changelog.txt

=========
Changelog
=========

The **signac** package follows `semantic versioning <https://semver.org/>`_.

Version 1
=========

Highlights
----------

 - Native integration of HDF5 files with the ``H5Store`` and ``H5StoreManager``, which are exposed as the ``job.data``, ``job.stores``, ``project.data``, and ``project.stores`` properties respectively.
 - The newly added ``signac.get_job()`` function makes it easier to obtain instances of ``Job`` by calling the function from within a job's workspace directory or by directly providing the path to the job's workspace directory. This is especially useful for interactive work or when accessing jobs which are outside of the current project.
 - Simplified export of project and job data to pandas dataframes *via* the ``to_dataframe()`` function.
 - Projects and job search results are displayed nicely in Jupyter Notebooks.
 - Support for compressed Collection files.


Next
----

Added
+++++

 - Add function to initialize a sample data space for testing purposes

Changed
+++++++

 - Implemented ``Project.__contains__`` check in constant time.

Fixed
+++++

 - Attempting to create a linked view for a Project on Windows now raises an informative error message.
 - Project configuration is initialized using ConfigObj, allowing the configuration to include commas and special characters (#251, #252).

Deprecated
++++++++++

 - In-memory modification of the project configuration, to be removed in 2.0 (#246).

Removed
+++++++

 - Dropped support for Python 2.7.


[1.2.0] -- 2019-07-22
---------------------

Added
+++++

 - Keep signac shell command history on a per-project basis (#134, #194).
 - Add ``read_json()`` and ``to_json()`` methods to ``Collection`` class (#104, #200).

Fixed
+++++

 - Fix issue where shallow copies of instances of ``Job`` would behave incorrectly (#153, #207).
 - Fix issue causing a failure of the automatic conversion of valid key types (#168, #205).
 - Improve the 'dots in keys' error message to make it easier to fix related issues (#170, #205).
 - Update the ``__repr__`` and ``__repr_html__`` implementations of the ``Project``, ``Job``, and ``JobsCursor`` classes (#193).
 - Reduce the logging verbosity about a missing default host key in the configuration (#201).
 - Fix issue with incorrect detection of dict-like files managed with the ``DictManager`` class (e.g. ``job.stores``) (#203).
 - Fix issue with generating views from the command line for projects with only one job (#208, #211).
 - Fix issue with heterogeneous types in state point values that are lists (#209, #210).

Deprecated
++++++++++

 - Support for Python 2.7 is deprecated with this version and will be removed in the next minor release. See the `Python 3 Statement <https://python3statement.org/>`_.


[1.1.0] -- 2019-05-19
---------------------

Added
+++++

 - Add command line options ``--sp`` and ``--doc`` for ``signac find`` that allow users to display key-value pairs of the state point and document in combination with the job id (#97, #146).
 - Improve the representation (return value of `repr()`) of instances of ``H5Group`` and ``SyncedAttrDict``.

Fixed
+++++
 - Fix: Searches for whole numbers will match all numerically matching integers regardless of whether they are stored as decimals or whole numbers (#169).
 - Fix: Passing an instance of dict to `H5Store.setdefault()` will return an instance of `H5Group` instead of a dict (#180).
 - Fix error with storing numpy arrays and scalars in a synced dictionary (e.g. `job.statepoint`, `job.document`) (#184).
 - Fix issue with ``ResourceWarning`` originating from unclosed instance of ``Collection`` (#186).
 - Fix issue with using the ``get_project()`` function with a relative path and ``search=False`` (#191).

Removed
+++++++

 - Support for Python version 3.4 (no longer tested).


