Merge pull request #112 from MolecularAI/release-3.7.0

Release 3.7.0

.github/workflows/tests.yml

@@ -2,28 +2,28 @@ name: tests
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Run
-      run: |
-        wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh |
-            bash -s -- --batch
-        conda env create -f env-dev.yml
-        conda run --name aizynth-dev poetry install -E all
-        conda run --name aizynth-dev inv full-tests
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        files: ./coverage.xml
-        directory: ./coverage/
-        name: codecov-aizynth
-        fail_ci_if_error: false
-        verbose: true
+      - uses: actions/checkout@v3
+      - name: Run
+        run: |
+          wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh |
+              bash -s -- --batch
+          conda env create -f env-dev.yml
+          conda run --name aizynth-dev poetry install -E all -E tf
+          conda run --name aizynth-dev inv full-tests
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          directory: ./coverage/
+          name: codecov-aizynth
+          fail_ci_if_error: false
+          verbose: true

.gitignore

@@ -143,3 +143,4 @@ coverage/
 # Files created by the tool
 smiles.txt
 config_local.yml
+devtools/seldon-output-*/

aizynthfinder/aizynthfinder.py

@@ -1,38 +1,40 @@
 """ Module containing a class that is the main interface the retrosynthesis tool.
 """
 from __future__ import annotations
+
 import time
 from collections import defaultdict
 from typing import TYPE_CHECKING
 
 from tqdm import tqdm
 
-# This must be imported first to setup logging for rdkit, tensorflow etc
-from aizynthfinder.utils.logging import logger
-from aizynthfinder.utils.loading import load_dynamic_class
-from aizynthfinder.context.config import Configuration
-from aizynthfinder.search.mcts import MctsSearchTree
-from aizynthfinder.reactiontree import ReactionTreeFromExpansion
 from aizynthfinder.analysis import (
-    TreeAnalysis,
     RouteCollection,
     RouteSelectionArguments,
+    TreeAnalysis,
 )
-from aizynthfinder.chem import Molecule, TreeMolecule, FixedRetroReaction
+from aizynthfinder.chem import FixedRetroReaction, Molecule, TreeMolecule
+from aizynthfinder.context.config import Configuration
+from aizynthfinder.reactiontree import ReactionTreeFromExpansion
 from aizynthfinder.search.andor_trees import AndOrSearchTreeBase
+from aizynthfinder.search.mcts import MctsSearchTree
 from aizynthfinder.utils.exceptions import MoleculeException
+from aizynthfinder.utils.loading import load_dynamic_class
+
+# This must be imported first to setup logging for rdkit, tensorflow etc
+from aizynthfinder.utils.logging import logger
 
 if TYPE_CHECKING:
+    from aizynthfinder.chem import RetroReaction
     from aizynthfinder.utils.type_utils import (
-        StrDict,
-        Optional,
-        Union,
         Callable,
+        Dict,
         List,
+        Optional,
+        StrDict,
         Tuple,
-        Dict,
+        Union,
     )
-    from aizynthfinder.chem import RetroReaction
 
 
 class AiZynthFinder:
@@ -230,17 +232,15 @@ def tree_search(self, show_progress: bool = False) -> float:
         self.search_stats["time"] = time_past
         return time_past
 
-    def _setup_search_tree(self):
+    def _setup_search_tree(self) -> None:
         self._logger.debug("Defining tree root: %s" % self.target_smiles)
         if self.config.search_algorithm.lower() == "mcts":
             self.tree = MctsSearchTree(
                 root_smiles=self.target_smiles, config=self.config
             )
         else:
             cls = load_dynamic_class(self.config.search_algorithm)
-            self.tree: AndOrSearchTreeBase = cls(
-                root_smiles=self.target_smiles, config=self.config
-            )
+            self.tree = cls(root_smiles=self.target_smiles, config=self.config)
 
 
 class AiZynthExpander:

