this post was submitted on 02 Aug 2024
341 points (97.5% liked)

Science Memes

11021 readers
3054 users here now

Welcome to c/science_memes @ Mander.xyz!

A place for majestic STEMLORD peacocking, as well as memes about the realities of working in a lab.

Rules

  1. Don't throw mud. Behave like an intellectual and remember the human.
  2. Keep it rooted (on topic).
  3. No spam.
  4. Infographics welcome, get schooled.

This is a science community. We use the Dawkins definition of meme.

Research Committee

Other Mander Communities

Science and Research

Biology and Life Sciences

Physical Sciences

Humanities and Social Sciences

Practical and Applied Sciences

Memes

Miscellaneous

founded 2 years ago
MODERATORS
[email protected]
[email protected]
[email protected]
341
Pandas (mander.xyz)
submitted 3 months ago by [email protected] to c/[email protected]
36 comments fedilink hide all child comments
 
you are viewing a single comment's thread
view the rest of the comments
[–] [email protected] 41 points 3 months ago (5 children)

Is 600 MB a lot for pandas? Of course, CSV isn't really optimal but I would've sworn pandas happily works with gigabytes of data.

[–] [email protected] 26 points 3 months ago* (last edited 3 months ago) (5 children)

What do you mean not optimal? This is quite literally the most popular format for any serious data handling and exchange. One byte per separator and newline is all you need. It is not compressed so allows you to stream as well. If you don't need tree structure it is massively better than others

[–] [email protected] 14 points 3 months ago

I think portability and easy parsing is the only advantage od CSV. It's definitely good enough (maybe even the best) for small datasets but if you have a lot of data you need a compressed binary format, something like parquet.

[–] [email protected] 8 points 3 months ago

But which separator is it, and which line ending? ASCII, UTF-8, UTF-16 or something else? What about quoting separators and line endings? Yes, there is an RFC, but a million programs were made before the RFC and won't change their ways now.

Also you can gzip CSV and still stream them.

[–] [email protected] 4 points 3 months ago (1 children)

Have you heard that there are great serialised file formats like .parquet from appache arrow, that can easily be used in typical data science packages like duckdb or polars. Perhaps it even works with pandas (although do not know it that well. I avoid pandas as much as possible as someone who comes from the R tidyverse and try to use polars more when I work in python, because it often feels more intuitive to work with for me.)

[–] [email protected] 1 points 3 months ago

I used to export my pandas DataFrames as pickles, but decided to test parquet and it was great. It was like 10x smaller and allowed me to had the the databases on a server directory instead of having to copy everything to the local machine.

[–] [email protected] 1 points 3 months ago

If you have a csv bigger than like 500mb you need more than 8gb of ram to open it

[–] [email protected] 1 points 3 months ago

Wait till you hear about WSV

[–] [email protected] 10 points 3 months ago (1 children)

It really depends on the machine that is running the code. Pandas will always have the entire thing loaded in memory, and while 600Mb is not a concern for our modern laptops running a single analysis at a time, it can get really messy if the person is not thinking about hardware limitations

[–] [email protected] 8 points 3 months ago (1 children)

Pandas supports lazy loading and can read files in chunks. Hell, even regular ole Python doesn't need to read the whole file at once with csv

[–] [email protected] 3 points 3 months ago* (last edited 3 months ago)

I didn't know about lazy loading, that's cool!

Then I guess that the meme doesn't apply anymore. Though I will state that (from my anedoctal experience) people that can use Panda's most advanced features* are also comfortable with other data processing frameworks (usually more suitable to large datasets**)

*Anything beyond the standard groupby - apply can be considered advanced, from the placrs I've been

**I feel the urge to note that 60Mb isn' lt a large dataset by any means, but I believe that's beyond the point

[–] [email protected] 8 points 3 months ago (1 children)

Is 600 MB a lot for pandas?

No, but it's easy to make a program in Python that doesn't like it.

[–] [email protected] 3 points 3 months ago

Oh, I know, believe me. I have some painful first-hand experience with such code.

[–] [email protected] 5 points 3 months ago (2 children)

I guess it's more of a critique of how bad CSV is for storing large data than pandas being inefficient

[–] [email protected] 13 points 3 months ago (2 children)

CSV is not optimal, but then someone shows up and gives you 60GB of JSON instead of 600MB of CSV.

[–] [email protected] 4 points 3 months ago

Why do you have to personally attack me like that?

[–] [email protected] 3 points 3 months ago

Or they dump their entire 6gb SQL database, customer info and all, into a SQL file that you have to load into a mariadb docker container when you just needed a subset that you were going to turn into csv anyway ☺️

[–] [email protected] 4 points 3 months ago

Fine! .csv.gz ftw!

[–] [email protected] 1 points 3 months ago (1 children)

It's more likely you'll eat up storage when you read a 600mb parquet and try to write it as CSV.

[–] [email protected] 1 points 3 months ago (1 children)

I mean, yeah, that's the point of compression. I don't quite get what you mean by that comment.

[–] [email protected] 1 points 3 months ago (1 children)

Ah I was trying to point out that CSV is the inefficient format. Reading a large amount of data from a more efficient format like parquet is more likely to cause trouble because the memory required can be more than the file size. CSV is the opposite where it will almost always use more disk space than is required to represent the data in memory.

[–] [email protected] 1 points 3 months ago

Right, true!