From 76bd0f7c2be3c243f298f4452fd6660bf1e42af1 Mon Sep 17 00:00:00 2001
From: Oleksii Leonov <mail@oleksiileonov.com>
Date: Thu, 23 Mar 2023 16:20:47 +0000
Subject: [PATCH 1/2] chore: apply isort to all files in project

---
 setup.py                                   |  1 +
 tests/cgu/test_convert.py                  | 14 ++++++-----
 tests/cgu/test_discgraph.py                |  5 ++--
 tests/cgu/test_iron.py                     |  2 +-
 tests/cgu/test_syngraph.py                 | 13 +++++++----
 tests/cgu/test_translate.py                | 23 ++++++++++--------
 tests/cheminfo/test_atom_mapping.py        | 15 ++++++++----
 tests/cheminfo/test_chemical_similarity.py |  9 ++++----
 tests/cheminfo/test_constructors.py        | 25 ++++++++++++--------
 tests/cheminfo/test_functions.py           | 27 ++++++++++++++++------
 tests/conftest.py                          |  1 +
 tests/interfaces/test_cli.py               |  2 +-
 tests/interfaces/test_facade.py            | 13 ++++++-----
 tests/interfaces/test_workflows.py         |  7 +++---
 tests/io/test_io_functions.py              |  1 +
 tests/rem/test_clustering.py               |  8 +++++--
 tests/rem/test_graph_distance.py           | 22 +++++++++++-------
 tests/rem/test_node_metrics.py             |  5 ++--
 tests/rem/test_route_descriptors.py        | 16 +++++++++----
 tests/rem/test_route_scoring.py            |  7 +++---
 20 files changed, 139 insertions(+), 77 deletions(-)

diff --git a/setup.py b/setup.py
index 8bf1ba9..6068493 100644
--- a/setup.py
+++ b/setup.py
@@ -1,2 +1,3 @@
 from setuptools import setup
+
 setup()
diff --git a/tests/cgu/test_convert.py b/tests/cgu/test_convert.py
index 7691d64..deedd08 100644
--- a/tests/cgu/test_convert.py
+++ b/tests/cgu/test_convert.py
@@ -1,11 +1,13 @@
-from linchemin.cgu.convert import converter
-from linchemin.cgu.translate import translator
-from linchemin.cgu.syngraph import (SynGraph, BipartiteSynGraph, MonopartiteReacSynGraph)
-
-import pytest
 import json
-from pathlib import Path
 import os
+from pathlib import Path
+
+import pytest
+
+from linchemin.cgu.convert import converter
+from linchemin.cgu.syngraph import (BipartiteSynGraph, MonopartiteReacSynGraph,
+                                    SynGraph)
+from linchemin.cgu.translate import translator
 
 
 def test_strategy_structure(ibm1_path):
diff --git a/tests/cgu/test_discgraph.py b/tests/cgu/test_discgraph.py
index 99fee61..2cfe6e1 100644
--- a/tests/cgu/test_discgraph.py
+++ b/tests/cgu/test_discgraph.py
@@ -1,7 +1,8 @@
+import pytest
+
 from linchemin.cgu.discgraph import DisconnectionGraph, MissingAtomMapping
-from linchemin.cheminfo.constructors import ChemicalEquationConstructor
 from linchemin.cgu.syngraph import MonopartiteReacSynGraph
-import pytest
+from linchemin.cheminfo.constructors import ChemicalEquationConstructor
 
 mapped_reactions = {'r1': 'CN(C)C=O.F[c:5]1[n:6][cH:7][cH:8][cH:9][c:10]1[F:11].O=C([O-])[O-].[CH3:1][CH:2]([CH3:3])['
                           'SH:4].[K+].[K+]>>[CH3:1][CH:2]([CH3:3])[S:4][c:5]1[n:6][cH:7][cH:8][cH:9][c:10]1[F:11]'}
diff --git a/tests/cgu/test_iron.py b/tests/cgu/test_iron.py
index 0648f83..70f80cf 100644
--- a/tests/cgu/test_iron.py
+++ b/tests/cgu/test_iron.py
@@ -1,4 +1,4 @@
-from linchemin.cgu.iron import Node, Edge, Direction, Iron
+from linchemin.cgu.iron import Direction, Edge, Iron, Node
 