aizynthfinder/analysis/__init__.py

@@ -1,5 +1,5 @@
 """ Sub-package containing analysis routines
 """
-from aizynthfinder.analysis.tree_analysis import TreeAnalysis
+from aizynthfinder.analysis.tree_analysis import TreeAnalysis  # isort: skip
 from aizynthfinder.analysis.routes import RouteCollection
 from aizynthfinder.analysis.utils import RouteSelectionArguments

aizynthfinder/analysis/routes.py

@@ -1,6 +1,7 @@
 """ Module containing classes to store and manipulate collections of synthetic routes.
 """
 from __future__ import annotations
+
 from typing import TYPE_CHECKING
 
 import numpy as np
@@ -11,24 +12,21 @@
 except ImportError:
     pass
 
-from aizynthfinder.analysis.utils import (
-    CombinedReactionTrees,
-    RouteSelectionArguments,
-)
-from aizynthfinder.reactiontree import SUPPORT_DISTANCES, ReactionTree
-from aizynthfinder.search.mcts import MctsSearchTree, MctsNode
 from aizynthfinder.analysis import TreeAnalysis
+from aizynthfinder.analysis.utils import CombinedReactionTrees, RouteSelectionArguments
+from aizynthfinder.reactiontree import SUPPORT_DISTANCES, ReactionTree
+from aizynthfinder.search.mcts import MctsNode, MctsSearchTree
 
 if TYPE_CHECKING:
+    from aizynthfinder.context.scoring import Scorer
     from aizynthfinder.utils.type_utils import (
-        StrDict,
-        PilImage,
-        Optional,
         Any,
         Dict,
+        Optional,
+        PilImage,
         Sequence,
+        StrDict,
     )
-    from aizynthfinder.context.scoring import Scorer
 
 
 class RouteCollection:

aizynthfinder/analysis/tree_analysis.py

@@ -1,33 +1,29 @@
 """ Module containing classes to perform analysis of the tree search results.
 """
 from __future__ import annotations
+
 from collections import defaultdict
 from typing import TYPE_CHECKING
 
-from aizynthfinder.chem import (
-    FixedRetroReaction,
-    hash_reactions,
-)
-from aizynthfinder.context.scoring import (
-    StateScorer,
-)
 from aizynthfinder.analysis.utils import RouteSelectionArguments
+from aizynthfinder.chem import FixedRetroReaction, hash_reactions
+from aizynthfinder.context.scoring import StateScorer
 from aizynthfinder.reactiontree import ReactionTree
-from aizynthfinder.search.mcts import MctsSearchTree, MctsNode
 from aizynthfinder.search.andor_trees import AndOrSearchTreeBase
+from aizynthfinder.search.mcts import MctsNode, MctsSearchTree
 
 if TYPE_CHECKING:
+    from aizynthfinder.chem import RetroReaction
+    from aizynthfinder.context.scoring import Scorer
     from aizynthfinder.utils.type_utils import (
-        StrDict,
-        Union,
-        Tuple,
         Any,
         Iterable,
-        Sequence,
         List,
+        Sequence,
+        StrDict,
+        Tuple,
+        Union,
     )
-    from aizynthfinder.context.scoring import Scorer
-    from aizynthfinder.chem import RetroReaction
 
 
 class TreeAnalysis:

aizynthfinder/analysis/utils.py

@@ -3,27 +3,19 @@
 To avoid clutter in that package, larger utility algorithms are placed herein.
 """
 from __future__ import annotations
-from dataclasses import dataclass
+
 from collections import defaultdict
+from dataclasses import dataclass
 from typing import TYPE_CHECKING
 
 import networkx as nx
 
-from aizynthfinder.chem import (
-    Molecule,
-    UniqueMolecule,
-    FixedRetroReaction,
-)
-from aizynthfinder.utils.image import make_visjs_page
+from aizynthfinder.chem import FixedRetroReaction, Molecule, UniqueMolecule
 from aizynthfinder.reactiontree import ReactionTree
+from aizynthfinder.utils.image import make_visjs_page
 
 if TYPE_CHECKING:
-    from aizynthfinder.utils.type_utils import (
-        Sequence,
-        Tuple,
-        StrDict,
-        FrameColors,
-    )
+    from aizynthfinder.utils.type_utils import FrameColors, Sequence, StrDict, Tuple
 
