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Update logging and fix #22 
1 parent bc2ec8d commit c767693

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‎docs/source/CHANGELOG.md‎

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@@ -10,12 +10,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Removed
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- 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.
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- Environmental variable `MOLDRUG_VERBOSE`
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### Changed
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- CLI has subspaces: `run` and `constraintconf`. The syntax `moldrug config.yml` changed to `moldrug run config.yml` and `constraintconf_moldrug ...` to `moldrug constraintconf ...`.
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- `GA` and `Local` now lies on the `opt` module. they can also be imported directly. E.g. `from moldrug import GA`.
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- Use logging instead of print.
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- 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.
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- The logging level at CLI is defined by the `verbose` (`V`) flag.
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- Move from `.rst` to `.md` on the documentation.
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- Update installation instructions.
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- Versioning: `Major.Minor.Patch` --> `Major.Minnor.Patch.postX` it helps to distinguish commits that are not yet included on the `Patch`.

‎docs/source/notebooks/advance-topics.ipynb‎

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‎docs/source/notebooks/constraint-docking.ipynb‎

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‎docs/source/notebooks/how-to.ipynb‎

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},
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{
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"outputs": [
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{
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"text": [
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"usage: moldrug run [-h] [-f [FITNESS]] [-c] [-V [VERBOSE]] yaml_file\n",
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"usage: moldrug run [-h] [-f [FITNESS]] [-c] [-V] yaml_file\n",
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"\n",
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"🚀 Main moldrug runner\n",
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"\n",
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" located in the working directory. This option is only\n",
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" compatible with moldrug.opt.GA; otherwise, a\n",
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" RuntimeError will be raised.\n",
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" -V [VERBOSE], --verbose [VERBOSE]\n"
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" -V, --verbose Increase verbosity (-V for INFO, -VV for DEBUG)\n"
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]
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}
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" 'deffnm']"
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"['crem.db.gz', 'config.yml', 'crem.db']"
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"2025-09-28 10:03:27,045 - moldrug - INFO - Started at Sun Sep 28 10:03:27 2025\n",
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"2025-09-28 10:03:27,045 - moldrug - INFO - You are using moldrug: 3.7.3.post34.dev0\n",
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"2025-09-28 19:30:09,521 - INFO - moldrug.cli - Started at Sun Sep 28 19:30:09 2025\n",
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"2025-09-28 19:30:09,521 - INFO - moldrug.cli - You are using moldrug: 3.7.3.post35.dev0\n",
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"\n",
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"2025-09-28 10:03:27,045 - moldrug - INFO - MoldrugRunHelper(yaml_file=config.yml, fitness=None, continuation=False, verbose=False)\n",
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"2025-09-28 19:30:09,521 - INFO - moldrug.cli - MoldrugRunHelper(yaml_file=config.yml, fitness=None, continuation=False, verbose=2)\n",
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"2025-09-28 10:03:29,471 - moldrug - INFO - Calculating cost function...\n",
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"100%|█████████████████████████████████████████████| 2/2 [00:06<00:00, 3.00s/it]\n",
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"2025-09-28 10:03:35,493 - moldrug - INFO - Finished at Sun Sep 28 10:03:35 2025.\n",
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"2025-09-28 19:30:11,871 - INFO - moldrug.opt - Calculating cost function...\n",
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"100%|█████████████████████████████████████████████| 2/2 [00:05<00:00, 2.69s/it]\n",
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"2025-09-28 19:30:17,272 - INFO - moldrug.opt - Finished at Sun Sep 28 19:30:17 2025.\n",
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"\n",
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"2025-09-28 10:03:35,502 - moldrug - INFO - File local_pop.sdf was createad!\n"
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"2025-09-28 19:30:17,282 - INFO - moldrug.utils - File local_pop.sdf was createad!\n"
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"! moldrug run config.yml -VV"
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"2025-09-28 10:03:37,081 - moldrug - INFO - Started at Sun Sep 28 10:03:37 2025\n",
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"2025-09-28 10:03:37,081 - moldrug - INFO - You are using moldrug: 3.7.3.post34.dev0\n",
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"2025-09-28 19:30:18,738 - INFO - moldrug.cli - Started at Sun Sep 28 19:30:18 2025\n",
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"2025-09-28 19:30:18,738 - INFO - moldrug.cli - You are using moldrug: 3.7.3.post35.dev0\n",
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"2025-09-28 10:03:37,081 - moldrug - INFO - MoldrugRunHelper(yaml_file=config_custom_fitness.yml, fitness=MyCustomFitness.py, continuation=False, verbose=False)\n",
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"2025-09-28 19:30:18,738 - INFO - moldrug.cli - MoldrugRunHelper(yaml_file=config_custom_fitness.yml, fitness=MyCustomFitness.py, continuation=False, verbose=2)\n",
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"2025-09-28 19:30:21,216 - INFO - moldrug.opt - Calculating cost function...\n",
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"2025-09-28 19:30:26,202 - INFO - moldrug.opt - Finished at Sun Sep 28 19:30:26 2025.\n",
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"2025-09-28 19:30:26,207 - INFO - moldrug.utils - File local_pop.sdf was createad!\n"
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"2025-09-28 10:03:48,921 - moldrug - INFO - Creating the first population with 20 members:\n",
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"2025-09-28 10:03:52,640 - moldrug - INFO - Acceptance rate: 20 / 20\n",
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"2025-09-28 10:05:46,607 - moldrug - INFO - The simulation finished successfully after 2 generations witha population of 20 individuals. A total number of 60 Individuals were seen during the simulation.\n",
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"2025-09-28 10:05:46,607 - moldrug - INFO - Initial Individual: Individual(idx = 0, smiles = CCCC(=O)OCCN, cost = 0.19688061076437202)\n",
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"2025-09-28 10:05:46,607 - moldrug - INFO - The cost function dropped in 0.18324133911690954 units.\n",
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"2025-09-28 10:05:46,607 - moldrug - INFO - Total time (2 generations): 120.52 (s).\n",
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