The signac package follows semantic versioning.
[1.8.0] – 2021-xx-xx¶
dump_statepointsare deprecated (#579, #197).
Project.indexmethod is deprecated (#591, #588).
JobSearchIndexclass is deprecated (#600).
indexargument is deprecated in
Projectmethods (#602, #588).
signac.citemodule is deprecated (#611, #592).
H5Store.modereturns the file mode (#607).
[1.7.0] – 2021-06-08¶
SyncedCollectionclass and subclasses to replace
JSONDictwith 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_writeparameter 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
Collectionindex 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.
- Optimized internal path joins to speed up project iteration (#515).
doc_filterarguments, which are replaced by namespaced filters. Due to their long history,
doc_filterarguments will still be accepted in signac 2.0 and will only be removed in 3.0 (#516).
- The modules
signac.core.synceddict.pyare deprecated in favor of the new
SyncedCollectionclasses and will be removed in signac 2.0 (#483).
- Corrected docstrings for
[1.6.0] – 2021-01-24¶
- Added documentation for
- Optimized job hash and equality checks (#442, #455).
- State points are loaded lazily when
Jobis opened by id (#238, #239).
Projectclasses 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).
- Zero-dimensional NumPy arrays can be used in state points and documents (#449).
[1.5.1] – 2020-12-19¶
- Support for h5py version 3 (#411).
- Added pyupgrade to pre-commit hooks (#413).
- Code is formatted with
isortpre-commit hooks (#415).
- Added macOS to CircleCI testing pipeline (#281, #414).
- Official support for Python 3.9 (#417).
- Optimized internal function
- 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¶
- Type annotations are validated during continuous integration (#313).
ProjectSchemaclass (#314, #324).
- Allow grouping by variables that are not present in all jobs in the project in
- Added parameters
flattento 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).
- Fix the
signac config verifycommand (previously broken) (#301, #302).
- Warnings now appear when raised by the
signacCLI (#317, #308).
- Fix dots in synchronization error messages (#375, #376).
- Deprecate the
Project, to be removed in 2.0 (#303, #308).
MainCrawlerclass has replaced the
MasterCrawlerclass. Both classes are deprecated (#342).
[1.4.0] – 2020-02-28¶
- Added Windows to platforms tested with continuous integration (#264, #266).
- Add command line option
signac sync(#280, #230).
- Workspace directory is created when
Projectis initialized (#267, #271).
- Changed testing framework from
- Refactored internal use of deprecated
get_statepointfunction (#227, #282).
- Fixed issues on Windows with
H5Store, project import/export, and operations that move files (#264, #266).
_SyncedDictobjects does not mutate nested dictionaries (#234, #269).
- Fixed issue with
project.dataaccess from separate instances of
- Fixed error when launching
signac shellif permissions are denied for
- Removed vendored
tqdmmodule and replaced it with a requirement (#289).
- Removed support for
rapidjsonas an alternative JSON library (#285, #287).
- Removed tuple of keys implementation of nested dictionaries (#272, #296).
[1.3.0] – 2019-12-20¶
- Official support for Python 3.8 (#258).
- Add properties
$ signac diffCLI 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).
Project.__contains__check in constant time (#231).
- 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).
- Deprecate the
Jobclasses in favor of the
idproperty, to be removed in 2.0 (#250).
- In-memory modification of the project configuration, to be removed in 2.0 (#246).
- Dropped support for Python 2.7 (#232).
[1.2.0] – 2019-07-22¶
- Keep signac shell command history on a per-project basis (#134, #194).
Collectionclass (#104, #200).
- Fix issue where shallow copies of instances of
Jobwould 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_html__implementations of the
- 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
- 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).
[1.1.0] – 2019-05-19¶
- Add command line options
signac findthat 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
- 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
ResourceWarningoriginating from unclosed instance of
- Fix issue with using the
get_project()function with a relative path and
- Support for Python version 3.4 (no longer tested).
