nanoset 0.2.1
A memory-optimized wrapper for Python sets likely to be empty.
License: MIT
Requires Python: >=3.5.*
Keywords: Python,set,memory,wrapper,optimisation

# `nanoset.py` [![starme](https://img.shields.io/github/stars/althonos/nanoset.py.svg?style=social&label=Star)](https://github.com/althonos/nanoset.py)

*A memory-optimized wrapper for Python sets likely to be empty.*

[![TravisCI](https://img.shields.io/travis/althonos/nanoset.py/master.svg?logo=travis&maxAge=600&style=flat-square)](https://travis-ci.org/althonos/nanoset.py/branches)
[![AppVeyor](https://img.shields.io/appveyor/ci/althonos/nanoset-py/master?logo=appveyor&style=flat-square&maxAge=600)](https://ci.appveyor.com/project/althonos/nanoset-py)
[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/)
[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/nanoset.py/)
[![PyPI](https://img.shields.io/pypi/v/nanoset.svg?style=flat-square&maxAge=600)](https://pypi.org/project/nanoset)
[![Crates](https://img.shields.io/crates/v/nanoset-py?style=flat-square&maxAge=600)](https://crates.io/crates/nanoset-py)
[![Wheel](https://img.shields.io/pypi/wheel/nanoset.svg?style=flat-square&maxAge=3600)](https://pypi.org/project/nanoset/#files)
[![Python Versions](https://img.shields.io/pypi/pyversions/nanoset.svg?style=flat-square&maxAge=600)](https://pypi.org/project/nanoset/#files)
[![Python Implementations](https://img.shields.io/pypi/implementation/nanoset.svg?style=flat-square&maxAge=600)](https://pypi.org/project/nanoset/#files)
[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/nanoset.py/blob/master/CHANGELOG.md)
[![GitHub issues](https://img.shields.io/github/issues/althonos/nanoset.py.svg?style=flat-square&maxAge=600)](https://github.com/althonos/nanoset.py/issues)

## ⏱️ TL;DR

Save up to 85% of the memory used by empty `set` instances in your code with
a single line of code:
```python
from nanoset import PicoSet as set
```

## �� Table of Contents

- [Overview](#-overview)
  * [About Python memory usage](#-about-python-memory-usage)
  * [Simple example usecase](#-simple-example-usecase)
  * [Implementation](#-implementation)
  * [Statistics](#-statistics)
- [Installing](#-installing)
- [API Reference](#-api-reference)
- [License](#-license)


## ��️ Overview

### �� About Python memory usage

Python is a great programming language (*fight me*), but sometimes you start
questioning why it does things in certain ways. Since Python 2.3, the standard
library provides the [`set`](https://docs.python.org/3.7/library/stdtypes.html#set)
collection, which is a specialized container for membership testing. On the
contrary to the ubiquitous [`list`](https://docs.python.org/3.7/library/stdtypes.html#list)
collection, `set` is not ordered (or, more accurately, *does not let you access
the order it stores the elements in*). The other feature of `set` is that just
like its mathematical counterpart, it does not allow duplicates, which is very
useful for some algorithms. However, **sets are memory-expensive**:
```python
>>> import sys
>>> sys.getsizeof(list())
56
>>> sys.getsizeof(set())
216
```

An empty set takes more than three times the memory of an empty list! For some
data structures or objects with a lot of `set` attributes, they can quickly
cause a very large part of the memory to be used for nothing. This is even more
sad when you are used to [Rust](https://www.rust-lang.org/), where most
[collections](https://doc.rust-lang.org/std/collections/) allocate lazily.
**This is where `nanoset` comes to the rescue:**
```python
>>> import nanoset
>>> sys.getsizeof(nanoset.NanoSet())
48
>>> sys.getsizeof(nanoset.PicoSet())
32
```

*Actually, that's a lie, but keep reading*.

