Micone

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

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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

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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``

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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

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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

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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