[1.0.0] – 2019-02-28¶
- Official support for Python 3.7.
H5StoreManagerclasses, which are useful for storing (numerical) array-like data with an HDF5-backend. These classes are exposed within the root namespace.
project.dataproperties which present an instance of
H5Storeto access numerical data within the job workspace and project root directory.
project.storesproperties, which present an instance of
H5StoreManagerto manage multiple instances of
H5Storeto store numerical array-like data within the project workspace and project root directory.
signac.Project.get_job()functions that allow users to get a job handle by switching into or providing the job’s workspace directory.
jobvariable is automatically set when opening a
signac shellfrom within a job’s workspace directory.
- Add the
signac shell -coption which allows the direct specification of Python commands to be executed within the shell.
- Automatic cast of
numpyarrays to lists when storing them within a
JSONDict, e.g., a
Collectionclass to manage collections stored in compressed files (gzip, zip, etc.).
- Enable deleting of
JSONDictkeys through the attribute interface, e.g.,
- Pretty HTML representation of instances of
JobsCursortargeted at Jupyter Notebooks (requires pandas, automatically enabled when installed).
to_dataframe()function to export the job state point and document data of a
JobsCursor, e.g., the result of
Project.find_jobs(), as a
- Dots (.) in keys are no longer allowed for
Collectionkeys (previously deprecated).
JSONDictmodule is exposed in the root namespace, which is useful for storing text-serializable data with a JSON-backend similar to the
Job.init()method returns the job to allow one-line job creation and initialization.
searchargument 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.
Collection.update()behavior such that existing documents with identical primary key are updated. Previously, a
KeyErrorwould be raised.
- Fix issue where the
Job.move()would trigger a confusing
DestinationExistsexception when trying to move jobs across devices / file systems.
- Fix issue that caused failures when the
python-rapidjsonpackage is installed. The
python-rapidjsonpackage 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.
- Removes the obsolete and deprecated
- The previously deprecated
Project.find_job_documents()functions have been removed.
Project.find_jobs()no longer accepts the obsolete
[0.9.5] – 2019-01-31¶
- 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¶
- Adds the
$ signac importcommand 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 exportcommand 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
- Adds the
signac.Project.temporary_project()context manager which creates a temporary project within the root project workspace.
signacto the default namespace when invoking
- Add option to specify a custom view path for the
- Iterables of documents used to construct a Collection no longer require an
- The default path for linked views has been adjusted to match the one used for data exports.
- 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¶
- 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.
- Fix issue where a job instance would not be properly updated after more than one state point reset.
[0.9.2] – 2017-12-18¶
- 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.
Project.check()method which checks for workspace corruption, but does not make any attempt to repair it.
Project.repair()method will attempt to repair jobs, that have been corrupted by manually renaming the job’s workspace directory.
- Enable the write_concern flag for the
- Allow to omit the specification of an authentication mechanism in the MongoDB host configuration.
- Fix critical issue in the
JSONDictimplementation 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¶
- Fix critical issue in the
SyncedAttrDictimplementation that would previously overwrite the underlying file if the first operation was a
[0.9.0] – 2017-10-28¶
- Introduction of
$ signac sync,
Job.sync()for the simplified and fine-grained synchronization of multiple project data spaces.
- Introduction of
$ signac schemaand
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
- Support for project-centralized data with the
Project.documentattribute and the
Project.fn()method for the wrapping of filenames within the project root directory.
- Added the
Job.reset()methods to clear or reset a job’s workspace data.
Job.documentnow use the same underlying data structure and provide the exact same API (copy with
()and access of keys as attributes).
Collectionclass 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.
[0.8.7] – 2017-10-05¶
- 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.
[0.8.5] – 2017-06-07¶
- The signac ids in the signac find –show view are no longer enclosed by quotation marks.
- 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¶
- 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.
$ signac findcommand supports a simple filter syntax, where key value pairs can be provided as individual arguments.
