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Clean up block warning paths#97

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Merged
jrfaeder merged 1 commit into from
May 12, 2026
Merged

Clean up block warning paths #97

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80 changes: 51 additions & 29 deletions bionetgen/modelapi/blocks.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
from typing import OrderedDict
except ImportError:
from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import Parameter, Compartment, Observable
from .structs import MoleculeType, Species, Function
from .structs import Rule, Action
Expand All@@ -14,6 +15,8 @@
except ImportError:
from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class ModelBlock:
Expand DownExpand Up@@ -105,10 +108,11 @@ def __setattr__(self, name, value) -> None:
if name in self.items.keys():
try:
new_value = float(value)
except (TypeError, ValueError):
self.items[name] = value
else:
changed = True
self.items[name] = new_value
except:
self.items[name] = value
if changed:
self._changes[name] = new_value
self.__dict__[name] = new_value
Expand DownExpand Up@@ -166,9 +170,13 @@ def add_item(self, item_tpl) -> None:
if isinstance(name, str):
try:
setattr(self, name, value)
except:
print("can't set {} to {}".format(name, value))
pass
except Exception as exc:
logger.warning(
f"Unable to bind attribute {name!r} for the {self.name} block;"
" the item remains available via block.items. "
f"Original error: {exc}",
loc=f"{__file__} : ModelBlock.add_item()",
)
# we just added an item to a block, let's assume we need
# to recompile if we have a compiled simulator
self._recompile = True
Expand DownExpand Up@@ -214,16 +222,20 @@ def __setattr__(self, name, value) -> None:
try:
# try a new value, we need to make sure
# to stop printing out the expression
value = float(value)
if self.items[name]["value"] != value:
new_value = float(value)
if self.items[name]["value"] != new_value:
changed = True
self.items[name]["value"] = value
self.items[name]["value"] = new_value
self.items[name].write_expr = False
except:
print(
"can't set parameter {} to {}".format(
self.items[name]["name"], value
)
value = new_value
except (TypeError, ValueError):
logger.warning(
"Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
self.items[name]["name"],
value,
self.items[name]["value"],
),
loc=f"{__file__} : ParameterBlock.__setattr__()",
)
if changed:
self._changes[name] = value
Expand DownExpand Up@@ -266,15 +278,19 @@ def __setattr__(self, name, value) -> None:
self.items[name]["name"] = value
else:
try:
value = float(value)
if self.items[name]["size"] != value:
new_value = float(value)
if self.items[name]["size"] != new_value:
changed = True
self.items[name]["size"] = value
except:
print(
"can't set compartment {} to {}".format(
self.items[name]["name"], value
)
self.items[name]["size"] = new_value
value = new_value
except (TypeError, ValueError):
logger.warning(
"Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
self.items[name]["name"],
value,
self.items[name]["size"],
),
loc=f"{__file__} : CompartmentBlock.__setattr__()",
)
if changed:
self._changes[name] = value
Expand DownExpand Up@@ -316,10 +332,13 @@ def __setattr__(self, name, value) -> None:
changed = True
self.items[name]["name"] = value
else:
print(
"can't set observable {} to {}".format(
self.items[name]["name"], value
)
logger.warning(
"Unable to set observable {!r} to {!r}; keeping existing observable {!r}".format(
self.items[name]["name"],
value,
self.items[name]["name"],
),
loc=f"{__file__} : ObservableBlock.__setattr__()",
)
if changed:
self._changes[name] = value
Expand DownExpand Up@@ -361,10 +380,13 @@ def __setattr__(self, name, value) -> None:
changed = True
self.items[name]["name"] = value
else:
print(
"can't set species {} to {}".format(
self.items[name]["name"], value
)
logger.warning(
"Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
self.items[name]["name"],
value,
self.items[name]["name"],
),
loc=f"{__file__} : SpeciesBlock.__setattr__()",
)
if changed:
self._changes[name] = value
Expand Down
81 changes: 52 additions & 29 deletions bionetgen/network/blocks.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
from typing import OrderedDict
except ImportError:
from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import NetworkParameter, NetworkCompartment, NetworkGroup
from .structs import NetworkSpecies, NetworkFunction, NetworkReaction
from .structs import NetworkEnergyPattern, NetworkPopulationMap
Expand All@@ -12,6 +13,8 @@
except ImportError:
from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class NetworkBlock:
Expand DownExpand Up@@ -42,6 +45,7 @@ class NetworkBlock:
def __init__(self) -> None:
self.name = "NetworkBlock"
self.comment = (None, None)
self._changes = OrderedDict()
self.items = OrderedDict()