[1.0.0] -- 2019-02-28
---------------------

Added
+++++

 - Official support for Python 3.7.
 - The ``H5Store`` and ``H5StoreManager`` classes, which are useful for storing (numerical) array-like data with an HDF5-backend. These classes are exposed within the root namespace.
 - The ``job.data`` and ``project.data`` properties which present an instance of ``H5Store`` to access numerical data within the job workspace and project root directory.
 - The ``job.stores`` and ``project.stores`` properties, which present an instance of ``H5StoreManager`` to manage multiple instances of ``H5Store`` to store numerical array-like data within the project workspace and project root directory.
 - The ``signac.get_job()`` and the ``signac.Project.get_job()`` functions that allow users to get a job handle by switching into or providing the job's workspace directory.
 - The ``job`` variable is automatically set when opening a ``signac shell`` from within a job's workspace directory.
 - Add the ``signac shell -c`` option which allows the direct specification of Python commands to be executed within the shell.
 - Automatic cast of ``numpy`` arrays to lists when storing them within a ``JSONDict``, e.g., a ``job.statepoint`` or ``job.document``.
 - Enable ``Collection`` class to manage collections stored in compressed files (gzip, zip, etc.).
 - Enable deleting of ``JSONDict`` keys through the attribute interface, e.g., ``del job.doc.foo``.
 - Pretty HTML representation of instances of ``Project`` and ``JobsCursor`` targeted at Jupyter Notebooks (requires pandas, automatically enabled when installed).
 - The ``to_dataframe()`` function to export the job state point and document data of a ``Project`` or a ``JobsCursor``, e.g., the result of ``Project.find_jobs()``, as a ``pandas.Dataframe`` (requires pandas).

Changed
+++++++

 - Dots (`.`) in keys are no longer allowed for ``JSONDict`` and ``Collection`` keys (previously deprecated).
 - The ``JSONDict`` module is exposed in the root namespace, which is useful for storing text-serializable data  with a JSON-backend similar to the ``job.statepoint`` or ``job.document``, etc.
 - The ``Job.init()`` method returns the job to allow one-line job creation and initialization.
 - The ``search`` argument was added to the ``signac.get_project()`` function, which when True (the default), will cause signac to search for a project within *and above* a specified root directory, not only within the root directory. The behavior without any arguments remains unchanged.

Fixed
+++++

 - Fix ``Collection.update()`` behavior such that existing documents with identical primary key are updated. Previously, a ``KeyError`` would be raised.
 - Fix issue where the ``Job.move()`` would trigger a confusing ``DestinationExists`` exception when trying to move jobs across devices / file systems.
 - Fix issue that caused failures when the ``python-rapidjson`` package is installed. The ``python-rapidjson`` package is used as the primary JSON-backend when installed.
 - Fix issue where schema with multiple keys would subset incorrectly if the list of jobs or statepoints was provided as an iterator rather than a sequence.

Removed
+++++++

 - Removes the obsolete and deprecated ``core.search_engine`` module.
 - The previously deprecated ``Project.find_statepoints()`` and ``Project.find_job_documents()`` functions have been removed.
 - The ``Project.find_jobs()`` no longer accepts the obsolete ``index`` argument.


Version 0.9
===========

Highlights
----------

 - Adds persistent state point index caching, which speeds up all functions that require indexing, for example the ``$ signac find`` command.
 - Adds the ``$ signac sync`` tool for synchronization of multiple **signac** projects.
 - Adds the ``$ signac schema`` function for the automatic detection of the implicit schema of a **signac** project.
 - Adds the ``$near`` operator to match numbers with up to a specific precision.
 - Adds functions for the import and export of data spaces.
 - Add functions for the management of data on the project level, as opposed to the job level.


[0.9.5] -- 2019-01-31
---------------------

Fixed
+++++

 - Ensure that the next() function can be called for a JobsIterator, e.g., `project.find()`.
 - Pickling issue that occurs when a _SyncedDict (job.statepoint, job.document, etc.) contains a list.
 - Issue with the readline module that would cause signac shell to fail on Windows operating systems.


[0.9.4] -- 2018-10-24
---------------------

Added
+++++

 - Adds the ``$ signac import`` command and the ``Project.import_from()`` method for the import of data spaces into a project workspace, such as a directory, a tarball, or a zip file.
 - Adds the ``$ signac export`` command and the ``Project.export_to()`` method for the export of project workspaces to an external location, such as a directory, a tarball, or a zip file.
 - Adds functionality for the rapid initialization of temporary projects with the ``signac.TemporaryProject`` context manager.
 - Adds the ``signac.Project.temporary_project()`` context manager which creates a temporary project within the root project workspace.
 - Add ``signac`` to the default namespace when invoking ``signac shell``.
 - Add option to specify a custom view path for the ``signac view``/ ``Project.create_linked_view()`` function.
 - Iterables of documents used to construct a Collection no longer require an ``_id`` field.

Changed
+++++++

 - The default path for linked views has been adjusted to match the one used for data exports.

