registry-factory 0.1.3
Registry pattern with factory for specifications to register generic modules.
License: MIT
Requires Python: <4.0,>=3.8
Keywords: registry, factory, codebase, module registry, accreditation system

# RegistryFactory

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An abstract implementation of the software design pattern called Registry proposed by Hartog and Svensson et. al. (2024),
providing a factory for creating registries to organize categorically similar modules.

**[Installation](#installation)**
| **[Dependencies](#dependencies)**
| **[Usage](#usage)**
| **[Citation](#citation)**

### Overview

The registry design pattern provides a way to organize modular
functionalities dynamically and achieve a unified, reusable, and interchangeable interface.
It extends the Factory design pattern without the explicit class dependency.
Additionally, the registry supports optional meta information such as versioning, accreditation,
testing, etc.
The UML diagrams show the differences between the factory and registry patterns.

<p align="center">
  <br>
  <img alt="UML diagram of the pattern" src="figures/registry_uml.png">
  <br>
<i>Created with BioRender.com</i>
 </p>

## Installation

The codebase can be installed from PyPI using `pip`, or your package manager of choice, with

```bash
$ pip install registry-factory
```

Or from a local clone, with

```bash
$ conda env create -f env-dev.yaml
$ conda activate registry_env
$ poetry install
```

## Dependencies

No third-party dependencies are required to use the minimal functionality of the RegistryFactory.

## Usage

The workflow of creating a registry is the following. 1) Identify a part of the code that can be
separated from the rest. 2) Modularize the section to be independent of the rest of the code. 3)
Create a registry from the RegistryFactory. 4) Register any modules that provide similar
functionalities. 5) Call the optional module from the registry from the main workflow. See below.

<p align="center">
  <br>
  <img alt="Workflow" src="figures/registry_creation.png" width="750">
  <br>
<i>Created with BioRender.com</i>
 </p>

Additional available options and use cases are described in the following sections. See also [examples](examples).

<!-- ### A basic registry -->
<details>
<summary> A basic registry </summary>
A simple registry is created as such.

```Python
from registry_factory.registry import Registry
```

Next, any models can be added to the registry as such.

```Python
import torch.nn as nn

@Registry.register("simple_model")
class SimpleModel(nn.Module):
    ...
```

</details>

<!-- ### Shared modules -->
<details>
<summary> Shared modules </summary>
To specify specific registries and have them share modules, we use the Factory class. Shared modules are modules that are used in multiple registries (e.g. a model and a module).

```Python
from registry_factory.factory import Factory

class Registries(Factory):
    ModelRegistry = Factory.create_registry("model_registry", shared=True)
    ModuleRegistry = Factory.create_registry("module_registry", shared=True)

@Registries.ModelRegistry.register("encoder")
class Encoder(nn.Module):
    ...

Registries.ModuleRegistry.get("encoder")
```

</details>

<!-- ### Arguments -->
<details>
<summary> Arguments </summary>
A registry can be created to store modules with arguments. The arguments can be set when registering a module.

```Python
from registry_factory.factory import Factory
from dataclasses import dataclass


class Registries(Factory):
    ModelRegistry = Factory.create_registry("model_registry", shared=True)

@Registries.ModelRegistry.register_arguments(key="simple_model")
@dataclass
class SimpleModelArguments:
    input_size: int
    output_size: int
```

Only dataclasses can be used as arguments for now.

</details>

<!-- ### Versioning and accreditation -->
<details>
<summary> Versioning and accreditation </summary>
Two examples of additional meta information that can be stored in a registry is module versioning
and accreditation regarding how and to who credit should be attributed the module.

Versioning can be used to keep track of changes in a module. The version can be set when registering a module.

```Python
from registry_factory.factory import Factory
from registry_factory.checks.versioning import Versioning

class Registries(Factory):
    ModelRegistry = Factory.create_registry(checks=[Versioning(forced=False)])

@Registries.ModelRegistry.register(call_name="simple_model", version="1.0.0")
class SimpleModel(nn.Module):
    ...

Registries.ModelRegistry.get("simple_model") # Error, version not specified.
Registries.ModelRegistry.get("simple_model", version="1.0.0") # Returns the module.
```

Accreditation can be used to keep track of how and to whom credit should be attributed for a given module.
The accreditation can be set when registering a module.

```Python
from registry_factory.factory import Factory
from registry_factory.checks.accreditation import Accreditation

class Registries(Factory):
    ModelRegistry = Factory.create_registry("model_registry", checks=[Accreditation(forced=False)])

@Registries.ModelRegistry.register(
    key="simple_model",
    author="Author name",
    credit_type="reference",
    additional_information="Reference published work in (link)."
)
class SimpleModel(nn.Module):
    ...

Registries.ModelRegistry.get("simple_model")  # Returns the module.
Registries.ModelRegistry.get_info("simple_model")  # Returns all meta information including the accreditation information.
```

The reason why the accreditation system can return an object without specification is because the accreditation system lacks "key" information.
In the versioning module, the version is the key information that is used to grab the module from the registry.
Without specifying the version the registry will not know which module to return.
Therefore, the author, credit type, and additional information are not key information in the accreditation system.
Without specifying the author, credit type, and additional information, the registry will still know which module to return.

