v0.14.2

v0.14.2

v0.5.0 [Escherichia coli]

Major update! Implementing the core pipeline functionality

Added

• NetworkGroup class represents a group of networks
• Config class to extract, process and store pipeline settings
• Command class is a wrapper for running subprocesses
• Process class for executing a pipeline process
• Pipeline class defines the pipeline and methods to run the pipeline
• Environments class that creates, lists and loads conda environments
• Logging functionality
• CLI interface for mindpipe

v0.4.2 [Escherichia coli]

Added

• dict property to Paramsclass
• verify_io method to Paramsclass
• update_location method to Params class
• get method to Params class
• Params class to config namespace

Changed

• ScriptTemplate.render now uses a default value of '{}' for template_data parameter
• Rename template_renderer.py to template.py

Fixed

• Input.location and Output.location are now of type pathlib.Path

v0.4.1 [Escherichia coli]

Changed

• Renamed ExternalProcessParamsSet class to ExternalParamsSet class
• Renamed InternalProcessParamsSet class to InternalParamsSet class
• Renamed ProcessParamsSet class to ParamsSet class
• Renamed ProcessParams class to Params class
• Updated dependencies - biom-format, dask, toml

Fixed

• Flake8 errors

v0.4.0 [Escherichia coli]

Pipeline settings parser and template render have been implemented.

Added

• Config - A class to store all the pipeline configuration
• InternalProcessParamsSet and ExternalProcessParamsSet for loading internal and external process params
• ProcessParams - A class to process and store parameters of pipeline processes
• DataTypes - A class to process and store datatypes
• external.toml to store the list of external pipeline processes
• internal.toml to store the list of internal pipeline processes
• datatypes.toml to store the list of pipeline supported datatypes
• ScriptTemplate - A class for templating nextflow scripts
• ConfigTemplate - A class for templating nextflow config files

Changed

• Simplified the internal and external settings files to contain minimum information
• correlation_table datatype renamed to interaction_table
• Modularize the default settings into separate files - datatypes.toml, internal.toml and external.toml

Fixed

• Filter DeprecationWarning and PendingDeprecationWarning in pytest configuration

v0.3.0 [Escherichia coli]

Added

• Network.__repr__ - object representation for the Network class
• Network.json method to convert network to a JSON string
• Network.write method to write network to a json file
• Network.graph property to return the nx.Graph representation of the network
• Network.load_json classmethod to load network from json file
• ElistType - Schema for edgelist
• NETWORK_CONVERTERS to convert networks to and from various formats
• Network.load_elist classmethod to load network from edge list file

Changed

• Type of "computational_metadata" to DictType(UnionType((StringType, FloatType)))
• "computational_metadata" now includes 'interaction_threshold', 'pvalue_threshold' and 'pvalue_correction'
• "abundance" is now not a required field for a node
• Refactor network models into 'network_schema' module

Fixed

• Type annotation for link_set in Network._create_network
• Test data is now from the same source (all FMT datasets are from deblur)
• Prevent re-correction of pvalues when loading from json or elist file

v0.2.4 [Escherichia coli]

Added

• travis-sphinx to automatically deploy 'sphinx' docs to gh-pages
• Custom JsonEncoder class to encode json network data

Changed

• sphix theme to sphinx_rtd_theme

Fixed

• Network._create_network now removes complementary links in undirected networks

v0.2.3 [Escherichia coli]

Added

• Network.load_data to create networks from files
• 'computational_metadata' to test data

Changed

• Add 'computational_metadata' to 'correlation_data' fixtures and tests

v0.2.2 [Escherichia coli]

Added

• Lineage.taxid property and tests
• NodesModel, LinksModel and NetworkmetadataModel
• Network class to read, write and manipulate networks and tests
• 'network_files' and 'correlation_data' fixtures for tests

Changed

• Keys for MetadataType class
• Incorporate new keys in 'metadata.json' in test data
• Changed MetadataType from 'BaseType' to 'Model'
• Renamed MetadataType -> MetadataModel

v0.2.1 [Escherichia coli]

Added

• ChildrenmapType class and tests

Changed

• Network metadata files for tests