bharurn / mimicpy

Python based tools for preparing MiMiC QM/MM simulations
GNU General Public License v3.0
1 stars 0 forks source link

prepqm input incombatible with pandas >2.0.0 #40

Open FloSeu opened 1 month ago

FloSeu commented 1 month ago

With pandas >2.0, the DataFrame.append() function, that was previously deprecated, was removed. Therefore, in the preqpm utility, the following error is produced when selecting atoms:


                    ***** MiMiCPy *****                  

                    Running version 0.2.1
    For more information type mimicpy [subcommand] --help 

=====> Running prepqm <=====

**Reading topology**

**Reading coordinates**  \Done

Please enter selection below. For more information type 'help'
> add (resname is LEU) and (resid is 364) and (name is C)
Traceback (most recent call last):
  File "/home/hildilab/anaconda3/envs/mimic/bin/mimicpy", line 8, in <module>
    sys.exit(main())
  File "/home/hildilab/anaconda3/envs/mimic/lib/python3.9/site-packages/mimicpy/__main__.py", line 761, in main
    args.func(args)
  File "/home/hildilab/anaconda3/envs/mimic/lib/python3.9/site-packages/mimicpy/__main__.py", line 225, in prepqm
    if check_user_input(user_input) == False:
  File "/home/hildilab/anaconda3/envs/mimic/lib/python3.9/site-packages/mimicpy/__main__.py", line 157, in check_user_input
    dispatch[command](selection)
  File "/home/hildilab/anaconda3/envs/mimic/lib/python3.9/site-packages/mimicpy/core/prepare.py", line 56, in add
    self.__qm_atoms = self.__qm_atoms.append(qdf)
  File "/home/hildilab/anaconda3/envs/mimic/lib/python3.9/site-packages/pandas/core/generic.py", line 6296, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'append'
bharurn commented 1 month ago

Thank for your interest in MiMiCPy and MiMiC. This repo has moved to https://gitlab.com/mimic-project/mimicpy. However, the issue you stated is still valid in the new repo. If you have a GitLab account, please repost the issue there: https://gitlab.com/mimic-project/mimicpy/-/issues/