Remove redundancies

.gitignore

@@ -102,6 +102,7 @@ ENV/
 
 # IDE configurations
 .idea/
+.vscode/
 
 # miscellaneous
 test_all_datasets.py

CONTRIBUTING.md

@@ -0,0 +1,49 @@
+# Contributing to `metalearn`
+
+## Adding New Metafeatures
+
+`metalearn` uses a caching mechanism to cache expensive computations that may need to be used again within the package by another function. Both resources (e.g. the dataset itself or a preprocessed version of it) and metafeatures (e.g. entropy, number of features) are cached by the system.
+
+When adding a new metafeature to the package, the function that computes that metafeature needs to be registered in the `resources_info` variable in [./metalearn/metafeatures/resources.py](./metalearn/metafeatures/resources.py), and passed to the call made to `_get_metafeature_ids` in that module as well. Before the function can be registered and passed though, it needs to be decorated with metadata by being passed through the `MetafeatureComputer` constructor (see example below). This allows the metafeatures returned by the function to be used intelligently by the package.
+
+Follow the example below to know how to write and register new metafeature(s). Note that a metafeature-computing function (e.g. `get_dataset_stats` as seen below) can compute and return more than one meta-feature.
+
+```python
+# Import needed utilities
+from metalearn.metafeatures.base import MetafeatureComputer
+from metalearn.metafeatures.constants import ProblemType, MetafeatureGroup
+
+# Declare the function that computes the metafeatures.
+def get_dataset_stats(X, column_types):
+    # Calculate metafeatures.
+    number_of_instances = X.shape[0]
+    number_of_features = X.shape[1]
+    # Return a tuple (here it's two metafeatures).
+    return (number_of_instances, number_of_features)
+
+# Decorate the metafeature-computing function with data
+# the package will use.
+get_dataset_stats = MetafeatureComputer(
+    # Pass the function into the `MetafeatureComputer`
+    # decorator.
+    computer=get_dataset_stats,
+    # Give each metafeature returned by the function a
+    # name for the cache to use (order here must match the
+    # order they are returned in by `computer`).
+    returns=[
+        "NumberOfInstances",
+        "NumberOfFeatures"
+    ],
+    # Associate a problem type with the new metafeatures.
+    problem_type=ProblemType.ANY,
+    # Associate one or more metafeature groups.
+    groups=[MetafeatureGroup.SIMPLE],
+    # Specify which values to pass to the function
+    # when calling it to compute the metafeatures.
+    # Here we are passing the cached resource called
+    # "X_raw" as the value for this function's "X" argument.
+    argmap={ "X": "X_raw" }
+)
+```
+
+By convention, all the decorated metafeature-computing functions in a module are aggregated at the bottom of the module into a list called `metafeature_computers`, which is then imported by [./metalearn/metafeatures/resources.py](./metalearn/metafeatures/resources.py) and added to that module's `resources_info` variable.

MANIFEST.in

@@ -1,2 +1 @@
-include metalearn/metafeatures/metafeatures.json
 include metalearn/metafeatures/metafeatures_schema.json

metalearn/__init__.py

@@ -1,2 +1,2 @@
 from .metafeatures.metafeatures import Metafeatures
-from .metafeatures.resources import METAFEATURE_CONFIG, METAFEATURES_JSON_SCHEMA
+from .metafeatures.resources import METAFEATURES_JSON_SCHEMA

