Merge pull request #229 from VlachosGroup/gui-dev

Complete GUI Overhaul

.github/workflows/run_tests.yml

@@ -10,7 +10,8 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
+    strategy:      
+      fail-fast: false
       matrix:
         python-version: ['3.7', '3.8', '3.9']
     name: Python ${{ matrix.python-version }} sample

aimsim/__init__.py

@@ -3,4 +3,4 @@
 from . import chemical_datastructures
 from . import utils
 
-__version__ = "1.0.3"
+__version__ = "1.1.0"

aimsim/chemical_datastructures/molecule_set.py

@@ -84,6 +84,7 @@ class MoleculeSet:
                 Spectral Embedding ('spectral_embedding')
 
     """
+
     def __init__(
         self,
         molecule_database_src,
@@ -396,6 +397,10 @@ def worker(thread_idx, n_mols, start_idx, end_idx, queue):  # pragma: no cover
                                 except NotInitializedError as e:
                                     e.message += "Similarity matrix could not be set "
                                     raise e
+                                except ValueError as e:
+                                    raise RuntimeError(
+                                        f'Unable to proccess molecule {molecule.mol_text}'
+                                    ) from e
                 queue.put(local_similarity_matrix)
                 return None
 
@@ -448,12 +453,17 @@ def worker(thread_idx, n_mols, start_idx, end_idx, queue):  # pragma: no cover
                             "Computing similarity of molecule num "
                             f"{target_mol_id + 1} against {source_mol_id + 1}"
                         )
-                    similarity_matrix[
-                        source_mol_id, target_mol_id
-                    ] = molecule.get_similarity_to(
-                        self.molecule_database[target_mol_id],
-                        similarity_measure=self.similarity_measure,
-                    )
+                    try:
+                        similarity_matrix[
+                            source_mol_id, target_mol_id
+                        ] = molecule.get_similarity_to(
+                            self.molecule_database[target_mol_id],
+                            similarity_measure=self.similarity_measure,
+                        )
+                    except ValueError as e:
+                        raise RuntimeError(
+                            f'Unable to proccess molecule {molecule.mol_text}'
+                        ) from e
 
         self.similarity_matrix = similarity_matrix
 

aimsim/ops/similarity_measures.py

@@ -254,7 +254,9 @@ def __call__(self, mol1_descriptor, mol2_descriptor):
             similarity_ (float): Similarity value
         """
         if not self._validate_fprint(mol1_descriptor) or not self._validate_fprint(mol2_descriptor):
-            raise ValueError('Molecule descriptor has no active bits')
+            raise ValueError(
+                f'Molecule descriptor ({mol1_descriptor.label_}) has no active bits.'
+            )
         similarity_ = None
         if self.metric == "l0_similarity":
             try:

aimsim/tasks/measure_search.py

@@ -168,7 +168,7 @@ def __call__(self,
                         n_threads=molecule_set_configs.get(
                             'n_threads', 1),
                         sampling_ratio=subsample_subset_size)
-                except (InvalidConfigurationError, ValueError) as e:
+                except (InvalidConfigurationError, ValueError, RuntimeError) as e:
                     if is_verbose:
                         print(f'Could not try {fingerprint_type} with '
                               f'similarity measure {similarity_measure} due to '