### �� Simple example usecase

Let's imagine we are building an ordered graph data structure, where we may
want to store [taxonomic data](https://en.wikipedia.org/wiki/Taxonomic_database),
or any other kind of hierarchy. We can simply define the graphs and its nodes
with the two following classes:

```python
class Graph:
    root: Node
    nodes: Dict[str, Node]

class Node:
    neighbors: Set[node]
```

This makes adding an edge and querying for an edge existence between two nodes
an `O(1)` operation, and iterating over all the nodes an `O(n)` operation, which
is mot likely what we want here. We use `set` and not `list` because we want to
avoid storing an edge in duplicate, which is a sensible choice. But now let's
look at the [statistics](https://terminologies.gfbio.org/terminology/?ontology=NCBITAXON)
of the [NCBITaxon](https://www.ncbi.nlm.nih.gov/taxonomy) project, the
database for Organismal Classification developed by the US National Center for
Biotechnology Information:

```ignore
 Metrics
    Number of classes*: 1595237
    Number of individuals: 0
    Number of properties: 0
    Classes without definition: 1595237
    Classes without label: 0
    Average number of children: 12
    Classes with a single child: 40319
    Maximum number of children: 41761
    Classes with more than 25 children: 0
    Classes with more than 1 parent: 0
    Maximum depth: 38
    Number of leaves**: 1130671
```

According to these, we are going to have **1,130,671** leaves for a total of
**1,595,237** nodes, which means **70.8%** of empty sets. Now you may think:

> Ok, I got this. But in this case, I just need a special case for leaves, where
> instead of storing an empty set of `neighbors`, I store a reference to `None`
> when that set would be empty. I can then replace that reference with an actual
> set only when I want to add new edges from that node. Problem solved!

Well, glad we are on the same level: this is what **`nanoset`** does for you!


### �� Implementation

Actually, it's not magic at all. Just imagine a class `NanoSet` that works as
a [proxy](https://www.tutorialspoint.com/python_design_patterns/python_design_patterns_proxy.htm)
to an actual Python `set` it wraps, but which is only allocated when some data
actually needs to be stored:

```python
class NanoSet(collections.abc.Set):

    def __init__(self, iterable=None):
        self.inner = None if iterable is None else set(iterable)

    def add(self, element):
        if self.inner is None:
            self.inner = set()
        self.inner.add(element)

    # ... the rest of the `set` API ...
```

That's about it! However, doing it like so in Python would not be super
efficient, as the resulting object would be **48** bytes. Using
[slots](http://book.pythontips.com/en/latest/__slots__magic.html), this can be
reduced to **40** bytes, which is on par to what we get with **`NanoSet`**.

**Note that these values are only when the inner set is empty!** When actually
allocating the set to store our values, we allocate an additional **232** bytes
of data. This means that using **`NanoSet`** creates an overhead, since a
non-empty set will now weigh **264** bytes (**248** bytes for **`PicoSet`**).

> Well, I was way better off with my approach of storing `Optional[Set]`
> everywhere then, I don't want to pay any additional cost for nonempty sets!

Sure. But that would mean changing your whole code. And actually, you may not
gain that much memory from doing that compared to using `nanoset`, since the
only time the wrapper performs badly is when you have a load factor of more than
90%. Furthermore, just to give you some perspective, `sys.getsizeof(1)` is
**28** bytes.

> By the way, you didn't mention `PicoSet`. How did you manage to get that down
> to **32** bytes, when a slotted Python object can't be less that **40** bytes?

Easy: `PicoSet` is basically `NanoSet`, but without an implementation of the
[Garbage Collector protocol](https://docs.python.org/3/c-api/gcsupport.html).
This saves us **8** bytes of object memory, but comes with a drawback: the
garbage collector cannot see the set allocated *inside* the `PicoSet`. This
does not change anything for execution, but debugging with a memory profiler
will be harder. Here is an example where we allocate **1,000,000** singletons
first with `NanoSet`, then with `PicoSet`, using
[`guppy3`](https://pypi.org/project/guppy3/) to check the heap:

```python
>>> l = [nanoset.NanoSet({x}) for x in range(1000000)]
>>> guppy.hpy().heap()
Partition of a set of 3036763 objects. Total size = 304996526 bytes.
 Index  Count   %     Size    %   Cumulative %  Kind (class / dict of class)
     0 1000044  33 216105248  71  216105248  71 set
     1 1000000  33  48000000  16  264105248  87 nanoset.NanoSet
     ...
     3     113   0   8716880   3  300851404  99 list
     ...
```
```python
>>> l = [nanoset.PicoSet({x}) for x in range(1000000)]
>>> guppy.hpy().heap()
Partition of a set of 1036905 objects. Total size = 44998965 bytes.
 Index  Count   %     Size   %   Cumulative  %  Kind (class / dict of class)
     0 1000000  96 32000000  71   32000000   71 nanoset.PicoSet
     1      96   0  8712752  24   32712752   89 list
     ...
```

