pandas.read_csv("iris.csv") FileNotFound

Description

Pandas read_csv gave FileNotFound error on example file iris.csv. I’m hope this is not a silly user error and I’m sorry in advance if it is.

Reproduce

• Create new notebook in examples folder
• import pandas as pd
• pd.read_csv("iris.csv")

Expected behavior

Load and display the content of iris.csv on screen

Context

• Operating System and version:
• MacOS 11.2.3
• MacBook Air (M1, 2020)
• Apple M1 chip
• Browser and version: Brave Version 1.24.84 Chromium: 90.0.4430.93 (Official Build) (arm64)
• JupyterLite version: can’t find version number but I did this today (2021/06/01) using JupyterLite for the first time

Browser Output

Dispose worker for kernel 7f928317-a338-41fb-9c00-6c1d041909fd
default.js:1228 Connection lost, reconnecting in 0 seconds.
_reconnect @ default.js:1228
reconnect @ default.js:516
restart @ default.js:487
async function (async)
restart @ default.js:484
restartKernel @ sessioncontext.js:298
restart @ sessioncontext.js:758
async function (async)
restart @ sessioncontext.js:733
onClick @ toolbar.js:343
y.createElement.onMouseDown @ toolbar.js:402
Be @ react-dom.production.min.js:52
Ke @ react-dom.production.min.js:52
(anonymous) @ react-dom.production.min.js:53
xr @ react-dom.production.min.js:100
Cr @ react-dom.production.min.js:101
(anonymous) @ react-dom.production.min.js:113
De @ react-dom.production.min.js:292
(anonymous) @ react-dom.production.min.js:50
Lr @ react-dom.production.min.js:105
Zn @ react-dom.production.min.js:75
Jn @ react-dom.production.min.js:74
n.unstable_runWithPriority @ scheduler.production.min.js:18
Bl @ react-dom.production.min.js:122
Me @ react-dom.production.min.js:292
Xn @ react-dom.production.min.js:73
pyodide.asm.js:9 Python initialization complete
pyodide.js:146 Loading matplotlib, cycler, six, kiwisolver, numpy, pillow, pyparsing, python-dateutil, pytz
pyodide.js:196 Loading matplotlib from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/matplotlib.js
pyodide.js:196 Loading cycler from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/cycler.js
pyodide.js:196 Loading six from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/six.js
pyodide.js:196 Loading kiwisolver from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/kiwisolver.js
pyodide.js:196 Loading numpy from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/numpy.js
pyodide.js:196 Loading pillow from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/pillow.js
pyodide.js:196 Loading pyparsing from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/pyparsing.js
pyodide.js:196 Loading python-dateutil from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/python-dateutil.js
pyodide.js:196 Loading pytz from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/pytz.js
pyodide.js:252 Loaded matplotlib, cycler, six, kiwisolver, numpy, pillow, pyparsing, python-dateutil, pytz
pyodide.js:146 Loading micropip, pyparsing, packaging
pyodide.js:196 Loading micropip from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/micropip.js
pyodide.js:184 pyparsing already loaded from default channel
pyodide.js:196 Loading packaging from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/packaging.js
pyodide.js:252 Loaded micropip, pyparsing, packaging
8ebb3553-36cc-44b7-9b0c-539a2f402d28:29 Pyolite kernel initialized, version 0.1.0
8ebb3553-36cc-44b7-9b0c-539a2f402d28:63 Inside worker {code: "import pandas as pd"}
pyodide.js:146 Loading pandas, numpy, python-dateutil, pytz
pyodide.js:196 Loading pandas from https://cdn.jsdelivr.net/pyodide/v0.17.0/full/pandas.js
pyodide.js:184 numpy already loaded from default channel
pyodide.js:184 python-dateutil already loaded from default channel
pyodide.js:184 pytz already loaded from default channel
pyodide.js:252 Loaded pandas, numpy, python-dateutil, pytz
8ebb3553-36cc-44b7-9b0c-539a2f402d28:63 Inside worker {code: "pd.read_csv("iris.csv")"}code: "pd.read_csv(\"iris.csv\")"__proto__: Object

[jtpio]

Thanks @mklilley for trying it out 👍

Looks like it’s related to not being able to do raw network request using the Python standard library.

As a workaround, something like the following could do the job maybe?

import pandas as pd
from js import fetch

URL = "https://support.staffbase.com/hc/en-us/article_attachments/360009197031/username.csv"

res = await fetch(URL)
text = await res.text()

filename = 'data.csv'

with open(filename, 'w') as f:
    f.write(text)

data = pd.read_csv(filename, sep=';')
data

[rth]

For those who find this and are trying to work with a binary file, here is an example of unpickling a file from a URL

Since Pyodide 0.19 (included in the latest JupyterLite) there is also the pyodide.http.pyfetch function aiming to make it a bit easier to work with JS fetch from Python. With it the above example would be,

from pyodide.http import pyfetch
import pickle, numpy

URL = "https://raw.githubusercontent.com/jmshea/digicom-jupyter/main/content/signals.pkl"
res = await pyfetch(URL)
stream = await res.bytes()

data = pickle.loads(stream)
data