Fixed
+++++

 - Fix issue where differently typed integer values stored within a Collection under the same key would not be indexed correctly. This issue affected the correct function of the `$type` operator for aforementioned cases and would lead to incorrect types in the Project schema detection algorithm for integer values.
 - Fix issue where jobs that are migrated (state point change), but are not initialized, were not properly updated.
 - Fix issue where changes to lists as part of synchronized dictionary, for example a state point or document would not be saved.
 - Fix non-deterministic issue occuring on network file systems when trying to open jobs where the user has no write access to the job workspace directory.

[0.9.3] -- 2018-06-14
---------------------

Added
+++++

 - Add `$near` operator to express queries for numerical values that match up to a certain precision.
 - Add the `$ signac shell` sub command to directly launch a Python interpreter within a project directory.

Fixed
+++++

 - Fix issue where a job instance would not be properly updated after more than one state point reset.

[0.9.2] -- 2017-12-18
---------------------

Added
+++++

  - Add provisional feature (persistent state point caching); calling the ``Project.update_cache()`` method will generate and store a persistent state point cache in the project root directory, which will increase the speed of many project iteration, search, and selection operations.
  - Add ``Project.check()`` method which checks for workspace corruption, but does not make any attempt to repair it.
  - The ``Project.repair()`` method will attempt to repair jobs, that have been corrupted by manually renaming the job's workspace directory.

Changed
+++++++

  - Enable the *write_concern* flag for the ``job.document``.
  - Allow to omit the specification of an authentication mechanism in the MongoDB host configuration.

Fixed
+++++

  - Fix critical issue in the ``JSONDict`` implementation that would previously overwrite the underlying file when attempting to store values that are not JSON serializable.
  - Fix issue where the ``Project.export()`` function would ignore the update argument when the index to export to would be a MongoDB collection.

[0.9.1] -- 2017-11-07
---------------------

Fixed
+++++

  - Fix critical issue in the ``SyncedAttrDict`` implementation that would previously overwrite the underlying file if the first operation was a ``__setitem__()`` operation.

[0.9.0] -- 2017-10-28
---------------------

Added
+++++

  - Introduction of ``$ signac sync``, ``Project.sync()``, and ``Job.sync()`` for the simplified and fine-grained synchronization of multiple project data spaces.
  - Introduction of ``$ signac schema`` and ``Project.detect_schema()`` for the automatic detection of the implicit and semi-structured state point schema of a project data space.
  - Simplified aggregation of jobs over projects and ``Project.find_jobs()`` results with the ``Project.groupby()`` function.
  - Support for project-centralized data with the ``Project.document`` attribute and the ``Project.fn()`` method for the wrapping of filenames within the project root directory.
  - Added the ``Job.clear()`` and the ``Job.reset()`` methods to clear or reset a job's workspace data.

Changed
+++++++

  - Both ``Job.statepoint`` and ``Job.document`` now use the same underlying data structure and provide the exact same API (copy with ``()`` and access of keys as attributes).
  - The ``Collection`` class uses an internal counter instead of UUIDs for the generation of primary keys (resulting in improved performance).
  - Major performance improvements (faster Collection, improved caching)
  - Overhaul of the reference documentation.

Version 0.8
===========

Highlights
----------

 - Adds boolean and arithmetic operators to search queries.
 - Major revision of the indexing system.
 - Adds ``$ signac document`` command line function.
 - Add the ``signac.Collection`` class for the management of persistent document collections.

[0.8.7] -- 2017-10-05
---------------------

Fixed
+++++

 - Fix an issue where the creation of linked views was non-deterministic in some cases.
 - Fix an issue where the creation of linked views would fail when the project contains job with state points that have lists as values.

[0.8.6] -- 2017-08-25
---------------------

Fixed
+++++

 - Fix Collection append truncation issue (see issue #66).

[0.8.5] -- 2017-06-07
---------------------

Changed
+++++++

 - The signac ids in the `signac find --show` view are no longer enclosed by quotation marks.

Fixed
+++++

 - Fix compatibility issue that broke the `signac find --view` and all `--pretty` commands on Python 2.7.
 - Fix issue where view directories would be incomplete in combination with heterogeneous state point schemas.

[0.8.4] -- 2017-05-19
---------------------

Added
+++++

 - All search queries on project and collection objects support various operators including: *$and*, *$or*, *$gt*, *$gte*, *$lt*, *$lte*, *$eq*, *$ne*, *$exists*, *$regex*, *$where*, *$in*, *$nin*, and *$type*.
 - The ``$ signac find`` command supports a simple filter syntax, where key value pairs can be provided as individual arguments.
 - The ``$ signac find`` command is extended by a *--show* option, to display the state point and the document contents directly. The contents are truncated to an adjustable depth to reduce output noise.
 - The ``$ signac view`` command has an additional filter option to select a sub data space directly without needing to pipe job ids.
 - The new ``$ signac document`` command can be used to display a job's document directly.

