

---
 bonobo/config/configurables.py          | 2 +-
 bonobo/config/services.py               | 2 --
 bonobo/examples/datasets/__main__.py    | 2 +-
 bonobo/execution/contexts/base.py       | 5 ++---
 bonobo/execution/strategies/executor.py | 6 +++---
 bonobo/nodes/io/csv.py                  | 3 +--
 bonobo/plugins/sentry.py                | 1 -
 bonobo/settings.py                      | 2 +-
 bonobo/util/environ.py                  | 1 -
 9 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/bonobo/config/configurables.py b/bonobo/config/configurables.py
index 20ceca5..98e21e7 100644
--- a/bonobo/config/configurables.py
+++ b/bonobo/config/configurables.py
@@ -72,7 +72,7 @@ class ConfigurableMeta(type):
 
 try:
     import _functools
-except:
+except ImportError:
     import functools
 
     PartiallyConfigured = functools.partial
diff --git a/bonobo/config/services.py b/bonobo/config/services.py
index 282d88f..eae3b8d 100644
--- a/bonobo/config/services.py
+++ b/bonobo/config/services.py
@@ -1,5 +1,3 @@
-import inspect
-import pprint
 import re
 import threading
 import types
diff --git a/bonobo/examples/datasets/__main__.py b/bonobo/examples/datasets/__main__.py
index 91f702d..a62ce33 100644
--- a/bonobo/examples/datasets/__main__.py
+++ b/bonobo/examples/datasets/__main__.py
@@ -51,7 +51,7 @@ if __name__ == '__main__':
                         s3.head_object(
                             Bucket='bonobo-examples', Key=s3_path
                         )
-                    except:
+                    except Exception:
                         s3.upload_file(
                             local_path,
                             'bonobo-examples',
diff --git a/bonobo/execution/contexts/base.py b/bonobo/execution/contexts/base.py
index b7f07c5..e071266 100644
--- a/bonobo/execution/contexts/base.py
+++ b/bonobo/execution/contexts/base.py
@@ -1,7 +1,6 @@
 import logging
 import sys
 from contextlib import contextmanager
-from logging import ERROR
 
 from bonobo.util import deprecated
 from bonobo.util.objects import Wrapper, get_name
@@ -13,7 +12,7 @@ def recoverable(error_handler):
     try:
         yield
     except Exception as exc:  # pylint: disable=broad-except
-        error_handler(*sys.exc_info(), level=ERROR)
+        error_handler(*sys.exc_info(), level=logging.ERROR)
 
 
 @contextmanager
@@ -21,7 +20,7 @@ def unrecoverable(error_handler):
     try:
         yield
     except Exception as exc:  # pylint: disable=broad-except
-        error_handler(*sys.exc_info(), level=ERROR)
+        error_handler(*sys.exc_info(), level=logging.ERROR)
         raise  # raise unrecoverableerror from exc ?
 
 
diff --git a/bonobo/execution/strategies/executor.py b/bonobo/execution/strategies/executor.py
index 1e2d45f..e900ce1 100644
--- a/bonobo/execution/strategies/executor.py
+++ b/bonobo/execution/strategies/executor.py
@@ -29,7 +29,7 @@ class ExecutorStrategy(Strategy):
         with self.create_executor() as executor:
             try:
                 context.start(self.get_starter(executor, futures))
-            except:
+            except Exception:
                 logger.critical('Exception caught while starting execution context.', exc_info=sys.exc_info())
 
             while context.alive:
@@ -53,14 +53,14 @@ class ExecutorStrategy(Strategy):
                 try:
                     with node:
                         node.loop()
-                except:
+                except Exception:
                     logging.getLogger(__name__).critical(
                         'Critical error in threadpool node starter.', exc_info=sys.exc_info()
                     )
 
             try:
                 futures.append(executor.submit(_runner))
-            except:
+            except Exception:
                 logging.getLogger(__name__).critical('futures.append', exc_info=sys.exc_info())
 
         return starter
diff --git a/bonobo/nodes/io/csv.py b/bonobo/nodes/io/csv.py
index d7d03fb..7900dca 100644
--- a/bonobo/nodes/io/csv.py
+++ b/bonobo/nodes/io/csv.py
@@ -1,12 +1,11 @@
 import csv
 
