File datasets.py has 512 lines of code (exceeds 250 allowed). Consider refactoring.

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import math
import torch
import torchvision.transforms as transforms
import torch.nn as nn
import torch.nn.functional as F

File lieGroups.py has 510 lines of code (exceeds 250 allowed). Consider refactoring.

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import torch
import numpy as np
from lie_conv.utils import export, Named

@export

File lieConv.py has 322 lines of code (exceeds 250 allowed). Consider refactoring.

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""" 
Note to the Reader:

In order to handle the generic spatial data we process features as a tuple: (coordinates,values,mask)
with shapes (bs,n,d), (bs,n,c), (bs,n) where bs is batchsize, n is the maximum number of points in the minibatch,

Function __init__ has 17 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(self, chin, ds_frac=1, num_outputs=1, k=1536, nbhd=np.inf,

Function __init__ has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

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    def __init__(self, data, included_species=None, num_pts=-1, normalize=True, shuffle=True, subtract_thermo=True):

        self.data = data

        if num_pts < 0:

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Function process_xyz_md17 has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

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def process_xyz_md17(datafile):
    """
    Read xyz file and return a molecular dict with number of atoms, energy, forces, coordinates and atom-type for the MD-17 dataset.

    Parameters

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Function makeTrainer has 15 arguments (exceeds 4 allowed). Consider refactoring.

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def makeTrainer(*, dataset=MnistRotDataset, network=ImgLieResnet, num_epochs=100,

Function prepare_dataset has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

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def prepare_dataset(datadir, dataset, subset=None, splits=None, cleanup=True, force_download=False):
    """
    Download and process dataset.

    Parameters

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Function makeTrainer has 11 arguments (exceeds 4 allowed). Consider refactoring.

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def makeTrainer(*, task='homo', device='cuda', lr=3e-3, bs=75, num_epochs=500,network=MolecLieResNet, 

Function __init__ has 11 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(self,chin=1,total_ds=1/64,num_layers=6,group=T(2),fill=1/32,k=256,

Function __init__ has 11 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(self,d=2,sys_dim=2,bn=False,num_layers=4,group=T(2),k=384,knn=False,nbhd=100,mean=True,center=True,**kwargs):

Function __init__ has 10 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(self,d=2,sys_dim=2,bn=False,num_layers=4,group=T(2),k=384,knn=False,nbhd=100,mean=True,**kwargs):

Function __init__ has 9 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(self,chin,chout,mc_samples=32,xyz_dim=3,ds_frac=1,knn_channels=None,act='swish',bn=False,mean=False):

Function gen_splits_gdb9 has 26 lines of code (exceeds 25 allowed). Consider refactoring.

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def gen_splits_gdb9(gdb9dir, cleanup=True):
    """
    Generate GDB9 training/validation/test splits used.

    First, use the file 'uncharacterized.txt' in the GDB9 figshare to find a

Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(self, root_dir=default_root_dir, train=True, download=True, n_systems=100, regen=False,

Function forward has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

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    def forward(self,inp,withquery=False):
        abq_pairs,vals,mask = inp
        dist = self.group.distance if self.group else lambda ab: norm(ab,dim=-1)
        if self.ds_frac!=1:
            if self.cache and self.cached_indices is None:

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Function process_xyz_files has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

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def process_xyz_files(data, process_file_fn, file_ext=None, file_idx_list=None, stack=True):
    """
    Take a set of datafiles and apply a predefined data processing script to each
    one. Data can be stored in a directory, tarfile, or zipfile. An optional
    file extension can be added.

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Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(self, root_dir=default_root_dir, train=True, download=True, n_systems=100, space_dim=2, regen=False,

Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(self,*args,group=T(3),ds_frac=1,fill=1/3,cache=False,knn=False,**kwargs):

Function prepare_dataset has 6 arguments (exceeds 4 allowed). Consider refactoring.

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def prepare_dataset(datadir, dataset, subset=None, splits=None, cleanup=True, force_download=False):