Changed
+++++++

 - Minor performance improvements.

[0.8.3] -- 2017-05-10
---------------------

Changed
+++++++

 - Raise ``ExportError`` when updating with an empty index.

Fixed
+++++

 - Fix command line logic issue with ``$signac config host``.
 - Fix bug, where ``Collection.replace_one()`` would ignore the upsert argument under specific conditions.

[0.8.2] -- 2017-04-19
---------------------

Fixed
+++++

 - Fixes a ``TypeError`` which occurred under specific conditions when calling ``Collection.find()`` with nested filter arguments.

[0.8.1] -- 2017-04-17
---------------------

Fixed
+++++

 - Fixes wide-spread typo (*indeces* -> *indexes*).

[0.8.0] -- 2017-04-16
---------------------

Overall major simplification of the generation of indexes and the management and searching of index collections without external database.

Added
+++++

 - Introduction of the ``Collection`` class for the management of document collections, such as indexes in memory and on disk.
 - Generation of file indexes directly via the ``signac.index_files()`` function.
 - Generation of master indexes directly via the ``signac.index()`` function and the ``$ signac index`` command.
 - The API of ``signac_access.py`` files has been simplified, including the possibility to use a blank file for a minimal configuration.
 - Use the ``$ signac project --access`` command to create a minimal access module in addition to ``Project.create_access_module()``.
 - The update of existing index collections has been simplified by using the ``export()`` function with the `update=True` argument, which means that stale documents (the associated file or state point no longer exists) are automatically identified and removed.
 - Added the ``Job.ws`` attribute, as short-cut for ``Job.workspace()``.
 - The ``Job.sp`` interface has a ``get()`` function which can be used to specify a default value in case that the requested key is not part of the state point.

Changed (breaking API)
++++++++++++++++++++++

 - The ``$ signac index`` command generates a master index instead of a project index. To generate a project index from the command line use ``$ signac project --index`` instead.
 - The ``SignacProjectCrawler`` class expects the project's root directory as first argument, not the workspace directory.
 - The ``get_crawlers()`` function defined within a ``signac_access.py`` access module is expected to yield crawler instances directly, not a mapping of crawler ids and instances.
 - The simplification of the ``signac_access.py`` module API is reflected in a reduction of arguments to the ``Project.create_access_module()`` method.

Changed (non-breaking)
++++++++++++++++++++++

 - The ``RegexFileCrawler``, ``SignacProjectCrawler`` and ``MasterCrawler`` classes were moved into the root namespace.
 - If a ``MasterCrawler`` object is instantiated with the ``raise_on_error`` argument set to True, any errors encountered during crawling are raised instead of ignored and skipped; this simplifies the debugging of erroneous access modules.
 - Improved error message for invalid configuration files.
 - Better error messages for invalid ``$ signac find`` queries.
 - Check a host configuration on the command line via ``$ signac host --test``.
 - A MongoDB database host configuration defaults to *none* when no authentication method is explicitly specified.
 - Using the ``--debug`` option in combination with ``$ signac index`` will show the traceback of errors encountered during indexing instead of ignoring them.
 - Instances of ``Job`` are hashable, making it possible to use them as dict keys for instance.
 - The representation of ``Job`` instances via ``repr()`` can actually serves as copy constructor command.
 - The project interface implementation performs all non-trivial search operations on an internally management index collection, which improves performance and simplifies the code base.

Deprecated
++++++++++

 - The ``DocumentSearchEngine`` class has been deprecated, its functionality is now provided by the ``Collection`` class.

Fixed
+++++

 - An issue related to exporting documents to MongoDB collections via pymongo in combination with Python 2.7 has been fixed.

Version 0.7
===========

Highlights
----------

 - Add support for Python 3.6, PyPy and PyPy3.
 - Make any instance of ``Project`` behave like an iterable (``for job in project``).
 - Introduction of the ``Job.sp`` attribute to access state point variables.
 - Revision of the linked view function, which now allows the update of previous views.
 - Support for searching by job document keys on the command line.
 - Add functions for moving and cloning jobs.
 - Add functions for changing a job's state point.
 - Enable opening of jobs by *abbreviated id*.

