Changelog¶

The signac package follows semantic versioning.

Version 2¶

[2.4.0] – 2025-xx-xx¶

Fixed¶

Schema detection when a state point value is a list of dictionaries having lists (#1030).

[2.3.0] – 2025-04-10¶

Added¶

Implemented JobsCursor.__getitem__ (#1017).

Fixed¶

Support for Numpy 2.0 in tests (#997).

Use tool.setuptools key in pyproject.toml (#1020).

Define build command in asv.conf.json to enable support for asv 0.6.2 and

later (#1021). - Documentation build process (#1001).

Changed¶

Improved performance of Project.detect_schema() (#1026).

[2.2.0] – 2024-02-13¶

Added¶

Official support for Python 3.12 (#957).

Job.cached_statepoint - cached and read only access to job state points. Faster than Job.statepoint (#975).

Changed¶

Restrict allowable tar file features in Python 3.12 (#957).

Linked views now can contain spaces and other characters except directory separators (#926).

Linked views now can be created on Windows, if ‘Developer mode’ is enabled (#430, #958).

Increase performance for many usage patterns (#975).

Fixed¶

Fixed parsing of $not query expressions on command line (#970).

Removed¶

Unused ruamel.yaml dependency (#981).

[2.1.0] – 2023-07-12¶

Changed¶

signac’s “synced collections” backend used for reading/writing JSON files has been moved to a separate package called synced_collections. See https://github.com/glotzerlab/synced_collections (#924).

[2.0.0] – 2023-03-30¶

Added¶

Official support for Python 3.11 (#875).

H5Store related errors are now included in the public API (#775).

Users can now access the project to which a job belongs with the Job.project attribute (#808).

Changed¶

Functions raising AssertionError now raise RuntimeError (#612).

State points and documents require keys to be of type str (#719).

The keyword _id of the Job constructor has been renamed to id_ (#681).

The signac schema to use version 2. This update involves a number of changes: - The project configuration is now stored at .signac/config instead of signac.rc or .signacrc (#678). - Schema versions are now identified by simple integers rather than semantic versioning style versions (#688). - Projects no longer have names and are identified solely by their root directories. This change also affects a number of public APIs where names are including, most prominently signac.init_project and Project.init_project. Projects can now be constructed with just a root directory rather than a preloaded config (#677, #684, #706). - Project workspaces are no longer configurable, but are instead always defined as a subdirectory of the Project’s root directory called workspace (#714).

Rather than searching upwards until the root, load_config will only load configuration files in the specified directory, which is assumed to be a project directory, as well as the user’s home directory (#711).

Changed the root parameter to path in the signac.get_project and signac.init_project functions and corresponding Project methods (#757, #758).

The prefix argument to $ signac view is now optional and can be provided with -p/--prefix (#653, #774).

Tests are run with xfail_strict = True (#850).

Detection of an invalid config will raise an error rather than a debug log (#855).

The package namespace has been flattened so that most functionality is directly available in the signac namespace (#756, #868).

The calc_id function has been moved from the hashing module to the job module (#873).

Tests are run with all warnings treated as errors (#871).

The contents of the syncutil module have been moved into sync (#869).

The project now leverages a fully pyproject.toml-driven build (#878).

Removed¶

The pre-SyncedCollection synchronized dictionary classes, including SyncedDict, SyncedAttrDict, and JSONDict (#577).

The old custom JSON encoder and dumps wrapper (#577).

The MPIPool and the filesystems.py module (#575).

The following Project methods: get_id, build_job_search_index, build_job_statepoint_index, find_job_ids, reset_statepoint, update_statepoint, create_access_module, index, dump_statepoints, get_statepoint, read_statepoints, write_statepoints, groupbydoc, root_directory, num_jobs (#574, #593, #599, #601, #752).

The following Job methods: get_id, workspace, ws, reset_statepoint (#578, #752).

The syncutil.copytree method (#581).

All Crawlers, including RegexFileCrawler, MainCrawler, MasterCrawler, SignacProjectCrawler, and BaseCrawler, in addition to all associated functionality in indexing.py (#580).

The cite.py module (#594).

The following types of exceptions: AuthenticationError, ExportError`, ``FetchError, PermissionsError (#595, #596).

All MongoDB database functionality, including the db subpackage, the connection, crypt, and host submodules in the common subpackage, and all associated configuration information (#576, #596).

The JobSearchIndex class (#587).

The ability to pass indexes to various Project methods (#599).

