🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError#92

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🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError #92

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dc45893
Refactor CSimulator error handling to use BNGLogger and BNGSimulatorE…
google-labs-jules[bot] Apr 13, 2026
c0fe1c8
chore: PR #92 remove forbidden artifacts and run black
akutuva21 Apr 13, 2026
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2 changes: 2 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -10,3 +10,5 @@ temp_testing/*
build
dist
Issues/rule_keywords/test_DeleteMolecules_changed.bngl
.jules/
__pycache__/
11 changes: 11 additions & 0 deletions bionetgen/core/exc.py
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Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -93,3 +93,14 @@ def __init__(
self.model = model
self.message = message
super().__init__(self.message)


class BNGSimulatorError(BNGError):
"""Error related to simulating a BNG model."""

def __init__(
self,
message="There was an issue simulating your BNG model",
):
self.message = message
super().__init__(self.message)
28 changes: 21 additions & 7 deletions bionetgen/simulator/csimulator.py
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Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -4,14 +4,17 @@
from distutils import ccompiler
from .bngsimulator import BNGSimulator
from bionetgen.main import BioNetGen
from bionetgen.core.exc import BNGCompileError
from bionetgen.core.exc import BNGCompileError, BNGSimulatorError
from bionetgen.core.utils.logging import BNGLogger

# This allows access to the CLIs config setup
app = BioNetGen()
app.setup()
conf = app.config["bionetgen"]
def_bng_path = conf["bngpath"]

logger = BNGLogger()


class RESULT(ctypes.Structure):
_fields_ = [
Expand DownExpand Up@@ -55,16 +58,24 @@ def set_species_init(self, arr):
"""
Set the initial species values array
"""
# TODO: Transition to BNGErrors and logging
assert len(arr) == self.num_spec_init
if len(arr) != self.num_spec_init:
logger.error(
f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
)
raise BNGSimulatorError(
f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
)
self.species_init = np.array(arr, dtype=np.float64)

def set_parameters(self, arr):
"""
Set the parameter values array
"""
# TODO: Transition to BNGErrors and logging
assert len(arr) == self.num_params
if len(arr) != self.num_params:
logger.error(f"Expected {self.num_params} parameters, got {len(arr)}")
raise BNGSimulatorError(
f"Expected {self.num_params} parameters, got {len(arr)}"
)
self.parameters = np.array(arr, dtype=np.float64)

def simulate(self, t_start=0, t_end=100, n_steps=100):
Expand DownExpand Up@@ -141,7 +152,9 @@ class CSimulator(BNGSimulator):
def __init__(self, model_file, generate_network=False):
# check cvode library paths
if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is None):
print("CVODE include and library paths are not set, compilation won't work")
logger.warning(
"CVODE include and library paths are not set, compilation won't work"
)
# let's load the model first
if isinstance(model_file, str):
# load model file
Expand All@@ -162,7 +175,8 @@ def __init__(self, model_file, generate_network=False):
)
os.chdir(cd)
else:
print(f"model format not recognized: {model_file}")
logger.error(f"model format not recognized: {model_file}")
raise BNGSimulatorError(f"model format not recognized: {model_file}")
# set compiler
self.compiler = ccompiler.new_compiler()
self.compiler.add_include_dir(conf.get("cvode_include"))
Expand Down
Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError#92

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 Closed

akutuva21
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commits into

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🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError
#92
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dc45893

Refactor CSimulator error handling to use BNGLogger and BNGSimulatorE…


google-labs-jules[bot] Apr 13, 2026
c0fe1c8

chore: PR #92 remove forbidden artifacts and run black


akutuva21 Apr 13, 2026

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2 changes: 2 additions & 0 deletions
.gitignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,3 +10,5 @@ temp_testing/*
build
dist
Issues/rule_keywords/test_DeleteMolecules_changed.bngl
.jules/
__pycache__/

11 changes: 11 additions & 0 deletions
bionetgen/core/exc.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,3 +93,14 @@ def __init__(
 self.model = model
 self.message = message
 super().__init__(self.message)


class BNGSimulatorError(BNGError):
 """Error related to simulating a BNG model."""

 def __init__(
 self,
 message="There was an issue simulating your BNG model",
 ):
 self.message = message
 super().__init__(self.message)

