sympy: lazy import sympy + SBML getSize compatibility fix#63

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Merged
jrfaeder merged 5 commits into from
Mar 17, 2026
Merged

sympy: lazy import sympy + SBML getSize compatibility fix #63

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46aeffa
sympy: lazy import sympy + SBML getSize compatibility fix
akutuva21 Mar 17, 2026
6a93f10
Refactor code to improve compatibility and maintainability:
akutuva21 Mar 17, 2026
c392f2b
CI fixes
akutuva21 Mar 17, 2026
9b7bd7a
CI and Black lint fixes
akutuva21 Mar 17, 2026
e3b7a2a
Black lint changes to match version used by CI
akutuva21 Mar 17, 2026
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14 changes: 7 additions & 7 deletions .github/workflows/ci.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -21,17 +21,17 @@ jobs:
fail-fast: false
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]
python-version: [3.7, 3.8]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache pip
uses: actions/cache@v2
uses: actions/cache@v4
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('requirements-dev.txt') }}
Expand All@@ -41,7 +41,7 @@ jobs:
- name: Install dependencies
run: |
if [ "$RUNNER_OS" == "Linux" ]; then
sudo apt-get -y install libncurses5-dev libncursesw5-dev libncurses5
sudo apt-get update && sudo apt-get -y install libncurses-dev
fi
python -m pip install --upgrade pip
pip install -r requirements-dev.txt
Expand DownExpand Up@@ -73,7 +73,7 @@ jobs:
uses: docker/login-action@v2
with:
registry: ghcr.io
username: ${{ secrets.GHCR_USER }}
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}

- name: Extract metadata (tags, labels) for Docker
Expand All@@ -86,7 +86,7 @@ jobs:
uses: docker/build-push-action@v4.0.0
with:
context: .
push: true
push: ${{ github.event_name != 'pull_request' }}
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}

Expand Down
4 changes: 1 addition & 3 deletions Dockerfile
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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,7 @@ LABEL org.opencontainers.image.source=https://github.com/RuleWorld/PyBioNetGen
LABEL org.opencontainers.image.description="PyBNG container"
LABEL org.opencontainers.image.licenses=MIT
RUN apt-get update && apt-get install -y \
libncurses5-dev \
libncursesw5-dev \
libncurses5
libncurses-dev
WORKDIR /src
COPY . /src
RUN pip install --no-cache-dir -r requirements.txt
Expand Down
4 changes: 2 additions & 2 deletions Issues/parameter_init/parameter_init.py
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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
import bionetgen
import bionetgen

parameter = bionetgen.modelapi.structs.Parameter("A0", "10")
print(parameter.gen_string())
print(parameter.gen_string())
4 changes: 2 additions & 2 deletions Issues/rule_keywords/run_pybng.py
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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import bionetgen

mname="test_deleteMolecules"
model= bionetgen.bngmodel(mname+".bngl")
mname = "test_deleteMolecules"
model= bionetgen.bngmodel(mname + ".bngl")
print(model)
20 changes: 20 additions & 0 deletions bionetgen/__init__.py
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Expand Up@@ -2,3 +2,23 @@
from .modelapi import bngmodel
from .modelapi.runner import run
from .simulator import sim_getter

# sympy is an expensive dependency to import. We delay importing the
# SympyOdes helpers until they are actually accessed.

__all__ = [
"defaults",
"bngmodel",
"run",
"sim_getter",
"SympyOdes",
"export_sympy_odes",
]


def __getattr__(name):
if name in {"SympyOdes", "export_sympy_odes"}:
from .modelapi.sympy_odes import SympyOdes, export_sympy_odes

return locals()[name]
raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
1 change: 0 additions & 1 deletion bionetgen/atomizer/atomizeTool.py
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Expand Up@@ -4,7 +4,6 @@

from bionetgen.core.utils.logging import BNGLogger, log_level


d = BNGDefaults()


Expand Down
7 changes: 3 additions & 4 deletions bionetgen/atomizer/atomizer/analyzeSBML.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,7 +6,6 @@
"""

import enum
import imp
from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore
import numpy as np
import json
Expand DownExpand Up@@ -820,9 +819,9 @@ def loadConfigFiles(self, fileName):
# deal with modifications
if "modificationDefinition" in reactionDefinition_new:
# TODO: Change file format to be nicer?
reactionDefinition[
"modificationDefinition"
] = reactionDefinition_new["modificationDefinition"]
reactionDefinition["modificationDefinition"] = (
reactionDefinition_new["modificationDefinition"]
)
# convert new JSON format to old data format
else:
reactionDefinition["modificationDefinition"] = {}
Expand Down
1 change: 0 additions & 1 deletion bionetgen/atomizer/atomizer/atomizationAux.py
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Expand Up@@ -3,7 +3,6 @@


class CycleError(Exception):

"""Exception raised for errors in the input.

Attributes:
Expand Down
1 change: 1 addition & 0 deletions bionetgen/atomizer/atomizer/detectOntology.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

import pprint
import difflib
from collections import Counter
Expand Down
18 changes: 9 additions & 9 deletions bionetgen/atomizer/atomizer/resolveSCT.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -113,9 +113,9 @@ def createSpeciesCompositionGraph(
# lexicalDependencyGraph[element], oldDependency))
"""
if self.database.dependencyGraph[element] != []:
self.database.alternativeDependencyGraph[
element
] = lexicalDependencyGraph[element]
self.database.alternativeDependencyGraph[element] = (
lexicalDependencyGraph[element]
)
else:
logMess(
"INFO:LAE009",
Expand DownExpand Up@@ -1464,9 +1464,9 @@ def selectBestCandidate(

tmpCandidates = namingTmpCandidates
if loginformation:
self.database.alternativeDependencyGraph[
reactant
] = tmpCandidates
self.database.alternativeDependencyGraph[reactant] = (
tmpCandidates
)
elif all(
sorted(x) == sorted(originalTmpCandidates[0])
for x in originalTmpCandidates
Expand DownExpand Up@@ -1568,9 +1568,9 @@ def selectBestCandidate(
namingTmpCandidates = tmpCandidates

else:
self.database.alternativeDependencyGraph[
reactant
] = namingtmpCandidates
self.database.alternativeDependencyGraph[reactant] = (
namingtmpCandidates
)
logMess(
"WARNING:SCT111",
"{0}:stoichiometry analysis:{1}:conflicts with and naming conventions:{2}:Selecting lexical analysis".format(
Expand Down
1 change: 1 addition & 0 deletions bionetgen/atomizer/contactMap.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

# import sys
# sys.path.insert(0, '../utils/')
import utils.consoleCommands as console
Expand Down
25 changes: 12 additions & 13 deletions bionetgen/atomizer/libsbml2bngl.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@

#!/usr/bin/env python
from collections import OrderedDict
from telnetlib import IP
import time
import libsbml
import bionetgen.atomizer.writer.bnglWriter as writer
Expand DownExpand Up@@ -438,9 +437,9 @@ def extractCompartmentStatistics(
for element in compartmentPairs:
if element[0][0] not in finalCompartmentPairs:
finalCompartmentPairs[element[0][0]] = {}
finalCompartmentPairs[element[0][0]][
tuple([element[0][1], element[1][1]])
] = compartmentPairs[element]
finalCompartmentPairs[element[0][0]][tuple([element[0][1], element[1][1]])] = (
compartmentPairs[element]
)
return finalCompartmentPairs


Expand DownExpand Up@@ -1457,16 +1456,16 @@ def analyzeHelper(
param = ["__epsilon__ 1e-100"] + param

if atomize:
commentDictionary[
"notes"
] = "'This is an atomized translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
commentDictionary["notes"] = (
"'This is an atomized translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
)
)
else:
commentDictionary[
"notes"
] = "'This is a plain translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
commentDictionary["notes"] = (
"'This is a plain translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
)
)
commentDictionary[
"notes"
Expand DownExpand Up@@ -1652,7 +1651,7 @@ def main():
metavar="FILE",
)

