pensieve 2022.4.20.1
Python library for organizing objects and dependencies in a graph structure
License: MIT
Requires Python: ~=3.6
Keywords: graph computation

# *Pensieve*
*Pensieve* is a Python library for organizing objects and dependencies in a graph structure.

"*One simply siphons the excess thoughts from one's mind, pours them into the basin, and examines them at one's leisure. It becomes easier to spot patterns and links, you understand, when they are in this form.*"</br>
&mdash;**Albus Dumbledore** (Harry Potter and the Goblet of Fire by J. K. Rowling)  
<p align="center">
  <img src="http://idin.ca/storage/python/pensieve/images/pensieve_600.jpg"/>
</p>

## Pensieve for Data

In [J. K. Rowling](https://en.wikipedia.org/wiki/J._K._Rowling)'s [words](https://en.wikipedia.org/wiki/Magical_objects_in_Harry_Potter#Pensieve): 
"*a witch or wizard can **extract** their own or another's memories, **store** them in the [Pensieve](https://en.wikipedia.org/wiki/Magical_objects_in_Harry_Potter#Pensieve), 
and **review** them later. It also **relieves the mind** when it becomes cluttered with information. 
Anyone can **examine** the memories in the Pensieve, which also allows viewers to fully immerse 
themselves in the memories*". 

Dealing with data during data wrangling and model generation in data science is like dealing with memories 
except that there is a lot more of back and forth and iteration when dealing with data. 
You constantly update parameters of your models, improve your data wrangling, 
and make changes to the ways you visualize or store data. 
As with most processes in data science, each step along the way may take a long time to finish
which forces you to avoid rerunning everything from scratch; this approach is very error-prone as some 
of the processes depend on others. To solve this problem I came up with the idea of a *Computation Graph* 
where the nodes represent data objects and the direction of edges indicate the dependency between them. 

After using Pensieve for some time myself, I have found it to be beneficial in several ways:
* error reduction, especially for data wrangling and model creation
* data object organization
* easy transfer of data
* coherent data processing and data pipelines
* data and model reproducibility
* parallel processing
* performance and cost analysis in terms of computation time and memory usage
* graphical visualization of data and processes
* most important of all: **relieving the mind**

Using pensieve is similar to using a dictionary:

```python
from pensieve import Pensieve
from math import pi

# initiate a pensieve
pensieve = Pensieve()

# store a "memory" (with 1 as its content) 
pensieve['radius'] = 5

# create a new memory made up of a precursor memory
# it is as easy as passing a defined function or a lambda to pensieve
pensieve['circumference'] = lambda radius: 2 * pi * radius
print(pensieve['circumference'])
```
outputs:

`31.41592653589793`

Changing the radius, in this example, will affect the circumference 
but it is only calculated when needed:
```python
pensieve['radius'] = 6
print(pensieve['circumference'])
```
outputs 

`37.69911184307752`


## Installation
```bash
pip install pensieve
```

## Usage
Pensieve stores *memories* and *functions* that define the relationship between memories.



## Concepts

### Memory
A `Pensieve` is a *computation graph* where the nodes hold values and edges 
show dependency between nodes. Each node is called a `Memory`.

Every *memory* has two important attributes:
- `key`: the name of the memory which should be identical
- `content`: the object the memory holds

Some memories have two other attributes:
- `precursors`: other memories a memory depends on
- `function`: a function that defines the relationship between a memory
and its precursors

There are two types of memories:
- *independent* memories (without precursors)
- *dependent* memories (with precursors)

### Storing a Memory
As explained above, you can work with pensieve similar to how you use a
dictionary. Adding a new item, *i.e.*, a memory and its content, to pensieve is
called *storing*. In fact the `Pensieve` class has a `store` method which 
can be used for storing new memories. However, we only use it for advanced
functionality. We do not use it as frequently because a new simpler notation 
introduced since version 2 makes working pensieve much more coherent. 
We will explain the `store` method and its notation in the *Advanced Usage* section.

### Retrieving a Memory
Retrieving the content of a memory is like getting an item from a dictionary.

```python
print(pensieve['circumference'])
```

### Independent Memories
An independent memory is like a root node in pensieve. It holds an object and
it does not depend on any other memory.

```python
from pensieve import Pensieve

pensieve = Pensieve()

pensieve['text'] = 'Hello World!'
pensieve['number'] = 1
pensieve['list_of_numbers'] = [1, 3, 2]
```
In the above example, *text*, *number*, and *list* are the names of three 
independent memories and their contents are 
the string `'Hello World'`, 
the integer `1`, 
and a list consisting of three integers.

### Dependent Memories and Precursors
A dependent memory is created from running a *function* on other dependent or
independent memories as the function's arguments. We call those memories, *precursors*;
*i.e.*, if a memory depends on another memory, the former is a *dependent* memory 
and the latter is its *precursor*.

The easiest way to define a dependent memory is by passing a function to pensieve
whose arguments match the names of precursors.

```python
def print_and_return_first_word(text):
    words = text.split()
    print(words[0])
    return words[0]
    
pensieve['first_word'] = print_and_return_first_word
```
In the above example, the `print_and_return_first_word` function accepts one argument:
`text` which is the name of the precursor.

You can also use a lambda, when possible, to define a dependent memory.

```python
pensieve['sorted_list'] = lambda list_of_numbers: sorted(list_of_numbers)
```

### Successors
Memories that depend on a memory are its *successors*. If a precursor is like a 
parent, a successor is like a child. 

