Micone

-------------------

Fixed
+++++
- ``NetworkGroup`` methods that return ``NetworkGroup`` objects now make use of the ``id_field`` parameter

-------------------

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

-------------------

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

-------------------

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

------------------

- 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.

------------------

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``