-from bonobo.config import Option, use_raw_input, use_context
+from bonobo.config import Option, use_context
 from bonobo.config.options import Method, RenamedOption
 from bonobo.constants import NOT_MODIFIED
 from bonobo.nodes.io.base import FileHandler
 from bonobo.nodes.io.file import FileReader, FileWriter
 from bonobo.util import ensure_tuple
-from bonobo.util.bags import BagType
 
 
 class CsvHandler(FileHandler):
diff --git a/bonobo/plugins/sentry.py b/bonobo/plugins/sentry.py
index 44799da..4704c0b 100644
--- a/bonobo/plugins/sentry.py
+++ b/bonobo/plugins/sentry.py
@@ -1,5 +1,4 @@
 from bonobo.plugins import Plugin
-from raven import Client
 
 
 class SentryPlugin(Plugin):
diff --git a/bonobo/settings.py b/bonobo/settings.py
index 799ba3d..d87a329 100644
--- a/bonobo/settings.py
+++ b/bonobo/settings.py
@@ -52,7 +52,7 @@ class Setting:
     def set(self, value):
         value = self.formatter(value) if self.formatter else value
         if self.validator and not self.validator(value):
-            raise ValidationError('Invalid value {!r} for setting {}.'.format(value, self.name))
+            raise ValidationError(self, 'Invalid value {!r} for setting {!r}.'.format(value, self.name))
         self.value = value
 
     def set_if_true(self, value):
diff --git a/bonobo/util/environ.py b/bonobo/util/environ.py
index b344d29..980d1db 100644
--- a/bonobo/util/environ.py
+++ b/bonobo/util/environ.py
@@ -57,7 +57,6 @@ def get_argument_parser(parser=None):
     :return:
     """
     if parser is None:
-        import argparse
         parser = argparse.ArgumentParser()
 
     # Store globally to be able to warn the user about the fact he's probably wrong not to pass a parser to

From 66451d03bb8effe95582c68e306839ca2eeefa47 Mon Sep 17 00:00:00 2001
From: Romain Dorgueil <romain@dorgueil.net>
Date: Sun, 22 Jul 2018 07:34:11 +0200
Subject: [PATCH 2/3] work in progress: working on nodes lifecycle.

---
 Makefile                                      |  2 +-
 bonobo/execution/contexts/base.py             |  3 +--
 bonobo/execution/contexts/graph.py            | 18 ++++++++++----
 bonobo/execution/contexts/node.py             | 24 ++++++++++---------
 requirements-dev.txt                          | 18 +++++++-------
 requirements-docker.txt                       | 17 +++++++------
 requirements-jupyter.txt                      | 13 +++++-----
 requirements-sqlalchemy.txt                   | 19 +++++++--------
 requirements.txt                              | 17 +++++++------
 setup.py                                      |  2 +-
 .../contexts/test_execution_contexts_graph.py |  6 ++---
 ...ode.py => test_execution_contexts_node.py} |  0
 12 files changed, 74 insertions(+), 65 deletions(-)
 rename tests/execution/contexts/{test_node.py => test_execution_contexts_node.py} (100%)

diff --git a/Makefile b/Makefile
index 29446bc..43c4934 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-# Generated by Medikit 0.6.3 on 2018-06-11.
+# Generated by Medikit 0.6.3 on 2018-07-22.
 # All changes will be overriden.
 # Edit Projectfile and run “make update” (or “medikit update”) to regenerate.
 
diff --git a/bonobo/execution/contexts/base.py b/bonobo/execution/contexts/base.py
index e071266..25cca26 100644
--- a/bonobo/execution/contexts/base.py
+++ b/bonobo/execution/contexts/base.py
@@ -53,8 +53,7 @@ class Lifecycle:
 
     @property
     def should_loop(self):
-        # TODO XXX started/stopped?
-        return not any((self.defunct, self.killed))
+        return self.alive and not any((self.defunct, self.killed))
 
     @property
     def status(self):
diff --git a/bonobo/execution/contexts/graph.py b/bonobo/execution/contexts/graph.py
index 3c029b5..b2362db 100644
--- a/bonobo/execution/contexts/graph.py
+++ b/bonobo/execution/contexts/graph.py
@@ -1,14 +1,19 @@
+import logging
 from functools import partial
+from queue import Empty
 from time import sleep
 
 from bonobo.config import create_container
 from bonobo.constants import BEGIN, END
+from bonobo.errors import InactiveReadableError
 from bonobo.execution import events
 from bonobo.execution.contexts.base import BaseContext
 from bonobo.execution.contexts.node import NodeExecutionContext
 from bonobo.execution.contexts.plugin import PluginExecutionContext
 from whistle import EventDispatcher
 