28 changes: 21 additions & 7 deletions
bionetgen/simulator/csimulator.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,14 +4,17 @@
from distutils import ccompiler
from .bngsimulator import BNGSimulator
from bionetgen.main import BioNetGen
from bionetgen.core.exc import BNGCompileError
from bionetgen.core.exc import BNGCompileError, BNGSimulatorError
from bionetgen.core.utils.logging import BNGLogger

# This allows access to the CLIs config setup
app = BioNetGen()
app.setup()
conf = app.config["bionetgen"]
def_bng_path = conf["bngpath"]

logger = BNGLogger()


class RESULT(ctypes.Structure):
 _fields_ = [
Expand DownExpand Up@@ -55,16 +58,24 @@ def set_species_init(self, arr):
 """
 Set the initial species values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_spec_init
 if len(arr) != self.num_spec_init:
 logger.error(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 raise BNGSimulatorError(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 self.species_init = np.array(arr, dtype=np.float64)

 def set_parameters(self, arr):
 """
 Set the parameter values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_params
 if len(arr) != self.num_params:
 logger.error(f"Expected {self.num_params} parameters, got {len(arr)}")
 raise BNGSimulatorError(
 f"Expected {self.num_params} parameters, got {len(arr)}"
 )
 self.parameters = np.array(arr, dtype=np.float64)

 def simulate(self, t_start=0, t_end=100, n_steps=100):
Expand DownExpand Up@@ -141,7 +152,9 @@ class CSimulator(BNGSimulator):
 def __init__(self, model_file, generate_network=False):
 # check cvode library paths
 if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is None):
 print("CVODE include and library paths are not set, compilation won't work")
 logger.warning(
 "CVODE include and library paths are not set, compilation won't work"
 )
 # let's load the model first
 if isinstance(model_file, str):
 # load model file
Expand All@@ -162,7 +175,8 @@ def __init__(self, model_file, generate_network=False):
 )
 os.chdir(cd)
 else:
 print(f"model format not recognized: {model_file}")
 logger.error(f"model format not recognized: {model_file}")
 raise BNGSimulatorError(f"model format not recognized: {model_file}")
 # set compiler
 self.compiler = ccompiler.new_compiler()
 self.compiler.add_include_dir(conf.get("cvode_include"))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError#92

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 Closed

akutuva21
wants to merge
2
commits into

from

 Closed


🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError
#92
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dc45893

Refactor CSimulator error handling to use BNGLogger and BNGSimulatorE…


google-labs-jules[bot] Apr 13, 2026
c0fe1c8

chore: PR #92 remove forbidden artifacts and run black


akutuva21 Apr 13, 2026

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2 changes: 2 additions & 0 deletions
.gitignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,3 +10,5 @@ temp_testing/*
build
dist
Issues/rule_keywords/test_DeleteMolecules_changed.bngl
.jules/
__pycache__/

11 changes: 11 additions & 0 deletions
bionetgen/core/exc.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,3 +93,14 @@ def __init__(
 self.model = model
 self.message = message
 super().__init__(self.message)


class BNGSimulatorError(BNGError):
 """Error related to simulating a BNG model."""

 def __init__(
 self,
 message="There was an issue simulating your BNG model",
 ):
 self.message = message
 super().__init__(self.message)

28 changes: 21 additions & 7 deletions
bionetgen/simulator/csimulator.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,14 +4,17 @@
from distutils import ccompiler
from .bngsimulator import BNGSimulator
from bionetgen.main import BioNetGen
from bionetgen.core.exc import BNGCompileError
from bionetgen.core.exc import BNGCompileError, BNGSimulatorError
from bionetgen.core.utils.logging import BNGLogger

# This allows access to the CLIs config setup
app = BioNetGen()
app.setup()
conf = app.config["bionetgen"]
def_bng_path = conf["bngpath"]

logger = BNGLogger()


class RESULT(ctypes.Structure):
 _fields_ = [
Expand DownExpand Up@@ -55,16 +58,24 @@ def set_species_init(self, arr):
 """
 Set the initial species values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_spec_init
 if len(arr) != self.num_spec_init:
 logger.error(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 raise BNGSimulatorError(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 self.species_init = np.array(arr, dtype=np.float64)

 def set_parameters(self, arr):
 """
 Set the parameter values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_params
 if len(arr) != self.num_params:
 logger.error(f"Expected {self.num_params} parameters, got {len(arr)}")
 raise BNGSimulatorError(
 f"Expected {self.num_params} parameters, got {len(arr)}"
 )
 self.parameters = np.array(arr, dtype=np.float64)