[0.7.1] -- 2017-01-09
---------------------

Added
+++++

 - When the ``python-rapidjson`` package is installed, it will be used for JSON encoding/decoding (experimental).

Changed
+++++++

 - All job move-related methods raise ``DestinationExistsError`` in case of destination conflicts.
 - Optimized ``$ signac find`` command.

Fixed
+++++

 - Fixed bug in ``$ signac statepoint``.
 - Suppress 'broken pipe error' message when using ``$ signac find`` for example in combination with ``$ head``.

[0.7.0] -- 2017-01-04
---------------------

Added
+++++

 - Add support for Python version 3.6.
 - Add support for PyPy and PyPy3.
 - Simplified iteration over project data spaces.
 - An existing linked view can be updated by executing the view command again.
 - Add attribute interface for the access and modification of job state points: ``Job.sp``.
 - Add function for moving and copying of jobs between projects.
 - All project related iterators support the ``len``-operator.
 - Enable iteration over all jobs with: ``for job in project:``.
 - Make ``len(project)`` an alias for ``project.num_jobs()``.
 - Add ``in``-operator to determine whether a job is initialized within a project.
 - Add ``Job.sp`` attribute to access and modify a job's state point.
 - The ``Project.open_job()`` method accepts abbreviated job ids.
 - Add ``Project.min_len_unique_id()`` method to determine the minimum length of job ids to be unique within the project's data space.
 - Add ``Job.move()`` method to move jobs between projects.
 - Add ``Project.clone()`` method to copy jobs between projects.
 - Add ``$ signac move`` and ``$ signac clone`` command line functions.
 - Add ``Job.reset_statepoint()`` method to reset a job's state point.
 - Add ``Job.update_statepoint()`` method to update a job's state point.
 - Add a ``Job.FN_DOCUMENT`` constant which defines the default filename of the job document file
 - The ``$ signac find`` command accepts a ``-d/--doc-filter`` option to filter by job document contents.
 - Add the ``Project.create_linked_view()`` method as replacement for the previously deprecated ``Project.create_view()`` method.

Changed
+++++++

 - Linked views use relative paths.
 - The *Guide* documentation chapter has been renamed to *Reference* and generally overhauled.
 - The *Quick Reference* documentation chapter has been extended.

Fixed
+++++

 - Fix error when using an instance of ``Job`` after calling ``Job.remove()``.
 - A project created in one the standard config directories (such as the home directory) does not take prevalence over project configurations in or above the current working directory.

Removed
+++++++

 - The *signac-gui* component has been removed.
 - The ``Project.create_linked_view()`` ``force`` argument is removed.
 - The ``Project.find_variable_parameters()`` method has been removed

Version 0.6
===========

Highlights
----------

 - General revision of the indexing and export system.
 - General consolidation including the removal of the *conversion framework*.

[0.6.2] -- 2017-12-15
---------------------

Added
+++++

 - Add instructions on how to acknowledge **signac** in publications to documentation.
 - Add cite module for the auto-generation of formatted references and BibTeX entries.

Removed
+++++++

 - Remove SSL authentication support.

[0.6.1] -- 2017-11-26
---------------------

Changed
+++++++

 - The ``Project.create_view()`` method triggers a ``DeprecationWarning`` instead of a ``PendingDeprecationWarning``.
 - The ``Project.find_variable_parameters()`` method triggers a ``DeprecationWarning`` instead of a ``PendingDeprecationWarning``.

Fixed
+++++

 - Make package more robust against PySide import errors.
 - Fix ``Project.__repr__`` method.
 - Fix critical bug in ``fs.GridFS`` class, which rendered it unusuable.
 - Fix issue in ``indexing.fetch()`` previously resulting in local paths being ignored.
 - Fix error ``signac.__all__`` namespace directive.

[0.6.0] -- 2016-11-18
---------------------

Added
+++++

 - Add the ``export_to_mirror()`` function for mirroring files.
 - Introduction of the ``signac.fs`` namespace to simplify the configuration of mirror filesystems.
 - Add *errors* module to root namespace. Many exceptions raised inherit from the base exception types defined within that module, making it easier to catch signac related errors.
 - Add the ``export_one()`` function for the export of a single index document; simplifies the implementation of custom export functions.
 - Opening an instance of ``Job`` with the ``open_job()`` method multiple times and entering a job context recursively is now well-defined behavior: Opening a job now adds the current working directory onto a stack, closing it switches into the directory on top of the stack.
 - The return type of ``Project.open_job()`` can be configured to make it easier to specialize projects with custom job types.

