Bugfix release 0.6.4

Merge branch 'release/0.6.4'

.travis.yml

@@ -15,4 +15,5 @@ script:
 branches:
   only:
     - master
+    - develop
     - /^release.*$/

README.rst

@@ -6,15 +6,15 @@ Sacred
     | *If an experiment is wasted*
     | *God gets quite irate*
 
-.. image:: https://zenodo.org/badge/doi/10.5281/zenodo.16386.svg
-    :target: http://dx.doi.org/10.5281/zenodo.16386
-    :alt: DOI for this release
-
-.. image:: http://img.shields.io/pypi/v/sacred.png
+.. image:: https://img.shields.io/pypi/v/sacred.svg
     :target: https://pypi.python.org/pypi/sacred
     :alt: Current PyPi Version
 
-.. image:: http://img.shields.io/badge/license-MIT-blue.png
+.. image:: https://img.shields.io/pypi/pyversions/sacred.svg
+    :target: https://pypi.python.org/pypi/sacred
+    :alt: Supported Python Versions
+
+.. image:: https://img.shields.io/badge/license-MIT-blue.png
     :target: http://choosealicense.com/licenses/mit/
     :alt: MIT licensed
 
@@ -34,10 +34,9 @@ Sacred
     :target: https://scrutinizer-ci.com/g/IDSIA/sacred/
     :alt: Code Scrutinizer Quality
 
-.. image:: https://pypip.in/wheel/sacred/badge.svg?style=flat
-    :target: https://pypi.python.org/pypi/sacred/
-    :alt: Wheel Status
-
+.. image:: https://zenodo.org/badge/doi/10.5281/zenodo.16386.svg
+    :target: http://dx.doi.org/10.5281/zenodo.16386
+    :alt: DOI for this release
 
 Sacred is a tool to help you configure, organize, log and reproduce experiments.
 It is designed to do all the tedious overhead work that you need to do around

docs/apidoc.rst

@@ -24,16 +24,17 @@ The Run Object
 .. autoclass:: sacred.run.Run
     :members:
     :undoc-members:
+    :special-members: __call__
 
 ConfigScope
 ===========
-.. autoclass:: sacred.config_scope.ConfigScope
+.. autoclass:: sacred.config.config_scope.ConfigScope
     :members:
     :undoc-members:
 
 ConfigDict
 ==========
-.. autoclass:: sacred.config_scope.ConfigDict
+.. autoclass:: sacred.config.config_dict.ConfigDict
     :members:
     :undoc-members:
 

sacred/__about__.py

@@ -5,7 +5,7 @@
 
 __all__ = ("__version__", "__author__", "__author_email__", "__url__")
 
-__version__ = "0.6.3"
+__version__ = "0.6.4"
 
 __author__ = 'Klaus Greff'
 __author_email__ = 'qwlouse@gmail.com'

sacred/config/config_summary.py

@@ -16,6 +16,16 @@ def __init__(self, added=(), modified=(), typechanged=(),
         self.ensure_coherence()
 
     def update_from(self, config_mod, path=''):
+        added = config_mod.added
+        updated = config_mod.modified
+        typechanged = config_mod.typechanged
+        self.added &= {join_paths(path, a) for a in added}
+        self.modified |= {join_paths(path, u) for u in updated}
+        self.typechanged.update({join_paths(path, k): v
+                                 for k, v in typechanged.items()})
+        self.ensure_coherence()
+
+    def update_add(self, config_mod, path=''):
         added = config_mod.added
         updated = config_mod.modified
         typechanged = config_mod.typechanged

sacred/config/custom_containers.py

@@ -27,13 +27,10 @@ def __contains__(self, item):
 
     def get(self, k, d=None):
         if dict.__contains__(self, k):
-            return dict.__getitem__(self, k)()
+            return dict.__getitem__(self, k)
         else:
             return self.fallback.get(k, d)
 
-    def has_key(self, item):
-        return self.__contains__(item)
-
     def items(self):
         raise NotImplementedError()
 
@@ -229,6 +226,7 @@ def revelation(self):
 
 
 SIMPLIFY_TYPE = {
+    type(None): type(None),
     bool: bool,
     float: float,
     int: int,
@@ -265,5 +263,7 @@ def revelation(self):
     SIMPLIFY_TYPE[np.bool_] = bool
 
 
-def type_changed(old_type, new_type):
-    return SIMPLIFY_TYPE[type(old_type)] != SIMPLIFY_TYPE[type(new_type)]
+def type_changed(old_value, new_value):
+    sot = SIMPLIFY_TYPE.get(type(old_value), type(old_value))
+    snt = SIMPLIFY_TYPE.get(type(new_value), type(new_value))
+    return sot != snt

sacred/experiment.py

@@ -31,13 +31,13 @@ class Ingredient(object):
     Ingredients can themselves use ingredients.
     """
 