 
 @dataclass

aizynthfinder/chem/__init__.py

@@ -2,22 +2,22 @@
 """
 from aizynthfinder.chem.mol import (
     Molecule,
+    MoleculeException,
     TreeMolecule,
     UniqueMolecule,
-    MoleculeException,
     none_molecule,
 )
 from aizynthfinder.chem.reaction import (
+    FixedRetroReaction,
     Reaction,
     RetroReaction,
-    TemplatedRetroReaction,
     SmilesBasedRetroReaction,
-    FixedRetroReaction,
+    TemplatedRetroReaction,
     hash_reactions,
 )
 from aizynthfinder.chem.serialization import (
-    MoleculeSerializer,
     MoleculeDeserializer,
-    serialize_action,
+    MoleculeSerializer,
     deserialize_action,
+    serialize_action,
 )

aizynthfinder/chem/mol.py

@@ -1,6 +1,7 @@
 """ Module containing classes to deal with Molecules - mostly wrappers around rdkit routines.
 """
 from __future__ import annotations
+
 from typing import TYPE_CHECKING
 
 import numpy as np
@@ -9,17 +10,16 @@
 
 from aizynthfinder.utils.exceptions import MoleculeException
 
-
 if TYPE_CHECKING:
     from aizynthfinder.utils.type_utils import (
+        Callable,
         Dict,
+        List,
         Optional,
-        Union,
-        Tuple,
         RdMol,
         Sequence,
-        List,
-        Callable,
+        Tuple,
+        Union,
     )
 
 

aizynthfinder/chem/reaction.py

@@ -1,35 +1,36 @@
 """ Module containing classes to deal with Reactions.
 """
 from __future__ import annotations
-import hashlib
+
 import abc
+import hashlib
 from functools import partial
 from typing import TYPE_CHECKING
 
 import numpy as np
-from rdkit import Chem
-from rdkit.Chem import AllChem
-from rdkit.Chem.rdchem import ChiralType, BondDir, BondStereo
 from rdchiral import main as rdc
 from rdchiral.bonds import get_atoms_across_double_bonds
 from rdchiral.initialization import BondDirOpposite
+from rdkit import Chem
+from rdkit.Chem import AllChem
+from rdkit.Chem.rdchem import BondDir, BondStereo, ChiralType
 
+from aizynthfinder.chem.mol import Molecule, MoleculeException, TreeMolecule
 from aizynthfinder.utils.logging import logger
-from aizynthfinder.chem.mol import MoleculeException, Molecule, TreeMolecule
 
 if TYPE_CHECKING:
+    from aizynthfinder.chem.mol import UniqueMolecule
     from aizynthfinder.utils.type_utils import (
-        Optional,
-        Union,
-        Tuple,
+        Any,
+        Iterable,
         List,
+        Optional,
         RdReaction,
-        StrDict,
-        Iterable,
-        Any,
         Set,
+        StrDict,
+        Tuple,
+        Union,
     )
-    from aizynthfinder.chem.mol import UniqueMolecule
 
 
 class _ReactionInterfaceMixin:

aizynthfinder/chem/serialization.py

@@ -1,14 +1,15 @@
 """ Module containing helper classes and routines for serialization.
 """
 from __future__ import annotations
+
 from typing import TYPE_CHECKING
 
 import aizynthfinder.chem
 from aizynthfinder.utils.loading import load_dynamic_class
 
 if TYPE_CHECKING:
-    from aizynthfinder.utils.type_utils import Optional, Sequence, Dict, Any, StrDict
     from aizynthfinder.chem import RetroReaction
+    from aizynthfinder.utils.type_utils import Any, Dict, Optional, Sequence, StrDict
 
 
 class MoleculeSerializer: