How to use a Python function defined in a separate file in a Python chunk in Rmarkdown?

So, I have a file called 'function.py' which includes the simple function:

def square(x):
 return x*x

I have a second bit of code like this:

from test import square
print(square(2))

If I store the second bit of code in a python file and run it in the terminal it works and gives the expected answer.

However, if I add a Python chunk in a Rmarkdown document like this:

```python
from test import square
print(square(2))
```

I get the error:

"Traceback (most recent call last):
File "/var/folders/g7/462tmml173nfzj0j8437t9_m0000gn/T/RtmptMA22N/chunk-code-48764cec023f.txt", line 1, in
from test import square
ImportError: cannot import name square"

The Rmarkdown file and the python file are in the same directory. Answers about the specific error message are about dependencies, but I don't see how that's relevant in my case?

I've searched the web and read documentation, but I think I am missing something important. Thank you for the help!

Edit:
Solved by specifically changing the path to the current working directory.

import sys, os
sys.path.append(os.getcwd())
import test
print(test.square(2))

edited Nov 14 '18 at 14:13

asked Nov 14 '18 at 13:04

D. de Jonge

237

Have you read and tried the solutions detailed in this GitHub issue thread?

– Mihai Chelaru
Nov 14 '18 at 13:08

Is test a folder ?

– Hcetipe
Nov 14 '18 at 13:11

1) The GitHub issue thread: yes, I have read this. The reticulate function that is given as solution is meant to be used in a R chunk, whereas I want to import within a Python chunk. The other solution of using "sys.path.append(os.path.join(os.path.dirname(file)))" is not quite clear to me; not sure how to implement it. 2) test is not a folder, test.py is a file with the function

– D. de Jonge
Nov 14 '18 at 13:39

You can try to put your test.py in a folder and then import like this : from yourfolder.test import *

– Hcetipe
Nov 14 '18 at 13:47

This solution does not work unfortunately. Am I missing something about what a module is exactly? Or am I missing something about how to define the location of the directory/file/function?

– D. de Jonge
Nov 14 '18 at 13:58

|
show 1 more comment

So, I have a file called 'function.py' which includes the simple function:

def square(x):
 return x*x

I have a second bit of code like this:

from test import square
print(square(2))

If I store the second bit of code in a python file and run it in the terminal it works and gives the expected answer.

However, if I add a Python chunk in a Rmarkdown document like this:

```python
from test import square
print(square(2))
```

I get the error:

"Traceback (most recent call last):
File "/var/folders/g7/462tmml173nfzj0j8437t9_m0000gn/T/RtmptMA22N/chunk-code-48764cec023f.txt", line 1, in
from test import square
ImportError: cannot import name square"

The Rmarkdown file and the python file are in the same directory. Answers about the specific error message are about dependencies, but I don't see how that's relevant in my case?

I've searched the web and read documentation, but I think I am missing something important. Thank you for the help!

Edit:
Solved by specifically changing the path to the current working directory.

import sys, os
sys.path.append(os.getcwd())
import test
print(test.square(2))

edited Nov 14 '18 at 14:13

asked Nov 14 '18 at 13:04

D. de Jonge

237

Have you read and tried the solutions detailed in this GitHub issue thread?

– Mihai Chelaru
Nov 14 '18 at 13:08

Is test a folder ?

– Hcetipe
Nov 14 '18 at 13:11

1) The GitHub issue thread: yes, I have read this. The reticulate function that is given as solution is meant to be used in a R chunk, whereas I want to import within a Python chunk. The other solution of using "sys.path.append(os.path.join(os.path.dirname(file)))" is not quite clear to me; not sure how to implement it. 2) test is not a folder, test.py is a file with the function

– D. de Jonge
Nov 14 '18 at 13:39

You can try to put your test.py in a folder and then import like this : from yourfolder.test import *

– Hcetipe
Nov 14 '18 at 13:47

This solution does not work unfortunately. Am I missing something about what a module is exactly? Or am I missing something about how to define the location of the directory/file/function?

– D. de Jonge
Nov 14 '18 at 13:58

|
show 1 more comment

So, I have a file called 'function.py' which includes the simple function:

def square(x):
 return x*x

I have a second bit of code like this:

from test import square
print(square(2))

If I store the second bit of code in a python file and run it in the terminal it works and gives the expected answer.

However, if I add a Python chunk in a Rmarkdown document like this:

```python
from test import square
print(square(2))
```

I get the error:

"Traceback (most recent call last):
File "/var/folders/g7/462tmml173nfzj0j8437t9_m0000gn/T/RtmptMA22N/chunk-code-48764cec023f.txt", line 1, in
from test import square
ImportError: cannot import name square"

The Rmarkdown file and the python file are in the same directory. Answers about the specific error message are about dependencies, but I don't see how that's relevant in my case?

I've searched the web and read documentation, but I think I am missing something important. Thank you for the help!

Edit:
Solved by specifically changing the path to the current working directory.

import sys, os
sys.path.append(os.getcwd())
import test
print(test.square(2))

edited Nov 14 '18 at 14:13

asked Nov 14 '18 at 13:04

D. de Jonge

237

So, I have a file called 'function.py' which includes the simple function:

def square(x):
 return x*x

I have a second bit of code like this:

from test import square
print(square(2))

If I store the second bit of code in a python file and run it in the terminal it works and gives the expected answer.