-    def __init__(self, path, ingredients=(), _generate_seed=False,
-                 _caller_globals=None):
+    def __init__(self, path, ingredients=(), _caller_globals=None):
         self.path = path
         self.cfgs = []
         self.named_configs = dict()
         self.ingredients = list(ingredients)
-        self.gen_seed = _generate_seed
+        self.logger = None
+        self.observers = []
         self.captured_functions = []
         self._is_traversing = False
         self.commands = OrderedDict()
@@ -211,6 +211,33 @@ def run_command(self, command_name, config_updates=None,
         self.current_run = None
         return run
 
+    def get_experiment_info(self):
+        """Get a dictionary with information about this experiment.
+
+        Contains:
+          * *name*: the name
+          * *sources*: a list of sources (filename, md5)
+          * *dependencies*: a list of package dependencies (name, version)
+          * *doc*: the docstring
+
+        :return: experiment information
+        :rtype: dict
+        """
+        dependencies = set()
+        sources = set()
+        for ing, _ in self._traverse_ingredients():
+            dependencies |= ing.dependencies
+            sources |= ing.sources
+
+        for dep in dependencies:
+            dep.fill_missing_version()
+
+        return dict(
+            name=self.path,
+            sources=[s.to_tuple() for s in sorted(sources)],
+            dependencies=[d.to_tuple() for d in sorted(dependencies)],
+            doc=self.doc)
+
     # ======================== Private Helpers ================================
 
     def _traverse_ingredients(self):
@@ -264,12 +291,8 @@ def __init__(self, name, ingredients=()):
         caller_globals = inspect.stack()[1][0].f_globals
         super(Experiment, self).__init__(path=name,
                                          ingredients=ingredients,
-                                         _generate_seed=True,
                                          _caller_globals=caller_globals)
-        self.name = name
         self.default_command = ""
-        self.logger = None
-        self.observers = []
         self.command(print_config)
         self.command(print_dependencies)
 
@@ -368,7 +391,7 @@ def run_commandline(self, argv=None):
                                     config_updates=config_updates,
                                     named_configs_to_use=named_configs,
                                     log_level=loglevel)
-        except:
+        except Exception:
             if args['--debug']:
                 import traceback
                 import pdb
@@ -388,7 +411,8 @@ def open_resource(self, filename):
         sure the file is stored in the database (but avoiding duplicates) along
         its path and md5 sum.
 
-        This function can only be called during a run.
+        This function can only be called during a run, and just calls the
+        :py:meth:`sacred.run.Run.open_resource` method.
 
         :param filename: name of the file that should be opened
         :type filename: str
@@ -405,7 +429,8 @@ def add_artifact(self, filename):
         run. In case of a MongoObserver that means storing the file in the
         database.
 
-        This function can only be called during a run.
+        This function can only be called during a run, and just calls the
+        :py:meth:`sacred.run.Run.add_artifact` method.
 
         :param filename: name of the file to be stored as artifact
         :type filename: str
@@ -419,41 +444,15 @@ def info(self):
 
         Only works during a run and is essentially a shortcut to:
 
+        .. code-block:: python
+
             @ex.capture
-            def my_captured_function(_run)
-                ...
+            def my_captured_function(_run):
+                # [...]
                 _run.info   # == ex.info
-
         """
         return self.current_run.info
 
-    def get_experiment_info(self):
-        """Get a dictionary with information about this experiment.
-
-        Contains:
-          * *name*: the name
-          * *sources*: a list of sources (filename, md5)
-          * *dependencies*: a list of package dependencies (name, version)
-          * *doc*: the docstring
-
-        :return: experiment information
-        :rtype: dict
-        """
-        dependencies = set()
-        sources = set()
-        for ing, _ in self._traverse_ingredients():
-            dependencies |= ing.dependencies
-            sources |= ing.sources
-
-        for dep in dependencies:
-            dep.fill_missing_version()
-
-        return dict(
-            name=self.name,
-            sources=[s.to_tuple() for s in sorted(sources)],
-            dependencies=[d.to_tuple() for d in sorted(dependencies)],
-            doc=self.doc)
-
     # =========================== Private Helpers =============================
 
     def _gather_commands(self):

sacred/initialize.py

@@ -102,7 +102,9 @@ def set_up_config(self):
         self.get_config_modifications()
 
     def get_config_modifications(self):
-        self.config_mods = ConfigSummary()
+        self.config_mods = ConfigSummary(
+            added={key
+                   for key, value in iterate_flattened(self.config_updates)})
         for cfg_summary in self.summaries:
             self.config_mods.update_from(cfg_summary)
 
@@ -211,13 +213,13 @@ def initialize_logging(experiment, scaffolding, loglevel=None):
         else:
             scaffold.logger = root_logger
 
