caefleury / pibiti-simulacoes Goto Github PK

Current test layout have a read function that gets data from a test data file. Reorganize the tests so that the read tests reads from a already working write test. Then add these data files to .gitignore.

• Reorganize test layout
• Run tests and verify changes
• Add test data files do .gitignore

• Ajustar o script para criar uma deleção 3x1 no centro da folha 5x5
  • Criar condições para os 3 átomos
  • Ajustar o número de átomos no arquivo .zyx após a deleção de uma molécula
• Ajustar o script para criar uma deleção 3x1 no centro da folha 15x15
• Dividr função de replicação
  • Criar uma função de rasgo que ja entenda os 3 tipos de moleculas alteradas
• Criar deleções para casos gerais
• Criar deleção maiores e de diferentes tipos

Currently, this codebase is not functional for general use as it relies on manually inputted, poorly documented specific data. To convert it into a package, it needs to be modularized and exportable, with all current manual entries handled as parameters.

• Research PyPI packages and their usage
• Reorganize the folder structure
• Translate all code to English
• Create a clear distinction between this package repository and the documentation repository
  • Update README.md

Currently the strain configuration files cannot be updated after they are created using the replication script. If the simulation runs and later we need to correct the strain.in files to create a simulation with the same parameters and different environments we would have to create a new simulation that would change the parameters (velocities). First create the test and update it upon every new functionality

• create a test for update_strain_configuration_file function
• create update_strain_configuration_file function on my_utils

• review guide for local PYTHONPATH definition
• update guide on virtual environment PYTHONPATH definition
• study the possiblity of using dockerfile ports to fix environment paths
• test for vscode, pycharm and idx