However, if I add a Python chunk in a Rmarkdown document like this:

```python
from test import square
print(square(2))
```

I get the error:

"Traceback (most recent call last):
File "/var/folders/g7/462tmml173nfzj0j8437t9_m0000gn/T/RtmptMA22N/chunk-code-48764cec023f.txt", line 1, in
from test import square
ImportError: cannot import name square"

The Rmarkdown file and the python file are in the same directory. Answers about the specific error message are about dependencies, but I don't see how that's relevant in my case?

I've searched the web and read documentation, but I think I am missing something important. Thank you for the help!

Edit:
Solved by specifically changing the path to the current working directory.

import sys, os
sys.path.append(os.getcwd())
import test
print(test.square(2))

python r-markdown

edited Nov 14 '18 at 14:13

asked Nov 14 '18 at 13:04

D. de Jonge

237

edited Nov 14 '18 at 14:13

asked Nov 14 '18 at 13:04

D. de Jonge

237

edited Nov 14 '18 at 14:13

asked Nov 14 '18 at 13:04

D. de Jonge

237

asked Nov 14 '18 at 13:04

D. de Jonge

237

asked Nov 14 '18 at 13:04

D. de Jonge

237

Have you read and tried the solutions detailed in this GitHub issue thread?

– Mihai Chelaru
Nov 14 '18 at 13:08

Is test a folder ?

– Hcetipe
Nov 14 '18 at 13:11

1) The GitHub issue thread: yes, I have read this. The reticulate function that is given as solution is meant to be used in a R chunk, whereas I want to import within a Python chunk. The other solution of using "sys.path.append(os.path.join(os.path.dirname(file)))" is not quite clear to me; not sure how to implement it. 2) test is not a folder, test.py is a file with the function

– D. de Jonge
Nov 14 '18 at 13:39

You can try to put your test.py in a folder and then import like this : from yourfolder.test import *

– Hcetipe
Nov 14 '18 at 13:47

This solution does not work unfortunately. Am I missing something about what a module is exactly? Or am I missing something about how to define the location of the directory/file/function?

– D. de Jonge
Nov 14 '18 at 13:58

|
show 1 more comment

Have you read and tried the solutions detailed in this GitHub issue thread?

– Mihai Chelaru
Nov 14 '18 at 13:08

Is test a folder ?

– Hcetipe
Nov 14 '18 at 13:11

1) The GitHub issue thread: yes, I have read this. The reticulate function that is given as solution is meant to be used in a R chunk, whereas I want to import within a Python chunk. The other solution of using "sys.path.append(os.path.join(os.path.dirname(file)))" is not quite clear to me; not sure how to implement it. 2) test is not a folder, test.py is a file with the function

– D. de Jonge
Nov 14 '18 at 13:39

You can try to put your test.py in a folder and then import like this : from yourfolder.test import *

– Hcetipe
Nov 14 '18 at 13:47

This solution does not work unfortunately. Am I missing something about what a module is exactly? Or am I missing something about how to define the location of the directory/file/function?

– D. de Jonge
Nov 14 '18 at 13:58

Have you read and tried the solutions detailed in this GitHub issue thread?

– Mihai Chelaru
Nov 14 '18 at 13:08

Is test a folder ?

– Hcetipe
Nov 14 '18 at 13:11

1) The GitHub issue thread: yes, I have read this. The reticulate function that is given as solution is meant to be used in a R chunk, whereas I want to import within a Python chunk. The other solution of using "sys.path.append(os.path.join(os.path.dirname(file)))" is not quite clear to me; not sure how to implement it. 2) test is not a folder, test.py is a file with the function

– D. de Jonge
Nov 14 '18 at 13:39

You can try to put your test.py in a folder and then import like this : from yourfolder.test import *

– Hcetipe
Nov 14 '18 at 13:47

This solution does not work unfortunately. Am I missing something about what a module is exactly? Or am I missing something about how to define the location of the directory/file/function?

– D. de Jonge
Nov 14 '18 at 13:58

|
show 1 more comment

1 Answer
1

active

oldest

votes

Solved by specifically changing the path to the current working directory.

import sys, os
sys.path.append(os.getcwd())
import test
print(test.square(2))

Answer was based on Python: Best way to add to sys.path relative to the current running script.

answered Nov 14 '18 at 14:13

D. de Jonge

237

add a comment |

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1 Answer
1

active

oldest

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1 Answer
1

active

oldest

votes

Solved by specifically changing the path to the current working directory.

import sys, os
sys.path.append(os.getcwd())
import test
print(test.square(2))

Answer was based on Python: Best way to add to sys.path relative to the current running script.

answered Nov 14 '18 at 14:13

D. de Jonge

237

add a comment |

Solved by specifically changing the path to the current working directory.

import sys, os
sys.path.append(os.getcwd())
import test
print(test.square(2))

Answer was based on Python: Best way to add to sys.path relative to the current running script.

answered Nov 14 '18 at 14:13

D. de Jonge

237

add a comment |

Solved by specifically changing the path to the current working directory.

import sys, os
sys.path.append(os.getcwd())
import test
print(test.square(2))

Answer was based on Python: Best way to add to sys.path relative to the current running script.

answered Nov 14 '18 at 14:13

D. de Jonge

237

Solved by specifically changing the path to the current working directory.

import sys, os
sys.path.append(os.getcwd())
import test
print(test.square(2))

Answer was based on Python: Best way to add to sys.path relative to the current running script.

answered Nov 14 '18 at 14:13

D. de Jonge

237

answered Nov 14 '18 at 14:13

D. de Jonge

237

answered Nov 14 '18 at 14:13

D. de Jonge

237

answered Nov 14 '18 at 14:13

D. de Jonge

237

add a comment |

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