requirements

requirements.txt

@@ -1,3 +1,4 @@
+aabbtree==2.8.1
 anyio==4.3.0
 appdirs==1.4.4
 appnope==0.1.4
@@ -38,6 +39,8 @@ fqdn==1.5.1
 fsspec==2024.3.1
 gauche==0.1.6
 gevent==24.2.1
+gmsh==4.12.2
+gmsh_interop==2021.1.1
 gpytorch==1.11
 graphein==1.7.6
 greenlet==3.0.3
@@ -73,18 +76,23 @@ line-profiler==4.1.2
 linear-operator==0.5.1
 loguru==0.7.2
 looseversion==1.1.2
+lsq-ellipse==2.2.1
 lxml==5.1.0
 markdown-it-py==3.0.0
 MarkupSafe==2.1.5
 matplotlib==3.8.3
 matplotlib-inline==0.1.6
 mdurl==0.1.2
+meshio==5.3.5
+MeshPy==2022.1.3
+microstructpy==1.5.9
 mistune==3.0.2
 ml-dtypes==0.3.2
 mmtf-python==1.1.3
 mpmath==1.3.0
 msgpack==1.0.8
 multipledispatch==1.0.0
+mypy-extensions==1.0.0
 nbclient==0.10.0
 nbconvert==7.16.3
 nbformat==5.10.3
@@ -99,6 +107,7 @@ packaging==24.0
 pandas==1.5.3
 pandocfilters==1.5.1
 parso==0.8.3
+pathspec==0.12.1
 pexpect==4.9.0
 pillow==10.2.0
 platformdirs==4.2.0
@@ -108,15 +117,20 @@ prompt-toolkit==3.0.43
 psutil==5.9.8
 ptyprocess==0.7.0
 pure-eval==0.2.2
+pybind11==2.11.1
 pycparser==2.21
 pydantic==1.10.14
 Pygments==2.17.2
+pygmsh==7.1.17
 pyparsing==3.1.2
+pyquaternion==0.9.9
 pyro-api==0.1.2
 pyro-ppl==1.9.0
 python-dateutil==2.9.0.post0
 python-json-logger==2.0.7
+pytools==2024.1.1
 pytz==2024.1
+pyvoro-mmalahe==1.3.4
 PyYAML==6.0.1
 pyzmq==25.1.2
 rdkit==2023.9.5

src/general_utils.py

@@ -48,7 +48,7 @@ def centered_2_norm(self, X: np.array, center: np.array) -> np.float32:
 
     def get_nsphere_and_sampled_boundary(
         self, radius: np.float32, center: np.ndarray, sample: int, eps: np.float32
-    ) -> [list, np.ndarray]:
+    ) -> List[list, np.ndarray]:
         representation = NSphere(r=radius, center=center)
         nsphere = representation.approximate()
         dim = center.shape[0]