 
 def test_direction():
diff --git a/tests/cgu/test_syngraph.py b/tests/cgu/test_syngraph.py
index c6939aa..ab716dc 100644
--- a/tests/cgu/test_syngraph.py
+++ b/tests/cgu/test_syngraph.py
@@ -1,10 +1,15 @@
-from linchemin.cgu.syngraph import (BipartiteSynGraph, MonopartiteReacSynGraph, MonopartiteMolSynGraph, merge_syngraph,
-                                    extract_reactions_from_syngraph)
-from linchemin.cgu.translate import translator
-from linchemin.cheminfo.constructors import ChemicalEquationConstructor, MoleculeConstructor
 import json
+
 import pytest
 
+from linchemin.cgu.syngraph import (BipartiteSynGraph, MonopartiteMolSynGraph,
+                                    MonopartiteReacSynGraph,
+                                    extract_reactions_from_syngraph,
+                                    merge_syngraph)
+from linchemin.cgu.translate import translator
+from linchemin.cheminfo.constructors import (ChemicalEquationConstructor,
+                                             MoleculeConstructor)
+
 
 def test_bipartite_syngraph_instance(az_path):
     """ To test that a BipartiteSynGraph instance is correctly generated. """
diff --git a/tests/cgu/test_translate.py b/tests/cgu/test_translate.py
index 349e0a7..3e32374 100644
--- a/tests/cgu/test_translate.py
+++ b/tests/cgu/test_translate.py
@@ -1,15 +1,20 @@
-from linchemin.cgu.iron import Iron, Node, Edge, Direction
-from linchemin.cgu.translate import (translator, ibm_dict_to_iron, get_available_formats, az_dict_to_iron,
-                                     get_available_data_models, get_output_formats, get_input_formats, TranslationError)
-from linchemin.cgu.syngraph import BipartiteSynGraph, MonopartiteReacSynGraph
-from linchemin.cheminfo.models import ChemicalEquation
 import json
-import pydot
-import networkx as nx
-import pytest
+import logging
 import os
 import unittest.mock
-import logging
+
+import networkx as nx
+import pydot
+import pytest
+
+from linchemin.cgu.iron import Direction, Edge, Iron, Node
+from linchemin.cgu.syngraph import BipartiteSynGraph, MonopartiteReacSynGraph
+from linchemin.cgu.translate import (TranslationError, az_dict_to_iron,
+                                     get_available_data_models,
+                                     get_available_formats, get_input_formats,
+                                     get_output_formats, ibm_dict_to_iron,
+                                     translator)
+from linchemin.cheminfo.models import ChemicalEquation
 
 
 def generate_iron_test_graph():
diff --git a/tests/cheminfo/test_atom_mapping.py b/tests/cheminfo/test_atom_mapping.py
index 8027b85..f25164b 100644
--- a/tests/cheminfo/test_atom_mapping.py
+++ b/tests/cheminfo/test_atom_mapping.py
@@ -1,11 +1,16 @@
-from linchemin.cheminfo.atom_mapping import pipeline_atom_mapping, perform_atom_mapping, get_available_mappers
-from linchemin.cgu.syngraph import extract_reactions_from_syngraph, MonopartiteReacSynGraph, merge_syngraph
-from linchemin.cgu.translate import translator
-
-import pytest
 import json
 import unittest.mock
 