$ signac findcommand 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.
$ signac viewcommand has an additional filter option to select a sub data space directly without needing to pipe job ids.
- The new
$ signac documentcommand can be used to display a job’s document directly.
- Minor performance improvements.
[0.8.3] – 2017-05-10¶
ExportErrorwhen updating with an empty index.
- 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¶
- Fixes a
TypeErrorwhich occurred under specific conditions when calling
Collection.find()with nested filter arguments.
[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.
- Introduction of the
Collectionclass for the management of document collections, such as indexes in memory and on disk.
- Generation of file indexes directly via the
- Generation of main indexes directly via the
signac.index()function and the
$ signac indexcommand.
- The API of
signac_access.pyfiles has been simplified, including the possibility to use a blank file for a minimal configuration.
- Use the
$ signac project --accesscommand to create a minimal access module in addition to
- 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.wsattribute, as short-cut for
Job.spinterface 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)¶
$ signac indexcommand generates a main index instead of a project index. To generate a project index from the command line use
$ signac project --indexinstead.
SignacProjectCrawlerclass expects the project’s root directory as first argument, not the workspace directory.
get_crawlers()function defined within a
signac_access.pyaccess module is expected to yield crawler instances directly, not a mapping of crawler ids and instances.
- The simplification of the
signac_access.pymodule API is reflected in a reduction of arguments to the
MainCrawlerclasses were moved into the root namespace.
- If a
MainCrawlerobject is instantiated with the
raise_on_errorargument 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 findqueries.
- 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
--debugoption in combination with
$ signac indexwill show the traceback of errors encountered during indexing instead of ignoring them.
- Instances of
Jobare hashable, making it possible to use them as dict keys for instance.
- The representation of
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.
DocumentSearchEngineclass has been deprecated, its functionality is now provided by the
- An issue related to exporting documents to MongoDB collections via pymongo in combination with Python 2.7 has been fixed.
[0.7.1] – 2017-01-09¶
- When the
python-rapidjsonpackage is installed, it will be used for JSON encoding/decoding (experimental).
- All job move-related methods raise
DestinationExistsErrorin case of destination conflicts.
$ signac findcommand.
- Fixed bug in
$ signac statepoint.
- Suppress ‘broken pipe error’ message when using
$ signac findfor example in combination with
[0.7.0] – 2017-01-04¶
- 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:
- Add function for moving and copying of jobs between projects.
- All project related iterators support the
- Enable iteration over all jobs with:
for job in project:.
len(project)an alias for
in-operator to determine whether a job is initialized within a project.
Job.spattribute to access and modify a job’s state point.
Project.open_job()method accepts abbreviated job ids.
Project.min_len_unique_id()method to determine the minimum length of job ids to be unique within the project’s data space.
Job.move()method to move jobs between projects.
Project.clone()method to copy jobs between projects.
$ signac moveand
$ signac clonecommand line functions.
Job.reset_statepoint()method to reset a job’s state point.
Job.update_statepoint()method to update a job’s state point.
- Add a
Job.FN_DOCUMENTconstant which defines the default filename of the job document file
$ signac findcommand accepts a
-d/--doc-filteroption to filter by job document contents.
- Add the
Project.create_linked_view()method as replacement for the previously deprecated
- 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.
- Fix error when using an instance of
- 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.
- The signac-gui component has been removed.
forceargument is removed.
Project.find_variable_parameters()method has been removed
[0.6.2] – 2017-12-15¶
- Add instructions on how to acknowledge signac in publications to documentation.
- Add cite module for the auto-generation of formatted references and BibTeX entries.
- Remove SSL authentication support.
[0.6.1] – 2017-11-26¶
Project.create_view()method triggers a
DeprecationWarninginstead of a
Project.find_variable_parameters()method triggers a
DeprecationWarninginstead of a
- Make package more robust against PySide import errors.