Changed
+++++++

 - The MasterCrawler logic has been simplified; their primary function is the compilation of index documents from slave crawlers, all export logic, including data mirroring is now provided by the ``signac.export()`` function.
 - Each index document is now uniquely coupled with only one file or data object, which is why ``signac.fetch()`` replaces ``signac.fetch_one()`` and the latter one has been deprecated and is currently an alias of the former one.
 - The ``signac.fetch()`` function always returns a file-like object, regardless of format definition.
 - The format argument in the crawler ``define()`` function is now optional and has now very well defined behavior for str types. It is encouraged to define a format with a str constant rather than a file-like object type.
 - The ``TextFile`` file-like object class definition in the formats module has been replaced with a constant of type ``str``.
 - The ``signac.export()`` function automatically delegates to specialized implementations such as ``export_pymongo()`` and is more robust against errors, such as broken connections.
 - The ``export_pymongo()`` function makes multiple automatic restart attempts when encountering errors.
 - Documentation: The tutorial is now based on signac-examples jupyter notebooks.
 - The ``contrib.crawler`` module has been renamed to contrib.indexing to better reflect the semantic context.
 - The ``signac.export()`` function now implements the logic for data linking and mirroring.
 - Provide default argument for '--indent' option for ``$ signac statepoint`` command.
 - Log, but do not reraise exceptions during ``MasterCrawler`` execution, making the compilation of master indexes more robust against errors.
 - The object representation of ``Job`` and ``Project`` instances is simplified.
 - The warning verbosity has been reduced when importing modules with optional dependencies.

Removed
+++++++

 - All modules related to the stale *conversion framework* feature have been removed resulting in a removal of the optional networkx dependency.
 - Multiple modules related to the *conversion framework* feature have been removed, including: ``contrib.formats_network``, ``contrib.conversion``, and ``contrib.adapters``.

Fixed
+++++

 - Opening instances of ``Job`` with the ``Job.open()`` method multiple times, equivalently entering the job context recursively, does not cause an error anymore, but instead the behavior is well-defined.

Version 0.5
===========

[0.5.0] -- 2016-08-31
---------------------

Added
+++++

 - New function: ``signac.init_project()`` simplifies project initialization within Python
 - Added optional ``root`` argument to ``signac.get_project()`` to simplify getting a project handle outside of the current working directory
 - Added optional argument to ``signac.get_project()``, to allow fetching of projects outside of the current working directory.
 - Added two class factory methods to `Project`: ``get_project()`` and ``init_project()``.

Changed
+++++++

 - The performance of project indexing and crawling has been improved.

Version 0.4
===========

[0.4.0] -- 2016-08-05
---------------------

Added
+++++

 - The performance of find operations can be greatly improved by using pre-generated job indexes.
 - New top-level commands: ``$ signac find``, ``$ signac index``, ``$ signac statepoint``, and ``$ signac view``.
 - New method: ``Project.create_linked_view()``
 - New method: ``Project.build_job_statepoint_index()``
 - New method: ``Project.build_job_search_index()``
 - The ``Project.find_jobs()`` method allows to filter by job document.

Changed
+++++++

 - The ``SignacProjectCrawler`` indexes all jobs, not only those with non-empty job documents.
 - The ``signac.fetch_one()`` function returns ``None`` if no associated object can be fetched.
 - The tutorial is restructured into multiple parts.
 - Instructions for installation are separated from the guide.

Removed
+++++++

 - Remove previously deprecated *crawl* keyword argument in index export functions.
 - Remove previously deprecated function common.config.write_config().

Version 0.3
===========

[0.3.0] -- 2016-06-23
---------------------

Added
+++++

 - Add contributing agreement and guidelines.

Changed
+++++++

 - Change license from MIT to BSD 3-clause license.

Version 0.2
===========

[0.2.9] -- 2016-06-06
---------------------

Added
+++++

 - Addition of the ``signac config`` command line API.
 - Password updates are encrypted with ``bcrypt`` when ``passlib`` is installed.
 - The user is prompted to enter missing credentials (username/password) in case that they are not stored in the configuration.
 - The ``$ signac confg`` tool provides the ``--update-pw`` argument, which allows users to update their own password.
 - Added MIT license, in addition, all source code files contain a short licensing header.

