uibcdf / bifree Goto Github PK

Should we base the project on the MOLSSI cookie-cutter.

We should spend a while reading about how to set the names or numbers of the versions.

@cramg, Let's open this task for you to learn how projects work on GitHub.

Please, please define the views "Priority", "Status", "Bugs" and "Next release" as we have in the project MolSysMT

Let's start working with forks, branches, and pull requests. This is what we will do from now on:

1- Make your own fork of this repository. Do not push changes straight to the uibcdf/OpenENM if not necessary. Do not work with this repo, work with your fork.
2- Clone your forked repository in your machine.
3- Any change, modification, implementation... do it in a new branch (different from main) in your fork.
4- Create and work with as many branches as you need. Once the implementation developed in your branch XXX has been finished, make a PR (Pull Request) from XXX (of your fork) to the branch main of the uibcdf repository.
5- PRs will be reviewed always by one of the main developers different from the author (at this point I review your PRs, and you mine).
6- Once a PR has been reviewed, accepted, and merged, you have to fetch the new changes from the main branch of uibcdf repo to your main branch (fork repo). Keep always your main branch of your fork updated with the main branch of this repository.

I am sure that you will have many doubts about this process. This is the place to ask. Courage! 💪🏻

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We should check the differences between using setuptools and numpy.distutils to configure the setup.py file. Which one should we use?

Although Poisson-Boltzmann is not our priority, we have to start thinking how this implementation should be. Let's use this issue to collect some ideas.

There is a widely used tool to solve the Poisson-Boltzmann equation of continuum electrostatics, its the APBS (Adaptive Poisson-Boltzmann Solver). Many tools depend on this APBS implementation (maybe amber does it as well). Although there is a registration process to use it, it is embedded in some other packages (how? who knows...). We should look for python libraries using this tool.

Here the paper of the last version.

APBS repo in GitHub
APBS documentation

PDB2PQR repo in GitHub # required to work with APBS
PDB2PQR documentation