+import pytest
+
+from linchemin.cgu.syngraph import (MonopartiteReacSynGraph,
+                                    extract_reactions_from_syngraph,
+                                    merge_syngraph)
+from linchemin.cgu.translate import translator
+from linchemin.cheminfo.atom_mapping import (get_available_mappers,
+                                             perform_atom_mapping,
+                                             pipeline_atom_mapping)
+
 
 def test_basic_factory(capfd):
     with pytest.raises(KeyError) as ke:
diff --git a/tests/cheminfo/test_chemical_similarity.py b/tests/cheminfo/test_chemical_similarity.py
index 904d9c8..b34f58b 100644
--- a/tests/cheminfo/test_chemical_similarity.py
+++ b/tests/cheminfo/test_chemical_similarity.py
@@ -1,8 +1,9 @@
-import linchemin.cheminfo.functions as cif
-from linchemin.cheminfo.chemical_similarity import (compute_reaction_fingerprint, compute_similarity,
-                                                    compute_mol_fingerprint)
 import pytest
-from rdkit.Chem import rdChemReactions, DataStructs
+from rdkit.Chem import DataStructs, rdChemReactions
+
+import linchemin.cheminfo.functions as cif
+from linchemin.cheminfo.chemical_similarity import (
+    compute_mol_fingerprint, compute_reaction_fingerprint, compute_similarity)
 
 
 def test_rdkit_reaction_fingerprints_basics_non_mapped_molecules():
diff --git a/tests/cheminfo/test_constructors.py b/tests/cheminfo/test_constructors.py
index 34bf3ce..63d693c 100644
--- a/tests/cheminfo/test_constructors.py
+++ b/tests/cheminfo/test_constructors.py
@@ -1,15 +1,22 @@
+import unittest
 from itertools import combinations
-from linchemin.cheminfo.constructors import (MoleculeConstructor, ChemicalEquationConstructor, RatamConstructor,
-                                             BadMapping, PatternConstructor, TemplateConstructor,
-                                             DisconnectionConstructor, calculate_molecular_hash_values,
-                                             UnavailableMolIdentifier)
-from linchemin.cheminfo.models import Template
-from linchemin.utilities import create_hash
+
+import pytest
+
+import linchemin.cheminfo.depiction as cid
 import linchemin.cheminfo.functions as cif
+from linchemin.cheminfo.constructors import (BadMapping,
+                                             ChemicalEquationConstructor,
+                                             DisconnectionConstructor,
+                                             MoleculeConstructor,
+                                             PatternConstructor,
+                                             RatamConstructor,
+                                             TemplateConstructor,
+                                             UnavailableMolIdentifier,
+                                             calculate_molecular_hash_values)
+from linchemin.cheminfo.models import Template
 from linchemin.IO import io as lio
-import linchemin.cheminfo.depiction as cid
-import unittest
-import pytest
+from linchemin.utilities import create_hash
 
 
 # Molecule tests
diff --git a/tests/cheminfo/test_functions.py b/tests/cheminfo/test_functions.py
index 8c25d40..c41bbdc 100644
--- a/tests/cheminfo/test_functions.py
+++ b/tests/cheminfo/test_functions.py
@@ -1,15 +1,28 @@
+import unittest
+
 import pytest
 from rdkit import Chem
 from rdkit.Chem import DataStructs, rdChemReactions
-import unittest
 
-from linchemin.cheminfo.constructors import ChemicalEquationConstructor, MoleculeConstructor
+from linchemin.cheminfo.constructors import (ChemicalEquationConstructor,
+                                             MoleculeConstructor)
+from linchemin.cheminfo.functions import (bstr_to_rdmol,
+                                          canonicalize_mapped_rdmol,
+                                          canonicalize_rdmol,
+                                          canonicalize_rdmol_lite,
+                                          compute_oxidation_numbers,
+                                          get_canonical_order,
+                                          has_mapped_products,
+                                          is_mapped_molecule,
+                                          mapping_diagnosis,
+                                          rdchiral_extract_template)
 from linchemin.cheminfo.functions import rdkit as rdkit
-from linchemin.cheminfo.functions import canonicalize_rdmol, get_canonical_order, rdmol_from_string, \
-    rdrxn_to_string, rdrxn_from_string, rdmol_to_bstr, bstr_to_rdmol, \
-    rdrxn_from_string, is_mapped_molecule, has_mapped_products, canonicalize_rdmol_lite,\
-    compute_oxidation_numbers, rdrxn_role_reassignment, rdrxn_to_rxn_mol_catalog, \
-    remove_rdmol_atom_mapping, rdchiral_extract_template, canonicalize_mapped_rdmol, mapping_diagnosis
+from linchemin.cheminfo.functions import (rdmol_from_string, rdmol_to_bstr,
+                                          rdrxn_from_string,
+                                          rdrxn_role_reassignment,
+                                          rdrxn_to_rxn_mol_catalog,
+                                          rdrxn_to_string,
+                                          remove_rdmol_atom_mapping)
 
