Changelog

0.11.6 (2022-04-05)

Fixed

• Calculation of correlations of bootstraps using fastspar (with temporary covariance parameter)

0.11.5 (2022-03-28)

Added

• Add obssum_thres parameter to Otu.rm_sparse_obs method to filter by sum of observation counts

Fixed

• The normalize_filter(off) module also does some filtering (with lax conditions) to ensure that the number of OTUs do not blow up.

0.11.3 (2022-01-12)

Fixed

• scaled_sum consensus method fixed to allow negative edges in the consensus

0.11.2 (2022-01-12)

Added

• NetworkGroup.to_network method to convert from nx.MultiGraph to nx.Graph

Fixed

• Make cids a default parameter in NetworkGroup.get_consensus_network

• Minor code refactoring

0.11.1 (2022-01-11)

Added

• slim parameter added to pvalue module to allow the user to forgo storage of correlation bootstrap files

0.11.0 (2021-12-16)

Fixed

• Network class now uses name to build the lineage of the node object instead of the taxid field. This prevents inconsistency between OTU tables and Networks of the same level

0.10.4 (2021-12-04)

Fixed

• NetworkGroup methods that return NetworkGroup objects now make use of the id_field parameter

0.10.3 (2021-12-03)

Fixed

• Network.get_adjacency_table now retrieves ids correctly

• simple_voting consensus method now takes sign of the edge into account

• propr modules now assigns correlation file name similar to other modules

• Fixed bug in mldm when sample metadata is a single column

0.10.2 (2021-12-01)

Added

• NetworkGroup object now supports the id_field parameter in constructor. Allowing combination of networks on fields other than taxid

• merge_pvalues and create_consensus now support the id_field parameter

Fixed

• remove_bimera module now uses external biom command to construct OTU table

0.10.0 (2021-11-23)

Added

• HARMONIES network inference method

• COZINE network inference method

• SPRING network inference method

• Pipeline output checking functionality - micone validate-results

• Parametrize some of the pipeline settings

Changed

• mldm runtime limit

Fixed

• normalize module is turned off by default

• Many bugs in the pipeline

0.9.0 (2021-10-30)

• Major overhaul of the pipeline to enable workflow to be implemented purely in nextflow

• As of writing the pipeline modules in the package do not work. Currently, to run the pipeline one needs to copy the contents of the pipelines folder to the destination, update the nextflow.config and run the pipeline.

0.7.0 (2021-03-04)

Added

• NetworkGroup method now supports an __add__ method

• FlashWeave.jl for network inference

• propr for network inference

• make_network module split into make_network_with_pvalue and make_network_wo_pvalue

Changed

• MAGMA network inference was removed because it has not been updated

• network_inference.direct modules will not support bootstrapping and pvalues in the future

Fixed

• Threading error due to database connection with NCBITaxa

0.6.0 (2021-02-04)

Stable update! All the tests pass and the pipelines work as expected

0.5.0 (2019-01-02)

Major update! Implemeting 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 micone

0.4.2 (2018-10-08)

Added

• dict property to ``Params``class

• verify_io method to ``Params``class

• 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

0.4.1 (2018-10-08)

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

0.4.0 (2018-10-06)

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

0.3.0 (2018-08-28)

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

0.2.4 (2018-08-23)

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

0.2.3 (2018-08-23)

Added

• Network.load_data to create networks from files

• ‘computational_metadata’ to test data

Changed

• Add ‘computational_metadata’ to ‘correlation_data’ fixtures and tests

0.2.2 (2018-08-22)

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

0.2.1 (2018-08-17)

Added

• ChildrenmapType class and tests

Changed

• Network metadata files for tests

0.2.0 (2018-08-17)

Added

• Lineage class

• Otu class

• OtuValidator class

• OtuSchema class

• taxmetadata_converter functions to convert to and from qiime1 and qiime2 taxonomy formats

0.1.0 (2018-06-30)

Added

• First release and initial commits