The following JobsCursor methods: groupbydoc, next (#601, #604).

The Project.config property is no longer mutable. Use the command line $ signac config to modify configuration (#608, #246, #244).

The config module and all its functions, all of which have been made private (#674, #753, #789, #847, #877).

Project subclasses can no longer define a Job subclass to use (#588, #693).

The Collection class (#664, #667, #683).

The project CLI subcommand (#752).

The --workspace option for the command line job subcommand (#752).

The ability to call Project.workspace, it is strictly a property now (#752).

ProjectSchema.__call__, ProjectSchema.detect (#752).

The --doc-filter option for several command line subcommands (#613, #795).

The public API of the synced_collection subpackage (#807, #790).

The warnings module (#815).

The signac.common.validate module (#853).

The Config class (#860).

The DictManager class (#858).

The signac.testing module (#863).

Zenodo is no longer updated (#903).

Version 1¶

[1.8.0] – 2022-10-05¶

Added¶

Official support for Python 3.10 (#631).

Benchmarks can be run using the asv (airspeed velocity) tool (#629).

Continuous integration tests run in parallel with pytest-xdist (#705).

The Project.path and Job.path properties (#685).

Changed¶

Schema migration is now performed on directories rather than signac projects and supports a wider range of schemas (#654).

Deprecated features now use FutureWarning instead of DeprecationWarning, which is hidden by default (#687, #691, #692).

Project names have a default in anticipation of removing names entirely. Project names will be removed in signac 2.0 (#644).

Project.workspace is now a property, not a method (#685).

Continuous integration uses GitHub Actions instead of CircleCI (#776, #788).

Raise errors in testing when DeprecatedWarning or FutureWarning is raised (#713).

Change GitHub PR to check for uncompleted tasks (i.e. unchecked checkboxes) (#686).

Deprecated¶

Project methods read_statepoints, write_statepoints, and dump_statepoints are deprecated (#579, #197).

Project.index method is deprecated (#591, #588).

JobSearchIndex class is deprecated (#600).

index argument is deprecated in Project methods (#602, #588).

signac.cite module is deprecated (#611, #592).

The config module and all its methods are deprecated (#675, #753, #814).

Accessing Project.workspace as a method, it should be accessed as a property (#685).

Project.num_jobs (#685).

ProjectSchema.__call__, ProjectSchema.detect (#685).

Fixed¶

H5Store.mode returns the file mode (#607).

User-provided path functions now raise an error if not unique (#666).

Collection class no longer raises an error when searching by a primary key that does not exist (#676).

Relative paths on Windows are not used if the current directory has no common prefix (#777).

get_project() now raises an error if provided a root directory that does not exist (#779, #792).

Catch internally raised warnings on use of deprecated password cache (#754).

Catch KeyError from multithreading error (#710).

Tests now properly show raised warnings (#603).

Removed¶

Removed upper bound of Python 4 on python_requires (#780, #781).

Dropped support for Python 3.6 and Python 3.7 (#715) following the recommended support schedules of NEP 29.

Dropped dependency on deprecation package (#687, #718).

Removed unused _extract utility function to avoid CVE-2007-4559 (#829).

[1.7.0] – 2021-06-08¶

Added¶

New SyncedCollection class and subclasses to replace JSONDict with more general support for different types of resources (such as MongoDB collections or Redis databases) and more complete support for different data types synchronized with files (#196, #234, #249, #316, #383, #397, #465, #484, #529, #530). This change introduces a minor-backwards incompatible change; for users making direct use of signac buffering, the force_write parameter is no longer respected. If the argument is passed, a warning will now be raised to indicate that it is ignored and will be removed in signac 2.0.

Unified querying for state point and document filters using ‘sp’ and ‘doc’ as prefixes (#332, #514). This change introduces a minor backwards-incompatible change to the Collection index schema (‘statepoint’->’sp’), but this does not affect any APIs, only indexes saved to file using a previous version of signac. Indexing APIs will be removed in signac 2.0.

Changed¶

Optimized internal path joins to speed up project iteration (#515).

Deprecated¶

doc_filter arguments, which are replaced by namespaced filters.

The modules signac.core.attrdict, signac.core.json, signac.core.jsondict, and signac.core.synceddict.py are deprecated in favor of the new SyncedCollection classes and will be removed in signac 2.0 (#483).

Fixed¶

Corrected docstrings for Job.update_statepoint and Project.update_statepoint (#506, #563).