+logger = logging.getLogger(__name__)
+
 
 class GraphExecutionContext(BaseContext):
     """
@@ -104,11 +109,16 @@ class GraphExecutionContext(BaseContext):
             sleep(self.TICK_PERIOD)
 
     def loop(self):
-        while self.should_loop:
-            self.tick()
-            for node in self.nodes:
-                if node.should_loop:
+        nodes = set(node for node in self.nodes if node.should_loop)
+        while self.should_loop and len(nodes):
+            self.tick(pause=False)
+            for node in list(nodes):
+                try:
                     node.step()
+                except Empty:
+                    continue
+                except InactiveReadableError:
+                    nodes.discard(node)
 
     def stop(self, stopper=None):
         super(GraphExecutionContext, self).stop()
diff --git a/bonobo/execution/contexts/node.py b/bonobo/execution/contexts/node.py
index 07cbf16..0affd29 100644
--- a/bonobo/execution/contexts/node.py
+++ b/bonobo/execution/contexts/node.py
@@ -120,20 +120,22 @@ class NodeExecutionContext(BaseContext, WithStatistics):
                 break
             except Empty:
                 sleep(TICK_PERIOD)  # XXX: How do we determine this constant?
-                continue
-            except (
-                    NotImplementedError,
-                    UnrecoverableError,
-            ):
-                self.fatal(sys.exc_info())  # exit loop
-            except Exception:  # pylint: disable=broad-except
-                self.error(sys.exc_info())  # does not exit loop
-            except BaseException:
-                self.fatal(sys.exc_info())  # exit loop
 
         logger.debug('Node loop ends for {!r}.'.format(self))
 
     def step(self):
+        try:
+            self._step()
+        except InactiveReadableError:
+            raise
+        except (NotImplementedError, UnrecoverableError, ):
+            self.fatal(sys.exc_info())  # exit loop
+        except Exception:  # pylint: disable=broad-except
+            self.error(sys.exc_info())  # does not exit loop
+        except BaseException:
+            self.fatal(sys.exc_info())  # exit loop
+
+    def _step(self):
         """
         A single step in the loop.
 
@@ -280,7 +282,7 @@ class NodeExecutionContext(BaseContext, WithStatistics):
         If Queue raises (like Timeout or Empty), stat won't be changed.
 
         """
-        input_bag = self.input.get()
+        input_bag = self.input.get(timeout=0)
 
