v2.2.0

[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

What's Changed

• Fix README example init command. by @bdice in #913
• Remove inaccurate guidance about doc filters being removed in 3.0. by @bdice in #916
• Add more descriptive error if sp and id are not provided by @cbkerr in #915
• Use synced_collections. by @bdice in #924
• Remove numcodecs from docs. by @bdice in #925
• CI: No longer test latest packages on Python 3.8 by @b-butler in #938

Full Changelog: v2.0.0...v2.1.0

2.0.0

[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).

1.8.0

[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 DeprecatedWarnings or FutureWarnings are 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

This release adds SyncedCollections, a new, performant, and flexible approach to syncing job state points and documents with an underlying resource. Thanks to all who contributed! 🎨

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. Due to their long history, doc_filter arguments will still be accepted in signac 2.0 and will only be removed in 3.0 (#516).
• 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

This release focuses on performance improvements and better docs. Large projects should see massive speedups (4-7x on an SSD) for iterating over the project and working with signac-flow. Now you can scale up your science! 🎨

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

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

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

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

Added

• Official support for Python 3.8 (#258).
• Add properties Project.id and Job.id (#250).
• Add signac.diff_jobs function 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).