[1.6.0] – 2021-01-24¶

Added¶

Implemented JobsCursor.__contains__ check (#449).

Added documentation for JobsCursor class (#475).

Changed¶

Optimized job hash and equality checks (#442, #455).

Optimized H5Store initialization (#443).

State points are loaded lazily when Job is opened by id (#238, #239).

Optimized Job and Project classes to cache internal properties and initialize on access (#451).

Python 3.6 is only tested with oldest dependencies (#474).

Improved documentation for updating and resetting state points (#444).

Deprecated¶

Deprecate syncutil.copytree method (#439).

Fixed¶

Zero-dimensional NumPy arrays can be used in state points and documents (#449).

[1.5.1] – 2020-12-19¶

Added¶

Support for h5py version 3 (#411).

Added pyupgrade to pre-commit hooks (#413).

Code is formatted with black and isort pre-commit hooks (#415).

Added macOS to CircleCI testing pipeline (#281, #414).

Official support for Python 3.9 (#417).

Changed¶

Optimized internal function _mkdir_p (#421).

Optimized performance of job initialization (#422).

Optimized performance of buffer storage (#428).

Optimized performance of creating/loading synced data structures (#429).

[1.5.0] – 2020-09-20¶

Added¶

Type annotations are validated during continuous integration (#313).

Added _repr_html_ method in ProjectSchema class (#314, #324).

Allow grouping by variables that are not present in all jobs in the project in JobsCursor.groupby (#321, #323).

Added parameters usecols and flatten to allow selection of columns and flattening of nested data when converting signac data into a pandas DataFrame (#327, #330).

Added support for pre-commit hooks (#355, #358).

Expanded CLI documentation (#187, #359, #377).

Changed¶

Docstrings are now written in numpydoc style.

Fixed¶

Fix the signac config verify command (previously broken) (#301, #302).

Warnings now appear when raised by the signac CLI (#317, #308).

Fix dots in synchronization error messages (#375, #376).

Deprecated¶

Deprecate the create_access_modules method in Project, to be removed in 2.0 (#303, #308).

The MainCrawler class has replaced the MasterCrawler class. Both classes are deprecated (#342).

Removed¶

Dropped support for Python 3.5 (#340). The signac project will follow the NEP 29 deprecation policy going forward.

Removed dependency on pytest-subtests (#379).

[1.4.0] – 2020-02-28¶

Added¶

Added Windows to platforms tested with continuous integration (#264, #266).

Add command line option -m/--merge for signac sync (#280, #230).

Changed¶

Workspace directory is created when Project is initialized (#267, #271).

Changed testing framework from unittest to pytest (#212, #275).

Refactored internal use of deprecated get_statepoint function (#227, #282).

Fixed¶

Fixed issues on Windows with H5Store, project import/export, and operations that move files (#264, #266).

Calling items or values on _SyncedDict objects does not mutate nested dictionaries (#234, #269).

Fixed issue with project.data access from separate instances of H5StoreManager (#274, #278).

Fixed error when launching signac shell if permissions are denied for .signac_shell_history (#279).

Removed¶

Removed vendored tqdm module and replaced it with a requirement (#289).

Removed support for rapidjson as an alternative JSON library (#285, #287).

Removed tuple of keys implementation of nested dictionaries (#272, #296).

[1.3.0] – 2019-12-20¶

Added¶

Official support for Python 3.8 (#258).

Add properties Project.id and Job.id (#250).

Add signac.diff_jobs function and $ signac diff CLI command to compare two or more state points (#248, #247).

Add function to initialize a sample data space for testing purposes (#215).

Add schema version to ensure compatibility and enable migrations in future package versions (#165, #253).

Changed¶

Implemented Project.__contains__ check in constant time (#231).

Fixed¶

Attempting to create a linked view for a Project on Windows now raises an informative error message (#214, #236).

Project configuration is initialized using ConfigObj, allowing the configuration to include commas and special characters (#251, #252).

Deprecated¶

Deprecate the get_id method in Project and Job classes in favor of the id property, to be removed in 2.0 (#250).

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

Removed¶

Dropped support for Python 2.7 (#232).

[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.

[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¶

[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¶

[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 main 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 main 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 MainCrawler classes were moved into the root namespace.

If a MainCrawler 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¶

[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¶

[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 MainCrawler logic has been simplified; their primary function is the compilation of index documents from subcrawlers, 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 MainCrawler execution, making the compilation of main 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.