octopipes 0.2.5
Pipeline library for AI workflows.

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# Octopipes
*Octopipes* is a pipeline library for AI workflows. Not only it allows
for easy definition of multi-step pipelines, but also handles testing
and collection of information of multiple workflows.

```bash
pip install octopipes
```

## Introduction
When using multiple-step (AI) pipelines, **octopipes** helps you define
workflows and work with workflows in an easy way. It allows for instance, adding post-workflow
hooks that can clean up GPU memory (or anything else).

Workflows are defined through the `Workflow` class, each workflow can contain a chain of `processes` (some common ones are already defined).
Every step of the pipeline is saved and can be used later. For easier managements of different outputs, we can provide an output handler for each 
specific step (Some basic ones are already defined as well such `BboxesHandler` etc.).

To run multiple workflows on the same input, you can use the `AggregateFlows` class for that. The library also provides a way to read datasets
and run benchmarks 

To keep `octopipes` ML library agnostic, it does not require `pytorch` or `tensorflow` to be installed
as it can work with both just fine.

## Get started
### Workflows
To add steps to a workflow, the class provides the `add` method which takes as input the function (process) and optionally
an OutputHandler. The whole workflow will act as the `|` (pipe) operator in Unix terminals by successively feeding the output of a process as
the input of the next process. To run a workflow, you just need to iterate over it with the appropriate input(s).
```
p1 -> p2 -> p3
```
In math terms, the workflow runs the function composition of all the steps.
```math
p3 \circ p2 \circ p1 (x)
```

This shows how to define and run a simple workflow:
```python
from octopipes.workflow import Workflow

# Define a workflow with two steps
wf = Workflow('wf_name').add(lambda x: x ** 2).add(lambda x: x - 4)
print(wf.nsteps)
# output: 1

# We can now run the workflow on a specific starting input value (in this case 4)
# `wf` will first run the input on the first function x ** 2, then run the second x - 4 with the result of the previous step.
# So in the first step of the iteration the result will be 16 (4 ** 2) then 12 (16 - 4)
wf_iter = wf(4)
for step, result in wf_iter:
    pass

# return a frozen instance of the workflow run.
# This is especially important, when working with memory intensive GPU workflows
frozen_res = wf_iter.freeze()

# Get the duration recap of each step of the workflow
wf_iter.recap()

# Define a workflow with some metadata attached
# this metadata can then be used to differentiate
# workflows with the same name but different params
wf = Workflow('wf_name', metadata={'thresh': 0.4}).add(lambda x: x ** 2)
```

#### Output handlers
When adding a new step that outputs a certain results that you want to be processed in a particular way, you can pass a class that
implements the `OutputHandler` interface.

The interface has 3 methods:
* **output_on_image**: used when outputting the results on an image (Used in computer vision mostly)
* **len_output**: give the output size of the result
* **to_json**: returns a serialized json object of the result

The library already provides some basic ones such as:
* BboxesHandler
* SegmentationMaskHandler
* CmapBboxesHandler
* CirclesHandler

Handlers are added this way. If None were supplied, `DefaultHandler` is used. *(In most cases a handler needs to be passed)*
```python
wf = Workflow('wf_name').add(some_func, some_handler)
```

#### Workflow steps with additional inputs
The `add` method can take an optional `requires` flag in cases a step needs additional inputs to work properly. This flag is comma separated string that declares the requires inputs needed for
a specific process. These requirements are then injected as separate arguments to the step (unpacked). Currently, the `requires` flag supposed two types of injections:
* Injections from previous steps (or initial input) -- These are declared by their order number (`0`, `1`, etc)
* Dependency injections that are independent of the flow of the pipeline. -- These are prefix with the letter `d` (`d0,d2`, etc.)

It is also possible to mix the `requires` with both types such as `0,d1,2` or `d0,1`. And the order in the requires flags is retained when injecting the arguments to the function.