- Fix critical bug in
fs.GridFSclass, which rendered it unusuable.
- Fix issue in
indexing.fetch()previously resulting in local paths being ignored.
- Fix error
[0.6.0] – 2016-11-18¶
- Add the
export_to_mirror()function for mirroring files.
- Introduction of the
signac.fsnamespace 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
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.
- 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
- Each index document is now uniquely coupled with only one file or data object, which is why
signac.fetch_one()and the latter one has been deprecated and is currently an alias of the former one.
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.
TextFilefile-like object class definition in the formats module has been replaced with a constant of type
signac.export()function automatically delegates to specialized implementations such as
export_pymongo()and is more robust against errors, such as broken connections.
export_pymongo()function makes multiple automatic restart attempts when encountering errors.
- Documentation: The tutorial is now based on signac-examples jupyter notebooks.
contrib.crawlermodule has been renamed to contrib.indexing to better reflect the semantic context.
signac.export()function now implements the logic for data linking and mirroring.
- Provide default argument for ‘–indent’ option for
$ signac statepointcommand.
- Log, but do not reraise exceptions during
MainCrawlerexecution, making the compilation of main indexes more robust against errors.
- The object representation of
Projectinstances is simplified.
- The warning verbosity has been reduced when importing modules with optional dependencies.
- 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:
- Opening instances of
Job.open()method multiple times, equivalently entering the job context recursively, does not cause an error anymore, but instead the behavior is well-defined.
[0.5.0] – 2016-08-31¶
- New function:
signac.init_project()simplifies project initialization within Python
- Added optional
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:
- The performance of project indexing and crawling has been improved.
[0.4.0] – 2016-08-05¶
- 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:
- New method:
- New method:
Project.find_jobs()method allows to filter by job document.
SignacProjectCrawlerindexes all jobs, not only those with non-empty job documents.
Noneif no associated object can be fetched.
- The tutorial is restructured into multiple parts.
- Instructions for installation are separated from the guide.
- Remove previously deprecated crawl keyword argument in index export functions.
- Remove previously deprecated function common.config.write_config().
[0.2.9] – 2016-06-06¶
- Addition of the
signac configcommand line API.
- Password updates are encrypted with
- The user is prompted to enter missing credentials (username/password) in case that they are not stored in the configuration.
$ signac confgtool provides the
--update-pwargument, which allows users to update their own password.
- Added MIT license, in addition, all source code files contain a short licensing header.
- Improved documentation on how to configure signac.
- The OSI classifiers are updated, including an upgrade of the development status to ‘4 - beta’.
- Nested job state points can no longer get corrupted. This bug occurred when trying to operate on nested state point mappings.
- Deprecated pymongo versions 2.x are no longer supported.
[0.2.8] – 2016-04-18¶
Projectis now in the root namespace.
index()method to Project.
Job, which prepends the job’s workspace path to a filename.
- The documentation contains a comprehensive tutorial
crawl()function yields only the index documents and not a tuple of (_id, doc).
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¶
[0.2.6] – 2016-02-20¶
- Sanitize filter argument in all
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.
define()class function only acts upon the actual specialization and not globally on all
- signac-gui does not crash when replica sets are configured.
[0.2.5] – 2016-02-10¶
signac.fetch_one()to top-level namespace.
- Added basic shell commands, see
$ signac --help.
- Allow opening of jobs by id:
- Mirror data while crawling.
- Use extra sources for
- 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
- Forwarding of pymongo host configuration via signac configuration.
- 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.
- Fixed hard import of pymongo bug (issue #24).
- Crawler issues with malformed documents.
[0.2.4] – 2016-01-11¶
Project.repair()function for projects with corrupted workspaces.
- Allow environment variables in workspace path definition.
- Check and fix config permission errors.
- Increase robustness of job manifest file creation.
- Fix project crawler deep directory issue (hotfix).
[0.2.1] – 2015-11-29¶
- 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
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.