Moldrug

Fixed

- Refactored changes for for meeko-0.5.0.
- Update docs.

Added

- A new environmental variable `MOLDRUG_VERBOSE` can be set to ask for more debug information.

Changed

- From `csf` to `toml` package configuration.
- Structure of the repo. Now `src/moldrug`.
- Improve [MolDrug-Dashboard](https://moldrug-dashboard.streamlit.app/).

Removed

- Support for conda package. Some dependencies had not ben installed properly. Fix in the future.

Added

- Continuation option to the command line.
- `moldrug.cli.CommandLineHelper` class to work with the parameters passed through the command line.
- `checkpoint` option to `moldrug.utils.GA`.
- [MolDrug-Dashboard](https://ale94mleon-moldrug-streamlitstreamlit-app-nltunu.streamlit.app) add-on. This is not included on the package itself, but could be used online or locally. In the case of locally you must check [Streamlit](https://streamlit.io/), the [requirements.txt](https://github.com/ale94mleon/MolDrug/blob/main/streamlit/requirements.txt) and the [app script](https://github.com/ale94mleon/MolDrug/blob/main/streamlit/streamlit_app.py).
- `retunr_mol` option to `utils.to_dataframe`

Changed

- The warnings are not printed for: `moldrug.fitness._vinadock` and `moldrug.constraintconf.generate_conformers`. Now, only at the end of a MolDrug simulation a note will be printed if the `error.tar.gz` file is created.
- `moldrug.utils.run` does not print extra info if the command fails. It only raises the corresponded `RuntimeError`.
- `moldrug.fitness.__vinadock` by `moldrug.fitness._vinadock`.
- Remove conformers that clash with the protein in case of score_only, for local_only vina will handle the clash.

Fixed

- Small bug during initialization of population with multiple `seed_mol`. Now `seed_mol` with the same amount of elements as `popsize` are not submitted to mutations, only evaluation.
- Problems with default parameters definition on the command line. Parameters with default values by the `type` of run defined in the configuration file are not needed to redefined any more; `moldrug.cli` will guess those.

Changed

- `moldrug.utils.__tar_errors__` by `moldrug.utils.tar_errors`.
- Default value of `moldrug.utils.tar_errors` is `error` instead of `.error`.
- `moldrug.constraintconf.generate_conformers` outputs warnings and errors to `error` instead of `.error`.
- `moldrug.fitness.__vinadock` by `moldrug.fitness._vinadock`.
- `moldrug.fitness._vinadock` outputs warnings and errors to `error` instead of `.error`.

Fixed

- The use of `moldrug.utils.tar_errors` inside of `moldrug.utils.Local` and `moldrug.utils.GA`.
- Clean code.

Fixed

- Improve docs.
- Cleaning of temporal files in /tmp directory. Now it is created temporal directories in the working directory with the pattern: `.costfunc_MolDrug_XXXXXXXX`.
- Cleaning errors. Now all warnings and errors are saved in .error directory and at the end they are compress to error.tar.gz

Fixed

- Bug: The initial individual was not printed properly.

Removed

- Redundant code in `moldrug.utils.GA`

Fix

- Bug: The output error name when constraint fails has a idx prefix. E.g. `33_conf_27_error.pbz2` now is: `idx_33_conf_27_error.pbz2`. Now it is easy to delete all of this files at the end of the simulation if they are not needed. (on the last version the naming was not changing)

Removed

- `moldrug.fitness.is_inside_box`
- Bug: `constraint_check_inside_box` option for the cost functions of `moldrug.fitness`