Merge pull request #854 from davidhassell/add-docs

Add missing docs

Author: davidhassell

cf/domain.py

@@ -1,5 +1,4 @@
 from math import prod
-from os import sep
 
 import cfdm
 import numpy as np
@@ -14,7 +13,6 @@
 from .functions import (
     _DEPRECATION_ERROR_ARG,
     _DEPRECATION_ERROR_METHOD,
-    abspath,
     indices_shape,
     parse_indices,
 )
@@ -125,43 +123,6 @@ def size(self):
             [domain_axis.get_size(0) for domain_axis in domain_axes.values()]
         )
 
-    def add_file_location(
-        self,
-        location,
-    ):
-        """Add a new file location in-place.
-
-        All data definitions that reference files are additionally
-        referenced from the given location.
-
-        .. versionadded:: 3.15.0
-
-        .. seealso:: `del_file_location`, `file_locations`
-
-        :Parameters:
-
-            location: `str`
-                The new location.
-
-        :Returns:
-
-            `str`
-                The new location as an absolute path with no trailing
-                path name component separator.
-
-        **Examples**
-
-        >>> f.add_file_location('/data/model/')
-        '/data/model'
-
-        """
-        location = abspath(location).rstrip(sep)
-
-        for c in self.constructs.filter_by_data(todict=True).values():
-            c.add_file_location(location)
-
-        return location
-
     def close(self):
         """Close all files referenced by the domain construct.
 
@@ -188,43 +149,6 @@ def close(self):
             removed_at="5.0.0",
         )  # pragma: no cover
 
-    def del_file_location(
-        self,
-        location,
-    ):
-        """Remove a file location in-place.
-
-        All data definitions that reference files will have references
-        to files in the given location removed from them.
-
-        .. versionadded:: 3.15.0
-
-        .. seealso:: `add_file_location`, `file_locations`
-
-        :Parameters:
-
-            location: `str`
-                 The file location to remove.
-
-        :Returns:
-
-            `str`
-                The removed location as an absolute path with no
-                trailing path name component separator.
-
-        **Examples**
-
-        >>> d.del_file_location('/data/model/')
-        '/data/model'
-
-        """
-        location = abspath(location).rstrip(sep)
-
-        for c in self.constructs.filter_by_data(todict=True).values():
-            c.del_file_location(location)
-
-        return location
-
     @classmethod
     def create_regular(cls, x_args, y_args, bounds=True):
         """
@@ -333,38 +257,6 @@ def create_regular(cls, x_args, y_args, bounds=True):
 
         return domain
 
-    def file_locations(
-        self,
-    ):
-        """The locations of files containing parts of the components data.
-
-        Returns the locations of any files that may be required to
-        deliver the computed data arrays of any of the component
-        constructs (such as dimension coordinate constructs, cell
-        measure constructs, etc.).
-
-        .. versionadded:: 3.15.0
-
-        .. seealso:: `add_file_location`, `del_file_location`
-
-        :Returns:
-
-            `set`
-                The unique file locations as absolute paths with no
-                trailing path name component separator.
-
-        **Examples**
-
-        >>> d.file_locations()
-        {'/home/data1', 'file:///data2'}
-
-        """
-        out = set()
-        for c in self.constructs.filter_by_data(todict=True).values():
-            out.update(c.file_locations())
-
-        return out
-
     @_inplace_enabled(default=False)
     def flip(self, axes=None, inplace=False):
         """Flip (reverse the direction of) domain axes.

docs/source/class.rst

@@ -24,6 +24,15 @@ Field list class
 
    cf.FieldList
 
+Domain class
+------------
+
+.. autosummary::
+   :nosignatures:
+   :toctree: class/
+
+   cf.Domain
+   
 Metadata component classes
 --------------------------
 
@@ -32,12 +41,14 @@ Metadata component classes
    :toctree: class/
 
    cf.AuxiliaryCoordinate
+   cf.CellConnectivity
    cf.CellMeasure
    cf.CellMethod
    cf.CoordinateReference
    cf.DimensionCoordinate
    cf.DomainAncillary
    cf.DomainAxis
+   cf.DomainTopology
    cf.FieldAncillary
 
 Constructs class
@@ -60,15 +71,6 @@ Coordinate component classes
    cf.CoordinateConversion
    cf.Datum
 
-Domain class
-------------
-
-.. autosummary::
-   :nosignatures:
-   :toctree: class/
-
-   cf.Domain
-   
 Data classes
 ------------
 

docs/source/class/cf.AuxiliaryCoordinate.rst

@@ -520,8 +520,8 @@ Groups
    ~cf.AuxiliaryCoordinate.nc_set_variable_groups
    ~cf.AuxiliaryCoordinate.nc_clear_variable_groups
 
-CFA
----
+Aggregation
+-----------
 
 .. rubric:: Methods
 
@@ -530,13 +530,8 @@ CFA
    :toctree: ../method/
    :template: method.rst
 
-   ~cf.AuxiliaryCoordinate.add_file_location
-   ~cf.AuxiliaryCoordinate.cfa_clear_file_substitutions
-   ~cf.AuxiliaryCoordinate.cfa_del_file_substitution
-   ~cf.AuxiliaryCoordinate.cfa_file_substitutions
-   ~cf.AuxiliaryCoordinate.cfa_update_file_substitutions
-   ~cf.AuxiliaryCoordinate.del_file_location
-   ~cf.AuxiliaryCoordinate.file_locations
+   ~cf.AuxiliaryCoordinate.file_directories
+   ~cf.AuxiliaryCoordinate.replace_directory
 