metalearn/metafeatures/base.py

@@ -0,0 +1,197 @@
+import inspect
+from typing import List, Callable, Dict, Union, Optional, Any
+import itertools
+from collections.abc import MutableMapping
+
+from metalearn.metafeatures.constants import ProblemType, MetafeatureGroup
+
+class ResourceComputer:
+
+    def __init__(
+        self,
+        computer: Callable,
+        returns: List[str],
+        argmap: Optional[Dict[str,Any]] = None
+    ) -> None:
+        """
+        Decorates ``computer``, a resource computing function
+        with metadata about that function.
+
+        Parameters
+        ----------
+        computer
+            The function that computes the resources.
+        returns
+            The names of the resources that ``computer`` returns, specified in
+            the same order as ``computer`` returns them.
+        argmap
+            A custom map of ``computer``'s argument names to the global resource names
+            that will be passed as ``computer``'s arguments when ``computer`` is called.
+        """
+
+        computer_args = inspect.getfullargspec(computer)
+        # TODO: If needed, add support for `computer` functions that
+        # use these types of arguments.
+        if (
+            computer_args.varargs is not None or
+            computer_args.varkw is not None or 
+            len(computer_args.kwonlyargs) > 0
+        ):
+            raise ValueError((
+                "ResourceComputer supports `computer` functions that "
+                "use positional arguments only in their function definition."
+            ))
+
+        self._computer = computer
+        self.returns = returns
+
+        self.argmap = {}
+
+        # reversing is needed because `self.defaults` gives the default
+        # argument values corresponding to the *last* `n` arguments in the
+        # function signature.
+        reversed_args = self.args[::-1]
+        reversed_defaults = self.defaults[::-1]
+        arg_default_pairs = itertools.zip_longest(reversed_args, reversed_defaults)
+
+        for local_name, default in arg_default_pairs:
+            # By default, just use the `computer` function's
+            # normal local argument names in the argmap,
+            # making sure to preserve default argument values
+            # when they are supplied.
+            if default is not None:
+                # The function has a default value for this arg;
+                # use that.
+                self.argmap[local_name] = default
+            else:
+                # This function has no default. Tell the system
+                # to pass in the global resource identified by
+                # this arg's ``local_name`` when calling this
+                # ``computer``.
+                self.argmap[local_name] = local_name
+
+        if argmap is not None:
+            # Now include any argument name or value overrides
+            # the developer has provided. Note: each value in `argmap`
+            # may be a global resource name (e.g. `"XSample"`) or
+            # a direct value for the argument (e.g. `5`)
+            self.argmap.update(argmap)
+
+
+    def __call__(self, *args, **kwargs):
+        """
+        Allows a ``ResourceComputer`` instance to be callable.
+        Just forwards all arguments on to self._computer.
+        """
+        return self._computer(*args, **kwargs)
+
+    @property
+    def args(self) -> list:
+        """Returns a list of the positional parameter names of self._computer"""
+        return inspect.getfullargspec(self._computer).args
+
+    @property
+    def defaults(self) -> list:
+        """
+        From https://docs.python.org/3/library/inspect.html#inspect.getfullargspec
+        [Returns] an n-tuple of default argument values corresponding to the last `n`
+        positional parameters [of self._computer].
+        """
+        defaults = inspect.getfullargspec(self._computer).defaults
+        return [] if defaults is None else defaults
+
+    @property
+    def name(self) -> str:
+        """Returns the function name of self._computer"""
+        return self._computer.__name__
+
+
+class MetafeatureComputer(ResourceComputer):
+
+    def __init__(
+        self,
+        computer: Callable,
+        returns: List[str], # TODO: Add support for passing just a string, not a list?
+        problem_type: ProblemType,
+        groups: List[MetafeatureGroup],
+        argmap: Optional[Dict[str,str]] = {}
+    ) -> None:
+        """
+        Decorates ``computer``, a metafeature computing function
+        with metadata about that function.
+
+        Parameters
+        ----------
+        computer
+            The function that computes the metafeatures.
+        returns
+            The names of the metafeatures that ``computer`` returns, specified in
+            the same order as ``computer`` returns them.
+        problem_type
+            The type of ML problem `computer`'s metafeatures can be computed for.
+        groups
+            The metafeature groups this computer's returned metafeatures belong to.
+            e.g. statistical, info-theoretic, simple, etc.
+        argmap
+            A custom map of ``computer``'s argument names to the global resource names
+            that will be passed as ``computer``'s arguments when ``computer`` is called.
+        """
+        super(MetafeatureComputer, self).__init__(computer, returns, argmap)
+        self.groups = groups
+        self.problem_type = problem_type
+
+
+class ResourceComputerMap(MutableMapping):
+    def __init__(self, computers: Union[ResourceComputer,List[ResourceComputer],None] = None) -> None:
+        """
+        Wraps a dictionary map of resource names to their computers.
+        Includes visibility into whether duplicate computers
+        are trying to become associated with a resource in the map e.g.
+        if a package developer has accidentally declared two computers
+        that return the same resource.
+        """
+        self._map: Dict[str,ResourceComputer] = {}
+        if computers is not None:
+            self.add(computers)
+
+    def add(self, computers: Union[ResourceComputer,List[ResourceComputer]]) -> None:
+        """
+        Adds more resource name/resource computer key/value
+        pairs to a resource map, throwing an error on duplicates.
+        """
+        if isinstance(computers, list):
+            for computer in computers:
+                self._add_one(computer)
+        elif isinstance(computers, ResourceComputer):
+            self._add_one(computers)
+        else:
+            raise ValueError("computers must be ResourceComputer or List[ResourceComputer]")
+
+    def __getitem__(self, key: str = None) -> ResourceComputer:
+        """Used for getting a resource from the map."""
+        return self._map[key]
+
+    def _add_one(self, computer: ResourceComputer) -> None:
+        if not isinstance(computer, ResourceComputer):
+            raise ValueError(f"computer is not a ResourceComputer; it is a {type(computer)}")
+
+        for resource_name in computer.returns:
+            self.__setitem__(resource_name, computer)
+
+    def __setitem__(self, resource_name: str, computer: ResourceComputer):
+        if resource_name in self._map:
+            raise ValueError(
+                f"duplicate computer '{computer.name}' provided for resource '{resource_name}', "
+                f"which is already present in the resouce map, registered "
+                f"by computer '{self._map[resource_name].name}'"
+            )
+        self._map[resource_name] = computer
+
+    def __iter__(self):
+        return iter(self._map)
+
+    def __len__(self):
+        return len(self._map)
+
+    def __delitem__(self, key: str):
+        raise TypeError("ResourceComputerMap does not support deletion of its ResourceComputers")