def __str__(self) -> str:
Expand DownExpand Up@@ -87,10 +91,11 @@ def __setattr__(self, name, value) -> None:
if name in self.items.keys():
try:
new_value = float(value)
except (TypeError, ValueError):
self.items[name] = value
else:
changed = True
self.items[name] = new_value
except:
self.items[name] = value
if changed:
self._changes[name] = new_value
self.__dict__[name] = new_value
Expand DownExpand Up@@ -129,9 +134,13 @@ def add_item(self, item_tpl) -> None:
if isinstance(name, str):
try:
setattr(self, name, value)
except:
# print("can't set {} to {}".format(name, value))
pass
except Exception as exc:
logger.warning(
f"Unable to bind attribute {name!r} for the {self.name} block;"
" the item remains available via block.items. "
f"Original error: {exc}",
loc=f"{__file__} : NetworkBlock.add_item()",
)
# we just added an item to a block, let's assume we need
# to recompile if we have a compiled simulator
self._recompile = True
Expand DownExpand Up@@ -174,16 +183,20 @@ def __setattr__(self, name, value) -> None:
try:
# try a new value, we need to make sure
# to stop printing out the expression
value = float(value)
if self.items[name]["value"] != value:
new_value = float(value)
if self.items[name]["value"] != new_value:
changed = True
self.items[name]["value"] = value
self.items[name]["value"] = new_value
self.items[name].write_expr = False
except:
print(
"can't set parameter {} to {}".format(
self.items[name]["name"], value
)
value = new_value
except (TypeError, ValueError):
logger.warning(
"Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
self.items[name]["name"],
value,
self.items[name]["value"],
),
loc=f"{__file__} : NetworkParameterBlock.__setattr__()",
)
if changed:
self._changes[name] = value
Expand DownExpand Up@@ -226,15 +239,19 @@ def __setattr__(self, name, value) -> None:
self.items[name]["name"] = value
else:
try:
value = float(value)
if self.items[name]["size"] != value:
new_value = float(value)
if self.items[name]["size"] != new_value:
changed = True
self.items[name]["size"] = value
except:
print(
"can't set compartment {} to {}".format(
self.items[name]["name"], value
)
self.items[name]["size"] = new_value
value = new_value
except (TypeError, ValueError):
logger.warning(
"Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
self.items[name]["name"],
value,
self.items[name]["size"],
),
loc=f"{__file__} : NetworkCompartmentBlock.__setattr__()",
)
if changed:
self._changes[name] = value
Expand DownExpand Up@@ -276,10 +293,13 @@ def __setattr__(self, name, value) -> None:
changed = True
self.items[name]["name"] = value
else:
print(
"can't set group {} to {}".format(
self.items[name]["name"], value
)
logger.warning(
"Unable to set group {!r} to {!r}; keeping existing group {!r}".format(
self.items[name]["name"],
value,
self.items[name]["name"],
),
loc=f"{__file__} : NetworkGroupBlock.__setattr__()",
)
if changed:
self._changes[name] = value
Expand DownExpand Up@@ -321,10 +341,13 @@ def __setattr__(self, name, value) -> None:
changed = True
self.items[name]["name"] = value
else:
print(
"can't set species {} to {}".format(
self.items[name]["name"], value
)
logger.warning(
"Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
self.items[name]["name"],
value,
self.items[name]["name"],
),
loc=f"{__file__} : NetworkSpeciesBlock.__setattr__()",
)
if changed:
self._changes[name] = value
Expand Down
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var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
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var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths#97

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 Merged

jrfaeder
merged 1 commit into

from

May 12, 2026
 Merged


Clean up block warning paths
#97
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80 changes: 51 additions & 29 deletions
bionetgen/modelapi/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import Parameter, Compartment, Observable
from .structs import MoleculeType, Species, Function
from .structs import Rule, Action
Expand All@@ -14,6 +15,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class ModelBlock:
Expand DownExpand Up@@ -105,10 +108,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -166,9 +170,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : ModelBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -214,16 +222,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : ParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -266,15 +278,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : CompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -316,10 +332,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set observable {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set observable {!r} to {!r}; keeping existing observable {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : ObservableBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -361,10 +380,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : SpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down

81 changes: 52 additions & 29 deletions
bionetgen/network/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import NetworkParameter, NetworkCompartment, NetworkGroup
from .structs import NetworkSpecies, NetworkFunction, NetworkReaction
from .structs import NetworkEnergyPattern, NetworkPopulationMap
Expand All@@ -12,6 +13,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class NetworkBlock:
Expand DownExpand Up@@ -42,6 +45,7 @@ class NetworkBlock:
 def __init__(self) -> None:
 self.name = "NetworkBlock"
 self.comment = (None, None)
 self._changes = OrderedDict()
 self.items = OrderedDict()

 def __str__(self) -> str:
Expand DownExpand Up@@ -87,10 +91,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -129,9 +134,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 # print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : NetworkBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -174,16 +183,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : NetworkParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -226,15 +239,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : NetworkCompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -276,10 +293,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set group {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set group {!r} to {!r}; keeping existing group {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkGroupBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -321,10 +341,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkSpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down
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Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths#97

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privacy statement. We’ll occasionally send you account related emails.