-    return root_logger.getChild(experiment.name)
+    return root_logger.getChild(experiment.path)
 
 
 def create_scaffolding(experiment):
     sorted_ingredients = gather_ingredients_topological(experiment)
     scaffolding = OrderedDict()
-    for ingredient in sorted_ingredients:
+    for ingredient in sorted_ingredients[:-1]:
         scaffolding[ingredient] = Scaffold(
             ingredient.cfgs,
             subrunners=OrderedDict([(scaffolding[m].path, scaffolding[m])
@@ -226,21 +228,31 @@ def create_scaffolding(experiment):
             captured_functions=ingredient.captured_functions,
             commands=ingredient.commands,
             named_configs=ingredient.named_configs,
-            generate_seed=ingredient.gen_seed)
+            generate_seed=False)
+
+    scaffolding[experiment] = Scaffold(
+        experiment.cfgs,
+        subrunners=OrderedDict([(scaffolding[m].path, scaffolding[m])
+                                for m in experiment.ingredients]),
+        path=experiment.path if experiment != experiment else '',
+        captured_functions=experiment.captured_functions,
+        commands=experiment.commands,
+        named_configs=experiment.named_configs,
+        generate_seed=True)
     return OrderedDict([(sc.path, sc) for sc in scaffolding.values()])
 
 
 def gather_ingredients_topological(ingredient):
     sub_ingredients = defaultdict(int)
-    for ingredient, depth in ingredient._traverse_ingredients():
-        sub_ingredients[ingredient] = max(sub_ingredients[ingredient], depth)
+    for sub_ing, depth in ingredient._traverse_ingredients():
+        sub_ingredients[sub_ing] = max(sub_ingredients[sub_ing], depth)
     return sorted(sub_ingredients, key=lambda x: -sub_ingredients[x])
 
 
-def get_config_modifications(scaffolding):
+def get_config_modifications(scaffolding, config_updates):
     config_modifications = ConfigSummary()
     for sc_path, scaffold in scaffolding.items():
-        config_modifications.update_from(scaffold.config_mods, path=sc_path)
+        config_modifications.update_add(scaffold.config_mods, path=sc_path)
     return config_modifications
 
 
@@ -273,7 +285,8 @@ def create_run(experiment, command_name, config_updates=None, log_level=None,
         scaffold.set_up_seed()  # partially recursive
 
     config = get_configuration(scaffolding)
-    config_modifications = get_config_modifications(scaffolding)
+    config_modifications = get_config_modifications(scaffolding,
+                                                    config_updates)
 
     experiment_info = experiment.get_experiment_info()
     host_info = get_host_info()

sacred/observers/__init__.py

@@ -2,12 +2,12 @@
 # coding=utf-8
 from __future__ import division, print_function, unicode_literals
 
-from sacred.observers.base import RunObserver, DebugObserver
+from sacred.observers.base import RunObserver
 import sacred.optional as opt
 
 if opt.has_pymongo:
     from sacred.observers.mongo import MongoObserver
 else:
     MongoObserver = opt.MissingDependencyMock('pymongo')
 
-__all__ = ('RunObserver', 'DebugObserver', 'MongoObserver')
+__all__ = ('RunObserver', 'MongoObserver')

sacred/observers/base.py

@@ -4,7 +4,7 @@
 
 __sacred__ = True  # marks files that should be filtered from stack traces
 
-__all__ = ('RunObserver', 'DebugObserver')
+__all__ = ('RunObserver',)
 
 
 class RunObserver(object):
@@ -31,26 +31,3 @@ def resource_event(self, filename):
 
     def artifact_event(self, filename):
         pass
-
-
-class DebugObserver(RunObserver):
-    def started_event(self, ex_info, host_info, start_time, config):
-        print('experiment_started_event')
-
-    def heartbeat_event(self, info, captured_out, beat_time):
-        print('experiment_info_updated')
-
-    def completed_event(self, stop_time, result):
-        print('experiment_completed_event')
-
-    def interrupted_event(self, interrupt_time):
-        print('experiment_interrupted_event')
-
-    def failed_event(self, fail_time, fail_trace):
-        print('experiment_failed_event')
-
-    def resource_event(self, filename):
-        print('resource_event: {}'.format(filename))
-
-    def artifact_event(self, filename):
-        print('artifact_event: {}'.format(filename))

sacred/observers/mongo.py

@@ -40,10 +40,9 @@ def transform_outgoing(self, son, collection):
         for (key, value) in son.items():
             if isinstance(value, dict):
                 if "_type" in value and value["_type"] == "ndarray":
-                    son[key] = pickle.loads(str(value["_value"]))
+                    son[key] = pickle.loads(value["_value"])
                 else:  # Again, make sure to recurse into sub-docs
-                    son[key] = self.transform_outgoing(value,
-                                                       collection)
+                    son[key] = self.transform_outgoing(value, collection)
         return son