 def simulate(self, t_start=0, t_end=100, n_steps=100):
Expand DownExpand Up@@ -141,7 +152,9 @@ class CSimulator(BNGSimulator):
 def __init__(self, model_file, generate_network=False):
 # check cvode library paths
 if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is None):
 print("CVODE include and library paths are not set, compilation won't work")
 logger.warning(
 "CVODE include and library paths are not set, compilation won't work"
 )
 # let's load the model first
 if isinstance(model_file, str):
 # load model file
Expand All@@ -162,7 +175,8 @@ def __init__(self, model_file, generate_network=False):
 )
 os.chdir(cd)
 else:
 print(f"model format not recognized: {model_file}")
 logger.error(f"model format not recognized: {model_file}")
 raise BNGSimulatorError(f"model format not recognized: {model_file}")
 # set compiler
 self.compiler = ccompiler.new_compiler()
 self.compiler.add_include_dir(conf.get("cvode_include"))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError#92

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akutuva21
wants to merge
2
commits into

from

 Closed


🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError
#92
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dc45893

Refactor CSimulator error handling to use BNGLogger and BNGSimulatorE…


google-labs-jules[bot] Apr 13, 2026
c0fe1c8

chore: PR #92 remove forbidden artifacts and run black


akutuva21 Apr 13, 2026

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2 changes: 2 additions & 0 deletions
.gitignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,3 +10,5 @@ temp_testing/*
build
dist
Issues/rule_keywords/test_DeleteMolecules_changed.bngl
.jules/
__pycache__/

11 changes: 11 additions & 0 deletions
bionetgen/core/exc.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,3 +93,14 @@ def __init__(
 self.model = model
 self.message = message
 super().__init__(self.message)


class BNGSimulatorError(BNGError):
 """Error related to simulating a BNG model."""

 def __init__(
 self,
 message="There was an issue simulating your BNG model",
 ):
 self.message = message
 super().__init__(self.message)

28 changes: 21 additions & 7 deletions
bionetgen/simulator/csimulator.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,14 +4,17 @@
from distutils import ccompiler
from .bngsimulator import BNGSimulator
from bionetgen.main import BioNetGen
from bionetgen.core.exc import BNGCompileError
from bionetgen.core.exc import BNGCompileError, BNGSimulatorError
from bionetgen.core.utils.logging import BNGLogger

# This allows access to the CLIs config setup
app = BioNetGen()
app.setup()
conf = app.config["bionetgen"]
def_bng_path = conf["bngpath"]

logger = BNGLogger()


class RESULT(ctypes.Structure):
 _fields_ = [
Expand DownExpand Up@@ -55,16 +58,24 @@ def set_species_init(self, arr):
 """
 Set the initial species values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_spec_init
 if len(arr) != self.num_spec_init:
 logger.error(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 raise BNGSimulatorError(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 self.species_init = np.array(arr, dtype=np.float64)

 def set_parameters(self, arr):
 """
 Set the parameter values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_params
 if len(arr) != self.num_params:
 logger.error(f"Expected {self.num_params} parameters, got {len(arr)}")
 raise BNGSimulatorError(
 f"Expected {self.num_params} parameters, got {len(arr)}"
 )
 self.parameters = np.array(arr, dtype=np.float64)

 def simulate(self, t_start=0, t_end=100, n_steps=100):
Expand DownExpand Up@@ -141,7 +152,9 @@ class CSimulator(BNGSimulator):
 def __init__(self, model_file, generate_network=False):
 # check cvode library paths
 if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is None):
 print("CVODE include and library paths are not set, compilation won't work")
 logger.warning(
 "CVODE include and library paths are not set, compilation won't work"
 )
 # let's load the model first
 if isinstance(model_file, str):
 # load model file
Expand All@@ -162,7 +175,8 @@ def __init__(self, model_file, generate_network=False):
 )
 os.chdir(cd)
 else:
 print(f"model format not recognized: {model_file}")
 logger.error(f"model format not recognized: {model_file}")
 raise BNGSimulatorError(f"model format not recognized: {model_file}")
 # set compiler
 self.compiler = ccompiler.new_compiler()
 self.compiler.add_include_dir(conf.get("cvode_include"))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError#92

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2
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🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError
#92
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dc45893