(options, _) = parser.parse_args()
options, _ = parser.parse_args()
# 144
rdfArray = []
# classificationArray = []
Expand Down
18 changes: 9 additions & 9 deletions bionetgen/atomizer/rulifier/componentGroups.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -681,9 +681,9 @@ def getContextRequirements(
requirementDependencies[molecule][
"doubleActivation"
].append(relationship)
processNodes[molecule]["doubleActivation"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
processNodes[molecule]["doubleActivation"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
)
elif not combination[0] and combination[1]:
if motif in ["ordering"]:
requirementDependencies[molecule][motif].remove(
Expand All@@ -700,14 +700,14 @@ def getContextRequirements(
requirementDependencies[molecule]["reprordering"].append(
relationship
)
processNodes[molecule]["reprordering"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
processNodes[molecule]["reprordering"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
)

elif not combination[0] and not combination[1]:
processNodes[molecule]["doubleRepression"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
processNodes[molecule]["doubleRepression"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
)
if motif == "repression":
requirementDependencies[molecule][motif].remove(
relationship
Expand Down
43 changes: 23 additions & 20 deletions bionetgen/atomizer/rulifier/postAnalysis.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -128,11 +128,11 @@ def getParticipatingReactions(self, molecule, componentPair, reactionDictionary)
for x in reactionDictionary[moleculeName][component]
if x in componentPair
]:
correlationList[
(component[0], componentComplement)
] = reactionDictionary[moleculeName][component][
componentComplement
]
correlationList[(component[0], componentComplement)] = (
reactionDictionary[moleculeName][component][
componentComplement
]
)
return correlationList

def getPairsFromMotif(self, motif1, motif2, excludedComponents):
Expand All@@ -146,10 +146,10 @@ def getPairsFromMotif(self, motif1, motif2, excludedComponents):
if len(self.motifMoleculeDict[element][molecule]) > 0:
for componentPair in self.motifMoleculeDict[element][molecule]:
if not any(x in excludedComponents for x in componentPair):
correlationList[
componentPair
] = self.getParticipatingReactions(
molecule, componentPair, self.patternXreactions
correlationList[componentPair] = (
self.getParticipatingReactions(
molecule, componentPair, self.patternXreactions
)
)
moleculeCorrelationList[molecule].update(correlationList)
return dict(moleculeCorrelationList)
Expand DownExpand Up@@ -283,10 +283,13 @@ def getClassification(keys, translator):
localAnalysisFlag = True
if not any(
[
molecule
in database.prunnedDependencyGraph[x][0]
if len(database.prunnedDependencyGraph[x]) > 0
else molecule in x
(
molecule
in database.prunnedDependencyGraph[x][0]
if len(database.prunnedDependencyGraph[x])
> 0
else molecule in x
)
for x in difference
]
):
Expand DownExpand Up@@ -372,9 +375,9 @@ def getContextMotifInformation(self):
"nullrequirement",
"exclusion",
]:
motifDictionary[
frozenset([requirementClass, requirementClass])
] = self.getPairsFromMotif(requirementClass, requirementClass, [])
motifDictionary[frozenset([requirementClass, requirementClass])] = (
self.getPairsFromMotif(requirementClass, requirementClass, [])
)
return motifDictionary

def getComplexReactions(self, threshold=2):
Expand DownExpand Up@@ -548,10 +551,10 @@ def runTests():
"nullrequirement",
"exclusion",
]:
motifDictionary[
(requirementClass, requirementClass)
] = modelLearning.getPairsFromMotif(
requirementClass, requirementClass, ["imod"]
motifDictionary[(requirementClass, requirementClass)] = (
modelLearning.getPairsFromMotif(
requirementClass, requirementClass, ["imod"]
)
)
if len(motifDictionary[(requirementClass, requirementClass)]) > 0:
print(
Expand Down
18 changes: 9 additions & 9 deletions bionetgen/atomizer/rulifier/stateTransitionDiagram.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -138,9 +138,9 @@ def isActive(state):
for species in centerUnit:
for element in species.split("."):
if element.split("(")[0].split("%")[0] not in sourceCounter:
sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
)
for component in moleculeDict[
element.split("(")[0].split("%")[0]
]:
Expand All@@ -158,9 +158,9 @@ def isActive(state):
for species in centerUnit:
for element in species.split("."):
if element.split("(")[0].split("%")[0] not in sourceCounter:
sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
)
for component in moleculeDict[
element.split("(")[0].split("%")[0]
]:
Expand All@@ -179,9 +179,9 @@ def isActive(state):
for species in productUnit:
for element in species.split("."):
if element.split("(")[0].split("%")[0] not in destinationCounter:
destinationCounter[
element.split("(")[0].split("%")[0]
] = Counter()
destinationCounter[element.split("(")[0].split("%")[0]] = (
Counter()
)
for component in moleculeDict[
element.split("(")[0].split("%")[0]
]:
Expand Down
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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sympy: lazy import sympy + SBML getSize compatibility fix#63

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 Merged

jrfaeder
merged 5 commits into

from

Mar 17, 2026
 Merged


sympy: lazy import sympy + SBML getSize compatibility fix
#63
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46aeffa

sympy: lazy import sympy + SBML getSize compatibility fix


akutuva21 Mar 17, 2026
6a93f10

Refactor code to improve compatibility and maintainability:


akutuva21 Mar 17, 2026
c392f2b

CI fixes


akutuva21 Mar 17, 2026
9b7bd7a

CI and Black lint fixes


akutuva21 Mar 17, 2026
e3b7a2a

Black lint changes to match version used by CI


akutuva21 Mar 17, 2026

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14 changes: 7 additions & 7 deletions
.github/workflows/ci.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,17 +21,17 @@ jobs:
 fail-fast: false
 matrix:
 os: [ubuntu-latest, windows-latest, macos-latest]
 python-version: [3.7, 3.8]
 python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 steps:
 - uses: actions/checkout@v2
 - uses: actions/checkout@v4
 with:
 fetch-depth: 0
 - name: Set up Python ${{ matrix.python-version }}
 uses: actions/setup-python@v2
 uses: actions/setup-python@v5
 with:
 python-version: ${{ matrix.python-version }}
 - name: Cache pip
 uses: actions/cache@v2
 uses: actions/cache@v4
 with:
 path: ~/.cache/pip
 key: ${{ runner.os }}-pip-${{ hashFiles('requirements-dev.txt') }}
Expand All@@ -41,7 +41,7 @@ jobs:
 - name: Install dependencies
 run: |
 if [ "$RUNNER_OS" == "Linux" ]; then
 sudo apt-get -y install libncurses5-dev libncursesw5-dev libncurses5
sudo apt-get update && sudo apt-get -y install libncurses-dev
 fi
 python -m pip install --upgrade pip
 pip install -r requirements-dev.txt
Expand DownExpand Up@@ -73,7 +73,7 @@ jobs:
 uses: docker/login-action@v2
 with:
 registry: ghcr.io
 username: ${{ secrets.GHCR_USER }}
 username: ${{ github.actor }}
 password: ${{ secrets.GITHUB_TOKEN }}

 - name: Extract metadata (tags, labels) for Docker
Expand All@@ -86,7 +86,7 @@ jobs:
 uses: docker/build-push-action@v4.0.0
 with:
 context: .
 push: true
 push: ${{ github.event_name != 'pull_request' }}
 tags: ${{ steps.meta.outputs.tags }}
 labels: ${{ steps.meta.outputs.labels }}

Expand Down

4 changes: 1 addition & 3 deletions
Dockerfile

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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,7 @@ LABEL org.opencontainers.image.source=https://github.com/RuleWorld/PyBioNetGen
LABEL org.opencontainers.image.description="PyBNG container"
LABEL org.opencontainers.image.licenses=MIT
RUN apt-get update && apt-get install -y \
 libncurses5-dev \
 libncursesw5-dev \
 libncurses5
 libncurses-dev
WORKDIR /src
COPY . /src
RUN pip install --no-cache-dir -r requirements.txt 
Expand Down

4 changes: 2 additions & 2 deletions
Issues/parameter_init/parameter_init.py

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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
import bionetgen
import bionetgen

parameter = bionetgen.modelapi.structs.Parameter("A0", "10")
print(parameter.gen_string())
print(parameter.gen_string())

4 changes: 2 additions & 2 deletions
Issues/rule_keywords/run_pybng.py

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import bionetgen

mname="test_deleteMolecules"
model= bionetgen.bngmodel(mname+".bngl")
mname = "test_deleteMolecules"
model= bionetgen.bngmodel(mname + ".bngl")
print(model)

20 changes: 20 additions & 0 deletions
bionetgen/__init__.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,3 +2,23 @@
from .modelapi import bngmodel
from .modelapi.runner import run
from .simulator import sim_getter

# sympy is an expensive dependency to import. We delay importing the
# SympyOdes helpers until they are actually accessed.

__all__ = [
 "defaults",
 "bngmodel",
 "run",
 "sim_getter",
 "SympyOdes",
 "export_sympy_odes",
]


def __getattr__(name):
 if name in {"SympyOdes", "export_sympy_odes"}:
 from .modelapi.sympy_odes import SympyOdes, export_sympy_odes

 return locals()[name]
 raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizeTool.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,6 @@

from bionetgen.core.utils.logging import BNGLogger, log_level


d = BNGDefaults()


Expand Down

7 changes: 3 additions & 4 deletions
bionetgen/atomizer/atomizer/analyzeSBML.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,7 +6,6 @@
"""

import enum
import imp
from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore
import numpy as np
import json
Expand DownExpand Up@@ -820,9 +819,9 @@ def loadConfigFiles(self, fileName):
 # deal with modifications
 if "modificationDefinition" in reactionDefinition_new:
 # TODO: Change file format to be nicer?
 reactionDefinition[
 "modificationDefinition"
] = reactionDefinition_new["modificationDefinition"]
 reactionDefinition["modificationDefinition"] = (
reactionDefinition_new["modificationDefinition"]
)
 # convert new JSON format to old data format
 else:
 reactionDefinition["modificationDefinition"] = {}
Expand Down

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizer/atomizationAux.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,6 @@


class CycleError(Exception):

 """Exception raised for errors in the input.

