Merge branch 'main' of https://github.com/saezlab/corneto

.gitignore

@@ -232,4 +232,4 @@ $RECYCLE.BIN/
 # Windows shortcuts
 *.lnk
 
-# End of https://www.toptal.com/developers/gitignore/api/windows,linux,python,visualstudiocode,jupyternotebooks
+# End of https://www.toptal.com/developers/gitignore/api/windows,linux,python,visualstudiocode,jupyternotebooks

.vscode/settings.json

@@ -5,4 +5,4 @@
     ],
     "python.testing.pytestEnabled": true,
     "python.testing.unittestEnabled": false
-}
+}

README.md

@@ -37,4 +37,3 @@ CORNETO is developed at the [Institute for Computational Biomedicine](https://sa
 PerMedCoE project ([permedcoe.eu](https://permedcoe.eu/)) agreement no. 951773.
 
 <img src="https://raw.githubusercontent.com/saezlab/.github/main/profile/logos/saezlab.png" alt="Saez lab logo" height="64px" style="height:64px; width:auto"> <img src="https://lcsb-biocore.github.io/COBREXA.jl/stable/assets/permedcoe.svg" alt="PerMedCoE logo" height="64px" style="height:64px; width:auto"> <img src="https://yt3.googleusercontent.com/ytc/AIf8zZSHTQJs12aUZjHsVBpfFiRyrK6rbPwb-7VIxZQk=s176-c-k-c0x00ffffff-no-rj" alt="UKHD logo" height="64px" style="height:64px; width:auto">  
-

corneto/__init__.py

@@ -1,12 +1,9 @@
 import sys
 
-from corneto._constants import *
-
 from corneto import _plotting as pl
-from corneto._graph import Graph, Attr, Attributes, EdgeType
+from corneto._constants import *
+from corneto._graph import Attr, Attributes, EdgeType, Graph
 from corneto._util import info
-from corneto.utils import Attr, Attributes
-
 from corneto.backend import DEFAULT_BACKEND, DEFAULT_SOLVER, available_backends
 from corneto.backend import DEFAULT_BACKEND as K
 from corneto.backend import DEFAULT_BACKEND as ops
@@ -20,6 +17,7 @@
     signaling,
     signflow_constraints,
 )
+from corneto.utils import Attr, Attributes
 
 __all__ = [
     "Attr",
@@ -30,7 +28,7 @@
     "DEFAULT_BACKEND",
     "available_backends",
     "K",
-    "ops"
+    "ops",
 ]
 
 

corneto/_core.py

@@ -1,13 +1,14 @@
 import abc
+from collections import OrderedDict
 from copy import deepcopy
+from itertools import chain
+from numbers import Number
+from typing import Any, Dict, Iterable, List, Optional, Set, Tuple
+
 import numpy as np
-from typing import Any, Optional, Iterable, Set, Tuple, Union, Dict, List
-from corneto._settings import sparsify
+
 from corneto._constants import *
-from corneto._decorators import jit
-from numbers import Number
-from collections import OrderedDict
-from itertools import chain
+from corneto._settings import sparsify
 
 
 def _set(e):
@@ -312,7 +313,7 @@ def to_graphviz(
             s, t = e
             s = list(s)
             if len(s) == 0:
-                s = f"*_{str(t)}"
+                s = f"*_{t!s}"
                 g.node(s, shape="point")
             elif len(s) == 1:
                 s = str(s[0])
@@ -322,7 +323,7 @@ def to_graphviz(
                 raise NotImplementedError("Represent- hyperedges as composite edges")
             t = list(t)
             if len(t) == 0:
-                t = f"{str(s)}_*"
+                t = f"{s!s}_*"
                 g.node(t, shape="point")
             elif len(t) == 1:
                 t = str(t[0])

corneto/_decorators.py

@@ -1,5 +1,6 @@
 from functools import wraps
 from typing import Callable
+
 from corneto._settings import LOGGER, USE_NUMBA
 
 
@@ -27,8 +28,7 @@ def _wrapped_func(*args, **kwargs):
 
 
 def _delegate(func):
-    """
-    A decorator that wraps a function to provide extended functionality
+    """A decorator that wraps a function to provide extended functionality
     when applied within a class. This decorator modifies the behavior
     of the function `func` to handle expression objects and delegate
     calls to their underlying representations, while maintaining a set of
@@ -74,6 +74,7 @@ def __add__(self, other):
             pass
     ```
     """
+
     @wraps(func)
     def _wrapper_func(self, *args, **kwargs):
         symbols = set()
@@ -97,9 +98,7 @@ def _wrapper_func(self, *args, **kwargs):
                 # if available. E.g., if function is __add__, checks if the backend
                 # expression has that function and uses it instead, this returns a
                 # new backend expression which is wrapped back to CORNETO expr.
-                return self._create(
-                    f(*args, **kwargs), symbols
-                )
+                return self._create(f(*args, **kwargs), symbols)
         return self._create(func(self, *args, **kwargs), symbols)
 
     return _wrapper_func

corneto/_graph.py

@@ -20,9 +20,10 @@
 )
 
 import numpy as np
-from corneto._types import Edge, CobraModel, NxDiGraph, NxGraph
-from corneto._util import unique_iter
+
 from corneto._io import import_cobra_model
+from corneto._types import CobraModel, Edge, NxDiGraph, NxGraph
+from corneto._util import unique_iter
 from corneto.utils import Attr, Attributes
 