On the second run, we have about the same order of allocated memory, saving
**16 MB** (**16** bytes saved by switching from `NanoSet` to `PicoSet` times
**1,000,000** instances). However, the garbage collector has no idea where
some of the memory is, because `PicoSet` hides the sets it allocates (this is
fine: it will be deallocated along with the `PicoSet`).

As such, I'd advise avoiding using `PicoSet` when debugging, which can be done
easily with Python's `__debug__` flag:
```python
if __debug__:
    from nanoset import NanoSet as set
else:
    from nanoset import PicoSet as set
```
This will cause `PicoSet` to be used instead of `NanoSet` when running Python
with the `-O` flag.


### �� Statistics

Okay, so let's do some maths. With `S = 232` the size of an allocated set,
`s` the size of the wrapper (`48` for `NanoSet`, `32` for `PicoSet`), the
`x` percentage of nonempty sets in our data structure, the relative size
of our sets is:

  * if we're using `set`: **S \* x / (S \* x) = 100%** (we use that as a reference)
  * if we're using `nanoset`: **((S + s) \* x + s \* (100 - x)) / (S \* x)**

This gives us the following graph, which shows how much memory you can save
depending of the ratio of empty sets you have at runtime:

![sizegraph](https://github.com/althonos/nanoset.py/raw/master/static/sizegraph.svg?sanitize=true)

If we get back to our NCBITaxon example, we have a total of **1,595,237** nodes
and **1,130,671** leaves, which means that by using sets we are allocating
**1,595,237 * 232 = 328.6 MiB** of memory simply for `set` after the whole
taxonomy is loaded. If we use `NanoSet` however, we
can reduce this to **168.7 MiB**, or even to **144.4 MiB** with `PicoSet`!
**We just saved about 45% memory just by using `NanoSet` in place of `set`.**


## �� Installing

This module is implemented in Rust, but native [Python wheels](https://pythonwheels.com/)
are compiled for the following platforms:

* Windows x86-64: CPython 3.5, 3.6, 3.7, 3.8
* Linux x86-64: CPython 3.5, 3.6, 3.7, 3.8
* OSX x86-64: CPython 3.5, 3.6, 3.7, 3.8

If you platform is not among these, you will need a
[working Rust `nightly` toolchain](https://www.rust-lang.org/tools/install)
as well as the [`setuptools-rust`](https://pypi.org/project/setuptools-rust/)
library installed to build the extension module.

Then, simply install with `pip`:
```console
$ pip install --user nanoset
```

## �� API Reference

Well, this is a comprehensive wrapper for `set`, so you can just read the
[standard library documentation](https://docs.python.org/3.7/library/stdtypes.html#set-types-set-frozenset).
Except for some very particular edge-cases, `NanoSet` and `PicoSet` both pass the
[`set` test suite](https://github.com/python/cpython/blob/master/Lib/test/test_set.py)
of [CPython](https://github.com/python/cpython).

There are however things you *can't* do:
- Subclassing a `PicoSet` or a `NanoSet`.
- Weakrefing a `PicoSet` or a `NanoSet`.
- Checking for membership in a plain `set` or `frozenset` with implicit
  conversion to `frozenset`.
- Creating a `dict` from a `PicoSet` or a `NanoSet` without rehashing keys.

## �� License

This library is provided under the open-source [MIT license](https://choosealicense.com/licenses/mit/).