 Attributes:
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/atomizer/detectOntology.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

import pprint
import difflib
from collections import Counter
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/atomizer/resolveSCT.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -113,9 +113,9 @@ def createSpeciesCompositionGraph(
 # lexicalDependencyGraph[element], oldDependency))
 """
 if self.database.dependencyGraph[element] != []:
 self.database.alternativeDependencyGraph[
 element
] = lexicalDependencyGraph[element]
 self.database.alternativeDependencyGraph[element] = (
lexicalDependencyGraph[element]
)
 else:
 logMess(
 "INFO:LAE009",
Expand DownExpand Up@@ -1464,9 +1464,9 @@ def selectBestCandidate(

 tmpCandidates = namingTmpCandidates
 if loginformation:
 self.database.alternativeDependencyGraph[
reactant
] = tmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
tmpCandidates
)
 elif all(
 sorted(x) == sorted(originalTmpCandidates[0])
 for x in originalTmpCandidates
Expand DownExpand Up@@ -1568,9 +1568,9 @@ def selectBestCandidate(
 namingTmpCandidates = tmpCandidates

 else:
 self.database.alternativeDependencyGraph[
reactant
] = namingtmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
namingtmpCandidates
)
 logMess(
 "WARNING:SCT111",
 "{0}:stoichiometry analysis:{1}:conflicts with and naming conventions:{2}:Selecting lexical analysis".format(
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/contactMap.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

# import sys
# sys.path.insert(0, '../utils/')
import utils.consoleCommands as console
Expand Down

25 changes: 12 additions & 13 deletions
bionetgen/atomizer/libsbml2bngl.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@

#!/usr/bin/env python
from collections import OrderedDict
from telnetlib import IP
import time
import libsbml
import bionetgen.atomizer.writer.bnglWriter as writer
Expand DownExpand Up@@ -438,9 +437,9 @@ def extractCompartmentStatistics(
 for element in compartmentPairs:
 if element[0][0] not in finalCompartmentPairs:
 finalCompartmentPairs[element[0][0]] = {}
 finalCompartmentPairs[element[0][0]][
tuple([element[0][1], element[1][1]])
] = compartmentPairs[element]
 finalCompartmentPairs[element[0][0]][tuple([element[0][1], element[1][1]])] = (
compartmentPairs[element]
)
 return finalCompartmentPairs


Expand DownExpand Up@@ -1457,16 +1456,16 @@ def analyzeHelper(
 param = ["__epsilon__ 1e-100"] + param

 if atomize:
 commentDictionary[
 "notes"
] = "'This is an atomized translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is an atomized translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 else:
 commentDictionary[
 "notes"
] = "'This is a plain translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is a plain translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 commentDictionary[
 "notes"
Expand DownExpand Up@@ -1652,7 +1651,7 @@ def main():
 metavar="FILE",
 )

(options, _) = parser.parse_args()
 options, _ = parser.parse_args()
 # 144
 rdfArray = []
 # classificationArray = []
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/componentGroups.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -681,9 +681,9 @@ def getContextRequirements(
 requirementDependencies[molecule][
 "doubleActivation"
 ].append(relationship)
 processNodes[molecule]["doubleActivation"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleActivation"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 elif not combination[0] and combination[1]:
 if motif in ["ordering"]:
 requirementDependencies[molecule][motif].remove(
Expand All@@ -700,14 +700,14 @@ def getContextRequirements(
 requirementDependencies[molecule]["reprordering"].append(
 relationship
 )
 processNodes[molecule]["reprordering"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["reprordering"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )

 elif not combination[0] and not combination[1]:
 processNodes[molecule]["doubleRepression"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleRepression"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 if motif == "repression":
 requirementDependencies[molecule][motif].remove(
 relationship
Expand Down

43 changes: 23 additions & 20 deletions
bionetgen/atomizer/rulifier/postAnalysis.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -128,11 +128,11 @@ def getParticipatingReactions(self, molecule, componentPair, reactionDictionary)
 for x in reactionDictionary[moleculeName][component]
 if x in componentPair
 ]:
 correlationList[
(component[0], componentComplement)
] = reactionDictionary[moleculeName][component][
componentComplement
]
 correlationList[(component[0], componentComplement)] = (
reactionDictionary[moleculeName][component][
 componentComplement
]
)
 return correlationList

 def getPairsFromMotif(self, motif1, motif2, excludedComponents):
Expand All@@ -146,10 +146,10 @@ def getPairsFromMotif(self, motif1, motif2, excludedComponents):
 if len(self.motifMoleculeDict[element][molecule]) > 0:
 for componentPair in self.motifMoleculeDict[element][molecule]:
 if not any(x in excludedComponents for x in componentPair):
 correlationList[
componentPair
] = self.getParticipatingReactions(
molecule, componentPair, self.patternXreactions
 correlationList[componentPair] = (
self.getParticipatingReactions(
 molecule, componentPair, self.patternXreactions
)
 )
 moleculeCorrelationList[molecule].update(correlationList)
 return dict(moleculeCorrelationList)
Expand DownExpand Up@@ -283,10 +283,13 @@ def getClassification(keys, translator):
 localAnalysisFlag = True
 if not any(
 [
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x]) > 0
 else molecule in x
 (
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x])
 > 0
 else molecule in x
 )
 for x in difference
 ]
 ):
Expand DownExpand Up@@ -372,9 +375,9 @@ def getContextMotifInformation(self):
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
frozenset([requirementClass, requirementClass])
] = self.getPairsFromMotif(requirementClass, requirementClass, [])
 motifDictionary[frozenset([requirementClass, requirementClass])] = (
self.getPairsFromMotif(requirementClass, requirementClass, [])
 )
 return motifDictionary

 def getComplexReactions(self, threshold=2):
Expand DownExpand Up@@ -548,10 +551,10 @@ def runTests():
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
(requirementClass, requirementClass)
] = modelLearning.getPairsFromMotif(
requirementClass, requirementClass, ["imod"]
 motifDictionary[(requirementClass, requirementClass)] = (
modelLearning.getPairsFromMotif(
 requirementClass, requirementClass, ["imod"]
)
 )
 if len(motifDictionary[(requirementClass, requirementClass)]) > 0:
 print(
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/stateTransitionDiagram.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -138,9 +138,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -158,9 +158,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -179,9 +179,9 @@ def isActive(state):
 for species in productUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in destinationCounter:
 destinationCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 destinationCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand Down
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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");
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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 Merged

jrfaeder
merged 5 commits into

from

Mar 17, 2026
 Merged


sympy: lazy import sympy + SBML getSize compatibility fix
#63
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46aeffa

sympy: lazy import sympy + SBML getSize compatibility fix


akutuva21 Mar 17, 2026
6a93f10

Refactor code to improve compatibility and maintainability:


akutuva21 Mar 17, 2026
c392f2b

CI fixes


akutuva21 Mar 17, 2026
9b7bd7a

CI and Black lint fixes


akutuva21 Mar 17, 2026
e3b7a2a

Black lint changes to match version used by CI


akutuva21 Mar 17, 2026

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14 changes: 7 additions & 7 deletions
.github/workflows/ci.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,17 +21,17 @@ jobs:
 fail-fast: false
 matrix:
 os: [ubuntu-latest, windows-latest, macos-latest]
 python-version: [3.7, 3.8]
 python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 steps:
 - uses: actions/checkout@v2
 - uses: actions/checkout@v4
 with:
 fetch-depth: 0
 - name: Set up Python ${{ matrix.python-version }}
 uses: actions/setup-python@v2
 uses: actions/setup-python@v5
 with:
 python-version: ${{ matrix.python-version }}
 - name: Cache pip
 uses: actions/cache@v2
 uses: actions/cache@v4
 with:
 path: ~/.cache/pip
 key: ${{ runner.os }}-pip-${{ hashFiles('requirements-dev.txt') }}
Expand All@@ -41,7 +41,7 @@ jobs:
 - name: Install dependencies
 run: |
 if [ "$RUNNER_OS" == "Linux" ]; then
 sudo apt-get -y install libncurses5-dev libncursesw5-dev libncurses5
sudo apt-get update && sudo apt-get -y install libncurses-dev
 fi
 python -m pip install --upgrade pip
 pip install -r requirements-dev.txt
Expand DownExpand Up@@ -73,7 +73,7 @@ jobs:
 uses: docker/login-action@v2
 with:
 registry: ghcr.io
 username: ${{ secrets.GHCR_USER }}
 username: ${{ github.actor }}
 password: ${{ secrets.GITHUB_TOKEN }}

 - name: Extract metadata (tags, labels) for Docker
Expand All@@ -86,7 +86,7 @@ jobs:
 uses: docker/build-push-action@v4.0.0
 with:
 context: .
 push: true
 push: ${{ github.event_name != 'pull_request' }}
 tags: ${{ steps.meta.outputs.tags }}
 labels: ${{ steps.meta.outputs.labels }}

Expand Down

4 changes: 1 addition & 3 deletions
Dockerfile

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,7 @@ LABEL org.opencontainers.image.source=https://github.com/RuleWorld/PyBioNetGen
LABEL org.opencontainers.image.description="PyBNG container"
LABEL org.opencontainers.image.licenses=MIT
RUN apt-get update && apt-get install -y \
 libncurses5-dev \
 libncursesw5-dev \
 libncurses5
 libncurses-dev
WORKDIR /src
COPY . /src
RUN pip install --no-cache-dir -r requirements.txt 
Expand Down

4 changes: 2 additions & 2 deletions
Issues/parameter_init/parameter_init.py

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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
import bionetgen
import bionetgen

parameter = bionetgen.modelapi.structs.Parameter("A0", "10")
print(parameter.gen_string())
print(parameter.gen_string())

4 changes: 2 additions & 2 deletions
Issues/rule_keywords/run_pybng.py

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import bionetgen

mname="test_deleteMolecules"
model= bionetgen.bngmodel(mname+".bngl")
mname = "test_deleteMolecules"
model= bionetgen.bngmodel(mname + ".bngl")
print(model)

20 changes: 20 additions & 0 deletions
bionetgen/__init__.py

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,3 +2,23 @@
from .modelapi import bngmodel
from .modelapi.runner import run
from .simulator import sim_getter

# sympy is an expensive dependency to import. We delay importing the
# SympyOdes helpers until they are actually accessed.