Refactor CSimulator error handling to use BNGLogger and BNGSimulatorE…


google-labs-jules[bot] Apr 13, 2026
c0fe1c8

chore: PR #92 remove forbidden artifacts and run black


akutuva21 Apr 13, 2026

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.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -10,3 +10,5 @@ temp_testing/*
build
dist
Issues/rule_keywords/test_DeleteMolecules_changed.bngl
.jules/
__pycache__/

11 changes: 11 additions & 0 deletions
bionetgen/core/exc.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,3 +93,14 @@ def __init__(
 self.model = model
 self.message = message
 super().__init__(self.message)


class BNGSimulatorError(BNGError):
 """Error related to simulating a BNG model."""

 def __init__(
 self,
 message="There was an issue simulating your BNG model",
 ):
 self.message = message
 super().__init__(self.message)

28 changes: 21 additions & 7 deletions
bionetgen/simulator/csimulator.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,14 +4,17 @@
from distutils import ccompiler
from .bngsimulator import BNGSimulator
from bionetgen.main import BioNetGen
from bionetgen.core.exc import BNGCompileError
from bionetgen.core.exc import BNGCompileError, BNGSimulatorError
from bionetgen.core.utils.logging import BNGLogger

# This allows access to the CLIs config setup
app = BioNetGen()
app.setup()
conf = app.config["bionetgen"]
def_bng_path = conf["bngpath"]

logger = BNGLogger()


class RESULT(ctypes.Structure):
 _fields_ = [
Expand DownExpand Up@@ -55,16 +58,24 @@ def set_species_init(self, arr):
 """
 Set the initial species values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_spec_init
 if len(arr) != self.num_spec_init:
 logger.error(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 raise BNGSimulatorError(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 self.species_init = np.array(arr, dtype=np.float64)

 def set_parameters(self, arr):
 """
 Set the parameter values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_params
 if len(arr) != self.num_params:
 logger.error(f"Expected {self.num_params} parameters, got {len(arr)}")
 raise BNGSimulatorError(
 f"Expected {self.num_params} parameters, got {len(arr)}"
 )
 self.parameters = np.array(arr, dtype=np.float64)

 def simulate(self, t_start=0, t_end=100, n_steps=100):
Expand DownExpand Up@@ -141,7 +152,9 @@ class CSimulator(BNGSimulator):
 def __init__(self, model_file, generate_network=False):
 # check cvode library paths
 if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is None):
 print("CVODE include and library paths are not set, compilation won't work")
 logger.warning(
 "CVODE include and library paths are not set, compilation won't work"
 )
 # let's load the model first
 if isinstance(model_file, str):
 # load model file
Expand All@@ -162,7 +175,8 @@ def __init__(self, model_file, generate_network=False):
 )
 os.chdir(cd)
 else:
 print(f"model format not recognized: {model_file}")
 logger.error(f"model format not recognized: {model_file}")
 raise BNGSimulatorError(f"model format not recognized: {model_file}")
 # set compiler
 self.compiler = ccompiler.new_compiler()
 self.compiler.add_include_dir(conf.get("cvode_include"))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError#92

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🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError
#92
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dc45893

Refactor CSimulator error handling to use BNGLogger and BNGSimulatorE…


google-labs-jules[bot] Apr 13, 2026
c0fe1c8

chore: PR #92 remove forbidden artifacts and run black


akutuva21 Apr 13, 2026

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2 changes: 2 additions & 0 deletions
.gitignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,3 +10,5 @@ temp_testing/*
build
dist
Issues/rule_keywords/test_DeleteMolecules_changed.bngl
.jules/
__pycache__/

11 changes: 11 additions & 0 deletions
bionetgen/core/exc.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,3 +93,14 @@ def __init__(
 self.model = model
 self.message = message
 super().__init__(self.message)


class BNGSimulatorError(BNGError):
 """Error related to simulating a BNG model."""

 def __init__(
 self,
 message="There was an issue simulating your BNG model",
 ):
 self.message = message
 super().__init__(self.message)

28 changes: 21 additions & 7 deletions
bionetgen/simulator/csimulator.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,14 +4,17 @@
from distutils import ccompiler
from .bngsimulator import BNGSimulator
from bionetgen.main import BioNetGen
from bionetgen.core.exc import BNGCompileError
from bionetgen.core.exc import BNGCompileError, BNGSimulatorError
from bionetgen.core.utils.logging import BNGLogger