 
 def test_build_rdrxn_from_smiles():
diff --git a/tests/conftest.py b/tests/conftest.py
index 6dd467e..4f354c3 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,4 +1,5 @@
 from pathlib import Path
+
 import pytest
 
 
diff --git a/tests/interfaces/test_cli.py b/tests/interfaces/test_cli.py
index c94591a..e411f92 100644
--- a/tests/interfaces/test_cli.py
+++ b/tests/interfaces/test_cli.py
@@ -1,5 +1,5 @@
-import unittest.mock
 import os
+import unittest.mock
 
 
 def test_cli_basic(capfd, cli):
diff --git a/tests/interfaces/test_facade.py b/tests/interfaces/test_facade.py
index 634f300..cfa4a99 100644
--- a/tests/interfaces/test_facade.py
+++ b/tests/interfaces/test_facade.py
@@ -1,11 +1,12 @@
-from linchemin.interfaces.facade import facade, facade_helper
-from linchemin.cgu.syngraph import MonopartiteReacSynGraph, BipartiteSynGraph
-from rdkit.Chem import rdChemReactions
+import json
+import unittest
+import unittest.mock
+
 import pandas as pd
+from rdkit.Chem import rdChemReactions
 
-import unittest.mock
-import unittest
-import json
+from linchemin.cgu.syngraph import BipartiteSynGraph, MonopartiteReacSynGraph
+from linchemin.interfaces.facade import facade, facade_helper
 
 
 def test_translate(ibm2_path):
diff --git a/tests/interfaces/test_workflows.py b/tests/interfaces/test_workflows.py
index 13b2da5..f028ae5 100644
--- a/tests/interfaces/test_workflows.py
+++ b/tests/interfaces/test_workflows.py
@@ -1,8 +1,9 @@
-from linchemin.interfaces.workflows import process_routes, get_workflow_options
-from linchemin.interfaces.facade import facade
+import unittest.mock
 
 import pytest
-import unittest.mock
+
+from linchemin.interfaces.facade import facade
+from linchemin.interfaces.workflows import get_workflow_options, process_routes
 
 
 @unittest.mock.patch('linchemin.IO.io.write_json')
diff --git a/tests/io/test_io_functions.py b/tests/io/test_io_functions.py
index 7b8efc7..e94ca6e 100644
--- a/tests/io/test_io_functions.py
+++ b/tests/io/test_io_functions.py
@@ -1,4 +1,5 @@
 import pytest
+
 from linchemin.IO import io as lio
 
 
diff --git a/tests/rem/test_clustering.py b/tests/rem/test_clustering.py
index ad6a60b..3069bbc 100644
--- a/tests/rem/test_clustering.py
+++ b/tests/rem/test_clustering.py
@@ -1,8 +1,12 @@
-from linchemin.rem.clustering import (clusterer, get_available_clustering, get_clustered_routes_metrics, ClusteringError)
-from linchemin.cgu.translate import translator
 import json
+
 import pytest
 
+from linchemin.cgu.translate import translator
+from linchemin.rem.clustering import (ClusteringError, clusterer,
+                                      get_available_clustering,
+                                      get_clustered_routes_metrics)
+
 
 def test_clusterer(az_path):
     graph = json.loads(open(az_path).read())
diff --git a/tests/rem/test_graph_distance.py b/tests/rem/test_graph_distance.py
index 596471c..ff7ef87 100644
--- a/tests/rem/test_graph_distance.py
+++ b/tests/rem/test_graph_distance.py
@@ -1,16 +1,22 @@
-from linchemin.rem.graph_distance import (graph_distance_factory, compute_nodes_fingerprints, build_similarity_matrix,
-                                          get_available_ged_algorithms, get_ged_default_parameters,
-                                          compute_distance_matrix, get_ged_parameters, GraphDistanceError)
-from linchemin.cgu.translate import translator
-from linchemin.cgu.convert import converter
-
 import json
-import pytest
+
 import networkx as nx
-import pandas as pd
 import numpy as np
+import pandas as pd
+import pytest
 from rdkit.Chem import rdChemReactions
 