__all__ = [
 "defaults",
 "bngmodel",
 "run",
 "sim_getter",
 "SympyOdes",
 "export_sympy_odes",
]


def __getattr__(name):
 if name in {"SympyOdes", "export_sympy_odes"}:
 from .modelapi.sympy_odes import SympyOdes, export_sympy_odes

 return locals()[name]
 raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizeTool.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,6 @@

from bionetgen.core.utils.logging import BNGLogger, log_level


d = BNGDefaults()


Expand Down

7 changes: 3 additions & 4 deletions
bionetgen/atomizer/atomizer/analyzeSBML.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,7 +6,6 @@
"""

import enum
import imp
from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore
import numpy as np
import json
Expand DownExpand Up@@ -820,9 +819,9 @@ def loadConfigFiles(self, fileName):
 # deal with modifications
 if "modificationDefinition" in reactionDefinition_new:
 # TODO: Change file format to be nicer?
 reactionDefinition[
 "modificationDefinition"
] = reactionDefinition_new["modificationDefinition"]
 reactionDefinition["modificationDefinition"] = (
reactionDefinition_new["modificationDefinition"]
)
 # convert new JSON format to old data format
 else:
 reactionDefinition["modificationDefinition"] = {}
Expand Down

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizer/atomizationAux.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,6 @@


class CycleError(Exception):

 """Exception raised for errors in the input.

 Attributes:
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/atomizer/detectOntology.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

import pprint
import difflib
from collections import Counter
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/atomizer/resolveSCT.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -113,9 +113,9 @@ def createSpeciesCompositionGraph(
 # lexicalDependencyGraph[element], oldDependency))
 """
 if self.database.dependencyGraph[element] != []:
 self.database.alternativeDependencyGraph[
 element
] = lexicalDependencyGraph[element]
 self.database.alternativeDependencyGraph[element] = (
lexicalDependencyGraph[element]
)
 else:
 logMess(
 "INFO:LAE009",
Expand DownExpand Up@@ -1464,9 +1464,9 @@ def selectBestCandidate(

 tmpCandidates = namingTmpCandidates
 if loginformation:
 self.database.alternativeDependencyGraph[
reactant
] = tmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
tmpCandidates
)
 elif all(
 sorted(x) == sorted(originalTmpCandidates[0])
 for x in originalTmpCandidates
Expand DownExpand Up@@ -1568,9 +1568,9 @@ def selectBestCandidate(
 namingTmpCandidates = tmpCandidates

 else:
 self.database.alternativeDependencyGraph[
reactant
] = namingtmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
namingtmpCandidates
)
 logMess(
 "WARNING:SCT111",
 "{0}:stoichiometry analysis:{1}:conflicts with and naming conventions:{2}:Selecting lexical analysis".format(
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/contactMap.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

# import sys
# sys.path.insert(0, '../utils/')
import utils.consoleCommands as console
Expand Down

25 changes: 12 additions & 13 deletions
bionetgen/atomizer/libsbml2bngl.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@

#!/usr/bin/env python
from collections import OrderedDict
from telnetlib import IP
import time
import libsbml
import bionetgen.atomizer.writer.bnglWriter as writer
Expand DownExpand Up@@ -438,9 +437,9 @@ def extractCompartmentStatistics(
 for element in compartmentPairs:
 if element[0][0] not in finalCompartmentPairs:
 finalCompartmentPairs[element[0][0]] = {}
 finalCompartmentPairs[element[0][0]][
tuple([element[0][1], element[1][1]])
] = compartmentPairs[element]
 finalCompartmentPairs[element[0][0]][tuple([element[0][1], element[1][1]])] = (
compartmentPairs[element]
)
 return finalCompartmentPairs


Expand DownExpand Up@@ -1457,16 +1456,16 @@ def analyzeHelper(
 param = ["__epsilon__ 1e-100"] + param

 if atomize:
 commentDictionary[
 "notes"
] = "'This is an atomized translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is an atomized translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 else:
 commentDictionary[
 "notes"
] = "'This is a plain translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is a plain translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 commentDictionary[
 "notes"
Expand DownExpand Up@@ -1652,7 +1651,7 @@ def main():
 metavar="FILE",
 )

(options, _) = parser.parse_args()
 options, _ = parser.parse_args()
 # 144
 rdfArray = []
 # classificationArray = []
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/componentGroups.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -681,9 +681,9 @@ def getContextRequirements(
 requirementDependencies[molecule][
 "doubleActivation"
 ].append(relationship)
 processNodes[molecule]["doubleActivation"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleActivation"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 elif not combination[0] and combination[1]:
 if motif in ["ordering"]:
 requirementDependencies[molecule][motif].remove(
Expand All@@ -700,14 +700,14 @@ def getContextRequirements(
 requirementDependencies[molecule]["reprordering"].append(
 relationship
 )
 processNodes[molecule]["reprordering"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["reprordering"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )

 elif not combination[0] and not combination[1]:
 processNodes[molecule]["doubleRepression"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleRepression"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 if motif == "repression":
 requirementDependencies[molecule][motif].remove(
 relationship
Expand Down

43 changes: 23 additions & 20 deletions
bionetgen/atomizer/rulifier/postAnalysis.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -128,11 +128,11 @@ def getParticipatingReactions(self, molecule, componentPair, reactionDictionary)
 for x in reactionDictionary[moleculeName][component]
 if x in componentPair
 ]:
 correlationList[
(component[0], componentComplement)
] = reactionDictionary[moleculeName][component][
componentComplement
]
 correlationList[(component[0], componentComplement)] = (
reactionDictionary[moleculeName][component][
 componentComplement
]
)
 return correlationList

 def getPairsFromMotif(self, motif1, motif2, excludedComponents):
Expand All@@ -146,10 +146,10 @@ def getPairsFromMotif(self, motif1, motif2, excludedComponents):
 if len(self.motifMoleculeDict[element][molecule]) > 0:
 for componentPair in self.motifMoleculeDict[element][molecule]:
 if not any(x in excludedComponents for x in componentPair):
 correlationList[
componentPair
] = self.getParticipatingReactions(
molecule, componentPair, self.patternXreactions
 correlationList[componentPair] = (
self.getParticipatingReactions(
 molecule, componentPair, self.patternXreactions
)
 )
 moleculeCorrelationList[molecule].update(correlationList)
 return dict(moleculeCorrelationList)
Expand DownExpand Up@@ -283,10 +283,13 @@ def getClassification(keys, translator):
 localAnalysisFlag = True
 if not any(
 [
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x]) > 0
 else molecule in x
 (
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x])
 > 0
 else molecule in x
 )
 for x in difference
 ]
 ):
Expand DownExpand Up@@ -372,9 +375,9 @@ def getContextMotifInformation(self):
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
frozenset([requirementClass, requirementClass])
] = self.getPairsFromMotif(requirementClass, requirementClass, [])
 motifDictionary[frozenset([requirementClass, requirementClass])] = (
self.getPairsFromMotif(requirementClass, requirementClass, [])
 )
 return motifDictionary

 def getComplexReactions(self, threshold=2):
Expand DownExpand Up@@ -548,10 +551,10 @@ def runTests():
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
(requirementClass, requirementClass)
] = modelLearning.getPairsFromMotif(
requirementClass, requirementClass, ["imod"]
 motifDictionary[(requirementClass, requirementClass)] = (
modelLearning.getPairsFromMotif(
 requirementClass, requirementClass, ["imod"]
)
 )
 if len(motifDictionary[(requirementClass, requirementClass)]) > 0:
 print(
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/stateTransitionDiagram.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -138,9 +138,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -158,9 +158,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -179,9 +179,9 @@ def isActive(state):
 for species in productUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in destinationCounter:
 destinationCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 destinationCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand Down
Loading
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('^' + ".*" + '

