Improve docstrings

Author: Verweijen

docs/source/api.rst

@@ -1,39 +1,45 @@
+===
 API
 ===
 
-InputData
----------
-.. automodule:: piargus.inputdata
+Input Specification
+===================
+
+Input data
+-------------------
+.. automodule:: piargus.inputspec
    :members: InputData, MetaData, MicroData, TableData, CodeList
    :show-inheritance:
 
 Hierarchies
 -----------
-.. automodule:: piargus.inputdata.hierarchy
-   :members: Hierarchy, TreeHierarchy, FlatHierarchy, LevelHierarchy
+.. automodule:: piargus.inputspec.hierarchy
+   :members: Hierarchy, TreeHierarchy, FlatHierarchy, LevelHierarchy, TreeHierarchyNode
    :show-inheritance:
 
-Safety rule
------------
-.. automodule:: piargus
-   :members: dominance_rule, percent_rule, frequency_rule, request_rule, zero_rule, missing_rule, weight_rule, manual_rule, p_rule, nk_rule,
-   :show-inheritance:
+Output Specification
+===================
 
-Output
+Tables
 ------
+.. automodule:: piargus.outputspec
+   :members: Table, Apriori, TreeRecode
+   :show-inheritance:
 
+Safety rule
+-----------
 .. automodule:: piargus
-   :members: Table, Apriori, TreeRecode
+   :members: dominance_rule, percent_rule, frequency_rule, request_rule, zero_rule, missing_rule, weight_rule, manual_rule, p_rule, nk_rule,
    :show-inheritance:
 
-Jobs
-----
+Result
+======
 .. automodule:: piargus
-   :members: Job, JobSetupError
+   :members: ArgusReport, TableResult
    :show-inheritance:
 
 Tau-Argus
----------
+=========
 .. automodule:: piargus
-   :members: TauArgus, BatchWriter
+   :members: TauArgus, BatchWriter, Job, JobSetupError
    :show-inheritance:

src/piargus/__init__.py

@@ -1,28 +1,31 @@
-from .argusreport import TauArgusException
 from .batchwriter import BatchWriter
 from .constants import *
-from .inputdata import InputData, MetaData, MicroData, TableData, CodeList
-from .inputdata.hierarchy import Hierarchy, FlatHierarchy, TreeHierarchy, \
+from .inputspec import InputData, MetaData, MicroData, TableData, CodeList
+from .inputspec.hierarchy import Hierarchy, FlatHierarchy, TreeHierarchy, \
     TreeHierarchyNode, Node, LevelHierarchy
 from .job import Job, JobSetupError
-from .table import Table, Apriori, TreeRecode
-from .table.safetyrule import *
+from .outputspec import Table, Apriori, TreeRecode
+from .outputspec.safetyrule import *
+from .result import TauArgusException, ArgusReport, TableResult
 from .tauargus import TauArgus
 
 __version__ = "1.0.2"
 
 __all__ = [
     "Apriori",
+    "TauArgus",
     "TauArgusException",
     "BatchWriter",
     "CodeList",
     "TreeRecode",
+    "Job",
+    "JobSetupError",
+
+    # Inputdata
     "InputData",
     "MetaData",
     "MicroData",
     "TableData",
-    "Job",
-    "JobSetupError",
 
     # Hierarchy
     "Hierarchy",
@@ -44,8 +47,13 @@
     "manual_rule",
     "p_rule",
     "nk_rule",
+
+    # Table
     "Table",
-    "TauArgus",
+
+    # Result
+    "ArgusReport",
+    "TableResult",
 
     # Constants
     "SAFE",

src/piargus/batchwriter.py

@@ -1,6 +1,6 @@
 from .constants import FREQUENCY_RESPONSE
-from .table.safetyrule import make_safety_rule
-from .utils import format_argument
+from .outputspec.safetyrule import make_safety_rule
+from .helpers import format_argument
 
 
 class BatchWriter:
@@ -22,19 +22,30 @@ def write_command(self, command, arg=None):
         return command, arg
 
     def logbook(self, log_file):
+        """Write LOGBOOK to batch file."""
         self.write_command('LOGBOOK', format_argument(log_file))
 
     def open_microdata(self, microdata):
+        """Write OPENMICRODATA to batch file."""
         return self.write_command("OPENMICRODATA", format_argument(microdata))
 
     def open_tabledata(self, tabledata):
+        """Write OPENTABLEDATA to batch file."""
         return self.write_command("OPENTABLEDATA", format_argument(tabledata))
 
     def open_metadata(self, metadata):
+        """Write METADATA to batch file."""
         return self.write_command("OPENMETADATA", format_argument(metadata))
 