</details>

<!-- ### Testing and Factory Patterns -->
<details>
<summary> Testing and Factory Patterns </summary>
We also provide defining tests and post-checks applied to all modules in a registry. Define test
or post checks as follows when creating the registry.

```Python
from registry_factory.factory import Factory
from registry_factory.checks.factory_pattern import FactoryPattern

class Pattern:
    """Test pattern."""

    def __init__(self):
        pass

    def hello_world(self):
        """Hello world."""
        print("Hello world")

class Registries(Factory):
    ModelRegistry = Factory.create_registry(
        "model_registry", shared=False, checks=[FactoryPattern(factory_pattern=Pattern, forced=False)]
    )

# No error, the module passes the test.
@ModelRegistry.register(key="hello_world")
class HelloWorld(Pattern):
    pass

# No error, the module passes the test.
@ModelRegistry.register(key="hello_world2")
class HelloWorld:
    def __init__(self):
        pass

    def hello_world(self):
        """Hello world."""
        print("Hello world")

# Error, the module does not pass the test.
@ModelRegistry.register(key="hello_world2")
class HelloWorld:
    def __init__(self):
        pass

    def goodday_world(self):
        """Good day world."""
        print("Good day world")
```

The factory also supports adding a callable test module to the registry. The callable test module can be specified to be called when a module is registered. The callable test module can be used to test the module when it is registered. The callable test module can be specified as follows when creating the registry.

```Python
from typing import Any
from registry_factory.factory import Factory
from registry_factory.checks.testing import Testing

class CallableTestModule:
    """Module to test."""

    def __init__(self, key: str, obj: Any, **kwargs):
        self.name = obj
        self.assert_name()

    def assert_name(self):
        assert self.name == "test", "Name is not test"



class Registries(Factory):
    ModelRegistry = Factory.create_registry(
        "model_registry", shared=False, checks=[Testing(test_module=CallableTestModule, forced=True)]
    )

Registries.ModelRegistry.register_prebuilt(key="name_test", obj="test") # No error, the module passes the test.
Registries.ModelRegistry.register_prebuilt(key="name_test", obj="not_test") # Error, the module doesn't pass the test.
```

</details>

<!-- ### Inserting hooks -->
<details>
<summary> Hooks insertions </summary>

Here we outline the use of registries in code to create hooks for outside users. The example given below contains a function unaccessible by users that have two options.

```Python
from registry_factory.registry import Registry

@Registry.register("option_1")
def option_1() -> int:
    return 1

@Registry.register("option_3")
def option_3() -> int:
    return 3

def _some_hidden_function(a: str) -> int:
    try:
        return print(Registry.get(f"option_{a}")())
    except Exception as e:
        raise RuntimeError("Error getting the option", e)
```

When a new users uses this code and selects option two, it will cause an error as it has not yet been implemented.

```Python
_some_hidden_function(1) # Returns 1
_some_hidden_function(3) # Returns 3
_some_hidden_function(2) # Error
```

Normally, this would be the end, but with registries, the user can easily create a new function that will solve the issue.

```Python
@Registry.register("option_2") # External user adds new option
def option_2() -> int:
    return 2

_some_hidden_function(2) # Returns 2
```

</details>

<!-- ### Compatibility wrapper -->

<details>
<summary> Compatibility wrapper </summary>

Another example of how to use registries, is to make two incompatible functions work through wrappers. Users can specify specific wrappers for functions and register them using the registry.

```Python
from registry_factory.factory import Factory

class Registries(Factory):
    ModelRegistry = Factory.create_registry(name="model_registry")

def func1():
    return "hello world"

def func2():
    return ["hello universe"]

def final_function(key: str) -> str:
    return Registries.ModelRegistry.get(key)()
```

Here the example will output the wrong versions if the objects are registered as is: one a string the other a list. You can easily use wrapper functions to register the objects in such a way that they output the correct types and become compatible.

```Python
# External user creates wrapper function to make both functions work with final function
def wrapper_function(func):
    def wrapper(*args, **kwargs):
        out = func(*args, **kwargs)
        if type(out) is list:
            return out[0]
        else:
            return out
    return wrapper

Registries.ModelRegistry.register_prebuilt(wrapper_function(func1), "world")
Registries.ModelRegistry.register_prebuilt(wrapper_function(func2), "universe")

print(final_function("world")) # -> Hello world
print(final_function("universe")) # -> Hello universe
```

</details>

## Citation

Our paper in which we propose the registry design pattern, on which this package is built, is currently
available as a preprint. If you use the design pattern or this package please cite our work accordingly.

[paper link]

<!-- ```
@inproceedings{hartog2023registry,
    title={Registry: a design pattern to promote code reuse in machine learning-based drug discovery},
    author={Hartog, Peter and Svensson, Emma and Mervin, Lewis and Genheden, Samuel and Engkvist, Ola and Tetko, Igor},
    year={2023},
    note={Preprint}
}
``` -->

### Funding

The work behind this package has received funding from the European Union’s Horizon 2020
research and innovation programme under the Marie Skłodowska-Curie
Actions, grant agreement “Advanced machine learning for Innovative Drug
Discovery (AIDD)” No 956832”. [Homepage](https://ai-dd.eu/).

![plot](figures/aidd.png)