Pypet

* StreamToLogger has moved to the pypetlogging.py module. The mplogging module was
deleted.

* The Network Manager now accepts custom network constructors

* A SingleRun can now provide a `v_filename` and `v_as_run` property.
Both cannot be changed and the latter simply returns the name of the run.

* Better testing on travis

* Better support for pandas 0.14.1

* Now you can import most of the objects directly from the *pypet* package, e.g.
``from pypet import Trajectory`` instead of ``from pypet.trajectory import Trajectory``.

* The storage service prints status updates for loading and storing trees

* v_as_run is not longer `None` for a trajectory but `run_ALL`

* The Queue storage writer now stores batches of single runs to avoid
re-opening of files as much as possible

* Faster Loading of data

* Support for PyTables 3.1.1

* *pypet* stores the name of the main script as a config parameter

* Data of Parameters can be accessed via `.data` or `param['data']`.
Same holds for results that only contain a single data item.

* Parameters provide the function `f_get_default` to return the default value
if the parameter is not empty.

* Large dictionaries and Object Tables are now split into chunks of 512 items

* In case an object table has more than 32 columns, another table is created to
store the data item types (which is faster than storing all of the types as
hdf5 node attributes)

* New auto load feature

* BUG FIX: When parameters are emptied, the default value is set to None (and no longer kept)

* Now items are only saved once, if the node already exist on disk, storage is refused
(Previously new data was added if it was not within the leaf before, but this can lead to
strange inconsistencies).

* BUG FIX: `f_has_children` of a group node, now returns the correct result

* Refactored continuing of trajectories. Now this is based on `dill` and works also
with data that cannot be pickled. `f_continue_run` is renamed `f_continue` to emphasize
this change in API

* Picking the search strategy and using `v_check_uniqueness` is no longer supported.
Sorry for the inconvenience. So forward search will always check if it finds 2 nodes
with the same name within the same depth, and skip search if the next tree depth is entered.

* `f_contains` of group nodes has per default `shortcuts=False`

* There exists now the abstract class `HasLogger` in pypetlogging.py that establishes
a unified logging framework

* Likewise the loggers of all network components are now private objects `_logger` and
so is the function `_set_logger`.

* BUG FIX: `f_get_run_information` now works without passing any arguments

* Trajectories no longer accept a `file_tile` on initialisation

* One can now decide if trajectories should be automatically stored and if
data should be cleaned up after every run

* BUG FIX: Storage of individual items during a single run do no longer require
a full storage of the single run container.

* If automatic storage is enabled, trajectories are now stored at the end of the experiment,
no longer before the starting of the single runs

* You can use the `$` character to decide where the HDF5 file tree should branch out for the
individual runs

* `v_creator_name` is now called `v_run_branch` (since single runs can also create
items that are not part of a run branch, so this is no longer misleading`.

* Results and parameters now issue a warning when they have been stored and you
change their data

* Parameters now have a property `v_explored` which is True for explored parameters
even if the range has been removed

* By default `backwards_search` is turned off!

* Brian parameters no longer store the `storage_mode` explicitly

* BUG FIX: Wildcard character now always defaults to `run_ALL` if trajectory is not set
to particular run

* BUG FIX: Now names with `XXXrun_` are again allowed only `run_` are forbidden.

* Annotations and Results now support __setitem__, which is analogue to `f_get` and `f_set`

* Group Nodes can now contain comments as well

* Comments are only stored to HDF5 if they are not the empty string

* Large Overview Tables are off by default

* BrianDurationParameter was removed and the annotations are used instead.
Use a normal BrianParameter and instead of `v_order` use `v_annotations.order`

* The user is advised to use `environment.f_run(manager.run_network)`, instead of
`environment.f_run(run_network, manager)`

* Now there is the distinction between `small`, `large`, and `summary` tables

* BrianMonitorResult: Mean and variance values of State and MultiState Monitors are only
extracted if they were recorded (which for newer BRIAN versions is only the case if you
do NOT record traces)

* Log Level can be passed to environment

* BUG FIX: Scalars are no longer autoconverted by the storage service to zero-length numpy arrays

* Names of loggers have been shortened

* The trajectory now contains the functions `f_delete_item` and `f_delete_items` to erase stuff
from disk. `f_remove_items` and `f_remove_item` no longer delete data from disk.

