* Org babel Python and R, table not transformed when :var is called ?
@ 2021-12-01 8:04 Sébastien Rey-Coyrehourcq
2021-12-02 11:10 ` Sébastien Rey-Coyrehourcq
2022-10-16 11:23 ` Ihor Radchenko
0 siblings, 2 replies; 3+ messages in thread
From: Sébastien Rey-Coyrehourcq @ 2021-12-01 8:04 UTC (permalink / raw)
To: emacs-orgmode
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Hi there,
Perhaps it's a bug, or something i don't understand, i post on reddit
(https://www.reddit.com/r/emacs/comments/r5yt4a/r_talking_with_python_using_orgtable_not_work/)
to see if people on org community know the problem.
I cross post here to see if it's a know bug or somethings ?
There is something i don't understand,
a difference between behavior of org-babel and org-mode when you use org
table to pass data using or not using :var.
|#+NAME:mypythoncode #+begin_src python :results value raw :output
:return tabulate(df, headers=df.columns, tablefmt='orgtbl') import numpy
as np import pandas as pd from tabulate import tabulate df =
pd.DataFrame(np.random.randint(0,10,size=(10, 4)), columns=list('ABCD'))
#+end_src #+RESULTS: mypythoncode | | A | B | C | D |
|---+---+---+---+---| | 0 | 0 | 9 | 6 | 0 | | 1 | 2 | 9 | 0 | 4 | | 2 |
9 | 6 | 0 | 1 | | 3 | 6 | 1 | 8 | 1 | | 4 | 4 | 2 | 1 | 4 | | 5 | 2 | 1
| 1 | 1 | | 6 | 4 | 8 | 9 | 0 | | 7 | 1 | 4 | 8 | 7 | | 8 | 9 | 3 | 2 |
5 | | 9 | 5 | 0 | 7 | 3 | #+NAME:lib-R #+HEADER: :var code=mypythoncode
#+begin_src R :results output library(ggplot2) library(dplyr)
library(lubridate) str(code) #+end_src #+RESULTS: lib-R : chr "| | A | B
| C | D |\n|----+-----+-----+-----+-----|\n| 0 | 8 | 0 | 5 | 2 |\n| 1 |
2 | "| __truncated__ |
As you see, the org table is not recognized as a dataframe by R.
If i replace by a basic org table :
|||#+NAME: any_data | | parameter | value | |---+-----------+-------| | 0
| heats | 30 | | 1 | heats | 30 | #+NAME:lib-R #+HEADER: :var
code=any_data #+begin_src R :results output library(ggplot2)
library(dplyr) library(lubridate) str(code) #+end_src #+RESULTS: lib-R :
'data.frame': 2 obs. of 3 variables: : $ X : int 0 1 : $ parameter: chr
"heats" "heats" : $ value : int 30 30 |||
That works...
Best regards,
||
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^ permalink raw reply [flat|nested] 3+ messages in thread* Re: Org babel Python and R, table not transformed when :var is called ?
2021-12-01 8:04 Org babel Python and R, table not transformed when :var is called ? Sébastien Rey-Coyrehourcq
@ 2021-12-02 11:10 ` Sébastien Rey-Coyrehourcq
2022-10-16 11:23 ` Ihor Radchenko
1 sibling, 0 replies; 3+ messages in thread
From: Sébastien Rey-Coyrehourcq @ 2021-12-02 11:10 UTC (permalink / raw)
To: emacs-orgmode, jeremiejuste
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Hi,
I found a solution using *Wrapping*, adding a #+NAME to #+RESULTS block
resolve the problem.
This is not defined / described into the doc, and actually i found this
process a little anti-intuitive. #+RESULTS has already a name,
resulting/linked from/to the execution of mypythoncode ...
Best regards
#+NAME: attr_wrap
#+BEGIN_SRC sh :var data="" :results output
echo "#+NAME: cities"
echo "$data"
#+END_SRC
#+NAME:mypythoncode
#+begin_src python :results value raw :output :post
attr_wrap(data=*this*) :return tabulate(df, headers=df.columns,
tablefmt='orgtbl')
import numpy as np
import pandas as pd
from tabulate import tabulate
df = pd.DataFrame(np.random.randint(0,10,size=(10, 4)),
columns=list('ABCD'))
#+end_src
Le 01/12/2021 à 09:04, Sébastien Rey-Coyrehourcq a écrit :
>
> Hi there,
>
> Perhaps it's a bug, or something i don't understand, i post on reddit
> (https://www.reddit.com/r/emacs/comments/r5yt4a/r_talking_with_python_using_orgtable_not_work/)
> to see if people on org community know the problem.