-    def specify_table(self, explanatory, response=FREQUENCY_RESPONSE, shadow=None, cost=None,
-                      labda=None):
+    def specify_table(
+        self,
+        explanatory,
+        response=FREQUENCY_RESPONSE,
+        shadow=None,
+        cost=None,
+        labda=None
+    ):
+        """Write SPECIFYTABLE to batch file."""
         explanatory_str = "".join([format_argument(v) for v in explanatory])
         response_str = format_argument(response)
         shadow_str = format_argument(shadow)
@@ -45,15 +56,18 @@ def specify_table(self, explanatory, response=FREQUENCY_RESPONSE, shadow=None, c
         return self.write_command('SPECIFYTABLE', options)
 
     def read_microdata(self):
+        """Write READMICRODATA to batch file."""
         return self.write_command("READMICRODATA")
 
     def read_table(self, compute_totals=None):
+        """Write READTABLE to batch file."""
         if compute_totals is None:
             return self.write_command("READTABLE")
         else:
             return self.write_command("READTABLE", int(compute_totals))
 
     def apriori(self, filename, table, separator=',', ignore_error=False, expand_trivial=True):
+        """Write APRIORI to batch file."""
         filename = format_argument(filename)
         table = format_argument(table)
         separator = format_argument(separator)
@@ -63,32 +77,39 @@ def apriori(self, filename, table, separator=',', ignore_error=False, expand_tri
         return self.write_command("APRIORI", arg)
 
     def recode(self, table, variable, file_or_treelevel):
+        """Write RECODE to batch file."""
         table = format_argument(table)
         variable = format_argument(variable)
         file_or_treelevel = format_argument(file_or_treelevel)
         arg = f"{table}, {variable}, {file_or_treelevel}"
         return self.write_command("RECODE", arg)
 
     def safety_rule(self, rule="", /, *, individual="", holding=""):
+        """Write SAFETYRULE to batch file."""
         rule = make_safety_rule(rule, individual=individual, holding=holding)
         return self.write_command('SAFETYRULE', rule)
 
     def suppress(self, method, table, *method_args):
+        """Write SUPPRESS to batch file."""
         args = ",".join(map(format_argument, [table, *method_args]))
         return self.write_command('SUPPRESS', f"{method}({args})")
 
     def write_table(self, table, kind, options, filename):
+        """Write WRITETABLE to batch file."""
         if hasattr(options, 'items'):
             options = "".join([k + {True: "+", False: "-"}[v] for k, v in options.items()])
 
         result = f"({table}, {kind}, {options}, {format_argument(filename)})"
         return self.write_command('WRITETABLE', result)
 
     def version_info(self, filename):
+        """Write VERSIONINFO to batch file."""
         return self.write_command("VERSIONINFO", format_argument(filename))
 
     def go_interactive(self):
+        """Write GOINTERACTIVE to batch file."""
         return self.write_command("GOINTERACTIVE")
 
     def clear(self):
+        """Write CLEAR to batch file."""
         return self.write_command("CLEAR")

src/piargus/utils.py src/piargus/helpers.py

@@ -12,6 +12,7 @@ class CodeList:
 
     @classmethod
     def from_cdl(cls, file):
+        """Read cdl file."""
         df = pd.read_csv(file, index_col=0, header=None)
         codelist = CodeList(df.iloc[:, 0])
         if isinstance(file, (str, Path)):
@@ -20,6 +21,7 @@ def from_cdl(cls, file):
         return codelist
 
     def __init__(self, codes):
+        """Create a codelist."""
         if hasattr(codes, 'keys'):
             self._codes = pd.Series(codes)
         else:
@@ -35,9 +37,11 @@ def __str__(self):
         return self.to_cdl()
 
     def __getitem__(self, key):
+        """Get label of a code."""
         return self._codes[key]
 
     def __setitem__(self, key, value):
+        """Set label of a code."""
         self._codes[key] = value
 
     def __iter__(self):
@@ -57,10 +61,12 @@ def keys(self):
         return self._codes.keys()
 
     def iter_codes(self):
+        """Iterate through codes."""
         for code in self._codes.index:
             yield code
 
     def to_cdl(self, file=None, length=0):
+        """Store codelist in cdl file."""
         codes = self._codes.copy()
         codes.index = codes.index.str.rjust(length)
         result = codes.to_csv(file, header=False)