         # Store or check input type
         if self._input_type is None:
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 704a481..be0cfb2 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,6 +1,6 @@
 -e .[dev]
 -r requirements.txt
-alabaster==0.7.10
+alabaster==0.7.11
 arrow==0.12.1
 atomicwrites==1.1.5
 attrs==18.1.0
@@ -13,7 +13,7 @@ cookiecutter==1.5.1
 coverage==4.5.1
 docutils==0.14
 future==0.16.0
-idna==2.6
+idna==2.7
 imagesize==1.0.0
 jinja2-time==0.2.0
 jinja2==2.10
@@ -22,20 +22,20 @@ more-itertools==4.2.0
 packaging==17.1
 pluggy==0.6.0
 poyo==0.4.1
-py==1.5.3
+py==1.5.4
 pygments==2.2.0
 pyparsing==2.2.0
 pytest-cov==2.5.1
-pytest-timeout==1.2.1
-pytest==3.6.1
+pytest-timeout==1.3.0
+pytest==3.6.3
 python-dateutil==2.7.3
-pytz==2018.4
-requests==2.18.4
+pytz==2018.5
+requests==2.19.1
 six==1.11.0
 snowballstemmer==1.2.1
 sphinx-sitemap==0.2
-sphinx==1.7.5
+sphinx==1.7.6
 sphinxcontrib-websupport==1.1.0
-urllib3==1.22
+urllib3==1.23
 whichcraft==0.4.1
 yapf==0.22.0
diff --git a/requirements-docker.txt b/requirements-docker.txt
index 08c0bf3..4600a77 100644
--- a/requirements-docker.txt
+++ b/requirements-docker.txt
@@ -7,24 +7,23 @@ chardet==3.0.4
 colorama==0.3.9
 docker-pycreds==0.3.0
 docker==2.7.0
-fs==2.0.23
-graphviz==0.8.3
-idna==2.6
+fs==2.0.25
+graphviz==0.8.4
+idna==2.7
 jinja2==2.10
 markupsafe==1.0
 mondrian==0.7.0
 packaging==17.1
-pbr==4.0.4
+pbr==4.1.1
 psutil==5.4.6
 pyparsing==2.2.0
 python-slugify==1.2.5
-pytz==2018.4
-requests==2.18.4
+pytz==2018.5
+requests==2.19.1
 semantic-version==2.6.0
 six==1.11.0
-stevedore==1.28.0
-typing==3.6.4
+stevedore==1.29.0
 unidecode==1.0.22
-urllib3==1.22
+urllib3==1.23
 websocket-client==0.48.0
 whistle==1.0.1
diff --git a/requirements-jupyter.txt b/requirements-jupyter.txt
index 38aef2a..7f6183f 100644
--- a/requirements-jupyter.txt
+++ b/requirements-jupyter.txt
@@ -10,7 +10,7 @@ ipykernel==4.8.2
 ipython-genutils==0.2.0
 ipython==6.4.0
 ipywidgets==6.0.1
-jedi==0.12.0
+jedi==0.12.1
 jinja2==2.10
 jsonschema==2.6.0
 jupyter-client==5.2.3
@@ -21,23 +21,24 @@ markupsafe==1.0
 mistune==0.8.3
 nbconvert==5.3.1
 nbformat==4.4.0
-notebook==5.5.0
+notebook==5.6.0
 pandocfilters==1.4.2
-parso==0.2.1
+parso==0.3.1
 pexpect==4.6.0
 pickleshare==0.7.4
+prometheus-client==0.3.0
 prompt-toolkit==1.0.15
-ptyprocess==0.5.2
+ptyprocess==0.6.0
 pygments==2.2.0
 python-dateutil==2.7.3
-pyzmq==17.0.0
+pyzmq==17.1.0
 qtconsole==4.3.1
 send2trash==1.5.0
 simplegeneric==0.8.1
 six==1.11.0
 terminado==0.8.1
 testpath==0.3.1
-tornado==5.0.2
+tornado==5.1
 traitlets==4.3.2
 wcwidth==0.1.7
 webencodings==0.5.1
diff --git a/requirements-sqlalchemy.txt b/requirements-sqlalchemy.txt
index 8d49e86..f80fd17 100644
--- a/requirements-sqlalchemy.txt
+++ b/requirements-sqlalchemy.txt
@@ -5,23 +5,22 @@ bonobo-sqlalchemy==0.6.0
 certifi==2018.4.16
 chardet==3.0.4
 colorama==0.3.9
-fs==2.0.23
-graphviz==0.8.3
-idna==2.6
+fs==2.0.25
+graphviz==0.8.4
+idna==2.7
 jinja2==2.10
 markupsafe==1.0
 mondrian==0.7.0
 packaging==17.1
-pbr==4.0.4
+pbr==4.1.1
 psutil==5.4.6
 pyparsing==2.2.0
 python-slugify==1.2.5
-pytz==2018.4
-requests==2.18.4
+pytz==2018.5
+requests==2.19.1
 six==1.11.0
-sqlalchemy==1.2.8
-stevedore==1.28.0
-typing==3.6.4
+sqlalchemy==1.2.10
+stevedore==1.29.0
 unidecode==1.0.22
-urllib3==1.22
+urllib3==1.23
 whistle==1.0.1
diff --git a/requirements.txt b/requirements.txt
index d4696d1..faed2d4 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,22 +3,21 @@ appdirs==1.4.3
 certifi==2018.4.16
 chardet==3.0.4
 colorama==0.3.9
-fs==2.0.23
-graphviz==0.8.3
-idna==2.6
+fs==2.0.25
+graphviz==0.8.4
+idna==2.7
 jinja2==2.10
 markupsafe==1.0
 mondrian==0.7.0
 packaging==17.1
-pbr==4.0.4
+pbr==4.1.1
 psutil==5.4.6
 pyparsing==2.2.0
 python-slugify==1.2.5
-pytz==2018.4
-requests==2.18.4
+pytz==2018.5
+requests==2.19.1
 six==1.11.0
-stevedore==1.28.0
-typing==3.6.4
+stevedore==1.29.0
 unidecode==1.0.22
-urllib3==1.22
+urllib3==1.23
 whistle==1.0.1
diff --git a/setup.py b/setup.py
index f9b7806..9e0aa4b 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,4 @@
-# Generated by Medikit 0.6.3 on 2018-06-11.
+# Generated by Medikit 0.6.3 on 2018-07-22.
 # All changes will be overriden.
 # Edit Projectfile and run “make update” (or “medikit update”) to regenerate.
 
diff --git a/tests/execution/contexts/test_execution_contexts_graph.py b/tests/execution/contexts/test_execution_contexts_graph.py
index 95b1ea4..e297c31 100644
--- a/tests/execution/contexts/test_execution_contexts_graph.py
+++ b/tests/execution/contexts/test_execution_contexts_graph.py
@@ -1,4 +1,5 @@
 from bonobo import Graph
+from bonobo.constants import EMPTY, BEGIN, END
 from bonobo.execution.contexts import GraphExecutionContext
 