Skip to content
sympy: lazy import sympy + SBML getSize compatibility fix#63

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 Merged

jrfaeder
merged 5 commits into

from

Mar 17, 2026
 Merged


sympy: lazy import sympy + SBML getSize compatibility fix
#63
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46aeffa

sympy: lazy import sympy + SBML getSize compatibility fix


akutuva21 Mar 17, 2026
6a93f10

Refactor code to improve compatibility and maintainability:


akutuva21 Mar 17, 2026
c392f2b

CI fixes


akutuva21 Mar 17, 2026
9b7bd7a

CI and Black lint fixes


akutuva21 Mar 17, 2026
e3b7a2a

Black lint changes to match version used by CI


akutuva21 Mar 17, 2026

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14 changes: 7 additions & 7 deletions
.github/workflows/ci.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,17 +21,17 @@ jobs:
 fail-fast: false
 matrix:
 os: [ubuntu-latest, windows-latest, macos-latest]
 python-version: [3.7, 3.8]
 python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 steps:
 - uses: actions/checkout@v2
 - uses: actions/checkout@v4
 with:
 fetch-depth: 0
 - name: Set up Python ${{ matrix.python-version }}
 uses: actions/setup-python@v2
 uses: actions/setup-python@v5
 with:
 python-version: ${{ matrix.python-version }}
 - name: Cache pip
 uses: actions/cache@v2
 uses: actions/cache@v4
 with:
 path: ~/.cache/pip
 key: ${{ runner.os }}-pip-${{ hashFiles('requirements-dev.txt') }}
Expand All@@ -41,7 +41,7 @@ jobs:
 - name: Install dependencies
 run: |
 if [ "$RUNNER_OS" == "Linux" ]; then
 sudo apt-get -y install libncurses5-dev libncursesw5-dev libncurses5
sudo apt-get update && sudo apt-get -y install libncurses-dev
 fi
 python -m pip install --upgrade pip
 pip install -r requirements-dev.txt
Expand DownExpand Up@@ -73,7 +73,7 @@ jobs:
 uses: docker/login-action@v2
 with:
 registry: ghcr.io
 username: ${{ secrets.GHCR_USER }}
 username: ${{ github.actor }}
 password: ${{ secrets.GITHUB_TOKEN }}

 - name: Extract metadata (tags, labels) for Docker
Expand All@@ -86,7 +86,7 @@ jobs:
 uses: docker/build-push-action@v4.0.0
 with:
 context: .
 push: true
 push: ${{ github.event_name != 'pull_request' }}
 tags: ${{ steps.meta.outputs.tags }}
 labels: ${{ steps.meta.outputs.labels }}

Expand Down

4 changes: 1 addition & 3 deletions
Dockerfile

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,7 @@ LABEL org.opencontainers.image.source=https://github.com/RuleWorld/PyBioNetGen
LABEL org.opencontainers.image.description="PyBNG container"
LABEL org.opencontainers.image.licenses=MIT
RUN apt-get update && apt-get install -y \
 libncurses5-dev \
 libncursesw5-dev \
 libncurses5
 libncurses-dev
WORKDIR /src
COPY . /src
RUN pip install --no-cache-dir -r requirements.txt 
Expand Down

4 changes: 2 additions & 2 deletions
Issues/parameter_init/parameter_init.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
import bionetgen
import bionetgen

parameter = bionetgen.modelapi.structs.Parameter("A0", "10")
print(parameter.gen_string())
print(parameter.gen_string())

4 changes: 2 additions & 2 deletions
Issues/rule_keywords/run_pybng.py

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import bionetgen

mname="test_deleteMolecules"
model= bionetgen.bngmodel(mname+".bngl")
mname = "test_deleteMolecules"
model= bionetgen.bngmodel(mname + ".bngl")
print(model)

20 changes: 20 additions & 0 deletions
bionetgen/__init__.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,3 +2,23 @@
from .modelapi import bngmodel
from .modelapi.runner import run
from .simulator import sim_getter

# sympy is an expensive dependency to import. We delay importing the
# SympyOdes helpers until they are actually accessed.

__all__ = [
 "defaults",
 "bngmodel",
 "run",
 "sim_getter",
 "SympyOdes",
 "export_sympy_odes",
]


def __getattr__(name):
 if name in {"SympyOdes", "export_sympy_odes"}:
 from .modelapi.sympy_odes import SympyOdes, export_sympy_odes

 return locals()[name]
 raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizeTool.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,6 @@

from bionetgen.core.utils.logging import BNGLogger, log_level


d = BNGDefaults()


Expand Down

7 changes: 3 additions & 4 deletions
bionetgen/atomizer/atomizer/analyzeSBML.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,7 +6,6 @@
"""

import enum
import imp
from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore
import numpy as np
import json
Expand DownExpand Up@@ -820,9 +819,9 @@ def loadConfigFiles(self, fileName):
 # deal with modifications
 if "modificationDefinition" in reactionDefinition_new:
 # TODO: Change file format to be nicer?
 reactionDefinition[
 "modificationDefinition"
] = reactionDefinition_new["modificationDefinition"]
 reactionDefinition["modificationDefinition"] = (
reactionDefinition_new["modificationDefinition"]
)
 # convert new JSON format to old data format
 else:
 reactionDefinition["modificationDefinition"] = {}
Expand Down

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizer/atomizationAux.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,6 @@


class CycleError(Exception):

 """Exception raised for errors in the input.

 Attributes:
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/atomizer/detectOntology.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

import pprint
import difflib
from collections import Counter
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/atomizer/resolveSCT.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -113,9 +113,9 @@ def createSpeciesCompositionGraph(
 # lexicalDependencyGraph[element], oldDependency))
 """
 if self.database.dependencyGraph[element] != []:
 self.database.alternativeDependencyGraph[
 element
] = lexicalDependencyGraph[element]
 self.database.alternativeDependencyGraph[element] = (
lexicalDependencyGraph[element]
)
 else:
 logMess(
 "INFO:LAE009",
Expand DownExpand Up@@ -1464,9 +1464,9 @@ def selectBestCandidate(

 tmpCandidates = namingTmpCandidates
 if loginformation:
 self.database.alternativeDependencyGraph[
reactant
] = tmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
tmpCandidates
)
 elif all(
 sorted(x) == sorted(originalTmpCandidates[0])
 for x in originalTmpCandidates
Expand DownExpand Up@@ -1568,9 +1568,9 @@ def selectBestCandidate(
 namingTmpCandidates = tmpCandidates

 else:
 self.database.alternativeDependencyGraph[
reactant
] = namingtmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
namingtmpCandidates
)
 logMess(
 "WARNING:SCT111",
 "{0}:stoichiometry analysis:{1}:conflicts with and naming conventions:{2}:Selecting lexical analysis".format(
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/contactMap.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

# import sys
# sys.path.insert(0, '../utils/')
import utils.consoleCommands as console
Expand Down

25 changes: 12 additions & 13 deletions
bionetgen/atomizer/libsbml2bngl.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@

#!/usr/bin/env python
from collections import OrderedDict
from telnetlib import IP
import time
import libsbml
import bionetgen.atomizer.writer.bnglWriter as writer
Expand DownExpand Up@@ -438,9 +437,9 @@ def extractCompartmentStatistics(
 for element in compartmentPairs:
 if element[0][0] not in finalCompartmentPairs:
 finalCompartmentPairs[element[0][0]] = {}
 finalCompartmentPairs[element[0][0]][
tuple([element[0][1], element[1][1]])
] = compartmentPairs[element]
 finalCompartmentPairs[element[0][0]][tuple([element[0][1], element[1][1]])] = (
compartmentPairs[element]
)
 return finalCompartmentPairs


Expand DownExpand Up@@ -1457,16 +1456,16 @@ def analyzeHelper(
 param = ["__epsilon__ 1e-100"] + param

 if atomize:
 commentDictionary[
 "notes"
] = "'This is an atomized translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is an atomized translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 else:
 commentDictionary[
 "notes"
] = "'This is a plain translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is a plain translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 commentDictionary[
 "notes"
Expand DownExpand Up@@ -1652,7 +1651,7 @@ def main():
 metavar="FILE",
 )

(options, _) = parser.parse_args()
 options, _ = parser.parse_args()
 # 144
 rdfArray = []
 # classificationArray = []
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/componentGroups.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -681,9 +681,9 @@ def getContextRequirements(
 requirementDependencies[molecule][
 "doubleActivation"
 ].append(relationship)
 processNodes[molecule]["doubleActivation"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleActivation"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 elif not combination[0] and combination[1]:
 if motif in ["ordering"]:
 requirementDependencies[molecule][motif].remove(
Expand All@@ -700,14 +700,14 @@ def getContextRequirements(
 requirementDependencies[molecule]["reprordering"].append(
 relationship
 )
 processNodes[molecule]["reprordering"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["reprordering"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )

 elif not combination[0] and not combination[1]:
 processNodes[molecule]["doubleRepression"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleRepression"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 if motif == "repression":
 requirementDependencies[molecule][motif].remove(
 relationship
Expand Down