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 Merged

jrfaeder
merged 1 commit into

from

May 12, 2026
 Merged


Clean up block warning paths
#97
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80 changes: 51 additions & 29 deletions
bionetgen/modelapi/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import Parameter, Compartment, Observable
from .structs import MoleculeType, Species, Function
from .structs import Rule, Action
Expand All@@ -14,6 +15,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class ModelBlock:
Expand DownExpand Up@@ -105,10 +108,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -166,9 +170,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : ModelBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -214,16 +222,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : ParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -266,15 +278,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : CompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -316,10 +332,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set observable {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set observable {!r} to {!r}; keeping existing observable {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : ObservableBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -361,10 +380,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : SpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down

81 changes: 52 additions & 29 deletions
bionetgen/network/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import NetworkParameter, NetworkCompartment, NetworkGroup
from .structs import NetworkSpecies, NetworkFunction, NetworkReaction
from .structs import NetworkEnergyPattern, NetworkPopulationMap
Expand All@@ -12,6 +13,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class NetworkBlock:
Expand DownExpand Up@@ -42,6 +45,7 @@ class NetworkBlock:
 def __init__(self) -> None:
 self.name = "NetworkBlock"
 self.comment = (None, None)
 self._changes = OrderedDict()
 self.items = OrderedDict()

 def __str__(self) -> str:
Expand DownExpand Up@@ -87,10 +91,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -129,9 +134,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 # print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : NetworkBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -174,16 +183,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : NetworkParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -226,15 +239,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : NetworkCompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -276,10 +293,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set group {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set group {!r} to {!r}; keeping existing group {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkGroupBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -321,10 +341,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkSpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
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found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths#97

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 Merged

jrfaeder
merged 1 commit into

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May 12, 2026
 Merged


Clean up block warning paths
#97
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80 changes: 51 additions & 29 deletions
bionetgen/modelapi/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import Parameter, Compartment, Observable
from .structs import MoleculeType, Species, Function
from .structs import Rule, Action
Expand All@@ -14,6 +15,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class ModelBlock:
Expand DownExpand Up@@ -105,10 +108,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -166,9 +170,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : ModelBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -214,16 +222,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : ParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -266,15 +278,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : CompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -316,10 +332,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set observable {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set observable {!r} to {!r}; keeping existing observable {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : ObservableBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -361,10 +380,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : SpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down

81 changes: 52 additions & 29 deletions
bionetgen/network/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import NetworkParameter, NetworkCompartment, NetworkGroup
from .structs import NetworkSpecies, NetworkFunction, NetworkReaction
from .structs import NetworkEnergyPattern, NetworkPopulationMap
Expand All@@ -12,6 +13,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class NetworkBlock:
Expand DownExpand Up@@ -42,6 +45,7 @@ class NetworkBlock:
 def __init__(self) -> None:
 self.name = "NetworkBlock"
 self.comment = (None, None)
 self._changes = OrderedDict()
 self.items = OrderedDict()

 def __str__(self) -> str:
Expand DownExpand Up@@ -87,10 +91,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -129,9 +134,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 # print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : NetworkBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -174,16 +183,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : NetworkParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -226,15 +239,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : NetworkCompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -276,10 +293,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set group {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set group {!r} to {!r}; keeping existing group {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkGroupBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -321,10 +341,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkSpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
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cleanLinks();
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var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths#97

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privacy statement. We’ll occasionally send you account related emails.