 T = TypeVar("T")
@@ -57,7 +58,8 @@ def _tpl(elements: Union[Any, Iterable[Any]]) -> Tuple[Any, ...]:
 
 class BaseGraph(abc.ABC):
     """BaseGraph class for graphs or hypergraphs with directed/undirected/mixed
-    and self edges"""
+    and self edges
+    """
 
     def __init__(self, default_edge_type: EdgeType = EdgeType.DIRECTED) -> None:
         """Initialize BaseGraph with default edge type.
@@ -647,7 +649,7 @@ class Graph(BaseGraph):
     default_edge_type
         Default edge type :class:`~corneto._graph.EdgeType`.
 
-    Examples
+    Examples:
     --------
     >>> graph = corneto.Graph()
     >>> graph.add_edge(1, 2)
@@ -688,7 +690,7 @@ def _add_edge(
     ) -> int:
         sv = frozenset(source)
         tv = frozenset(target)
-        #uv = sv | tv
+        # uv = sv | tv
         edge = (sv, tv)
         self._edges.append(edge)
         idx = len(self._edges) - 1

corneto/_io.py

@@ -1,19 +1,18 @@
 from pathlib import Path
 from typing import (
-    List,
+    Dict,
     Iterable,
-    Tuple,
+    List,
     Optional,
-    Dict,
     Set,
+    Tuple,
     Union,
-    TypeVar,
-    Any,
-    TYPE_CHECKING,
 )
-from corneto._types import TupleSIF, CobraModel
+
 import numpy as np
 
+from corneto._types import CobraModel, TupleSIF
+
 
 def _read_sif(
     sif_file: Union[str, Path],
@@ -54,7 +53,9 @@ def _read_sif_iter(
             if has_header and i == 0:
                 continue
             if len(line) <= 2:
-                raise ValueError(f"Invalid SIF line: {line}: expected at least 3 columns")
+                raise ValueError(
+                    f"Invalid SIF line: {line}: expected at least 3 columns"
+                )
             s, d, t = [line[idx] for idx in column_order]
             if discard_self_loops and s == t:
                 continue
@@ -95,7 +96,7 @@ def _get_reaction_species(reactions: Dict[str, Dict[str, int]]) -> Set[str]:
 
 
 def _stoichiometry(
-    reactions: Dict[str, Dict[str, int]]
+    reactions: Dict[str, Dict[str, int]],
 ) -> Tuple[np.ndarray, List[str], List[str]]:
     reactions_ids = list(reactions.keys())
     compounds_ids = list(_get_reaction_species(reactions))
@@ -173,7 +174,7 @@ def import_cobra_model(model: CobraModel) -> Tuple[np.ndarray, np.ndarray, np.nd
                 # Try to create a list
                 import re
 
-                subsys = re.findall("\['(.*?)'\]", subsys)
+                subsys = re.findall(r"\['(.*?)'\]", subsys)
                 if len(subsys) == 0:
                     subsys = rxn.subsystem
             # A list containing a numpy array?
@@ -222,8 +223,7 @@ def import_cobra_model(model: CobraModel) -> Tuple[np.ndarray, np.ndarray, np.nd
 
 
 def _is_url(url):
-    """
-    Determine if the provided string is a valid url
+    """Determine if the provided string is a valid url
     :param url: string
     :return: True if the string is a URL
     """
@@ -243,8 +243,8 @@ def _download(url_file):
 
     if not _is_url(url_file):
         raise ValueError("Invalid url")
-    import tempfile
     import os
+    import tempfile
     from urllib.request import urlopen
 
     ext = pathlib.Path(url_file).suffix

corneto/_legacy.py

@@ -488,7 +488,7 @@ def select(
         if isinstance(ids, int) or isinstance(ids, str):
             ids = [ids]
         if not isinstance(ids, list):
-            raise ValueError(f"ids must be a list of ints or strings")
+            raise ValueError("ids must be a list of ints or strings")
         for id in ids:
             if isinstance(id, int):
                 nids.append(id)
@@ -998,7 +998,7 @@ def legacy_graphviz(
         s, t = e
         s = list(s)
         if len(s) == 0:
-            s = f"*_{str(t)}"
+            s = f"*_{t!s}"
             g.node(s, shape="point")
         elif len(s) == 1:
             s = str(s[0])
@@ -1008,7 +1008,7 @@ def legacy_graphviz(
             raise NotImplementedError("Represent- hyperedges as composite edges")
         t = list(t)
         if len(t) == 0:
-            t = f"{str(s)}_*"
+            t = f"{s!s}_*"
             g.node(t, shape="point")
         elif len(t) == 1:
             t = str(t[0])

corneto/_nx.py

@@ -1,7 +1,8 @@
+import warnings
+from typing import Any, Dict, Iterable, Optional
+
 from corneto._legacy import ReNet
 from corneto._types import StrOrInt
-from typing import Any, Dict, List, Optional, Iterable, Union
-import warnings
 