src/piargus/inputdata/__init__.py src/piargus/inputspec/__init__.py

@@ -12,6 +12,7 @@ class FlatHierarchy(Hierarchy):
     is_hierarchical = False
 
     def __init__(self, *, total_code=DEFAULT_TOTAL_CODE):
+        """Create a FlatHierarchy."""
         self.total_code = total_code
 
     def __repr__(self):

src/piargus/inputdata/codelist.py src/piargus/inputspec/codelist.py

@@ -14,6 +14,7 @@ class LevelHierarchy(Hierarchy):
     is_hierarchical = True
 
     def __init__(self, levels, *, total_code: str = DEFAULT_TOTAL_CODE):
+        """Create a tree hierarchy."""
         self.levels = [int(level) for level in levels]
         self.total_code = total_code
 

src/piargus/inputdata/hierarchy/__init__.py src/piargus/inputspec/hierarchy/__init__.py

@@ -18,6 +18,7 @@ class TreeHierarchy(Hierarchy):
     is_hierarchical = True
 
     def __init__(self, tree=None, *, total_code: str = DEFAULT_TOTAL_CODE, indent='@'):
+        """Create a tree hierarchy."""
         if not isinstance(tree, TreeHierarchyNode):
             tree = TreeHierarchyNode(total_code, tree)
         self.root = tree
@@ -40,18 +41,25 @@ def __hash__(self):
 
     @property
     def total_code(self) -> str:
+        """The code used as a total."""
         return self.root.code
 
     @total_code.setter
     def total_code(self, value):
         self.root.code = value
 
     def get_node(self, path) -> Optional["TreeHierarchyNode"]:
-        """Return single Node, None if it doesn't exist, ValueError if path not unique."""
+        """Obtain a node within the hierarchy.
+
+        Return single Node, None if it doesn't exist, ValueError if path not unique."""
         return self.root.path.get(path)
 
     def create_node(self, path) -> "TreeHierarchyNode":
-        """Return single Node, None if it doesn't exist, ValueError if path not unique."""
+        """Create a node within the hierarchy.
+
+        The newly created node is returned.
+        If the node already existed, the existing one is returned.
+        """
         return self.root.path.create(path)
 
     @property
@@ -71,6 +79,7 @@ def code_length(self):
 
     @classmethod
     def from_hrc(cls, file, indent='@', total_code=DEFAULT_TOTAL_CODE):
+        """Create hierarchy from a hrc-file."""
         if isinstance(file, (str, Path)):
             with open(file) as reader:
                 hierarchy = cls.from_hrc(reader, indent, total_code)
@@ -82,6 +91,7 @@ def from_hrc(cls, file, indent='@', total_code=DEFAULT_TOTAL_CODE):
         return cls(root, indent=indent)
 
     def to_hrc(self, file=None, length=0):
+        """Write hierarchy to a hrc-file."""
         if file is None:
             file = io.StringIO(newline=os.linesep)
             self.to_hrc(file, length)
@@ -122,9 +132,11 @@ def to_relations(self, child_name="code", parent_name="parent"):
         return serializer.to_relations(self.root)
 
     def to_image(self, **kwargs):
+        """Export the hierarchy file as an image."""
         return self.root.to_image(**kwargs)
 
     def to_pillow(self, **kwargs):
+        """Export the hierarchy file as a Pillow image."""
         if hasattr(self.root, 'to_pillow'):
             # Newer versions
             return self.root.to_pillow(**kwargs)
@@ -151,6 +163,7 @@ def __init__(self, code=None, children=(), parent=None):
 
     @property
     def code(self):
+        """Which code belongs to this node."""
         return self.identifier
 
     @code.setter

src/piargus/inputdata/hierarchy/flathierarchy.py src/piargus/inputspec/hierarchy/flathierarchy.py

@@ -62,6 +62,7 @@ def __init__(
 
     @abc.abstractmethod
     def to_csv(self, target):
+        """Save data to a file in the csv-format which tau-argus requires."""
         raise NotImplementedError
 
     @abc.abstractmethod
@@ -106,6 +107,7 @@ def resolve_column_lengths(self, default=DEFAULT_COLUMN_LENGTH):
 
     @property
     def hierarchies(self):
+        """The hierarchies attached to input data."""
         return self._hierarchies
 
     @hierarchies.setter
@@ -115,6 +117,7 @@ def hierarchies(self, value):
 
     @property
     def codelists(self):
+        """The codelists attached to input data."""
         return self._codelists
 
     @codelists.setter