Specializing dantro Classes#

This page shows a few examples of how to specialize dantro classes to your liking. This step is an important aspect of adapting dantro to work with the data structures that you are frequently using, which is beneficial for good integration into your workflow.

Note

The code snippets shown on this page are implemented as test cases to assert that they function as intended. To have a look at the full source code used in the examples below, you can download the relevant file or view it online.

Note that the integration into the test framework requires some additional code in those files, e.g. to generate dummy data.

Specializing a data container#

As an example, let’s look at the implementation of the MutableSequenceContainer, a container that is meant to store mutable sequences:

# Import the python abstract base class we want to adhere to
from collections.abc import MutableSequence

# Import base container class and the mixins we would like to use
from dantro.base import BaseDataContainer
from dantro.mixins import CheckDataMixin, CollectionMixin, ItemAccessMixin

class MutableSequenceContainer(CheckDataMixin,
                               ItemAccessMixin,
                               CollectionMixin,
                               BaseDataContainer,
                               MutableSequence):
    """The MutableSequenceContainer stores sequence-like mutable data"""

The steps to arrive at this point are as follows:

The collections.abc python module is also used by python to specify the interfaces for python-internal classes. In the documentation it says that the MutableSequence inherits from Sequence and has the following abstract methods: __getitem__, __setitem__, __delitem__, __len__, and insert.

As we want the resulting container to adhere to this interface, we set MutableSequence as the first class to inherit from. The BaseDataContainer is what makes this object a dantro data container. It implements some of the required methods to concur with the MutableSequence interface but leaves others abstract.

Now, we need to supply implementations of these abstract methods. That is the job of the following two (reading from right to left) mixin classes. In this case, the Sequence interface has to be fulfilled. As a Sequence is nothing more than a Collection with item access, we can fulfill this by inheriting from the CollectionMixin and the ItemAccessMixin.

The CheckDataMixin is an example of how functionality can be added to the container while still adhering to the interface. This mixin checks the provided data before storing it and allows specifying whether unexpected data should lead to warnings or exceptions; for an example, see below

Some methods will remain abstract, in this case: insert. These need to be manually defined; the MutableSequenceContainer‘s insert() method does exactly that, thus becoming a fully non-abstract class:

def insert(self, idx: int, val) -> None:
    """Insert an item at a given position.

    Args:
        idx (int): The index before which to insert
        val: The value to insert
    """
    self.data.insert(idx, val)

Using a specialized data container#

Once defined, instantiation of a custom container works the same way as for other data containers:

dc = MutableSequenceContainer(name="my_mutable_sequence",
                              data=[4, 8, 16])

# Insert values
dc.insert(0, 2)
dc.insert(0, 1)

# Item access and collection interface
assert 16 in dc
assert 32 not in dc
assert dc[0] == 1

for num in dc:
    print(num, end=", ")
# prints:  1, 2, 4, 8, 16,

Configuring mixins#

Many mixins allow some form of configuration. This typically happens via class variables.

Let’s define a new container that strictly requires its stored data to be a list, i.e. an often-used mutable sequence type. We can use the already-included CheckDataMixin such that it checks a type. To do so, we set the DATA_EXPECTED_TYPES to only allow list and we set DATA_UNEXPECTED_ACTION to raise an exception if this is not the case.

class StrictlyListContainer(MutableSequenceContainer):
    """A MutableSequenceContainer that allows only a list as data"""
    DATA_EXPECTED_TYPES = (list,)     # as tuple or None (allow all)
    DATA_UNEXPECTED_ACTION = 'raise'  # can be: raise, warn, ignore

# This will work
some_list = StrictlyListContainer(name="some_list", data=["foo", "bar"])

# The following will fail
with pytest.raises(TypeError):
    StrictlyListContainer(name="some_tuple", data=("foo", "bar"))

with pytest.raises(TypeError):
    StrictlyListContainer(name="some_tuple", data="just some string")

Other mixins provide other class variables for specializing behavior. Consult the documentation or the source code to find out which ones.

Note

The class variables typically define the default behavior for a certain specialized type. However, depending on the mixin, its behavior might also depend on runtime information, e.g. specified in __init__.

Warning

We advise against overwriting class variables during the lifetime of an object.