43 changes: 23 additions & 20 deletions
bionetgen/atomizer/rulifier/postAnalysis.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -128,11 +128,11 @@ def getParticipatingReactions(self, molecule, componentPair, reactionDictionary)
 for x in reactionDictionary[moleculeName][component]
 if x in componentPair
 ]:
 correlationList[
(component[0], componentComplement)
] = reactionDictionary[moleculeName][component][
componentComplement
]
 correlationList[(component[0], componentComplement)] = (
reactionDictionary[moleculeName][component][
 componentComplement
]
)
 return correlationList

 def getPairsFromMotif(self, motif1, motif2, excludedComponents):
Expand All@@ -146,10 +146,10 @@ def getPairsFromMotif(self, motif1, motif2, excludedComponents):
 if len(self.motifMoleculeDict[element][molecule]) > 0:
 for componentPair in self.motifMoleculeDict[element][molecule]:
 if not any(x in excludedComponents for x in componentPair):
 correlationList[
componentPair
] = self.getParticipatingReactions(
molecule, componentPair, self.patternXreactions
 correlationList[componentPair] = (
self.getParticipatingReactions(
 molecule, componentPair, self.patternXreactions
)
 )
 moleculeCorrelationList[molecule].update(correlationList)
 return dict(moleculeCorrelationList)
Expand DownExpand Up@@ -283,10 +283,13 @@ def getClassification(keys, translator):
 localAnalysisFlag = True
 if not any(
 [
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x]) > 0
 else molecule in x
 (
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x])
 > 0
 else molecule in x
 )
 for x in difference
 ]
 ):
Expand DownExpand Up@@ -372,9 +375,9 @@ def getContextMotifInformation(self):
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
frozenset([requirementClass, requirementClass])
] = self.getPairsFromMotif(requirementClass, requirementClass, [])
 motifDictionary[frozenset([requirementClass, requirementClass])] = (
self.getPairsFromMotif(requirementClass, requirementClass, [])
 )
 return motifDictionary

 def getComplexReactions(self, threshold=2):
Expand DownExpand Up@@ -548,10 +551,10 @@ def runTests():
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
(requirementClass, requirementClass)
] = modelLearning.getPairsFromMotif(
requirementClass, requirementClass, ["imod"]
 motifDictionary[(requirementClass, requirementClass)] = (
modelLearning.getPairsFromMotif(
 requirementClass, requirementClass, ["imod"]
)
 )
 if len(motifDictionary[(requirementClass, requirementClass)]) > 0:
 print(
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/stateTransitionDiagram.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -138,9 +138,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -158,9 +158,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -179,9 +179,9 @@ def isActive(state):
 for species in productUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in destinationCounter:
 destinationCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 destinationCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand Down
Loading
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
sympy: lazy import sympy + SBML getSize compatibility fix#63

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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to your account

 Merged

jrfaeder
merged 5 commits into

from

Mar 17, 2026
 Merged


sympy: lazy import sympy + SBML getSize compatibility fix
#63
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5 commits


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46aeffa

sympy: lazy import sympy + SBML getSize compatibility fix


akutuva21 Mar 17, 2026
6a93f10

Refactor code to improve compatibility and maintainability:


akutuva21 Mar 17, 2026
c392f2b

CI fixes


akutuva21 Mar 17, 2026
9b7bd7a

CI and Black lint fixes


akutuva21 Mar 17, 2026
e3b7a2a

Black lint changes to match version used by CI


akutuva21 Mar 17, 2026

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Filter by extension
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14 changes: 7 additions & 7 deletions
.github/workflows/ci.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,17 +21,17 @@ jobs:
 fail-fast: false
 matrix:
 os: [ubuntu-latest, windows-latest, macos-latest]
 python-version: [3.7, 3.8]
 python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 steps:
 - uses: actions/checkout@v2
 - uses: actions/checkout@v4
 with:
 fetch-depth: 0
 - name: Set up Python ${{ matrix.python-version }}
 uses: actions/setup-python@v2
 uses: actions/setup-python@v5
 with:
 python-version: ${{ matrix.python-version }}
 - name: Cache pip
 uses: actions/cache@v2
 uses: actions/cache@v4
 with:
 path: ~/.cache/pip
 key: ${{ runner.os }}-pip-${{ hashFiles('requirements-dev.txt') }}
Expand All@@ -41,7 +41,7 @@ jobs:
 - name: Install dependencies
 run: |
 if [ "$RUNNER_OS" == "Linux" ]; then
 sudo apt-get -y install libncurses5-dev libncursesw5-dev libncurses5
sudo apt-get update && sudo apt-get -y install libncurses-dev
 fi
 python -m pip install --upgrade pip
 pip install -r requirements-dev.txt
Expand DownExpand Up@@ -73,7 +73,7 @@ jobs:
 uses: docker/login-action@v2
 with:
 registry: ghcr.io
 username: ${{ secrets.GHCR_USER }}
 username: ${{ github.actor }}
 password: ${{ secrets.GITHUB_TOKEN }}

 - name: Extract metadata (tags, labels) for Docker
Expand All@@ -86,7 +86,7 @@ jobs:
 uses: docker/build-push-action@v4.0.0
 with:
 context: .
 push: true
 push: ${{ github.event_name != 'pull_request' }}
 tags: ${{ steps.meta.outputs.tags }}
 labels: ${{ steps.meta.outputs.labels }}

Expand Down

4 changes: 1 addition & 3 deletions
Dockerfile

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,7 @@ LABEL org.opencontainers.image.source=https://github.com/RuleWorld/PyBioNetGen
LABEL org.opencontainers.image.description="PyBNG container"
LABEL org.opencontainers.image.licenses=MIT
RUN apt-get update && apt-get install -y \
 libncurses5-dev \
 libncursesw5-dev \
 libncurses5
 libncurses-dev
WORKDIR /src
COPY . /src
RUN pip install --no-cache-dir -r requirements.txt 
Expand Down

4 changes: 2 additions & 2 deletions
Issues/parameter_init/parameter_init.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
import bionetgen
import bionetgen

parameter = bionetgen.modelapi.structs.Parameter("A0", "10")
print(parameter.gen_string())
print(parameter.gen_string())

4 changes: 2 additions & 2 deletions
Issues/rule_keywords/run_pybng.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import bionetgen

mname="test_deleteMolecules"
model= bionetgen.bngmodel(mname+".bngl")
mname = "test_deleteMolecules"
model= bionetgen.bngmodel(mname + ".bngl")
print(model)

20 changes: 20 additions & 0 deletions
bionetgen/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,3 +2,23 @@
from .modelapi import bngmodel
from .modelapi.runner import run
from .simulator import sim_getter

# sympy is an expensive dependency to import. We delay importing the
# SympyOdes helpers until they are actually accessed.

__all__ = [
 "defaults",
 "bngmodel",
 "run",
 "sim_getter",
 "SympyOdes",
 "export_sympy_odes",
]


def __getattr__(name):
 if name in {"SympyOdes", "export_sympy_odes"}:
 from .modelapi.sympy_odes import SympyOdes, export_sympy_odes

 return locals()[name]
 raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizeTool.py

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,6 @@

from bionetgen.core.utils.logging import BNGLogger, log_level


d = BNGDefaults()


Expand Down

7 changes: 3 additions & 4 deletions
bionetgen/atomizer/atomizer/analyzeSBML.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,7 +6,6 @@
"""

import enum
import imp
from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore
import numpy as np
import json
Expand DownExpand Up@@ -820,9 +819,9 @@ def loadConfigFiles(self, fileName):
 # deal with modifications
 if "modificationDefinition" in reactionDefinition_new:
 # TODO: Change file format to be nicer?
 reactionDefinition[
 "modificationDefinition"
] = reactionDefinition_new["modificationDefinition"]
 reactionDefinition["modificationDefinition"] = (
reactionDefinition_new["modificationDefinition"]
)
 # convert new JSON format to old data format
 else:
 reactionDefinition["modificationDefinition"] = {}
Expand Down

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizer/atomizationAux.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,6 @@


class CycleError(Exception):

 """Exception raised for errors in the input.

 Attributes:
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/atomizer/detectOntology.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

import pprint
import difflib
from collections import Counter
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/atomizer/resolveSCT.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -113,9 +113,9 @@ def createSpeciesCompositionGraph(
 # lexicalDependencyGraph[element], oldDependency))
 """
 if self.database.dependencyGraph[element] != []:
 self.database.alternativeDependencyGraph[
 element
] = lexicalDependencyGraph[element]
 self.database.alternativeDependencyGraph[element] = (
lexicalDependencyGraph[element]
)
 else:
 logMess(
 "INFO:LAE009",
Expand DownExpand Up@@ -1464,9 +1464,9 @@ def selectBestCandidate(

 tmpCandidates = namingTmpCandidates
 if loginformation:
 self.database.alternativeDependencyGraph[
reactant
] = tmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
tmpCandidates
)
 elif all(
 sorted(x) == sorted(originalTmpCandidates[0])
 for x in originalTmpCandidates
Expand DownExpand Up@@ -1568,9 +1568,9 @@ def selectBestCandidate(
 namingTmpCandidates = tmpCandidates

 else:
 self.database.alternativeDependencyGraph[
reactant
] = namingtmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
namingtmpCandidates
)
 logMess(
 "WARNING:SCT111",
 "{0}:stoichiometry analysis:{1}:conflicts with and naming conventions:{2}:Selecting lexical analysis".format(
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/contactMap.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

