betters warning files

Author: ale94mleon

docs/source/CHANGELOG.md

@@ -7,12 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [unreleased]
 
-## [3.2.4] - 2020.12.20
+## [3.2.6] - 2020.12.20
 
 ### 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
 
 ## [3.2.2] - 2020.12.12
 

moldrug/_version.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 # We will use semantic version (major, minor, patch)
-__version_tuple__ = version_tuple = (3, 2, 4)
+__version_tuple__ = version_tuple = (3, 2, 5)
 __version__ = version = '.'.join([str(i) for i in __version_tuple__])

moldrug/constraintconf.py

@@ -126,6 +126,9 @@ def generate_conformers(mol: Chem.rdchem.Mol,
         mol with with generated conformers. In case some Exception ocurred, it returns mol without conformers and write in the
         current directory generate_conformers_error.log with the nature of the Exception.
     """
+    # Creating the error directory if needed
+    if not os.path.isdir('.error'):
+        os.makedirs('.error')
     # if SMILES to be fixed are not given, assume to the MCS
     if ref_smi:
         if not Chem.MolFromSmiles(ref_smi):
@@ -167,8 +170,8 @@ def generate_conformers(mol: Chem.rdchem.Mol,
     except Exception as e:
         print(e)
         cwd = os.getcwd()
-        warnings.warn(f"generate_conformers failed. Check the file {os.path.join(cwd, 'generate_conformers_error.pbz2')}")
-        compressed_pickle('generate_conformers_error', e)
+        warnings.warn(f"generate_conformers failed. Check the file {os.path.join(cwd, '.error/generate_conformers_error.pbz2')}")
+        compressed_pickle('.error/generate_conformers_error', e)
         mol.RemoveAllConformers()
         return mol
 

moldrug/fitness.py

@@ -236,6 +236,10 @@ def __vinadock(
     """
 
     constraint_type = constraint_type.lower()
+
+    # Creating the error directory if needed
+    if not os.path.isdir('.error'):
+        os.makedirs('.error')
     # Creating the working directory if needed
     if not os.path.exists(wd):
         os.makedirs(wd)
@@ -314,8 +318,8 @@ def __vinadock(
                         'boxcenter': boxcenter,
                         'boxsize': boxsize,
                     }
-                    utils.compressed_pickle(f'idx_{Individual.idx}_conf_{conf.GetId()}_error', error)
-                    warnings.warn(f"\nVina failed! Check: idx_{Individual.idx}_conf_{conf.GetId()}_error.pbz2 file.\n")
+                    utils.compressed_pickle(f'.error/idx_{Individual.idx}_conf_{conf.GetId()}_error', error)
+                    warnings.warn(f"\nVina failed! Check: idx_{Individual.idx}_conf_{conf.GetId()}_error.pbz2 file in error.\n")
                     vina_score_pdbqt = (np.inf, preparator.write_pdbqt_string())
                     return vina_score_pdbqt
 
@@ -361,8 +365,8 @@ def __vinadock(
                 'boxcenter': boxcenter,
                 'boxsize': boxsize,
             }
-            utils.compressed_pickle(f'{Individual.idx}_error', error)
-            warnings.warn(f"\nVina failed! Check: {Individual.idx}_error.pbz2 file.\n")
+            utils.compressed_pickle(f'.error/{Individual.idx}_error', error)
+            warnings.warn(f"\nVina failed! Check: {Individual.idx}_error.pbz2 file in error.\n")
 
             vina_score_pdbqt = (np.inf, 'VinaFailed')
             return vina_score_pdbqt

moldrug/utils.py

@@ -841,6 +841,19 @@ def __make_kwargs_copy__(costfunc, costfunc_kwargs,):
         kwargs_copy['wd'] = costfunc_jobs_tmp_dir.name
     return kwargs_copy, costfunc_jobs_tmp_dir
 
+def __tar_errors__(error_path:str = '.error'):
+    """Clena of errors the working directory
+
+    Parameters
+    ----------
+    error_path : str
+        Where the error are storged.
+    """
+    if os.path.isdir(error_path):
+        if os.listdir(error_path):
+            shutil.make_archive('error', 'gztar', error_path)
+        shutil.rmtree(error_path)
+
 
 class Local:
     """For local search
@@ -945,6 +958,8 @@ def __call__(self, njobs:int = 1, pick:int = None):
 
