CDO

I understood my mistake ...
(thanks cdo.debug = True)
Do not forget this "s" to options= ...

hi Romain!
yeah, unfortunately there is no warning for unknown keywords. Maybe I should implement this.

On Cdo{rbpy} you can find some examples for python usage.

hth
ralf

Romain:

May I ask how you were even able to get cdo working in Python? Are you using a specific IDE or was there a website that helped? I have been trying for days and I have not yet found a good source for even getting it started. I do have it installed as version 1.5.3.

Any help would be appreciated.

Thanks,

KL

Hi Kyle,
I'm using PyCharm CE and my "bible" is [[https://code.mpimet.mpg.de/projects/cdo/embedded/index.html]].
I have installed cdo with

pip install cdo netcdf4 xarray

Your file.py must be contains

from cdo import *
# OR
# from cdo import Cdo

cdo = Cdo()
#cdo.debug = True """ can be useful to help for solve errors """ 

# Commands
cdo.operator('parameters',
             options=XXX, """ if need """ 
             input=infile,
             output=outfile)

I don't know much more for now

Thank you for your assistance. I use spyder and unfortunately that pip install cdo netcdf4 xarray did not solve my issue. For some reason I get this error:

signal.siginterrupt(signal.SIGINT, False)
AttributeError: module 'signal' has no attribute 'siginterrupt'

Thanks for your help though. I'll figure it out one day!

@Kyle: Which version of python do you use?

signal.siginterrup() was introduced in python 2.6 and is still there in 3.8

Romain LE LAMER wrote:

Hi Kyle,
I'm using PyCharm CE and my "bible" is [[https://code.mpimet.mpg.de/projects/cdo/embedded/index.html]].

Amen!! ;-)

@Ralf Thehos: I am running Python 3.7.6.

I am on macOS and a friend also has the same problem (with my script) as you Kyle, and he is on Windows ...
My question is therefore are you under Windows also ?

Me:
macOS v10.15.6
python v3.8.5
cdo v1.9.8

$ cdo --version
Climate Data Operators version 1.9.8 (https://mpimet.mpg.de/cdo)
System: x86_64-apple-darwin19.4.0
CXX Compiler: clang++ -std=gnu++11 -g -O2  -D_THREAD_SAFE -pthread
CXX version : Apple clang version 11.0.3 (clang-1103.0.32.59)
C Compiler: clang -g -O2  -D_THREAD_SAFE -pthread -D_THREAD_SAFE -D_THREAD_SAFE -pthread
C version : Apple clang version 11.0.3 (clang-1103.0.32.59)
F77 Compiler: gfortran -g -O2
F77 version : GNU Fortran (Homebrew GCC 9.3.0_1) 9.3.0
Features: 8GB 4threads C++11 Fortran DATA PTHREADS HDF5 NC4/HDF5 OPeNDAP SZ SSE4_2
Libraries: HDF5/1.12.0
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5 
     CDI library version : 1.9.8
 cgribex library version : 1.9.4
 ecCodes library version : 2.18.0
  NetCDF library version : 4.7.4 of Jul  2 2020 22:40:24 $
    hdf5 library version : 1.12.0
    exse library version : 1.4.1
    FILE library version : 1.8.3

A friend :
Windows 10
python v3.8.5

cdo --version not possible

Oop's it is not good ...
You must have at least these packages

pip list
Package         Version
--------------- ---------
cdo             1.5.3
cftime          1.2.1
netCDF4         1.5.4
numpy           1.19.1
pandas          1.1.0
pip             20.1.1
python-dateutil 2.8.1
pytz            2020.1
six             1.15.0
wheel           0.34.2
xarray          0.16.0

I come back to the error encountered by Kyle and a friend (who uses my script)
As I indicated above it is under Windows 10, at Python v3.8.5 and via pip it installed cdo netcdf4 and xarray

C:\BIN\Python\python.exe D:/Temp/main.py
Traceback (most recent call last):
  File "D:/Temp/main.py", line 112, in <module>
    cdo = Cdo()
  File "C:\BIN\Python\lib\site-packages\cdo.py", line 170, in _init_
    signal.siginterrupt(signal.SIGINT, False)
AttributeError: module 'signal' has no attribute 'siginterrupt'
Process finished with exit code 1

My conclusion (after testing) is that it is necessary to have the cdo binary installed locally.
• For UNIX systems, it must be compiled or installed via the system's package manager (me on macOS I used Homebrew (brew install cdo))
• For Windows systems, it is necessary to do this via Cygwin.