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 Merged

jrfaeder
merged 1 commit into

from

May 12, 2026
 Merged


Clean up block warning paths
#97
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80 changes: 51 additions & 29 deletions
bionetgen/modelapi/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import Parameter, Compartment, Observable
from .structs import MoleculeType, Species, Function
from .structs import Rule, Action
Expand All@@ -14,6 +15,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class ModelBlock:
Expand DownExpand Up@@ -105,10 +108,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -166,9 +170,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : ModelBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -214,16 +222,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : ParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -266,15 +278,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : CompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -316,10 +332,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set observable {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set observable {!r} to {!r}; keeping existing observable {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : ObservableBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -361,10 +380,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : SpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down

81 changes: 52 additions & 29 deletions
bionetgen/network/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import NetworkParameter, NetworkCompartment, NetworkGroup
from .structs import NetworkSpecies, NetworkFunction, NetworkReaction
from .structs import NetworkEnergyPattern, NetworkPopulationMap
Expand All@@ -12,6 +13,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class NetworkBlock:
Expand DownExpand Up@@ -42,6 +45,7 @@ class NetworkBlock:
 def __init__(self) -> None:
 self.name = "NetworkBlock"
 self.comment = (None, None)
 self._changes = OrderedDict()
 self.items = OrderedDict()

 def __str__(self) -> str:
Expand DownExpand Up@@ -87,10 +91,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -129,9 +134,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 # print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : NetworkBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -174,16 +183,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : NetworkParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -226,15 +239,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : NetworkCompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -276,10 +293,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set group {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set group {!r} to {!r}; keeping existing group {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkGroupBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -321,10 +341,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkSpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down
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// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
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tryTheater();
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var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
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}, 1000);
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observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths#97

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 Merged

jrfaeder
merged 1 commit into

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May 12, 2026
 Merged


Clean up block warning paths
#97
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80 changes: 51 additions & 29 deletions
bionetgen/modelapi/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import Parameter, Compartment, Observable
from .structs import MoleculeType, Species, Function
from .structs import Rule, Action
Expand All@@ -14,6 +15,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class ModelBlock:
Expand DownExpand Up@@ -105,10 +108,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -166,9 +170,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : ModelBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -214,16 +222,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : ParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -266,15 +278,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : CompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -316,10 +332,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set observable {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set observable {!r} to {!r}; keeping existing observable {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : ObservableBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -361,10 +380,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : SpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down

81 changes: 52 additions & 29 deletions
bionetgen/network/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import NetworkParameter, NetworkCompartment, NetworkGroup
from .structs import NetworkSpecies, NetworkFunction, NetworkReaction
from .structs import NetworkEnergyPattern, NetworkPopulationMap
Expand All@@ -12,6 +13,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class NetworkBlock:
Expand DownExpand Up@@ -42,6 +45,7 @@ class NetworkBlock:
 def __init__(self) -> None:
 self.name = "NetworkBlock"
 self.comment = (None, None)
 self._changes = OrderedDict()
 self.items = OrderedDict()

 def __str__(self) -> str:
Expand DownExpand Up@@ -87,10 +91,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -129,9 +134,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 # print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : NetworkBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -174,16 +183,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : NetworkParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -226,15 +239,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : NetworkCompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -276,10 +293,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set group {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set group {!r} to {!r}; keeping existing group {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkGroupBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -321,10 +341,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkSpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down
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// Remove or un-stick sticky/fixed headers that block content
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function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
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}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths#97

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privacy statement. We’ll occasionally send you account related emails.

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 Merged

jrfaeder
merged 1 commit into

from

May 12, 2026
 Merged


Clean up block warning paths
#97
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80 changes: 51 additions & 29 deletions
bionetgen/modelapi/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import Parameter, Compartment, Observable
from .structs import MoleculeType, Species, Function
from .structs import Rule, Action
Expand All@@ -14,6 +15,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class ModelBlock:
Expand DownExpand Up@@ -105,10 +108,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -166,9 +170,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : ModelBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -214,16 +222,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : ParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -266,15 +278,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : CompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -316,10 +332,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set observable {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set observable {!r} to {!r}; keeping existing observable {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : ObservableBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -361,10 +380,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : SpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down

81 changes: 52 additions & 29 deletions
bionetgen/network/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import NetworkParameter, NetworkCompartment, NetworkGroup
from .structs import NetworkSpecies, NetworkFunction, NetworkReaction
from .structs import NetworkEnergyPattern, NetworkPopulationMap
Expand All@@ -12,6 +13,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class NetworkBlock:
Expand DownExpand Up@@ -42,6 +45,7 @@ class NetworkBlock:
 def __init__(self) -> None:
 self.name = "NetworkBlock"
 self.comment = (None, None)
 self._changes = OrderedDict()
 self.items = OrderedDict()

 def __str__(self) -> str:
Expand DownExpand Up@@ -87,10 +91,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -129,9 +134,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 # print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : NetworkBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -174,16 +183,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : NetworkParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -226,15 +239,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : NetworkCompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -276,10 +293,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set group {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set group {!r} to {!r}; keeping existing group {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkGroupBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -321,10 +341,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkSpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
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applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
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Clean up block warning paths#97