metalearn/metafeatures/common_operations.py

@@ -3,6 +3,8 @@
 
 from scipy.stats import skew, kurtosis
 
+import metalearn.metafeatures.constants as consts
+
 def profile_distribution(data):
     """
     Compute the mean, standard deviation, min, quartile1, quartile2, quartile3, and max of a vector
@@ -16,21 +18,21 @@ def profile_distribution(data):
     features = dictionary containing the min, max, mean, and standard deviation
     """
     if len(data) == 0:
-        return (data, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan)
+        return (np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan)
     else:
         ddof = 1 if len(data) > 1 else 0
         dist_mean = np.mean(data)
         dist_stdev = np.std(data, ddof=ddof)
         dist_min, dist_quartile1, dist_quartile2, dist_quartile3, dist_max = np.percentile(data, [0,25,50,75,100])
         dist_skew = skew(data)
         dist_kurtosis = kurtosis(data)
-    return (data, dist_mean, dist_stdev, dist_skew, dist_kurtosis, dist_min, dist_quartile1, dist_quartile2, dist_quartile3, dist_max)
+    return (dist_mean, dist_stdev, dist_skew, dist_kurtosis, dist_min, dist_quartile1, dist_quartile2, dist_quartile3, dist_max)
 
 def get_numeric_features(dataframe, column_types):
-    return [feature for feature in dataframe.columns if column_types[feature] == "NUMERIC"]
+    return [feature for feature in dataframe.columns if column_types[feature] == consts.NUMERIC]
 
 def get_categorical_features(dataframe, column_types):
-    return [feature for feature in dataframe.columns if column_types[feature] == "CATEGORICAL"]
+    return [feature for feature in dataframe.columns if column_types[feature] == consts.CATEGORICAL]
 
 def dtype_is_numeric(dtype):
     return "int" in str(dtype) or "float" in str(dtype)

metalearn/metafeatures/constants.py

@@ -0,0 +1,27 @@
+from enum import Enum
+
+# Constant Enums
+class ProblemType(Enum):
+    CLASSIFICATION = "classification"
+    REGRESSION = "regression"
+    ANY = "any"
+
+class MetafeatureGroup(Enum):
+    ALL = "all"
+    SIMPLE = "simple"
+    TEXT = "text"
+    STATISTICAL = "statistical"
+    INFO_THEORETIC = "info_theoretic"
+    LANDMARKING = "landmarking"
+    MODEL_BASED = "model_based"
+    TARGET_DEPENDENT = "target_dependent"
+
+# Constant strings
+VALUE_KEY = 'value'
+COMPUTE_TIME_KEY = 'compute_time'
+NUMERIC = "NUMERIC"
+TEXT = "TEXT"
+CATEGORICAL = "CATEGORICAL"
+NO_TARGETS = "NO_TARGETS"
+NUMERIC_TARGETS = "NUMERIC_TARGETS"
+TIMEOUT = "TIMEOUT"