# import sys
# sys.path.insert(0, '../utils/')
import utils.consoleCommands as console
Expand Down

25 changes: 12 additions & 13 deletions
bionetgen/atomizer/libsbml2bngl.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@

#!/usr/bin/env python
from collections import OrderedDict
from telnetlib import IP
import time
import libsbml
import bionetgen.atomizer.writer.bnglWriter as writer
Expand DownExpand Up@@ -438,9 +437,9 @@ def extractCompartmentStatistics(
 for element in compartmentPairs:
 if element[0][0] not in finalCompartmentPairs:
 finalCompartmentPairs[element[0][0]] = {}
 finalCompartmentPairs[element[0][0]][
tuple([element[0][1], element[1][1]])
] = compartmentPairs[element]
 finalCompartmentPairs[element[0][0]][tuple([element[0][1], element[1][1]])] = (
compartmentPairs[element]
)
 return finalCompartmentPairs


Expand DownExpand Up@@ -1457,16 +1456,16 @@ def analyzeHelper(
 param = ["__epsilon__ 1e-100"] + param

 if atomize:
 commentDictionary[
 "notes"
] = "'This is an atomized translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is an atomized translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 else:
 commentDictionary[
 "notes"
] = "'This is a plain translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is a plain translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 commentDictionary[
 "notes"
Expand DownExpand Up@@ -1652,7 +1651,7 @@ def main():
 metavar="FILE",
 )

(options, _) = parser.parse_args()
 options, _ = parser.parse_args()
 # 144
 rdfArray = []
 # classificationArray = []
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/componentGroups.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -681,9 +681,9 @@ def getContextRequirements(
 requirementDependencies[molecule][
 "doubleActivation"
 ].append(relationship)
 processNodes[molecule]["doubleActivation"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleActivation"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 elif not combination[0] and combination[1]:
 if motif in ["ordering"]:
 requirementDependencies[molecule][motif].remove(
Expand All@@ -700,14 +700,14 @@ def getContextRequirements(
 requirementDependencies[molecule]["reprordering"].append(
 relationship
 )
 processNodes[molecule]["reprordering"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["reprordering"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )

 elif not combination[0] and not combination[1]:
 processNodes[molecule]["doubleRepression"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleRepression"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 if motif == "repression":
 requirementDependencies[molecule][motif].remove(
 relationship
Expand Down

43 changes: 23 additions & 20 deletions
bionetgen/atomizer/rulifier/postAnalysis.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -128,11 +128,11 @@ def getParticipatingReactions(self, molecule, componentPair, reactionDictionary)
 for x in reactionDictionary[moleculeName][component]
 if x in componentPair
 ]:
 correlationList[
(component[0], componentComplement)
] = reactionDictionary[moleculeName][component][
componentComplement
]
 correlationList[(component[0], componentComplement)] = (
reactionDictionary[moleculeName][component][
 componentComplement
]
)
 return correlationList

 def getPairsFromMotif(self, motif1, motif2, excludedComponents):
Expand All@@ -146,10 +146,10 @@ def getPairsFromMotif(self, motif1, motif2, excludedComponents):
 if len(self.motifMoleculeDict[element][molecule]) > 0:
 for componentPair in self.motifMoleculeDict[element][molecule]:
 if not any(x in excludedComponents for x in componentPair):
 correlationList[
componentPair
] = self.getParticipatingReactions(
molecule, componentPair, self.patternXreactions
 correlationList[componentPair] = (
self.getParticipatingReactions(
 molecule, componentPair, self.patternXreactions
)
 )
 moleculeCorrelationList[molecule].update(correlationList)
 return dict(moleculeCorrelationList)
Expand DownExpand Up@@ -283,10 +283,13 @@ def getClassification(keys, translator):
 localAnalysisFlag = True
 if not any(
 [
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x]) > 0
 else molecule in x
 (
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x])
 > 0
 else molecule in x
 )
 for x in difference
 ]
 ):
Expand DownExpand Up@@ -372,9 +375,9 @@ def getContextMotifInformation(self):
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
frozenset([requirementClass, requirementClass])
] = self.getPairsFromMotif(requirementClass, requirementClass, [])
 motifDictionary[frozenset([requirementClass, requirementClass])] = (
self.getPairsFromMotif(requirementClass, requirementClass, [])
 )
 return motifDictionary

 def getComplexReactions(self, threshold=2):
Expand DownExpand Up@@ -548,10 +551,10 @@ def runTests():
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
(requirementClass, requirementClass)
] = modelLearning.getPairsFromMotif(
requirementClass, requirementClass, ["imod"]
 motifDictionary[(requirementClass, requirementClass)] = (
modelLearning.getPairsFromMotif(
 requirementClass, requirementClass, ["imod"]
)
 )
 if len(motifDictionary[(requirementClass, requirementClass)]) > 0:
 print(
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/stateTransitionDiagram.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -138,9 +138,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -158,9 +158,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -179,9 +179,9 @@ def isActive(state):
 for species in productUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in destinationCounter:
 destinationCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 destinationCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand Down
Loading
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('^' + ".*" + '

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sympy: lazy import sympy + SBML getSize compatibility fix#63

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 Merged

jrfaeder
merged 5 commits into

from

Mar 17, 2026
 Merged


sympy: lazy import sympy + SBML getSize compatibility fix
#63
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46aeffa

sympy: lazy import sympy + SBML getSize compatibility fix


akutuva21 Mar 17, 2026
6a93f10

Refactor code to improve compatibility and maintainability:


akutuva21 Mar 17, 2026
c392f2b

CI fixes


akutuva21 Mar 17, 2026
9b7bd7a

CI and Black lint fixes


akutuva21 Mar 17, 2026
e3b7a2a

Black lint changes to match version used by CI


akutuva21 Mar 17, 2026

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14 changes: 7 additions & 7 deletions
.github/workflows/ci.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,17 +21,17 @@ jobs:
 fail-fast: false
 matrix:
 os: [ubuntu-latest, windows-latest, macos-latest]
 python-version: [3.7, 3.8]
 python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 steps:
 - uses: actions/checkout@v2
 - uses: actions/checkout@v4
 with:
 fetch-depth: 0
 - name: Set up Python ${{ matrix.python-version }}
 uses: actions/setup-python@v2
 uses: actions/setup-python@v5
 with:
 python-version: ${{ matrix.python-version }}
 - name: Cache pip
 uses: actions/cache@v2
 uses: actions/cache@v4
 with:
 path: ~/.cache/pip
 key: ${{ runner.os }}-pip-${{ hashFiles('requirements-dev.txt') }}
Expand All@@ -41,7 +41,7 @@ jobs:
 - name: Install dependencies
 run: |
 if [ "$RUNNER_OS" == "Linux" ]; then
 sudo apt-get -y install libncurses5-dev libncursesw5-dev libncurses5
sudo apt-get update && sudo apt-get -y install libncurses-dev
 fi
 python -m pip install --upgrade pip
 pip install -r requirements-dev.txt
Expand DownExpand Up@@ -73,7 +73,7 @@ jobs:
 uses: docker/login-action@v2
 with:
 registry: ghcr.io
 username: ${{ secrets.GHCR_USER }}
 username: ${{ github.actor }}
 password: ${{ secrets.GITHUB_TOKEN }}

 - name: Extract metadata (tags, labels) for Docker
Expand All@@ -86,7 +86,7 @@ jobs:
 uses: docker/build-push-action@v4.0.0
 with:
 context: .
 push: true
 push: ${{ github.event_name != 'pull_request' }}
 tags: ${{ steps.meta.outputs.tags }}
 labels: ${{ steps.meta.outputs.labels }}

Expand Down

4 changes: 1 addition & 3 deletions
Dockerfile

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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,7 @@ LABEL org.opencontainers.image.source=https://github.com/RuleWorld/PyBioNetGen
LABEL org.opencontainers.image.description="PyBNG container"
LABEL org.opencontainers.image.licenses=MIT
RUN apt-get update && apt-get install -y \
 libncurses5-dev \
 libncursesw5-dev \
 libncurses5
 libncurses-dev
WORKDIR /src
COPY . /src
RUN pip install --no-cache-dir -r requirements.txt 
Expand Down

4 changes: 2 additions & 2 deletions
Issues/parameter_init/parameter_init.py

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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
import bionetgen
import bionetgen

parameter = bionetgen.modelapi.structs.Parameter("A0", "10")
print(parameter.gen_string())
print(parameter.gen_string())

4 changes: 2 additions & 2 deletions
Issues/rule_keywords/run_pybng.py

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import bionetgen

mname="test_deleteMolecules"
model= bionetgen.bngmodel(mname+".bngl")
mname = "test_deleteMolecules"
model= bionetgen.bngmodel(mname + ".bngl")
print(model)

20 changes: 20 additions & 0 deletions
bionetgen/__init__.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,3 +2,23 @@
from .modelapi import bngmodel
from .modelapi.runner import run
from .simulator import sim_getter

# sympy is an expensive dependency to import. We delay importing the
# SympyOdes helpers until they are actually accessed.