>
> I cross post here to see if it's a know bug or somethings ?
>
> There is something i don't understand,
> a difference between behavior of org-babel and org-mode when you use
> org table to pass data using or not using :var.
>
> |#+NAME:mypythoncode #+begin_src python :results value raw :output
> :return tabulate(df, headers=df.columns, tablefmt='orgtbl') import
> numpy as np import pandas as pd from tabulate import tabulate df =
> pd.DataFrame(np.random.randint(0,10,size=(10, 4)),
> columns=list('ABCD')) #+end_src #+RESULTS: mypythoncode | | A | B | C
> | D | |---+---+---+---+---| | 0 | 0 | 9 | 6 | 0 | | 1 | 2 | 9 | 0 | 4
> | | 2 | 9 | 6 | 0 | 1 | | 3 | 6 | 1 | 8 | 1 | | 4 | 4 | 2 | 1 | 4 | |
> 5 | 2 | 1 | 1 | 1 | | 6 | 4 | 8 | 9 | 0 | | 7 | 1 | 4 | 8 | 7 | | 8 |
> 9 | 3 | 2 | 5 | | 9 | 5 | 0 | 7 | 3 | #+NAME:lib-R #+HEADER: :var
> code=mypythoncode #+begin_src R :results output library(ggplot2)
> library(dplyr) library(lubridate) str(code) #+end_src #+RESULTS: lib-R
> : chr "| | A | B | C | D |\n|----+-----+-----+-----+-----|\n| 0 | 8 |
> 0 | 5 | 2 |\n| 1 | 2 | "| __truncated__ |
>
> As you see, the org table is not recognized as a dataframe by R.
>
> If i replace by a basic org table :
>
> |||#+NAME: any_data | | parameter | value | |---+-----------+-------| |
> 0 | heats | 30 | | 1 | heats | 30 | #+NAME:lib-R #+HEADER: :var
> code=any_data #+begin_src R :results output library(ggplot2)
> library(dplyr) library(lubridate) str(code) #+end_src #+RESULTS: lib-R
> : 'data.frame': 2 obs. of 3 variables: : $ X : int 0 1 : $ parameter:
> chr "heats" "heats" : $ value : int 30 30 |||
>
> That works...
>
> Best regards,
>
> ||
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^ permalink raw reply [flat|nested] 3+ messages in thread* Re: Org babel Python and R, table not transformed when :var is called ?
2021-12-01 8:04 Org babel Python and R, table not transformed when :var is called ? Sébastien Rey-Coyrehourcq
2021-12-02 11:10 ` Sébastien Rey-Coyrehourcq
@ 2022-10-16 11:23 ` Ihor Radchenko
1 sibling, 0 replies; 3+ messages in thread
From: Ihor Radchenko @ 2022-10-16 11:23 UTC (permalink / raw)
To: sebastien.rey-coyrehourcq; +Cc: emacs-orgmode
Sébastien Rey-Coyrehourcq <sebastien.rey-coyrehourcq@univ-rouen.fr>
writes:
> Perhaps it's a bug, or something i don't understand, i post on reddit
> (https://www.reddit.com/r/emacs/comments/r5yt4a/r_talking_with_python_using_orgtable_not_work/)
> to see if people on org community know the problem.
>
> I cross post here to see if it's a know bug or somethings ?
>
> There is something i don't understand,
> a difference between behavior of org-babel and org-mode when you use org
> table to pass data using or not using :var.
>
> |#+NAME:mypythoncode #+begin_src python :results value raw :output
> :return tabulate(df, headers=df.columns, tablefmt='orgtbl')
AFAIU, your tabulate call returns string, not a python table. So, :var
assignment indeed assigns a string. The returned string also happens to
use Org table format, which is why results block is an Org table.
By putting #+NAME to results block, you will be referring to its Org
syntax, which is then converted from Org table to R table, in contrast
to from Python result string to R string.
--
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>
^ permalink raw reply [flat|nested] 3+ messages in thread
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2021-12-01 8:04 Org babel Python and R, table not transformed when :var is called ? Sébastien Rey-Coyrehourcq
2021-12-02 11:10 ` Sébastien Rey-Coyrehourcq
2022-10-16 11:23 ` Ihor Radchenko
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