czbenchmarks.datasets.types
===========================

.. py:module:: czbenchmarks.datasets.types


Attributes
----------

.. autoapisummary::

   czbenchmarks.datasets.types.DataValue


Classes
-------

.. autoapisummary::

   czbenchmarks.datasets.types.Organism
   czbenchmarks.datasets.types.DataTypeSpec
   czbenchmarks.datasets.types.DataType


Module Contents
---------------

.. py:class:: Organism(name: str, prefix: str)

   Bases: :py:obj:`enum.Enum`


   Create a collection of name/value pairs.

   Example enumeration:

   >>> class Color(Enum):
   ...     RED = 1
   ...     BLUE = 2
   ...     GREEN = 3

   Access them by:

   - attribute access::

   >>> Color.RED
   <Color.RED: 1>

   - value lookup:

   >>> Color(1)
   <Color.RED: 1>

   - name lookup:

   >>> Color['RED']
   <Color.RED: 1>

   Enumerations can be iterated over, and know how many members they have:

   >>> len(Color)
   3

   >>> list(Color)
   [<Color.RED: 1>, <Color.BLUE: 2>, <Color.GREEN: 3>]

   Methods can be added to enumerations, and members can have their own
   attributes -- see the documentation for details.


   .. py:attribute:: HUMAN
      :value: ('homo_sapiens', 'ENSG')



   .. py:attribute:: MOUSE
      :value: ('mus_musculus', 'ENSMUSG')



   .. py:attribute:: TROPICAL_CLAWED_FROG
      :value: ('xenopus_tropicalis', 'ENSXETG')



   .. py:attribute:: AFRICAN_CLAWED_FROG
      :value: ('xenopus_laevis', 'ENSXLAG')



   .. py:attribute:: ZEBRAFISH
      :value: ('danio_rerio', 'ENSDARG')



   .. py:attribute:: MOUSE_LEMUR
      :value: ('microcebus_murinus', 'ENSMICG')



   .. py:attribute:: WILD_BOAR
      :value: ('sus_scrofa', 'ENSSSCG')



   .. py:attribute:: CRAB_EATING_MACAQUE
      :value: ('macaca_fascicularis', 'ENSMFAG')



   .. py:attribute:: RHESUS_MACAQUE
      :value: ('macaca_mulatta', 'ENSMMUG')



   .. py:attribute:: PLATYPUS
      :value: ('ornithorhynchus_anatinus', 'ENSOANG')



   .. py:attribute:: OPOSSUM
      :value: ('monodelphis_domestica', 'ENSMODG')



   .. py:attribute:: GORILLA
      :value: ('gorilla_gorilla', 'ENSGGOG')



   .. py:attribute:: CHIMPANZEE
      :value: ('pan_troglodytes', 'ENSPTRG')



   .. py:attribute:: MARMOSET
      :value: ('callithrix_jacchus', 'ENSCJAG')



   .. py:attribute:: CHICKEN
      :value: ('gallus_gallus', 'ENSGALG')



   .. py:attribute:: RABBIT
      :value: ('oryctolagus_cuniculus', 'ENSOCUG')



   .. py:attribute:: FRUIT_FLY
      :value: ('drosophila_melanogaster', 'FBgn')



   .. py:attribute:: RAT
      :value: ('rattus_norvegicus', 'ENSRNOG')



   .. py:attribute:: NAKED_MOLE_RAT
      :value: ('heterocephalus_glaber', 'ENSHGLG')



   .. py:attribute:: CAENORHABDITIS_ELEGANS
      :value: ('caenorhabditis_elegans', 'WBGene')



   .. py:attribute:: YEAST
      :value: ('saccharomyces_cerevisiae', '')



   .. py:attribute:: MALARIA_PARASITE
      :value: ('plasmodium_falciparum', 'PF3D7')



   .. py:attribute:: SEA_LAMPREY
      :value: ('petromyzon_marinus', 'ENSPMAG')



   .. py:attribute:: FRESHWATER_SPONGE
      :value: ('spongilla_lacustris', 'ENSLPGG')



   .. py:attribute:: CORAL
      :value: ('stylophora_pistillata', 'LOC')



   .. py:attribute:: SEA_URCHIN
      :value: ('lytechinus_variegatus', '')



   .. py:method:: __str__()


   .. py:method:: __repr__()


   .. py:property:: name

      The name of the Enum member.


   .. py:property:: prefix


.. py:class:: DataTypeSpec

   Specification for a data type in the system


   .. py:attribute:: name
      :type:  str


   .. py:attribute:: dtype
      :type:  Type


   .. py:attribute:: description
      :type:  str


   .. py:attribute:: is_input
      :type:  bool
      :value: True



.. py:class:: DataType(*args, **kwds)

   Bases: :py:obj:`enum.Enum`


   Create a collection of name/value pairs.

   Example enumeration:

   >>> class Color(Enum):
   ...     RED = 1
   ...     BLUE = 2
   ...     GREEN = 3

   Access them by:

   - attribute access::

   >>> Color.RED
   <Color.RED: 1>

   - value lookup:

   >>> Color(1)
   <Color.RED: 1>

   - name lookup:

   >>> Color['RED']
   <Color.RED: 1>

   Enumerations can be iterated over, and know how many members they have:

   >>> len(Color)
   3

   >>> list(Color)
   [<Color.RED: 1>, <Color.BLUE: 2>, <Color.GREEN: 3>]

   Methods can be added to enumerations, and members can have their own
   attributes -- see the documentation for details.


   .. py:attribute:: METADATA


   .. py:attribute:: ANNDATA


   .. py:attribute:: ORGANISM


   .. py:attribute:: EMBEDDING


   .. py:attribute:: CONDITION_KEY


   .. py:attribute:: SPLIT_KEY


   .. py:attribute:: PERTURBATION_PRED


   .. py:attribute:: PERTURBATION_TRUTH


   .. py:property:: spec
      :type: DataTypeSpec



   .. py:property:: dtype
      :type: Type



   .. py:property:: description
      :type: str



   .. py:property:: is_input
      :type: bool



   .. py:property:: is_output
      :type: bool



   .. py:method:: __hash__()


   .. py:method:: __eq__(other)


   .. py:method:: __str__()


   .. py:method:: __repr__()


.. py:data:: DataValue