         # Clean directory
         costfunc_jobs_tmp_dir.cleanup()
+        # Tar errors
+        __tar_errors__('error')
 
         # Printing how long was the simulation
         print(f"Finished at {datetime.datetime.now().strftime('%c')}.\n")
@@ -1381,6 +1396,9 @@ def __call__(self, njobs:int = 1):
         print(f"The cost function dropped in {self.InitIndividual - self.pop[0]} units.")
         print(f"\n{50*'=+'}\n")
 
+        # Tar errors
+        __tar_errors__('error')
+
         # Printing how long was the simulation
         print(f"Total time ({self.maxiter} generations): {time.time() - ts:>5.2f} (s).\nFinished at {datetime.datetime.now().strftime('%c')}.\n")
 

tests/test_moldrug.py

@@ -93,7 +93,6 @@ def test_single_receptor_command_line():
 
     os.chdir(cwd)
 
-
 def test_multi_receptor(maxiter = 1, popsize = 2, njobs = 3, NumbCalls = 1):
     out = utils.GA(
         seed_mol=[Chem.MolFromSmiles(ligands.r_x0161), Chem.MolFromSmiles(ligands.r_x0161)],
@@ -144,8 +143,6 @@ def test_multi_receptor(maxiter = 1, popsize = 2, njobs = 3, NumbCalls = 1):
     vina_out.chunks[0].write()
     os.chdir(cwd)
 
-
-
 def test_local_command_line():
     Config = {
         "main": {
@@ -186,7 +183,6 @@ def test_local_command_line():
     print(result.to_dataframe())
     os.chdir(cwd)
 
-
 @pytest.mark.filterwarnings("ignore:\nVina failed")
 def test_fitness_module():
     individual = utils.Individual(Chem.MolFromSmiles(ligands.r_x0161))
@@ -251,13 +247,12 @@ def test_fitness_module():
         boxcenter = boxes.r_x0161['A']['boxcenter'], boxsize = boxes.r_x0161['A']['boxsize'],)
 
     # Clean
-    os.remove('0_error.pbz2')
-
+    utils.__tar_errors__()
+    os.remove('error.tar.gz')
 
 def test_home():
     home.home(dataDir='data')
 
-
 def test_get_sim_utils():
     from rdkit.Chem import AllChem
     mols = []
@@ -268,14 +263,12 @@ def test_get_sim_utils():
         ref_fps.append(AllChem.GetMorganFingerprintAsBitVect(mol, 2))
     utils.get_sim(mols, ref_fps)
 
-
 def test_lipinski():
     mol = Chem.MolFromSmiles('CCCO')
     utils.lipinski_filter(Chem.MolFromSmiles('BrCC(COCN)CC(Br)CC(Cl)CCc1ccccc1CCCC(NCCCO)'))
     utils.lipinski_filter(mol)
     utils.lipinski_profile(mol)
 
-
 def test_Individual():
     I1 = utils.Individual(Chem.MolFromSmiles('CC'), cost=10)
     I2 = utils.Individual(Chem.MolFromSmiles('CCO'), cost=2)
@@ -297,8 +290,6 @@ def test_Individual():
     assert divmod(I1, I2) == (5,0)
     assert I1**I2 == 100
 
-
-
 def test_miscellanea():
     obj0 = []
     for i in range(0,50):
@@ -339,6 +330,7 @@ def test_miscellanea():
 #     print(os.listdir(tmp_path.name))
 
 #     print(local.to_dataframe())
+
 def test_constraintconf():
     from moldrug.constraintconf import constraintconf
     with Chem.SDWriter(os.path.join(tmp_path.name, 'fix.sdf')) as w:
@@ -353,6 +345,9 @@ def test_constraintconf():
         fix= os.path.join(tmp_path.name, 'fix.sdf'),
         out = os.path.join(tmp_path.name, 'conf.sdf')
     )
+    # Clean
+    utils.__tar_errors__()
+
 def test_generate_conformers():
     from moldrug.constraintconf import generate_conformers
     from rdkit.Chem import AllChem
@@ -363,6 +358,9 @@ def test_generate_conformers():
     AllChem.MMFFOptimizeMolecule(ref)
     generate_conformers(Chem.RemoveHs(mol), Chem.RemoveHs(ref), 50)
 
+    # Clean
+    utils.__tar_errors__()
+
 
 if __name__ == '__main__':
     pass