remove typing_extension dependency (#378)

* remove typing_extension dependency

* formatting changes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.requirements/base.in

@@ -19,7 +19,6 @@ pyyaml!=6.0.0,!=5.4.0,!=5.4.1
 scikit-learn
 scipy>=1.8
 tqdm
-typing_extensions==4.5.0
 wget
 xarray
 jaxtyping

CHANGELOG.md

@@ -3,6 +3,7 @@
 ### Bugfixes
 
 * Fix bug where the `deprotonate` argument is not wired up to `graphein.protein.graphs.construct_graphs`. [#375](https://github.com/a-r-j/graphein/pull/375)
+* Remove `typing_extension` as dependency since we now only support Python >=3.8 and `Literal` is included in `typing` there.
 
 ### 1.7.6
 

graphein/molecule/config.py

@@ -13,7 +13,6 @@
 
 from deepdiff import DeepDiff
 from pydantic import BaseModel
-from typing_extensions import Literal
 
 from graphein.molecule.edges.atomic import add_atom_bonds
 from graphein.molecule.edges.distance import (
@@ -24,6 +23,12 @@
 from graphein.molecule.features.nodes.atom_type import atom_type_one_hot
 from graphein.utils.config import PartialMatchOperator, PathMatchOperator
 
+try:
+    from typing import Literal
+except ImportError:
+    from typing_extensions import Literal
+
+
 GraphAtoms = Literal[
     "C",
     "H",

graphein/protein/config.py

@@ -14,12 +14,16 @@
 
 from deepdiff import DeepDiff
 from pydantic import BaseModel, validator
-from typing_extensions import Literal
 
 from graphein.protein.edges.distance import add_peptide_bonds
 from graphein.protein.features.nodes.amino_acid import meiler_embedding
 from graphein.utils.config import PartialMatchOperator, PathMatchOperator
 
+try:
+    from typing import Literal
+except ImportError:
+    from typing_extensions import Literal
+
 
 class DSSPConfig(BaseModel):
     executable: str = "mkdssp"

graphein/protein/graphs.py

@@ -23,7 +23,6 @@
 from loguru import logger as log
 from rich.progress import Progress
 from tqdm.contrib.concurrent import process_map
-from typing_extensions import Literal
 
 from graphein.protein.config import GetContactsConfig, ProteinGraphConfig
 from graphein.protein.edges.distance import (
@@ -47,6 +46,11 @@
     compute_edges,
 )
 
+try:
+    from typing import Literal
+except ImportError:
+    from typing_extensions import Literal
+
 
 def subset_structure_to_rna(
     df: pd.DataFrame,

graphein/utils/utils.py

@@ -18,7 +18,12 @@
 import pandas as pd
 import xarray as xr
 from Bio.Data.IUPACData import protein_letters_3to1
-from typing_extensions import Literal
+
+try:
+    from typing import Literal
+except ImportError:
+    from typing_extensions import Literal
+
 
 AggregationType: List["sum", "mean", "max", "min", "median"]
 """Types of aggregations for features."""