+from linchemin.cgu.convert import converter
+from linchemin.cgu.translate import translator
+from linchemin.rem.graph_distance import (GraphDistanceError,
+                                          build_similarity_matrix,
+                                          compute_distance_matrix,
+                                          compute_nodes_fingerprints,
+                                          get_available_ged_algorithms,
+                                          get_ged_default_parameters,
+                                          get_ged_parameters,
+                                          graph_distance_factory)
+
 
 def test_similarity_factory(az_path):
     # Test similarity with oneself with monopartite syngraphs and factory workflow
diff --git a/tests/rem/test_node_metrics.py b/tests/rem/test_node_metrics.py
index a689551..90ee51b 100644
--- a/tests/rem/test_node_metrics.py
+++ b/tests/rem/test_node_metrics.py
@@ -1,7 +1,8 @@
-from linchemin.rem.node_metrics import node_score_calculator, reaction_mapping
-from linchemin.cheminfo.constructors import ChemicalEquationConstructor
 import pytest
 
+from linchemin.cheminfo.constructors import ChemicalEquationConstructor
+from linchemin.rem.node_metrics import node_score_calculator, reaction_mapping
+
 
 def test_factory():
     smile1 = 'CC(O)=O.CN>>CNC(C)=O'
diff --git a/tests/rem/test_route_descriptors.py b/tests/rem/test_route_descriptors.py
index b750190..0c2eb32 100644
--- a/tests/rem/test_route_descriptors.py
+++ b/tests/rem/test_route_descriptors.py
@@ -1,11 +1,17 @@
-from linchemin.cgu.convert import converter
-from linchemin.rem.route_descriptors import (find_path, descriptor_calculator, is_subset, find_duplicates,
-                                             get_nodes_consensus, get_available_descriptors, DescriptorError)
-from linchemin.cgu.syngraph import SynGraph, merge_syngraph, MonopartiteReacSynGraph
 import json
-from linchemin.cgu.translate import translator
+
 import pytest
 
+from linchemin.cgu.convert import converter
+from linchemin.cgu.syngraph import (MonopartiteReacSynGraph, SynGraph,
+                                    merge_syngraph)
+from linchemin.cgu.translate import translator
+from linchemin.rem.route_descriptors import (DescriptorError,
+                                             descriptor_calculator,
+                                             find_duplicates, find_path,
+                                             get_available_descriptors,
+                                             get_nodes_consensus, is_subset)
+
 
 def test_unavailable_metrics(ibm1_path):
     """ To test that a KeyError is raised if an unavailable metrics is requested. """
diff --git a/tests/rem/test_route_scoring.py b/tests/rem/test_route_scoring.py
index c53c266..7fb46c1 100644
--- a/tests/rem/test_route_scoring.py
+++ b/tests/rem/test_route_scoring.py
@@ -1,8 +1,9 @@
-from linchemin.rem.route_scoring import route_scorer
-from linchemin.cgu.translate import translator
+import json
 
 import pytest
-import json
+
+from linchemin.cgu.translate import translator
+from linchemin.rem.route_scoring import route_scorer
 
 
 def test_scoring_factory(ibm1_path):

From 1d742a5455365a0fd4297bf44a45b0ed703849c4 Mon Sep 17 00:00:00 2001
From: Oleksii Leonov <mail@oleksiileonov.com>
Date: Thu, 23 Mar 2023 16:21:25 +0000
Subject: [PATCH 2/2] ci: turn on isort pre-commit check for all files

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 05c9758..9636da6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -23,7 +23,7 @@ repos:
     rev: 5.12.0
     hooks:
       - id: isort
-        files: '^src/.*\.pyi?$'
+        files: '.*\.pyi?$'
   - repo: https://github.com/asottile/pyupgrade
     rev: v3.3.1
     hooks: