delete redundant code in GAmol

ale94mleon · Dec 12, 2022 · a12c8b9 · a12c8b9
1 parent 692795e
commit a12c8b9
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Showing 4 changed files with 33 additions and 21 deletions.
diff --git a/Contrib/adme_models/test.ipynb b/Contrib/adme_models/test.ipynb
@@ -115,7 +115,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) \n[GCC 10.3.0]"
   },
   "orig_nbformat": 4,
   "vscode": {

diff --git a/docs/source/CHANGELOG.md b/docs/source/CHANGELOG.md
@@ -7,13 +7,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [unreleased]
 
-### Fix
+## [3.2.2] - 2020.12.12
+
+### Fixed
 
 - Bug: The initial individual was not printed properly.
 
+### Removed
+
+- Redundant code in `moldrug.utils.GA`
+
 ## [3.2.0] - 2022.11.28
 
-### Fix
+### Fixed
 
 - 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)
 
@@ -35,7 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - 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.
 
-### Fix
+### Fixed
 
 - Clean code.
 - Improve docs.
@@ -265,7 +271,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Minor code cleaning.
 - Better code covered during testing
 
-[unreleased]: https://github.com/ale94mleon/MolDrug/compare/3.2.0...HEAD
+[unreleased]: https://github.com/ale94mleon/MolDrug/compare/3.2.2...HEAD
+[3.2.2]: https://github.com/ale94mleon/MolDrug/compare/3.2.0...3.2.2
 [3.2.0]: https://github.com/ale94mleon/MolDrug/compare/3.1.0...3.2.0
 [3.1.0]: https://github.com/ale94mleon/MolDrug/compare/3.0.3...3.1.0
 [3.0.3]: https://github.com/ale94mleon/MolDrug/compare/3.0.1...3.0.3

diff --git a/moldrug/_version.py b/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, 1)
+__version_tuple__ = version_tuple = (3, 2, 2)
 __version__ = version = '.'.join([str(i) for i in __version_tuple__])
diff --git a/moldrug/utils.py b/moldrug/utils.py
@@ -997,7 +997,6 @@ def roulette_wheel_selection(p:List[float]):
     ind = np.argwhere(r <= c)
     return ind[0][0]
 
-
 def to_dataframe(individuals:List[Individual]):
     """Create a DataFrame from individuals.
 
@@ -1063,7 +1062,7 @@ def __init__(self, seed_mol:Union[Chem.rdchem.Mol, Iterable[Chem.rdchem.Mol]],
         ValueError
             In case of incorrect definition of mutate_crem_kwargs. It must be None or a dict instance.
         """
-        self.__moldrug_version = __version__
+        self.__moldrug_version__ = __version__
         if mutate_crem_kwargs is None:
             mutate_crem_kwargs = dict()
         elif not isinstance(mutate_crem_kwargs, dict):
@@ -1141,8 +1140,8 @@ def __call__(self, njobs:int = 1):
         self.NumCalls += 1
 
         # Check version of MolDrug
-        if self.__moldrug_version != __version__:
-            warn.warning(f"{self.__class__.__name__} was initialized with moldrug-{self.__moldrug_version} but was called with moldrug-{__version__}")
+        if self.__moldrug_version__ != __version__:
+            warn.warning(f"{self.__class__.__name__} was initialized with moldrug-{self.__moldrug_version__} but was called with moldrug-{__version__}")
 
         # Here we will update if needed some parameters for the crem operations that could change between different calls.
         # We need to return the molecule, so we override the possible user definition respect to this keyword
@@ -1202,10 +1201,7 @@ def __call__(self, njobs:int = 1):
             # Creating the arguments
             args_list = []
             # Make a copy of the self.costfunc_kwargs
-            kwargs_copy = self.costfunc_kwargs.copy()
-            if 'wd' in getfullargspec(self.costfunc).args:
-                costfunc_jobs = tempfile.TemporaryDirectory(prefix='costfunc')
-                kwargs_copy['wd'] = costfunc_jobs.name
+            kwargs_copy = self.__make_kwargs_copy__()
 
             for individual in self.pop:
                 args_list.append((individual, kwargs_copy))
@@ -1236,8 +1232,6 @@ def __call__(self, njobs:int = 1):
                 'generated':len(self.pop[:])
             }
 
-            if 'wd' in getfullargspec(self.costfunc).args: shutil.rmtree(costfunc_jobs.name)
-
             # Print some information of the initial population
             print(f"Initial Population: Best Individual: {min(self.pop)}")
             print(f"Accepted rate: {self.acceptance[self.NumGens]['accepted']} / {self.acceptance[self.NumGens]['generated']}\n")
@@ -1296,10 +1290,7 @@ def __call__(self, njobs:int = 1):
                 # Creating the arguments
                 args_list = []
                 # Make a copy of the self.costfunc_kwargs
-                kwargs_copy = self.costfunc_kwargs.copy()
-                if 'wd' in getfullargspec(self.costfunc).args:
-                    costfunc_jobs = tempfile.TemporaryDirectory(prefix='costfunc')
-                    kwargs_copy['wd'] = costfunc_jobs.name
+                kwargs_copy = self.__make_kwargs_copy__()
 
                 NumbOfSawIndividuals = len(self.SawIndividuals)
                 for (i, individual) in enumerate(popc):
@@ -1324,7 +1315,6 @@ def __call__(self, njobs:int = 1):
                             f"=========Parellel=========:\n {e1}\n"\
                             f"==========Serial==========:\n {e2}"
                             )
-                if 'wd' in getfullargspec(self.costfunc).args: shutil.rmtree(costfunc_jobs.name)
 
             # Merge, Sort and Select
             self.pop += popc
@@ -1421,6 +1411,21 @@ def mutate(self, individual:Individual):
             mol = Chem.AddHs(mol)
         return Individual(mol)
 
+    def __make_kwargs_copy__(self):
+        """Make a copy of the self.costfunc_kwargs.
+        It creates a temporal directory.
+
+        Returns
+        -------
+        dict
+            A copy of self.costfunc_kwargs with wd changed if needed
+        """
+        kwargs_copy = self.costfunc_kwargs.copy()
+        if 'wd' in getfullargspec(self.costfunc).args:
+            costfunc_jobs = tempfile.TemporaryDirectory(prefix='costfunc')
+            kwargs_copy['wd'] = costfunc_jobs.name
+        return kwargs_copy
+
     def pickle(self, title:str, compress = False):
         """Method to pickle the whole GA class