# This allows access to the CLIs config setup
app = BioNetGen()
app.setup()
conf = app.config["bionetgen"]
def_bng_path = conf["bngpath"]

logger = BNGLogger()


class RESULT(ctypes.Structure):
 _fields_ = [
Expand DownExpand Up@@ -55,16 +58,24 @@ def set_species_init(self, arr):
 """
 Set the initial species values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_spec_init
 if len(arr) != self.num_spec_init:
 logger.error(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 raise BNGSimulatorError(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 self.species_init = np.array(arr, dtype=np.float64)

 def set_parameters(self, arr):
 """
 Set the parameter values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_params
 if len(arr) != self.num_params:
 logger.error(f"Expected {self.num_params} parameters, got {len(arr)}")
 raise BNGSimulatorError(
 f"Expected {self.num_params} parameters, got {len(arr)}"
 )
 self.parameters = np.array(arr, dtype=np.float64)

 def simulate(self, t_start=0, t_end=100, n_steps=100):
Expand DownExpand Up@@ -141,7 +152,9 @@ class CSimulator(BNGSimulator):
 def __init__(self, model_file, generate_network=False):
 # check cvode library paths
 if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is None):
 print("CVODE include and library paths are not set, compilation won't work")
 logger.warning(
 "CVODE include and library paths are not set, compilation won't work"
 )
 # let's load the model first
 if isinstance(model_file, str):
 # load model file
Expand All@@ -162,7 +175,8 @@ def __init__(self, model_file, generate_network=False):
 )
 os.chdir(cd)
 else:
 print(f"model format not recognized: {model_file}")
 logger.error(f"model format not recognized: {model_file}")
 raise BNGSimulatorError(f"model format not recognized: {model_file}")
 # set compiler
 self.compiler = ccompiler.new_compiler()
 self.compiler.add_include_dir(conf.get("cvode_include"))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError#92

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to your account

 Closed

akutuva21
wants to merge
2
commits into

from

 Closed


🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError
#92
Show file tree
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dc45893

Refactor CSimulator error handling to use BNGLogger and BNGSimulatorE…


google-labs-jules[bot] Apr 13, 2026
c0fe1c8

chore: PR #92 remove forbidden artifacts and run black


akutuva21 Apr 13, 2026

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2 changes: 2 additions & 0 deletions
.gitignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,3 +10,5 @@ temp_testing/*
build
dist
Issues/rule_keywords/test_DeleteMolecules_changed.bngl
.jules/
__pycache__/

11 changes: 11 additions & 0 deletions
bionetgen/core/exc.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,3 +93,14 @@ def __init__(
 self.model = model
 self.message = message
 super().__init__(self.message)


class BNGSimulatorError(BNGError):
 """Error related to simulating a BNG model."""

 def __init__(
 self,
 message="There was an issue simulating your BNG model",
 ):
 self.message = message
 super().__init__(self.message)

28 changes: 21 additions & 7 deletions
bionetgen/simulator/csimulator.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,14 +4,17 @@
from distutils import ccompiler
from .bngsimulator import BNGSimulator
from bionetgen.main import BioNetGen
from bionetgen.core.exc import BNGCompileError
from bionetgen.core.exc import BNGCompileError, BNGSimulatorError
from bionetgen.core.utils.logging import BNGLogger

# This allows access to the CLIs config setup
app = BioNetGen()
app.setup()
conf = app.config["bionetgen"]
def_bng_path = conf["bngpath"]

logger = BNGLogger()


class RESULT(ctypes.Structure):
 _fields_ = [
Expand DownExpand Up@@ -55,16 +58,24 @@ def set_species_init(self, arr):
 """
 Set the initial species values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_spec_init
 if len(arr) != self.num_spec_init:
 logger.error(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 raise BNGSimulatorError(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 self.species_init = np.array(arr, dtype=np.float64)

 def set_parameters(self, arr):
 """
 Set the parameter values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_params
 if len(arr) != self.num_params:
 logger.error(f"Expected {self.num_params} parameters, got {len(arr)}")
 raise BNGSimulatorError(
 f"Expected {self.num_params} parameters, got {len(arr)}"
 )
 self.parameters = np.array(arr, dtype=np.float64)