 # TODO: Pass default style to plotting methods
 _default_style = {
@@ -79,8 +80,8 @@ def plot(
 ):
     try:
         import matplotlib.pyplot as plt
-        from matplotlib.patches import ArrowStyle
         import networkx as nx
+        from matplotlib.patches import ArrowStyle
     except ImportError:
         raise ImportError("matplotlib and networkx are required for plotting")
 
@@ -94,7 +95,7 @@ def plot(
             pos = nx.nx_pydot.graphviz_layout(G, prog="dot")
         except Exception as err:
             warnings.warn(
-                f"Failed to use graphviz with dot layout: {str(err)}. Using spring_layout instead."
+                f"Failed to use graphviz with dot layout: {err!s}. Using spring_layout instead."
             )
             pos = nx.spring_layout(G)
 
@@ -185,7 +186,7 @@ def to_nxgraph(
     reactions: Optional[Iterable[StrOrInt]] = None,
 ):
     try:
-        from networkx import DiGraph, set_node_attributes, set_edge_attributes
+        from networkx import DiGraph, set_edge_attributes, set_node_attributes
     except ImportError:
         raise ImportError(
             "NetworkX is required to convert a Reaction Network to a networkx graph."

corneto/_plotting.py

@@ -1,8 +1,10 @@
-from typing import Any, Dict, Optional, Literal
-from corneto._graph import BaseGraph, Attr, EdgeType
-from corneto.backend._base import EXPR_NAME_FLOW
+from typing import Any, Dict, Literal, Optional
+
 import numpy as np
 
+from corneto._graph import Attr, BaseGraph, EdgeType
+from corneto.backend._base import EXPR_NAME_FLOW
+
 
 def clip_quantiles(arr, q):
     if q < 0 or q > 1:
@@ -14,7 +16,7 @@ def clip_quantiles(arr, q):
 
 def vertex_style(
     P,
-    G, # TODO: G should not be required
+    G,  # TODO: G should not be required
     vertex_var: str = "vertex_values",
     negative_color: str = "dodgerblue4",
     positive_color: str = "firebrick4",

corneto/_settings.py

@@ -1,9 +1,10 @@
 import logging
 import os
 import sys
-import numpy as np
 from importlib.util import find_spec
 
+import numpy as np
+
 LOGGER = logging.getLogger("__corneto__")
 LOGGER.setLevel(logging.INFO)
 LOGGER.propagate = False

corneto/_types.py

@@ -1,6 +1,7 @@
-from typing import TYPE_CHECKING, FrozenSet, Tuple, Union, Any, TypeVar
-from corneto._settings import LOGGER
 import importlib
+from typing import TYPE_CHECKING, Any, FrozenSet, Tuple, TypeVar, Union
+
+from corneto._settings import LOGGER
 
 Edge = Tuple[FrozenSet[Any], FrozenSet[Any]]
 StrOrInt = Union[str, int]

corneto/_typing.py

@@ -1,4 +1,4 @@
-from typing import Union, Tuple
+from typing import Tuple, Union
 
 StrOrInt = Union[str, int]
 TupleSIF = Tuple[str, int, str]

corneto/_util.py

@@ -40,7 +40,7 @@ def get_latest_version(
         if match:
             version = match.group(1)
             return version
-    except Exception as e:
+    except Exception:
         return None
 
 
@@ -49,8 +49,6 @@ def _support_html_output(force_html: bool = False):
     # and https://github.com/tqdm/tqdm/blob/0bb91857eca0d4aea08f66cf1c8949abe0cd6b7a/tqdm/notebook.py#L38
     try:
         from IPython import get_ipython
-        from IPython.core.display import display
-        from IPython.display import HTML
 
         ipy = get_ipython()
         if ipy is None:
@@ -115,7 +113,7 @@ def _get_info() -> Dict[str, Dict]:
 
         info["graphviz_version"]["message"] = f"v{graphviz.__version__}"
         info["graphviz_version"]["value"] = graphviz.__version__
-    except Exception as e:
+    except Exception:
         pass
     info["repo_url"] = {
         "title": "Repository",
@@ -189,7 +187,7 @@ def _info():
     if DEFAULT_BACKEND:
         print("Default backend (corneto.K):", str(DEFAULT_BACKEND))
         print(
-            f"Available solvers for {str(DEFAULT_BACKEND)}:",
+            f"Available solvers for {DEFAULT_BACKEND!s}:",
             ", ".join([s for s in DEFAULT_BACKEND.available_solvers()]),
         )
     else: