________________ [doctest] flexynesis.data.read_stringdb_links _________________
807 value format with a header row, and at least the columns 'protein1', 'protein2', and 'combined_score'.
808 top_neighbors (int, optional): The number of top interactions to return for each protein. Defaults to 5.
809
810 Returns:
811 pd.DataFrame: A DataFrame with columns 'protein1' and 'protein2' representing the top interactions
812 for each protein. Each protein and partner identifier is simplified by stripping to the last
813 element after splitting by ".".
814
815 Example:
816 >>> read_stringdb_links('string_interactions.txt', top_neighbors=3)
UNEXPECTED EXCEPTION: FileNotFoundError(2, 'No such file or directory')
Traceback (most recent call last):
File "/gnu/store/jjcka1g6sk2cvwx8nm4fdwpdq3vll0v0-python-3.10.7/lib/python3.10/doctest.py", line 1350, in __run
exec(compile(example.source, filename, "single",
File "<doctest flexynesis.data.read_stringdb_links[0]>", line 1, in <module>
File "/tmp/guix-build-flexynesis-0.2.10.drv-0/source/flexynesis/data.py", line 820, in read_stringdb_links
df = pd.read_csv(fname, header=0, sep=" ")
File "/gnu/store/imagx3cs7qzbh1ys54gskn0szgdmszxj-python-pandas-2.1.1/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 948, in read_csv
return _read(filepath_or_buffer, kwds)
File "/gnu/store/imagx3cs7qzbh1ys54gskn0szgdmszxj-python-pandas-2.1.1/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 611, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/gnu/store/imagx3cs7qzbh1ys54gskn0szgdmszxj-python-pandas-2.1.1/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1448, in __init__
self._engine = self._make_engine(f, self.engine)
File "/gnu/store/imagx3cs7qzbh1ys54gskn0szgdmszxj-python-pandas-2.1.1/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1705, in _make_engine
self.handles = get_handle(
File "/gnu/store/imagx3cs7qzbh1ys54gskn0szgdmszxj-python-pandas-2.1.1/lib/python3.10/site-packages/pandas/io/common.py", line 863, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: 'string_interactions.txt'
/tmp/guix-build-flexynesis-0.2.10.drv-0/source/flexynesis/data.py:816: UnexpectedException
_____________________ [doctest] flexynesis.modules.flexGCN _____________________
169 'GAT' for Graph Attention Network, 'SAGE' for GraphSAGE, and 'GC' for generic Graph Convolution.
170 Defaults to 'GC'.
171 act (str, optional): Type of activation function to use. Supported types include 'relu', 'sigmoid',
172 'leakyrelu', 'tanh', and 'gelu'. Defaults to 'relu'.
173
174 Raises:
175 ValueError: If an unsupported activation function or convolution type is specified.
176
177 Example:
178 >>> model = flexGCN(node_count=100, node_feature_count=5, node_embedding_dim=64, output_dim=10,
UNEXPECTED EXCEPTION: SyntaxError("'(' was never closed", ('<doctest flexynesis.modules.flexGCN[0]>', 1, 16, 'model = flexGCN(node_count=100, node_feature_count=5, node_embedding_dim=64, output_dim=10, \n', 1, 0))
Traceback (most recent call last):
File "/gnu/store/jjcka1g6sk2cvwx8nm4fdwpdq3vll0v0-python-3.10.7/lib/python3.10/doctest.py", line 1350, in __run
exec(compile(example.source, filename, "single",
File "<doctest flexynesis.modules.flexGCN[0]>", line 1
model = flexGCN(node_count=100, node_feature_count=5, node_embedding_dim=64, output_dim=10,
^
SyntaxError: '(' was never closed
/tmp/guix-build-flexynesis-0.2.10.drv-0/source/flexynesis/modules.py:178: UnexpectedException
If these are not valid doctests then pytest should be configured to skip them.
When running pytest I get these doctest failures:
If these are not valid doctests then pytest should be configured to skip them.