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 toOtu.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 fromnx.MultiGraph
tonx.Graph
Fixed
Make
cids
a default parameter inNetworkGroup.get_consensus_network
Minor code refactoring
0.11.1 (2022-01-11)
Added
slim
parameter added topvalue
module to allow the user to forgo storage of correlation bootstrap files
0.11.0 (2021-12-16)
Fixed
Network
class now usesname
to build the lineage of the node object instead of thetaxid
field. This prevents inconsistency between OTU tables and Networks of the same level
0.10.4 (2021-12-04)
Fixed
NetworkGroup
methods that returnNetworkGroup
objects now make use of theid_field
parameter
0.10.3 (2021-12-03)
Fixed
Network.get_adjacency_table
now retrieves ids correctlysimple_voting
consensus method now takes sign of the edge into accountpropr
modules now assigns correlation file name similar to other modulesFixed bug in
mldm
when sample metadata is a single column
0.10.2 (2021-12-01)
Added
NetworkGroup
object now supports theid_field
parameter in constructor. Allowing combination of networks on fields other thantaxid
merge_pvalues
andcreate_consensus
now support theid_field
parameter
Fixed
remove_bimera
module now uses externalbiom
command to construct OTU table
0.10.0 (2021-11-23)
Added
HARMONIES
network inference methodCOZINE
network inference methodSPRING
network inference methodPipeline output checking functionality -
micone validate-results
Parametrize some of the pipeline settings
Changed
mldm
runtime limit
Fixed
normalize
module is turned off by defaultMany 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 thenextflow.config
and run the pipeline.
0.7.0 (2021-03-04)
Added
NetworkGroup
method now supports an__add__
methodFlashWeave.jl
for network inferencepropr
for network inferencemake_network
module split intomake_network_with_pvalue
andmake_network_wo_pvalue
Changed
MAGMA
network inference was removed because it has not been updatednetwork_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 networksConfig
class to extract, process and store pipeline settingsCommand
class is a wrapper for running subprocessesProcess
class for executing a pipeline processPipeline
class defines the pipeline and methods to run the pipelineEnvironments
class that creates, lists and loads conda environmentsLogging functionality
CLI interface for micone
0.4.2 (2018-10-08)
Added
Changed
ScriptTemplate.render
now uses a default value of ‘{}’ fortemplate_data
parameterRename
template_renderer.py
totemplate.py
Fixed
Input.location
andOutput.location
are now of typepathlib.Path
0.4.1 (2018-10-08)
Changed
Renamed
ExternalProcessParamsSet
class toExternalParamsSet
classRenamed
InternalProcessParamsSet
class toInternalParamsSet
classRenamed
ProcessParamsSet
class toParamsSet
classRenamed
ProcessParams
class toParams
classUpdated 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 configurationInternalProcessParamsSet
andExternalProcessParamsSet
for loading internal and external process paramsProcessParams
- A class to process and store parameters of pipeline processesDataTypes
- A class to process and store datatypesexternal.toml
to store the list of external pipeline processesinternal.toml
to store the list of internal pipeline processesdatatypes.toml
to store the list of pipeline supported datatypesScriptTemplate
- A class for templating nextflow scriptsConfigTemplate
- A class for templating nextflow config files
Changed
Simplified the internal and external settings files to contain minimum information
correlation_table
datatype renamed tointeraction_table
Modularize the default settings into separate files - datatypes.toml, internal.toml and external.toml
Fixed
Filter
DeprecationWarning
andPendingDeprecationWarning
in pytest configuration
0.3.0 (2018-08-28)
Added
Network.__repr__
- object representation for theNetwork
classNetwork.json
method to convert network to aJSON
stringNetwork.write
method to write network to a json fileNetwork.graph
property to return thenx.Graph
representation of the networkNetwork.load_json
classmethod to load network from json fileElistType
- Schema for edgelistNETWORK_CONVERTERS
to convert networks to and from various formatsNetwork.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 togh-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 testsNodesModel
,LinksModel
andNetworkmetadataModel
Network
class to read, write and manipulate networks and tests‘network_files’ and ‘correlation_data’ fixtures for tests
Changed
Keys for
MetadataType
classIncorporate 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
classOtu
classOtuValidator
classOtuSchema
classtaxmetadata_converter
functions to convert to and fromqiime1
andqiime2
taxonomy formats
0.1.0 (2018-06-30)
Added
First release and initial commits