I think a cdo developer will confirm this conclusion.

@Romain:

Yes I am also using windows. I've tried to get CDO to work with Spyder, Pycharm, and cygwin now but to no avail. I did update all my packages to be exactly the same way that you did Romain, but for some reason I still get the error even in Pycharm

Traceback (most recent call last):
File "C:\Users\kylel\Anaconda3\envs\cdo\lib\site-packages\IPython\core\interactiveshell.py", line 3417, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-3-237a1757623c>", line 1, in <module>
cdo = Cdo()
File "C:\Users\kylel\Anaconda3\envs\cdo\lib\site-packages\cdo.py", line 170, in init
signal.siginterrupt(signal.SIGINT, False)
AttributeError: module 'signal' has no attribute 'siginterrupt'.

I tried to install Ubuntu through the VM Virtual Machine, but unfortunately computers really dislike me and there are errors in the download :(.

Hi Kyle
Use this tutorial to install correctly cygwin + cdo
=> [[https://opencpn.org/wiki/dokuwiki/doku.php?id=opencpn:supplementary_software:cdo:windows_8.1#:~:text='cdo.exe'%20is%20extracted,running%20the%20batch%20file%20'Cygwin.]]

hi!

There is not CDO binary for the native Windows system. Hence you cannot use python/anaconda/pip to call CDO through cdo.py, because there is no CDO on plain Windows.
For Windows there are two option

• cygwin (Thx for the link, Roman)
• the Windows Subsystem for Linux and install cdo with

  sudo apt-get install cdo

The windows version of python doesn't seem to have this part of the signal module - sorry for missing the fact, that you work under windows directly.

Hi Ralf & Kyle
I did not know Windows Subsystem for Linux (WSL) at all but I find it to be THE solution to adopt.
It is extremely easy to implement (compared to Cygwin)
Thanks for that

hi Roman!

yes, it's a lot easier IMO. the only disadvantage is, that you won't get the latest release out-of-the-box. But for most applications this will not be needed.
The other question is, whether Microsoft is willing to support this on the long run. Many years ago there was a Unix Subsystem, but totally outdated and a Microsoft employer told me, he would use cygwin instead.

Maybe this has changed now - debian/ubuntu is well maintained, Microsoft updates the ubuntu version.

In case of problems using WSL please let me know. I am curious how a real world setup works in there.

cheers
ralf

I think you have to do it in a simple way, that is to say you should not try to make Windows and Linux communicate, you have to run everything from Linux.
If Windows gives the possibility of running a Linux so easily it is a bit of the death of Windows (and it's not me that will bother )

Thank you all for your input. After many hours, I have finally been able to run CDO through the Ubuntu Desktop app!

Here were my steps for anyone else in the future who tries to install it:

After first opening and creating your username:
sudo apt-get update and sudo apt-get upgrade

Install CDO
sudo apt-get install cdo

Try cdo - v if you get this error:
cdo: error while loading shared libraries: libQt5Core.so.5: cannot open shared object file: No such file or directory

Then:
sudo strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5

Then you have to move your file you want to edit into the actual Desktop folder. Then cdo operators will work.

I maybe shouldn't have posted this here considering the title of the post is Python syntax for cdo commands, but this may be much quicker for others if they have a hard time figuring it out.

hi Kyle!

no worries - it's good that we have it here! thx for the info

best wishes
ralf