 def simulate(self, t_start=0, t_end=100, n_steps=100):
Expand DownExpand Up@@ -141,7 +152,9 @@ class CSimulator(BNGSimulator):
 def __init__(self, model_file, generate_network=False):
 # check cvode library paths
 if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is None):
 print("CVODE include and library paths are not set, compilation won't work")
 logger.warning(
 "CVODE include and library paths are not set, compilation won't work"
 )
 # let's load the model first
 if isinstance(model_file, str):
 # load model file
Expand All@@ -162,7 +175,8 @@ def __init__(self, model_file, generate_network=False):
 )
 os.chdir(cd)
 else:
 print(f"model format not recognized: {model_file}")
 logger.error(f"model format not recognized: {model_file}")
 raise BNGSimulatorError(f"model format not recognized: {model_file}")
 # set compiler
 self.compiler = ccompiler.new_compiler()
 self.compiler.add_include_dir(conf.get("cvode_include"))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError#92

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 Closed

akutuva21
wants to merge
2
commits into

from

 Closed


🧹 [code health improvement] Refactor CSimulator to use BNGLogger and BNGSimulatorError
#92
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dc45893

Refactor CSimulator error handling to use BNGLogger and BNGSimulatorE…


google-labs-jules[bot] Apr 13, 2026
c0fe1c8

chore: PR #92 remove forbidden artifacts and run black


akutuva21 Apr 13, 2026

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2 changes: 2 additions & 0 deletions
.gitignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,3 +10,5 @@ temp_testing/*
build
dist
Issues/rule_keywords/test_DeleteMolecules_changed.bngl
.jules/
__pycache__/

11 changes: 11 additions & 0 deletions
bionetgen/core/exc.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,3 +93,14 @@ def __init__(
 self.model = model
 self.message = message
 super().__init__(self.message)


class BNGSimulatorError(BNGError):
 """Error related to simulating a BNG model."""

 def __init__(
 self,
 message="There was an issue simulating your BNG model",
 ):
 self.message = message
 super().__init__(self.message)

28 changes: 21 additions & 7 deletions
bionetgen/simulator/csimulator.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,14 +4,17 @@
from distutils import ccompiler
from .bngsimulator import BNGSimulator
from bionetgen.main import BioNetGen
from bionetgen.core.exc import BNGCompileError
from bionetgen.core.exc import BNGCompileError, BNGSimulatorError
from bionetgen.core.utils.logging import BNGLogger

# This allows access to the CLIs config setup
app = BioNetGen()
app.setup()
conf = app.config["bionetgen"]
def_bng_path = conf["bngpath"]

logger = BNGLogger()


class RESULT(ctypes.Structure):
 _fields_ = [
Expand DownExpand Up@@ -55,16 +58,24 @@ def set_species_init(self, arr):
 """
 Set the initial species values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_spec_init
 if len(arr) != self.num_spec_init:
 logger.error(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 raise BNGSimulatorError(
 f"Expected {self.num_spec_init} initial species values, got {len(arr)}"
 )
 self.species_init = np.array(arr, dtype=np.float64)

 def set_parameters(self, arr):
 """
 Set the parameter values array
 """
 # TODO: Transition to BNGErrors and logging
 assert len(arr) == self.num_params
 if len(arr) != self.num_params:
 logger.error(f"Expected {self.num_params} parameters, got {len(arr)}")
 raise BNGSimulatorError(
 f"Expected {self.num_params} parameters, got {len(arr)}"
 )
 self.parameters = np.array(arr, dtype=np.float64)

 def simulate(self, t_start=0, t_end=100, n_steps=100):
Expand DownExpand Up@@ -141,7 +152,9 @@ class CSimulator(BNGSimulator):
 def __init__(self, model_file, generate_network=False):
 # check cvode library paths
 if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is None):
 print("CVODE include and library paths are not set, compilation won't work")
 logger.warning(
 "CVODE include and library paths are not set, compilation won't work"
 )
 # let's load the model first
 if isinstance(model_file, str):
 # load model file
Expand All@@ -162,7 +175,8 @@ def __init__(self, model_file, generate_network=False):
 )
 os.chdir(cd)
 else:
 print(f"model format not recognized: {model_file}")
 logger.error(f"model format not recognized: {model_file}")
 raise BNGSimulatorError(f"model format not recognized: {model_file}")
 # set compiler
 self.compiler = ccompiler.new_compiler()
 self.compiler.add_include_dir(conf.get("cvode_include"))
Expand Down
Loading