Split up requirements for rxn and graph

feaurisations/kernels.

.github/ISSUE_TEMPLATES/bug_report.md

@@ -28,7 +28,7 @@ If applicable, add screenshots to help explain your problem.
 
 - OS: [e.g. iOS]
 - Python Version
-- Graphein Version [e.g. 22] & how it was installed
+- Gauche Version [e.g. 1.0.0] & how it was installed
 
 **Additional context**
 Add any other context about the problem here.

.requirements/base.in

@@ -4,7 +4,6 @@ scikit-learn
 rdkit
 tqdm
 selfies
-graphein
 torch
 gpytorch
 botorch

.requirements/graphs.in

@@ -0,0 +1 @@
+graphein

.requirements/rxn.in

@@ -0,0 +1,2 @@
+rxnfp
+drfp

gauche/dataloader/molprop_loader.py

@@ -47,10 +47,7 @@ def validate(
         """
 
         invalid_mols = np.array(
-            [
-                True if MolFromSmiles(x) is None else False
-                for x in self.features
-            ]
+            [True if MolFromSmiles(x) is None else False for x in self.features]
         )
         if np.any(invalid_mols):
             print(
@@ -88,9 +85,7 @@ def validate(
                 for smiles in self.features
             ]
 
-    def featurize(
-        self, representation: Union[str, Callable], **kwargs
-    ) -> None:
+    def featurize(self, representation: Union[str, Callable], **kwargs) -> None:
         """Transforms SMILES into the specified molecular representation.
 
         :param representation: the desired molecular representation, one of [ecfp_fingerprints, fragments, ecfp_fragprints, molecular_graphs, bag_of_smiles, bag_of_selfies, mqn] or a callable that takes a list of SMILES strings as input and returns the desired featurization.
@@ -151,9 +146,7 @@ def featurize(
         elif representation == "bag_of_selfies":
             from gauche.representations.strings import bag_of_characters
 
-            self.features = bag_of_characters(
-                self.features, selfies=True, **kwargs
-            )
+            self.features = bag_of_characters(self.features, selfies=True, **kwargs)
 
         elif representation == "bag_of_smiles":
             from gauche.representations.strings import bag_of_characters

pyproject.toml

@@ -26,7 +26,7 @@ force_grid_wrap = 0
 include_trailing_comma = true
 line_length = 79 # match our custom config above
 multi_line_output = 3
-src_paths = ["graphein", "test"]
+src_paths = ["gauche", "test"]
 float_to_top = true
 use_parentheses = true
 

setup.py

@@ -11,6 +11,7 @@
 
 HERE = os.path.abspath(os.path.dirname(__file__))
 
+
 def read(*parts):
     # intentionally *not* adding an encoding option to open
     return codecs.open(os.path.join(HERE, *parts), "r").read()
@@ -54,25 +55,23 @@ def read_requirements(*parts) -> List[str]:
 
 INSTALL_REQUIRES: List[str] = read_requirements(".requirements/base.in")
 EXTRA_REQUIRES: Dict[str, List[str]] = {
+    "rxn": read_requirements(".requirements/rxn.in"),
+    "graphs": read_requirements(".requirements/graphs.in"),
     "dev": read_requirements(".requirements/dev.in"),
     "docs": read_requirements(".requirements/docs.in"),
-    "cpu": read_requirements(".requirements/cpu.in"),
-    "cu116": read_requirements(".requirements/cu116.in"),
-    "cu117": read_requirements(".requirements/cu117.in"),
 }
+
 # Add all requires
 all_requires: List[str] = []
 for k, v in EXTRA_REQUIRES.items():
-    if k not in ["cu116", "cu117"]:
+    if k not in ["dev", "docs"]:
         all_requires.extend(v)
 EXTRA_REQUIRES["all"] = list(set(all_requires))
 
 
 def find_version(*file_paths):
     version_file = read(*file_paths)
-    version_match = re.search(
-        r"^__version__ = ['\"]([^'\"]*)['\"]", version_file, re.M
-    )
+    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", version_file, re.M)
     if version_match:
         return version_match.group(1)
     raise RuntimeError("Unable to find version string.")
@@ -86,7 +85,7 @@ def find_version(*file_paths):
 setup(
     name="gauche",
     version=version,
-    description="Gaussian Process Library for Molecules, Proteins and General Chemistry in PyTorch.",
+    description="Gaussian Process Library for Molecules, Chemical Reactions and Proteins.",
     long_description=readme,
     long_description_content_type="text/markdown",
     license="MIT",

tests/test_dataloaders/test_molprop_loader.py

@@ -52,7 +52,9 @@ def test_benchmark_loader(dataset, representation, kwargs):
     """
 
     dataset_root = os.path.abspath(
-        os.path.join("..", "..", "data", "property_prediction")
+        os.path.join(
+            os.path.abspath(__file__), "..", "..", "..", "data", "property_prediction"
+        )
     )
 
     # load through benchmark loading method
@@ -89,7 +91,7 @@ def test_invalid_data():
 
     dataloader = MolPropLoader()
     dataloader.read_csv(
-        path=os.path.join(os.getcwd(), "invalid_molprop_data.csv"),
+        path=os.path.join(os.path.abspath(__file__), "invalid_molprop_data.csv"),
         smiles_column="SMILES",
         label_column="labels",
     )

tests/test_dataloaders/test_reaction_loader.py

@@ -82,7 +82,7 @@ def test_invalid_data():
 
     dataloader = ReactionLoader()
     dataloader.read_csv(
-        path=os.path.join(os.getcwd(), "invalid_reaction_data.csv"),
+        path=os.path.join(os.path.abspath(__file__), "invalid_reaction_data.csv"),
         reactant_column=["ligand", "additive", "base", "aryl halide"],
         label_column="yield",
     )