* Loading and deletions of items can now be made with SingleRuns as well.

* f_iter_nodes now iterates by default recursively all nodes

* A group node now supports __iter__ which simply calls f_iter_nodes NON recursively

* The structure of the trees are slightly changed. Results and derived parameters added
with the trajectory are no longer assigned the prefix `trajectory`.
Results and derived parameters added during single runs are now sorted into
`runs.run_XXXXXXXXX`.

* Useless shortcuts have been removed.

* New *Backwards* search functionality

* New `f_get_all` functionality to find all items in a tree matching a particular
search string

* Pandas Series and Panels are now supported, too!

* Now Pypet allows compression of HDF5 files, this can yield a massive reduction in
memory space.

* `tr`, `cr`, `current_run`, `param`, `dparam` are no longer supported as a shortcuts

* __getitem__ is equivalent to __getattr__

* Now one can specify a maximum depth for accessing items.

* Now one can specify if shortcuts, i.e. hopping over parts of the tree, are allowed.

* New trajectroy attributes `v_backwards_search`, `v_max_depth`, `v_shortcuts` and
`v_iter_recursive`. `v_iter_recursive` specifies the behavior of `__iter__`.

* `__contains__` now greps is arguments from the attributes `v_max_depth` and `v_shortcuts`.

* `log_stdout` parameter of the Environment determines if STDOUT and STDERROR will be logged
to files. Can be disabled to allow better usage of pypet with interactive consoles.

* git commits only happen on changes and not all the time

* Now one can specify CPU, RAM and Swap cap levels if no pool is used.
If these cap levels are crossed *pypet* won't start new processes.

* `f_load` now has an argument `load_all` to quickly load all subtrees with the same setting.
Also `f_load` now accepts a filename as well

* New post-processing and pipeline modes!

* BUG FIX: Now `f_run` and `f_continue_run` of an environment return the results
produced by `runfunc`

* You can enforce a type convert for exploration

* Added lazy_debug option for the environment

* If you don't specify a filename, the environment defaults to a file with the name of
the trajectory

* New multiprocessing mode (`use_pool=False` for environment) to spawn individual processes
for each run. Useful if data cannot be pickled.

* New Brian framework with NetworkManager, NetworkComponent, NetworkAnalyser,
NetworkRunner and DurationParameter

* Components, Analysers and the network runner of the manager are now publicly available

* Every component now provides the function `set_logger` to enable logging and instantiate a
logger for `self.logger`

* DefaultReplacementError is now called PresettingError

* Now the runtime of single runs is measured and stored.

* __getitem__ of the trajectory always returns the instance and fast access is not applied

* PickleResult and PickleParameter support the choice of protocol

* Explored Sparse matrices are stored under a slightly different name to disk.

* BUG FIX: BFS works properly

* BUG FIX: f_iter_runs is now affected if f_as_run is chosen

* Annotations support __iter__

* Annotations support __getitem__

* BrianMonitorResult, the property and columns 'times' for the Spike and StateSpikeMonitor
has been renamed 'spiketimes'.

* Results support __iter__

* BrianMonitorResult, the name of state variables in array mode
is changed to varname+'_%Xd', instead of varname+'_idx%08d', and 'spiketimes_%08d' to
'spiketimes_%Xd' and X is chosen in accordance with the number of neurons

* BUG FIX: nested_equal now supports Object Tables containing numpy arrays

* Better categorizations of the utility functions

* Comments are no longer limited in size

* New Brian Result

* Storage Service - in case of purging - now sets the comment to the result with the lowest index,
in case of multiprocessing.

* Old API names are kept, but emit a depricated warning.

* The exploration array is now termed range. Accordingly, the function `f_is_array` is
renamed `f_has_range` and `f_get_array` renamed to `f_get_range`.

* v_leaf renamed to v_is_leaf

* f_is_root renamed to v_is_root and changed to property

* v_fast_accessible renamed to f_supports_fast_access and changed to function

* v_parameter changed to v_is_parameter