**Previous input injection**

In cases where a workflow step requires inputs from previous steps other than the one strictly before it, we can inject whose inputs using the `requires` flag. 
The flag is a series of comma separated step numbers like (`0`, `0,1,2`) where 0 is the first input of the workflow and 1 the output of the first step.

To understand this flag, let's suppose that we have such a requirement:
```
(input) -> p1 -> p2 -> p3
```
Now let's say p3 not only requires the output of `p2` but also the first `input` (The initial starting value when running the workflow). In this case when defining your
workflow you can specify a `requires` flag `requires='0'` that will inject `input` as the second argument to your
process.

```python
.add(lambda p2, input: some_calculation(input, p2), requires='0')
```

Note that the order of the steps in the `requires` flag is retained when injecting the arguments, and the previous
step of the workflow is ignored in case it is present in `requires` as it is automatically injected by default.

**Dependency injections**

In some cases you might need a workflow to use some data or dependency further down in the workflow without having to propagate that variable through all your steps. This is where you
can use the `requires` flag of the `add` method to tell octopipes to inject dependencies as arguments to a specific step. The way to specify them is to prefix the dependency number with
the letter `d`. So `d0,d2` would inject the dependency number 0 and 2 to your step.

After declaring where the dependencies should be injected, you simply has to specify them when running the workflow:
```
wf = Workflow('name').add(lambda x y: x + y, requires='d0')
wf_iter = wf(input=get_input(), dependencies=[dependency0, dependency1])
```

### AggregateFlows
`AggregateFlows` allows running **multiple** workflows on the same input. This is usually used when either benchmarking multiple
pipelines at the same time or wanting to select the "best" output out of different workflows.

```python
from octopipes.workflow import Workflow
from octopipes.aggreage_flows import AggregateFlows

wf1 = Workflow('wf_name').add(some_func, some_handler)
wf2 = Workflow('wf_name').add(some_func, some_handler)

flows = AggregateFlows(input, workflows=[wf1, wf2])
flows.run_workflows()

# get results for wf1
flows.results[0]
```

### Benchmark
As the name suggest, `Benchmark` allows testing your workflows on a dataset and then being able to calculate easily your metrics.
Depending on the batch size of the dataset loader, the tests will be run simultaneously (as many processes as the batch size). Take note
however that as of now, a single `AggregateFlow` is run synchronously.

If you're using `pytorch` or `tensorflow`, some memory freeing hooks might be needed. For that, you can pass an instance of
`DefaultAggregateFlowsFactory` with the specific hooks needed. Otherwise, you can always define implement your own `AggregateFlowsFactory`.

Here's a simple example:
```python
from octopipes.workflow import Workflow
from octopipes.benchmark import Benchmark

dataloader = ...

wf1 = Workflow('wf1_name').add(some_func, some_handler)
wf2 = Workflow('wf2_name').add(some_func, some_handler)

bench = Benchmark(dataloader=dataloader, workflows=[wf1, wf2])
bench.run_tests()
```

## Requirements & Installation
The module is tested against versions `>=3.10`. However, this requirement is due to using type hinting so the module can be
altered to work on lower version of the interpreter.

Installing the package is pretty standard:
```sh
git clone https://github.com/octomiro/octopipes

pip install -r requirements.txt
# or requirements.in

pip install -r dev-requirements.in

# Running tests
pytest
# or
tox
```
## Contributions 
PRs are more than welcome! If the change is big enough to require some discussion, it's better to open an issue for it.
To keep the history of the repo clean, all PRs are rebased instead of merged so make sure everything is correct be submitting anything.

## Why Octopipes?
This library was born from a need to define, benchmark, and debug in an easy way workflows that use foundational models. In the course of
our work, we did not find something that met that need in terms of flexibility or features. So we created octopipes internally, and decided
to open source it.

Octopipes is developed and maintained by [octomiro](https://octomiro.ai), an AI company that makes ERP systems intelligent.