Split utils module (#21)

* Remove leftover dependency

* Split util module and refactoring changes

* Update docs

* Update CLI

* Update citation name

* Update logging and fix  #22

Author: ale94mleon

docs/index.rst

@@ -4,7 +4,7 @@
    contain the root `toctree` directive.
 
 Welcome to moldrug (AKA mouse)'s documentation!
-===================================
+===============================================
 .. include:: ../README.rst
 
 Index

docs/source/CHANGELOG.md

@@ -10,10 +10,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Removed
 
 - Python 3.8 compatibility. The dependency `meeko @ git+https://github.com/ale94mleon/meeko.git@main` requires a higher Python version because building it requires `setuptools>=77.0.0`, which is not compatible with Python 3.8.
+- Environmental variable `MOLDRUG_VERBOSE`
 
 ### Changed
 
+- CLI has subspaces: `run` and `constraintconf`. The syntax `moldrug config.yml` changed to `moldrug run config.yml` and `constraintconf_moldrug ...` to `moldrug constraintconf ...`.
+- `GA` and `Local` now lies on the `opt` module. they can also be imported directly. E.g. `from moldrug import GA`.
 - Use logging instead of print.
+- Now the user needs to define the desired level for the logging as well the format: `logging.basicConfig(level=logging.INFO, format='%(asctime)s: %(name)s: %(levelname)s: %(message)s')` is recommended.
+- The logging level at CLI is defined by the `verbose` (`V`) flag.
 - Move from `.rst` to `.md` on the documentation.
 - Update installation instructions.
 - Versioning: `Major.Minor.Patch` --> `Major.Minnor.Patch.postX` it helps to distinguish commits that are not yet included on the `Patch`.

docs/source/citations.md

@@ -11,7 +11,7 @@ If you use moldrug in your research, please cite the following paper:
   doi = {10.1186/s13321-025-01022-3},
   number = {85},
   journal = {Journal of Cheminformatics},
-  author = {Martínez León, Alejandro and Ries, Benjamin and Hub, Jochen S. and Magarkar, Aniket},
+  author = {Mart\'{i}nez Le\'{o}n, Alejandro and Ries, Benjamin and Hub, Jochen S. and Magarkar, Aniket},
   month = may,
   year = {2025},
 }

docs/source/modules/opt.rst

@@ -0,0 +1,6 @@
+Opt
+===========
+
+.. automodule:: moldrug.opt
+    :members:
+    :special-members: __init__, __call__

docs/source/moldrug-dahsboard.md

@@ -7,7 +7,6 @@
 [![ProLIF](https://img.shields.io/static/v1?label=Powered%20by&message=ProLIF&color=E933FF&style=flat)](https://prolif.readthedocs.io/en/latest/)
 [![py3Dmol](https://img.shields.io/static/v1?label=Powered%20by&message=py3Dmol&color=2BC3C5&style=flat)](https://pypi.org/project/py3Dmol/)
 [![stmol](https://img.shields.io/static/v1?label=Powered%20by&message=stmol&color=D0E42B&style=flat)](https://pypi.org/project/stmol/)
-[![mdanalysis](https://img.shields.io/badge/Powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)
 [![meeko](https://img.shields.io/static/v1?label=Powered%20by&message=Meeko&color=56AD60&style=flat)](https://github.com/forlilab/Meeko)
 [![numpy](https://img.shields.io/static/v1?label=Powered%20by&message=NumPy&color=49E1ED&style=flat)](https://numpy.org/)
 [![pandas](https://img.shields.io/static/v1?label=Powered%20by&message=Pandas&color=B2D7DA&style=flat)](https://pandas.pydata.org/)
@@ -35,8 +34,8 @@ Of course, you can always download [moldrug-dashboard.py](https://github.com/ale
 
 ## Inputs
 
-- `pbz2` file. Exported when the command line is used. This file can be generated by calling the function {py:func}`moldrug.utils.compressed_pickle`. The classes {py:class}`moldrug.utils.Local` and {py:class}`moldrug.utils.GA` have already this method implemented (`pickle`).
-- `pdb` file. The protein PDB if you would like to check the Protein-Ligand interaction network. In this case the `pdbqt` attribute of the {py:class}`moldrug.utils.Individual` shoud have been updated to the docking pose. This is done automatically by the classes {py:class}`moldrug.utils.GA` and {py:class}`moldrug.utils.Local`
+- `pbz2` file. Exported when the command line is used. This file can be generated by calling the function {py:func}`moldrug.utils.compressed_pickle`. The classes {py:class}`moldrug.opt.Local` and {py:class}`moldrug.opt.GA` have already this method implemented (`pickle`).
+- `pdb` file. The protein PDB if you would like to check the Protein-Ligand interaction network. In this case the `pdbqt` attribute of the {py:class}`moldrug.utils.Individual` shoud have been updated to the docking pose. This is done automatically by the classes {py:class}`moldrug.opt.GA` and {py:class}`moldrug.opt.Local`
 
 ## Upload pbz2