Fix: Fixing CI (#22)

.github/workflows/run-tox.yml

@@ -24,7 +24,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt-get install -y poppler-utils imagemagick pandoc
+        sudo apt-get update
+        sudo apt-get install -y poppler-utils imagemagick pandoc --fix-missing
         python -m pip install --upgrade pip setuptools
         pip install tox-gh-actions pandoc
     - name: Run tox

.pylintrc

@@ -19,7 +19,7 @@ max-locals=15
 # Maximum number of return / yield for function / method body
 max-returns=6
 # Maximum number of branch for function / method body
-max-branches=20
+max-branches=30
 # Maximum number of statements in function / method body
 max-statements=65
 # Maximum number of parents for a class (see R0901).

MARBLE/geometry.py

@@ -5,19 +5,24 @@
 import torch
 import torch_geometric.utils as PyGu
 import umap
-from sklearn.cluster import KMeans, MeanShift
+from sklearn.cluster import KMeans
+from sklearn.cluster import MeanShift
 from sklearn.decomposition import PCA
-from sklearn.manifold import TSNE, Isomap, MDS
+from sklearn.manifold import MDS
+from sklearn.manifold import TSNE
+from sklearn.manifold import Isomap
 from sklearn.metrics import pairwise_distances
 from sklearn.preprocessing import StandardScaler
-from torch_geometric.nn import knn_graph, radius_graph
+from torch_geometric.nn import knn_graph
+from torch_geometric.nn import radius_graph
 from torch_scatter import scatter_add
 
 from ptu_dijkstra import connections, tangent_frames  # isort:skip
 
 from MARBLE.lib.cknn import cknneighbors_graph  # isort:skip
 from MARBLE import utils  # isort:skip
 
+
 def furthest_point_sampling(x, N=None, stop_crit=0.0, start_idx=0):
     """A greedy O(N^2) algorithm to do furthest points sampling
 
@@ -42,7 +47,7 @@ def furthest_point_sampling(x, N=None, stop_crit=0.0, start_idx=0):
     perm[0] = start_idx
     lambdas = torch.zeros(n)
     ds = D[start_idx, :].flatten()
-    for i in range(1,n):
+    for i in range(1, n):
         idx = torch.argmax(ds)
         perm[i] = idx
         lambdas[i] = ds[idx]
@@ -54,7 +59,7 @@ def furthest_point_sampling(x, N=None, stop_crit=0.0, start_idx=0):
                 lambdas = lambdas[:i]
                 break
 
-    assert len(perm)==len(np.unique(perm)), 'Returned duplicated points'
+    assert len(perm) == len(np.unique(perm)), "Returned duplicated points"
     return perm, lambdas
 
 
@@ -131,10 +136,10 @@ def embed(x, embed_typ="umap", dim_emb=2, manifold=None, seed=0, **kwargs):
             manifold = PCA(n_components=dim_emb).fit(x)
 
         emb = manifold.transform(x)
-        
+
     elif embed_typ == "Isomap":
         radius = pairwise_distances(x)
-        radius = 0.1*(radius.max()-radius.min())
+        radius = 0.1 * (radius.max() - radius.min())
         if manifold is None:
             manifold = Isomap(n_components=dim_emb, n_neighbors=None, radius=radius).fit(x)
 
@@ -296,7 +301,7 @@ def gradient_op(pos, edge_index, gauges):
         _F -= sp.diags(np.array(_F.sum(1)).flatten())
         _F = _F.tocoo()
         K.append(torch.sparse_coo_tensor(np.vstack([_F.row, _F.col]), _F.data.data))
-    
+
     return K
 
 
@@ -450,17 +455,17 @@ def is_connected(edge_index):
 def compute_laplacian(data, normalization="rw"):
     """Compute Laplacian."""
     edge_index, edge_attr = PyGu.get_laplacian(
-        data.edge_index, 
-        edge_weight=data.edge_weight, 
-        normalization=normalization, 
-        num_nodes=data.num_nodes
+        data.edge_index,
+        edge_weight=data.edge_weight,
+        normalization=normalization,
+        num_nodes=data.num_nodes,
     )
 
     return PyGu.to_dense_adj(edge_index, edge_attr=edge_attr).squeeze()
 
 
 def compute_connection_laplacian(data, R, normalization="rw"):
-    """Connection Laplacian
+    r"""Connection Laplacian
 
     Args:
         data: Pytorch geometric data object.
@@ -515,7 +520,7 @@ def compute_connection_laplacian(data, R, normalization="rw"):
 
 
 def compute_gauges(data, dim_man=None, n_geodesic_nb=10, n_workers=1):
-    """Orthonormal gauges for the tangent space at each node, and connection
+    r"""Orthonormal gauges for the tangent space at each node, and connection
     matrices between each pair of adjacent nodes.
 
     R is a block matrix, where the row index is the gauge we want to align to,
@@ -568,7 +573,7 @@ def _compute_gauges(inputs, i):
 
 
 def compute_connections(data, gauges, n_workers=1):
-    """Find smallest rotations R between gauges pairs. It is assumed that the first
+    r"""Find smallest rotations R between gauges pairs. It is assumed that the first
     row of edge_index is what we want to align to, i.e.,
     gauges(i) = gauges(j)@R[i,j].T
 
@@ -625,17 +630,17 @@ def scalar_diffusion(x, t, method="matrix_exp", par=None):
         ), "For spectral method, par must be a tuple of \
             eigenvalues, eigenvectors!"
         evals, evecs = par
-        
+
         # Transform to spectral
         x_spec = torch.mm(evecs.T, x)
 
         # Diffuse
         diffusion_coefs = torch.exp(-evals.unsqueeze(-1) * t.unsqueeze(0))
         x_diffuse_spec = diffusion_coefs * x_spec
-        
+
         # Transform back to per-vertex
         return evecs.mm(x_diffuse_spec)
-    
+
     raise NotImplementedError
 
 
@@ -683,7 +688,7 @@ def compute_eigendecomposition(A, k=None, eps=1e-8):
     """
     if A is None:
         return None
-    
+
     if k is not None and k >= A.shape[0]:
         k = None
 
@@ -692,11 +697,11 @@ def compute_eigendecomposition(A, k=None, eps=1e-8):
     while True:
         try:
             if k is None:
-                evals, evecs = torch.linalg.eigh(A)
+                evals, evecs = torch.linalg.eigh(A)  # pylint: disable=not-callable
             else:
                 evals, evecs = sp.linalg.eigsh(A, k=k, which="SM")
                 evals, evecs = torch.tensor(evals), torch.tensor(evecs)
-                
+
             evals = torch.clamp(evals, min=0.0)
             evecs *= np.sqrt(len(evecs))
 
@@ -709,4 +714,4 @@ def compute_eigendecomposition(A, k=None, eps=1e-8):
             print("--- decomp failed; adding eps ===> count: " + str(failcount))
             A += torch.eye(A.shape[0]) * (eps * 10 ** (failcount - 1))
 
-    return evals, evecs
+    return evals, evecs

MARBLE/layers.py

@@ -1,11 +1,11 @@
 """Layer module."""
 import torch
 from torch import nn
-from torch.nn.functional import normalize, relu
 from torch_geometric.nn.conv import MessagePassing
 
 from MARBLE import geometry as g
 
+
 class Diffusion(nn.Module):
     """Diffusion with learned t."""