 
@@ -49,9 +50,8 @@ def test_lifecycle_of_graph_with_recoverable_error():
 def test_lifecycle_of_graph_with_unrecoverable_error():
     graph = Graph([1, 2, 3], raise_an_unrecoverrable_error, print)
     with GraphExecutionContext(graph) as context:
-        assert context.started
-        assert context.alive
-        assert not context.stopped
+        assert context.started and context.alive and not context.stopped
+        context.write(BEGIN, EMPTY, END)
         context.loop()
     assert context.started
     assert not context.alive
diff --git a/tests/execution/contexts/test_node.py b/tests/execution/contexts/test_execution_contexts_node.py
similarity index 100%
rename from tests/execution/contexts/test_node.py
rename to tests/execution/contexts/test_execution_contexts_node.py

From 4e2cb29fc2a5137123a6f9e4be0d870f083aa068 Mon Sep 17 00:00:00 2001
From: Romain Dorgueil <romain@dorgueil.net>
Date: Sun, 22 Jul 2018 07:54:22 +0200
Subject: [PATCH 3/3] Formatting.

---
 bonobo/config/configurables.py    |  1 +
 bonobo/execution/contexts/node.py | 14 +++++++++++---
 bonobo/registry.py                |  2 ++
 3 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/bonobo/config/configurables.py b/bonobo/config/configurables.py
index 98e21e7..81defaa 100644
--- a/bonobo/config/configurables.py
+++ b/bonobo/config/configurables.py
@@ -77,6 +77,7 @@ except ImportError:
 
     PartiallyConfigured = functools.partial
 else:
+
     class PartiallyConfigured(_functools.partial):
         @property  # TODO XXX cache this
         def _options_values(self):
diff --git a/bonobo/execution/contexts/node.py b/bonobo/execution/contexts/node.py
index 0affd29..c8d7733 100644
--- a/bonobo/execution/contexts/node.py
+++ b/bonobo/execution/contexts/node.py
@@ -30,6 +30,7 @@ class NodeExecutionContext(BaseContext, WithStatistics):
     a service implementation, or a value holder).
 
     """
+
     def __init__(self, wrapped, *, parent=None, services=None, _input=None, _outputs=None):
         """
         Node execution context has the responsibility fo storing the state of a transformation during its execution.
@@ -92,11 +93,15 @@ class NodeExecutionContext(BaseContext, WithStatistics):
                     # Not normal to have a partially configured object here, so let's warn the user instead of having get into
                     # the hard trouble of understanding that by himself.
                     raise TypeError(
-                        'Configurables should be instanciated before execution starts.\nGot {!r}.\n'.format(self.wrapped)
+                        'Configurables should be instanciated before execution starts.\nGot {!r}.\n'.format(
+                            self.wrapped
+                        )
                     ) from exc
                 else:
                     raise TypeError(
-                        'Configurables should be instanciated before execution starts.\nGot {!r}.\n'.format(self.wrapped)
+                        'Configurables should be instanciated before execution starts.\nGot {!r}.\n'.format(
+                            self.wrapped
+                        )
                     )
             self._stack.setup(self)
         except Exception:
@@ -128,7 +133,10 @@ class NodeExecutionContext(BaseContext, WithStatistics):
             self._step()
         except InactiveReadableError:
             raise
-        except (NotImplementedError, UnrecoverableError, ):
+        except (
+                NotImplementedError,
+                UnrecoverableError,
+        ):
             self.fatal(sys.exc_info())  # exit loop
         except Exception:  # pylint: disable=broad-except
             self.error(sys.exc_info())  # does not exit loop
diff --git a/bonobo/registry.py b/bonobo/registry.py
index fba0c53..f45da4f 100644
--- a/bonobo/registry.py
+++ b/bonobo/registry.py
@@ -89,6 +89,7 @@ class Registry:
 
 default_registry = Registry()
 
+
 def create_reader(name, *args, format=None, registry=default_registry, **kwargs):
     """
     Create a reader instance, guessing its factory using filename (and eventually format).
@@ -103,6 +104,7 @@ def create_reader(name, *args, format=None, registry=default_registry, **kwargs)
     """
     return registry.get_reader_factory_for(name, format=format)(name, *args, **kwargs)
 
+
 def create_writer(name, *args, format=None, registry=default_registry, **kwargs):
     """
     Create a writer instance, guessing its factory using filename (and eventually format).