error in import abilib about abipy

[gmatteo]

In the new version of pymatgen, SlotPickleMixin has been removed thus breaking backward compatibility.
A patch addressing the problem has been merged in #253 and will be made available in v0.9.3

For the time being, one has to install an older version of pymargen with e.g.:

pip install pymatgen==2022.9.8

See also this pymatgen issue

[rajeshatiitm]

I have successfully installed the abipy using "pip install abipy --user".
Using ipython I can test the installation is ok like "from abipy import abilab"

However, I can not execute abiopen.py in Ubuntu terminal! it says command not found.

Could you please help me to find out what I am doing wrong?

Thanks!

[gmatteo]

Could you please help me to find out what I am doing wrong?

You are using conda to manage your python installation so you need to activate the conda environment where abipy has been installed with e.g.:

conda activate my_pymatgen

in order to have the python scripts in $PATH.

PS: The --user option is not needed when conda envs are used.
To install python packages in a conda env, activate the env then use

conda install abipy -c conda-forge

or

pip install abipy

[rajeshatiitm]

I did the following:
-->conda install pymatgen==2022.9.8
-->conda create --name my_pymatgen python
-->conda activate my_pymatgen
-->conda create --name abienv python=3.10
-->conda activate abienv
-->conda config --add channels conda-forge
-->conda install abipy -c conda-forge

then I tested as before in ipython "from abipy import abilab" and it works. I can even see that abipy is installed where it says

"The following NEW packages will be installed
abipy conda-forge/noarch::abipy-0.9.2-pyhd8ed1ab_0 None"

then I executed in terminal $ abipy and it says "abipy: command not found

Any help please!

[gmatteo]

then I executed in terminal $ abipy and it says "abipy: command not found

Abipy is the name of the python package so it's normal that you cannot invoke it directly from the shell.
There are several scripts that can be used to post-process the data directly from the shell: abistruct.py, abiopen.py, etc.

For the full list of scripts installed by abipy see this page

[rajeshatiitm]

Hi Gmatteo,

I can work with abilab in jupyter notbook, it works nicely, but I can not execute in terminal. I get the following error
$ abiopen.py --help
Traceback (most recent call last):
File "/home/rdutta/anaconda3/bin/abiopen.py", line 4, in
import('pkg_resources').run_script('abipy==0.9.2', 'abiopen.py')
File "/home/rdutta/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 662, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/rdutta/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1447, in run_script
raise ResolutionError(
pkg_resources.ResolutionError: Script 'scripts/abiopen.py' not found in metadata at '/home/rdutta/.local/lib/python3.9/site-packages/abipy-0.9.2.dist-info'

[rajeshatiitm]

However, I can manually copy that abiopen.py into the working directory (where I am working on example), then it works with command ./abiopen.py.

I don't know why does it not work just as $abiopen.py ?