 Aliases
 -------
@@ -721,11 +716,18 @@ Deprecated
    :toctree: ../method/
    :template: method.rst
 
+   ~cf.AuxiliaryCoordinate.add_file_location
    ~cf.AuxiliaryCoordinate.asdatetime
    ~cf.AuxiliaryCoordinate.asreftime
+   ~cf.AuxiliaryCoordinate.cfa_clear_file_substitutions
+   ~cf.AuxiliaryCoordinate.cfa_del_file_substitution
+   ~cf.AuxiliaryCoordinate.cfa_file_substitutions
+   ~cf.AuxiliaryCoordinate.cfa_update_file_substitutions
    ~cf.AuxiliaryCoordinate.chunk
+   ~cf.AuxiliaryCoordinate.del_file_location
    ~cf.AuxiliaryCoordinate.delprop
    ~cf.AuxiliaryCoordinate.expand_dims
+   ~cf.AuxiliaryCoordinate.file_locations
    ~cf.AuxiliaryCoordinate.files
    ~cf.AuxiliaryCoordinate.get_filenames
    ~cf.AuxiliaryCoordinate.getprop

docs/source/class/cf.Bounds.rst

@@ -418,8 +418,8 @@ NetCDF
    ~cf.Bounds.nc_hdf5_chunksizes
    ~cf.Bounds.nc_set_hdf5_chunksizes
 
-CFA
----
+Aggregation
+-----------
 
 .. rubric:: Methods
 
@@ -428,13 +428,8 @@ CFA
    :toctree: ../method/
    :template: method.rst
 
-   ~cf.Bounds.add_file_location
-   ~cf.Bounds.cfa_clear_file_substitutions
-   ~cf.Bounds.cfa_del_file_substitution
-   ~cf.Bounds.cfa_file_substitutions
-   ~cf.Bounds.cfa_update_file_substitutions
-   ~cf.Bounds.del_file_location
-   ~cf.Bounds.file_locations
+   ~cf.Bounds.file_directories
+   ~cf.Bounds.replace_directory
 
 Aliases
 -------
@@ -632,13 +627,21 @@ Deprecated
    :toctree: ../method/
    :template: method.rst
 
+
+   ~cf.Bounds.add_file_location
    ~cf.Bounds.asdatetime
    ~cf.Bounds.asreftime
    ~cf.Bounds.attributes
+   ~cf.Bounds.cfa_clear_file_substitutions
+   ~cf.Bounds.cfa_del_file_substitution
+   ~cf.Bounds.cfa_file_substitutions
+   ~cf.Bounds.cfa_update_file_substitutions
    ~cf.Bounds.chunk
+   ~cf.Bounds.del_file_location
    ~cf.Bounds.delprop
    ~cf.Bounds.dtvarray
    ~cf.Bounds.expand_dims
+   ~cf.Bounds.file_locations   
    ~cf.Bounds.getprop
    ~cf.Bounds.get_filenames
    ~cf.Bounds.hasbounds

docs/source/class/cf.BoundsFromNodesArray.rst

@@ -0,0 +1,58 @@
+.. currentmodule:: cf
+.. default-role:: obj
+
+cf.BoundsFromNodesArray
+=======================
+
+----
+
+.. autoclass:: cf.BoundsFromNodesArray
+   :no-members:
+   :no-inherited-members:
+
+.. rubric:: Methods
+
+.. autosummary::
+   :nosignatures:
+   :toctree: ../method/
+   :template: method.rst
+
+   ~cf.BoundsFromNodesArray.__init__
+   ~cf.BoundsFromNodesArray.compressed_dimensions
+   ~cf.BoundsFromNodesArray.conformed_data
+   ~cf.BoundsFromNodesArray.copy
+   ~cf.BoundsFromNodesArray.get_attributes
+   ~cf.BoundsFromNodesArray.get_Subarray
+   ~cf.BoundsFromNodesArray.get_calendar
+   ~cf.BoundsFromNodesArray.get_cell_dimension
+   ~cf.BoundsFromNodesArray.get_compressed_axes
+   ~cf.BoundsFromNodesArray.get_compressed_dimension
+   ~cf.BoundsFromNodesArray.get_compression_type
+   ~cf.BoundsFromNodesArray.get_filenames
+   ~cf.BoundsFromNodesArray.get_node_coordinates
+   ~cf.BoundsFromNodesArray.get_start_index
+   ~cf.BoundsFromNodesArray.get_subspace
+   ~cf.BoundsFromNodesArray.get_units
+   ~cf.BoundsFromNodesArray.source
+   ~cf.BoundsFromNodesArray.subarray_parameters
+   ~cf.BoundsFromNodesArray.subarray_shapes
+   ~cf.BoundsFromNodesArray.subarrays
+   ~cf.BoundsFromNodesArray.to_dask_array
+   ~cf.BoundsFromNodesArray.to_memory
+      
+.. rubric:: Attributes
+
+.. autosummary::
+   :nosignatures:
+   :toctree: ../attribute/	    
+   :template: at
+
+   ~cf.BoundsFromNodesArray.Units
+   ~cf.BoundsFromNodesArray.array
+   ~cf.BoundsFromNodesArray.compressed_array
+   ~cf.BoundsFromNodesArray.dtype
+   ~cf.BoundsFromNodesArray.ndim
+   ~cf.BoundsFromNodesArray.shape
+   ~cf.BoundsFromNodesArray.size
+   
+