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 Merged

jrfaeder
merged 1 commit into

from

May 12, 2026
 Merged


Clean up block warning paths
#97
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80 changes: 51 additions & 29 deletions
bionetgen/modelapi/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import Parameter, Compartment, Observable
from .structs import MoleculeType, Species, Function
from .structs import Rule, Action
Expand All@@ -14,6 +15,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class ModelBlock:
Expand DownExpand Up@@ -105,10 +108,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -166,9 +170,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : ModelBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -214,16 +222,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : ParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -266,15 +278,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : CompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -316,10 +332,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set observable {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set observable {!r} to {!r}; keeping existing observable {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : ObservableBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -361,10 +380,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : SpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down

81 changes: 52 additions & 29 deletions
bionetgen/network/blocks.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,7 @@
 from typing import OrderedDict
except ImportError:
 from collections import OrderedDict
from bionetgen.core.utils.logging import BNGLogger
from .structs import NetworkParameter, NetworkCompartment, NetworkGroup
from .structs import NetworkSpecies, NetworkFunction, NetworkReaction
from .structs import NetworkEnergyPattern, NetworkPopulationMap
Expand All@@ -12,6 +13,8 @@
except ImportError:
 from collections import OrderedDict

logger = BNGLogger()


###### BLOCK OBJECTS ######
class NetworkBlock:
Expand DownExpand Up@@ -42,6 +45,7 @@ class NetworkBlock:
 def __init__(self) -> None:
 self.name = "NetworkBlock"
 self.comment = (None, None)
 self._changes = OrderedDict()
 self.items = OrderedDict()

 def __str__(self) -> str:
Expand DownExpand Up@@ -87,10 +91,11 @@ def __setattr__(self, name, value) -> None:
 if name in self.items.keys():
 try:
 new_value = float(value)
 except (TypeError, ValueError):
 self.items[name] = value
 else:
 changed = True
 self.items[name] = new_value
 except:
 self.items[name] = value
 if changed:
 self._changes[name] = new_value
 self.__dict__[name] = new_value
Expand DownExpand Up@@ -129,9 +134,13 @@ def add_item(self, item_tpl) -> None:
 if isinstance(name, str):
 try:
 setattr(self, name, value)
 except:
 # print("can't set {} to {}".format(name, value))
 pass
 except Exception as exc:
 logger.warning(
 f"Unable to bind attribute {name!r} for the {self.name} block;"
 " the item remains available via block.items. "
 f"Original error: {exc}",
 loc=f"{__file__} : NetworkBlock.add_item()",
 )
 # we just added an item to a block, let's assume we need
 # to recompile if we have a compiled simulator
 self._recompile = True
Expand DownExpand Up@@ -174,16 +183,20 @@ def __setattr__(self, name, value) -> None:
 try:
 # try a new value, we need to make sure
 # to stop printing out the expression
value = float(value)
 if self.items[name]["value"] != value:
new_value = float(value)
 if self.items[name]["value"] != new_value:
 changed = True
 self.items[name]["value"] = value
 self.items[name]["value"] = new_value
 self.items[name].write_expr = False
 except:
 print(
 "can't set parameter {} to {}".format(
 self.items[name]["name"], value
 )
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set parameter {!r} to {!r}; keeping existing value {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["value"],
 ),
 loc=f"{__file__} : NetworkParameterBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -226,15 +239,19 @@ def __setattr__(self, name, value) -> None:
 self.items[name]["name"] = value
 else:
 try:
value = float(value)
 if self.items[name]["size"] != value:
new_value = float(value)
 if self.items[name]["size"] != new_value:
 changed = True
 self.items[name]["size"] = value
 except:
 print(
 "can't set compartment {} to {}".format(
 self.items[name]["name"], value
 )
 self.items[name]["size"] = new_value
 value = new_value
 except (TypeError, ValueError):
 logger.warning(
 "Unable to set compartment {!r} to {!r}; keeping existing size {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["size"],
 ),
 loc=f"{__file__} : NetworkCompartmentBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -276,10 +293,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set group {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set group {!r} to {!r}; keeping existing group {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkGroupBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand DownExpand Up@@ -321,10 +341,13 @@ def __setattr__(self, name, value) -> None:
 changed = True
 self.items[name]["name"] = value
 else:
 print(
 "can't set species {} to {}".format(
 self.items[name]["name"], value
 )
 logger.warning(
 "Unable to set species {!r} to {!r}; keeping existing species {!r}".format(
 self.items[name]["name"],
 value,
 self.items[name]["name"],
 ),
 loc=f"{__file__} : NetworkSpeciesBlock.__setattr__()",
 )
 if changed:
 self._changes[name] = value
Expand Down
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