In the above example, `sorted_list` is a successor of `list_of_numbers`.

### Staleness
If one or more precursors of a memory change, the memory and all its successors becomes *stale*. 
A stale memory is only refreshed when needed and if after calculation, it is found out
that the content has not changed, the successors go back to being up-to-date, but if 
the content has in fact changed, the stay stale and will be updated when needed.

**Note**: if a memory is stale, retrieving its content will update it.

## Visualization

```python
from pensieve import Pensieve
from pandas import DataFrame, concat
from numpy.random import randint, seed

# set seed for the randint function
seed(17)

# set up a pensieve with a top-bottom (tb) representation
# the top-bottom graph_direction is purely aesthetic
# you can also use lr for left to right or rl for right to left or bottom-top
pensieve = Pensieve(graph_direction='tb')

# choose the number of columns for two dataframes
pensieve['number_of_columns'] = 9

# create generic names for the columns, in this case x_1, x_2, ...
pensieve['column_names'] = lambda number_of_columns: [
    f'x_{i + 1}' for i in range(number_of_columns)
]

# choose the range of random values, and store them as a dictionary 
pensieve['value_range'] = {'low': 1, 'high': 5}

# define a function that creates a dataframe with the above parameters
def create_dataframe(column_names, value_range, number_of_rows):
    return DataFrame({
        column: randint(
            low=value_range['low'], 
            high=value_range['high'], 
            size=number_of_rows
        )
        for column in column_names
    })

# create the first dataframe
pensieve['data_1'] = lambda column_names, value_range: create_dataframe(
    column_names=column_names, value_range=value_range, number_of_rows=5
)

# create the second dataframe
pensieve['data_2'] = lambda column_names, value_range: create_dataframe(
    column_names=column_names, value_range=value_range, number_of_rows=3
)

# concatenate the two dataframes
pensieve['data_1_and_2'] = lambda data_1, data_2: concat(
    objs=[data_1, data_2], 
    sort=False
)

# choose a coefficient for a future multiplication
pensieve['coefficient'] = 5

# define a function that sums all the values in each row and 
# multiplies the result by the coefficient
def sum_and_multiply(data_1_and_2, coefficient):
    data = data_1_and_2.copy()
    data['summation'] = data.apply(sum, axis=1)
    data['coefficient'] = coefficient
    data['y'] = data['summation'] * data['coefficient']
    return data

# get the result of the sum_and_multiply function
pensieve['result'] = sum_and_multiply

# display the pensieve
display(pensieve) 
# or simply pensieve at the end of a jupyter notebook cell
```

<p align="center">
  <img 
    src="http://idin.ca/storage/python/pensieve/images/pensieve_visualization.png"
    width=60%
  />
</p>



## Advanced Usage

### Parallel Processing
```python
from pensieve import Pensieve
from time import sleep
from datetime import datetime

# as in other libraries, num_threads=-1 means 
# using as many threads as available

start_time = datetime.now()
pensieve = Pensieve(num_threads=-1, evaluate=False)

pensieve['x'] = 1
pensieve['y'] = 10
pensieve['z'] = 2
pensieve['w'] = 20

def add_with_delay(x, y):
    print(f'adding {x} and {y}, slowly, at {datetime.now()}')
    sleep(1)
    return x + y
    
pensieve['x_plus_y'] = add_with_delay
pensieve['z_plus_w'] = lambda z, w: add_with_delay(x=z, y=w)
# we had to use a lambda for this one because the arguments
# of the add_with_delay function are different

pensieve['all_the_four'] = lambda x_plus_y, z_plus_w: add_with_delay(x=x_plus_y, y=z_plus_w)
elapsed = datetime.now() - start_time
print('Nothing has been calculated yet. Elapsed time:', elapsed)

print('Getting all_the_four forces the calculation of everything')

start_time = datetime.now()
print('Result of adding the four numbers:', pensieve['all_the_four'])
elapsed = datetime.now() - start_time
print('Elapsed time:', elapsed)
```
The above code produces the following output:
```
Nothing has been calculated yet. Elapsed time: 0:00:00.000716
Getting all_the_four forces the calculation of everything
adding 2 and 20, slowly, at 2019-12-15 21:33:55.063888
adding 1 and 10, slowly, at 2019-12-15 21:33:55.064526
adding 11 and 22, slowly, at 2019-12-15 21:33:56.188258
Result of adding the four numbers: 33
Elapsed time: 0:00:02.341677
```
Two of the calculations were executed in parallel: `x + y` and `z + w`. 
With an overhead of `0.34` seconds, the three calculations took `2.34` seconds.

Let's see what happens if we do it the ordinary way:
```python
start_time = datetime.now()
x = 1
y = 10
z = 2
w = 20
x_plus_y = add_with_delay(x, y)
z_plus_w = add_with_delay(z, w)
all_the_four = add_with_delay(x_plus_y, z_plus_w)
print('Result of adding the four numbers:', all_the_four)
elapsed = datetime.now() - start_time
print('Elapsed time:', elapsed)
```
This time the following output is produced:
```
adding 1 and 10, slowly, at 2019-12-15 21:38:11.618910
adding 2 and 20, slowly, at 2019-12-15 21:38:12.620105
adding 11 and 22, slowly, at 2019-12-15 21:38:13.625195
Result of adding the four numbers: 33
Elapsed time: 0:00:03.011291
```
With an overhead of `0.01` seconds, the three calculations 
ran one after the other and took `3.01` seconds.

### The `store` Method
***TBD***