Changed
+++++++

 - Improved documentation on how to configure signac.
 - The OSI classifiers are updated, including an upgrade of the development status to '4 - beta'.

Fixed
+++++

 - Nested job state points can no longer get corrupted. This bug occurred when trying to operate on nested state point mappings.

Deprecated
++++++++++

 - Deprecated pymongo versions 2.x are no longer supported.

[0.2.8] -- 2016-04-18
---------------------

Added
+++++

 - ``Project`` is now in the root namespace.
 - Add ``index()`` method to `Project`.
 - Add ``create_access_module()`` method to ``Project``.
 - Add ``find_variable_parameters()`` method to ``Project``.
 - Add ``fn()`` method to ``Job``, which prepends the job's workspace path to a filename.
 - The documentation contains a comprehensive tutorial

Changed
+++++++

 - The ``crawl()`` function yields only the index documents and not a tuple of (_id, doc).
 - ``export()`` and ``export_pymongo()`` expect the index documents as first argument, not a crawler instance. The old API is still supported, but will trigger a DeprecationWarning.

[0.2.7] -- 2016-02-29
---------------------

Added
+++++

 - Add ``job.isfile()`` method

Changed
+++++++

 - Optimize ``project.find_statepoints()`` and ``project.repair()`` functions.

[0.2.6] -- 2016-02-20
---------------------

Added
+++++

 - Add ``job.reset_statepoint()`` and `job.update_statepoint()`
 - Add ``job.remove()`` function

Changed
+++++++

 - Sanitize filter argument in all ``project.find_*()`` methods.
 - The ``job.statepoint()`` function accurately represents saved statepoints, e.g. tuples are represented as lists, as there is no difference between tuples and lists in JSON.
 - signac-gui does not block on database operations.
 - signac-gui allows reload of databases and collections of connected hosts.

Fixed
+++++

 - ``RegexFileCrawler`` ``define()`` class function only acts upon the actual specialization and not globally on all ``RegexFileCrawler`` classes.
 - signac-gui does not crash when replica sets are configured.

[0.2.5] -- 2016-02-10
---------------------

Added
+++++

 - Added ``signac.get_project()``, ``signac.get_database()``, ``signac.fetch()`` and ``signac.fetch_one()`` to top-level namespace.
 - Added basic shell commands, see ``$ signac --help``.
 - Allow opening of jobs by id: ``project.open_job(id='abc123...')``.
 - Mirror data while crawling.
 - Use extra sources for ``fetch()`` and ``fetch_one()``.
 - Add file system handler: ``LocalFS``, handler for local file system.
 - Add file system handler: ``GridFS``, handler for MongoDB GridFS file system.
 - Crawler tags, to control which crawlers are used for a specific index.
 - Allow explicit job workspace creation with ``job.init()``.
 - Forwarding of pymongo host configuration via **signac** configuration.

Changed
+++++++

 - Major reorganization of the documentation, split into: Overview, Guide, Quick Reference and API.
 - Documentation: Add notes for system administrators about advanced indexing.
 - Warn about outdated pymongo versions.
 - Set *zip_safe* flag to true in *setup.py*.
 - Remove dependency on six module, by adding it to the common subpackage.

Deprecated
++++++++++

Fixed
+++++

 - Fixed hard import of pymongo bug (issue #24).
 - Crawler issues with malformed documents.

[0.2.4] -- 2016-01-11
---------------------

Added
+++++

 - Implement ``Project.repair()`` function for projects with corrupted workspaces.
 - Allow environment variables in workspace path definition.
 - Check and fix config permission errors.

Changed
+++++++

 - Increase robustness of job manifest file creation.

Fixed
+++++

 - Fix project crawler deep directory issue (hotfix).

[0.2.3] -- 2015-12-09
---------------------

Fixed
+++++

 - Fix a few bugs related to project views.

[0.2.2] -- 2015-11-30
---------------------

Fixed
+++++

 - Fix ``SignacProjectCrawler`` ``super()`` bug.

[0.2.1] -- 2015-11-29
---------------------

Added
+++++

 - Add support for Python 2.7
 - Add signac-gui (early alpha)
 - Allow specification of relative and default workspace paths
 - Add the ability to create project views
 - Add ``Project.find_*()`` functions to search the workspace
 - Add function to write and read state point hash tables

[0.2.0] -- 2015-11-05
---------------------

 - Major consolidation of the package.
 - Remove all hard dependencies, but six.