Specializing the DataManager#

This works in essentially the same way: A DataManager is specialized by adding data_loaders mixin classes.

import dantro
from dantro.data_loaders import PickleLoaderMixin, YamlLoaderMixin

class MyDataManager(PickleLoaderMixin,
                    YamlLoaderMixin,
                    dantro.DataManager):
    """A DataManager specialization that can load pickle and yaml data"""

That’s all.

For more information, see The DataManager.

Hint

It’s not strictly required to define a new DataManager class to use loader mixins: The DataManager is aware of all registered data loaders and can access them via the DATA_LOADERS registry.

However, if you plan on extending it, it may be the more convenient approach to define this custom class and include mixins.

Note

When using specialized container classes such a custom DataManager is also the place to configure data loaders to use those classes. For example, when using the Hdf5LoaderMixin, the _HDF5-prefixed class variables can be set to use the specialized container classes rather than the defaults.

Note

For an integration example, you can have a look at the data manager used in utopya.

Adding data loaders#

Adding a custom data loader is simple. As an example, let’s look at how a data loader mixin for plain text files (TextLoaderMixin) is implemented in dantro:

"""Defines a loader mixin to load plain text files"""

from ..containers import StringContainer
from ._registry import add_loader


class TextLoaderMixin:
    """A mixin for :py:class:`~dantro.data_mngr.DataManager` that supports
    loading of plain text files."""

    @add_loader(TargetCls=StringContainer, register_aliases=["text"])
    def _load_plain_text(
        filepath: str, *, TargetCls: type, **load_kwargs
    ) -> StringContainer:
        """Loads the content of a plain text file into a
        :py:class:`~dantro.containers.general.StringContainer`.

        Args:
            filepath (str): Where the plain text file is located
            TargetCls (type): The class constructor
            **load_kwargs: Passed on to :py:func:`open`

        Returns:
            StringContainer: The reconstructed StringContainer
        """
        with open(filepath, **load_kwargs) as f:
            data = f.read()

        return TargetCls(data=data, attrs=dict(filepath=filepath))

So basically:

  1. Import the add_loader decorator from dantro.data_loaders

  2. Define your mixin class

  3. Add a method named _load_<name> and decorate it with @add_loader(TargetCls=SomeClass).

    Note

    Here, you have to decide for a target type for the return value of the loader. This can be any dantro container or group type, see dantro.containers or dantro.groups.

    If there is no suitable container type, you can either specialize one yourself. Alternatively, the PassthroughContainer always works.

  4. Fill in the method’s body to implement the loading of your data.

  5. Initialize and return the TargetCls object, passing the loaded data to it.

Specializing the PlotManager#

The plot manager can be specialized to support further functionality simply by overloading methods that may or may not invoke the parent methods. However, given the complexity of the plot manager, there is no guide on how to do this exactly: It depends a lot on what you want to achieve.

In a simple situation, a specialized PlotManager may simply overwrite some default values via the class variables. This could, for instance, be the plot function resolver, which defaults to PlotFuncResolver:

import dantro

class MyPlotFuncResolver(dantro.plot.utils.PlotFuncResolver):
    """A custom plot function resolver class"""

    BASE_PKG = "my_custom_package.plot_functions"
    """For relative module imports, regard this as the base package.
    A plot configuration ``module`` argument starting with a ``.`` is
    looked up in that module.

    Note that this needs to be an importable module.
    """

class MyPyPlotManager(dantro.PlotManager):
    """My custom plot manager"""

    PLOT_FUNC_RESOLVER = MyPlotFuncResolver
    """Use a custom plot function resolver"""

Note

For an operational example in a more complex framework setting, see the specialization used in the utopya project. There, the PlotManager is extended such that a number of custom module paths are made available for import.

Specializing BasePlotCreator#

As described in Plot Creators, dantro already supplies a range of plot creators. Furthermore, dantro provides the BasePlotCreator, which provides an interface and a lot of the commonly used functionality.

Specialization thus can be of two kinds:

  1. Using an existing plot creator and configuring it to your needs.

  2. Implementing a whole new plot creator, e.g. because you desire to use a different plotting backend.

In general, we recommend to refer to the implementation of existing dantro.plot.creators as examples for how this can be achieved. We are happy to support the implementation of new plot creators, so feel free to post an issue to the project page.

Note

After specializing a plot creator, make sure to let the PlotManager (or your specialization of it) know about your new creator class. You can do so by extending its CREATORS mapping.

Also see the integration guide for an overview.