__all__ = [
 "defaults",
 "bngmodel",
 "run",
 "sim_getter",
 "SympyOdes",
 "export_sympy_odes",
]


def __getattr__(name):
 if name in {"SympyOdes", "export_sympy_odes"}:
 from .modelapi.sympy_odes import SympyOdes, export_sympy_odes

 return locals()[name]
 raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizeTool.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,6 @@

from bionetgen.core.utils.logging import BNGLogger, log_level


d = BNGDefaults()


Expand Down

7 changes: 3 additions & 4 deletions
bionetgen/atomizer/atomizer/analyzeSBML.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,7 +6,6 @@
"""

import enum
import imp
from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore
import numpy as np
import json
Expand DownExpand Up@@ -820,9 +819,9 @@ def loadConfigFiles(self, fileName):
 # deal with modifications
 if "modificationDefinition" in reactionDefinition_new:
 # TODO: Change file format to be nicer?
 reactionDefinition[
 "modificationDefinition"
] = reactionDefinition_new["modificationDefinition"]
 reactionDefinition["modificationDefinition"] = (
reactionDefinition_new["modificationDefinition"]
)
 # convert new JSON format to old data format
 else:
 reactionDefinition["modificationDefinition"] = {}
Expand Down

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizer/atomizationAux.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,6 @@


class CycleError(Exception):

 """Exception raised for errors in the input.

 Attributes:
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/atomizer/detectOntology.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

import pprint
import difflib
from collections import Counter
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/atomizer/resolveSCT.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -113,9 +113,9 @@ def createSpeciesCompositionGraph(
 # lexicalDependencyGraph[element], oldDependency))
 """
 if self.database.dependencyGraph[element] != []:
 self.database.alternativeDependencyGraph[
 element
] = lexicalDependencyGraph[element]
 self.database.alternativeDependencyGraph[element] = (
lexicalDependencyGraph[element]
)
 else:
 logMess(
 "INFO:LAE009",
Expand DownExpand Up@@ -1464,9 +1464,9 @@ def selectBestCandidate(

 tmpCandidates = namingTmpCandidates
 if loginformation:
 self.database.alternativeDependencyGraph[
reactant
] = tmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
tmpCandidates
)
 elif all(
 sorted(x) == sorted(originalTmpCandidates[0])
 for x in originalTmpCandidates
Expand DownExpand Up@@ -1568,9 +1568,9 @@ def selectBestCandidate(
 namingTmpCandidates = tmpCandidates

 else:
 self.database.alternativeDependencyGraph[
reactant
] = namingtmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
namingtmpCandidates
)
 logMess(
 "WARNING:SCT111",
 "{0}:stoichiometry analysis:{1}:conflicts with and naming conventions:{2}:Selecting lexical analysis".format(
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/contactMap.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

# import sys
# sys.path.insert(0, '../utils/')
import utils.consoleCommands as console
Expand Down

25 changes: 12 additions & 13 deletions
bionetgen/atomizer/libsbml2bngl.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@

#!/usr/bin/env python
from collections import OrderedDict
from telnetlib import IP
import time
import libsbml
import bionetgen.atomizer.writer.bnglWriter as writer
Expand DownExpand Up@@ -438,9 +437,9 @@ def extractCompartmentStatistics(
 for element in compartmentPairs:
 if element[0][0] not in finalCompartmentPairs:
 finalCompartmentPairs[element[0][0]] = {}
 finalCompartmentPairs[element[0][0]][
tuple([element[0][1], element[1][1]])
] = compartmentPairs[element]
 finalCompartmentPairs[element[0][0]][tuple([element[0][1], element[1][1]])] = (
compartmentPairs[element]
)
 return finalCompartmentPairs


Expand DownExpand Up@@ -1457,16 +1456,16 @@ def analyzeHelper(
 param = ["__epsilon__ 1e-100"] + param

 if atomize:
 commentDictionary[
 "notes"
] = "'This is an atomized translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is an atomized translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 else:
 commentDictionary[
 "notes"
] = "'This is a plain translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is a plain translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 commentDictionary[
 "notes"
Expand DownExpand Up@@ -1652,7 +1651,7 @@ def main():
 metavar="FILE",
 )

(options, _) = parser.parse_args()
 options, _ = parser.parse_args()
 # 144
 rdfArray = []
 # classificationArray = []
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/componentGroups.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -681,9 +681,9 @@ def getContextRequirements(
 requirementDependencies[molecule][
 "doubleActivation"
 ].append(relationship)
 processNodes[molecule]["doubleActivation"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleActivation"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 elif not combination[0] and combination[1]:
 if motif in ["ordering"]:
 requirementDependencies[molecule][motif].remove(
Expand All@@ -700,14 +700,14 @@ def getContextRequirements(
 requirementDependencies[molecule]["reprordering"].append(
 relationship
 )
 processNodes[molecule]["reprordering"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["reprordering"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )

 elif not combination[0] and not combination[1]:
 processNodes[molecule]["doubleRepression"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleRepression"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 if motif == "repression":
 requirementDependencies[molecule][motif].remove(
 relationship
Expand Down

43 changes: 23 additions & 20 deletions
bionetgen/atomizer/rulifier/postAnalysis.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -128,11 +128,11 @@ def getParticipatingReactions(self, molecule, componentPair, reactionDictionary)
 for x in reactionDictionary[moleculeName][component]
 if x in componentPair
 ]:
 correlationList[
(component[0], componentComplement)
] = reactionDictionary[moleculeName][component][
componentComplement
]
 correlationList[(component[0], componentComplement)] = (
reactionDictionary[moleculeName][component][
 componentComplement
]
)
 return correlationList

 def getPairsFromMotif(self, motif1, motif2, excludedComponents):
Expand All@@ -146,10 +146,10 @@ def getPairsFromMotif(self, motif1, motif2, excludedComponents):
 if len(self.motifMoleculeDict[element][molecule]) > 0:
 for componentPair in self.motifMoleculeDict[element][molecule]:
 if not any(x in excludedComponents for x in componentPair):
 correlationList[
componentPair
] = self.getParticipatingReactions(
molecule, componentPair, self.patternXreactions
 correlationList[componentPair] = (
self.getParticipatingReactions(
 molecule, componentPair, self.patternXreactions
)
 )
 moleculeCorrelationList[molecule].update(correlationList)
 return dict(moleculeCorrelationList)
Expand DownExpand Up@@ -283,10 +283,13 @@ def getClassification(keys, translator):
 localAnalysisFlag = True
 if not any(
 [
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x]) > 0
 else molecule in x
 (
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x])
 > 0
 else molecule in x
 )
 for x in difference
 ]
 ):
Expand DownExpand Up@@ -372,9 +375,9 @@ def getContextMotifInformation(self):
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
frozenset([requirementClass, requirementClass])
] = self.getPairsFromMotif(requirementClass, requirementClass, [])
 motifDictionary[frozenset([requirementClass, requirementClass])] = (
self.getPairsFromMotif(requirementClass, requirementClass, [])
 )
 return motifDictionary

 def getComplexReactions(self, threshold=2):
Expand DownExpand Up@@ -548,10 +551,10 @@ def runTests():
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
(requirementClass, requirementClass)
] = modelLearning.getPairsFromMotif(
requirementClass, requirementClass, ["imod"]
 motifDictionary[(requirementClass, requirementClass)] = (
modelLearning.getPairsFromMotif(
 requirementClass, requirementClass, ["imod"]
)
 )
 if len(motifDictionary[(requirementClass, requirementClass)]) > 0:
 print(
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/stateTransitionDiagram.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -138,9 +138,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -158,9 +158,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -179,9 +179,9 @@ def isActive(state):
 for species in productUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in destinationCounter:
 destinationCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 destinationCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand Down
Loading
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
sympy: lazy import sympy + SBML getSize compatibility fix#63

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 Merged

jrfaeder
merged 5 commits into

from

Mar 17, 2026
 Merged


sympy: lazy import sympy + SBML getSize compatibility fix
#63
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46aeffa

sympy: lazy import sympy + SBML getSize compatibility fix


akutuva21 Mar 17, 2026
6a93f10

Refactor code to improve compatibility and maintainability:


akutuva21 Mar 17, 2026
c392f2b

CI fixes


akutuva21 Mar 17, 2026
9b7bd7a

CI and Black lint fixes


akutuva21 Mar 17, 2026
e3b7a2a

Black lint changes to match version used by CI


akutuva21 Mar 17, 2026

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14 changes: 7 additions & 7 deletions
.github/workflows/ci.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,17 +21,17 @@ jobs:
 fail-fast: false
 matrix:
 os: [ubuntu-latest, windows-latest, macos-latest]
 python-version: [3.7, 3.8]
 python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 steps:
 - uses: actions/checkout@v2
 - uses: actions/checkout@v4
 with:
 fetch-depth: 0
 - name: Set up Python ${{ matrix.python-version }}
 uses: actions/setup-python@v2
 uses: actions/setup-python@v5
 with:
 python-version: ${{ matrix.python-version }}
 - name: Cache pip
 uses: actions/cache@v2
 uses: actions/cache@v4
 with:
 path: ~/.cache/pip
 key: ${{ runner.os }}-pip-${{ hashFiles('requirements-dev.txt') }}
Expand All@@ -41,7 +41,7 @@ jobs:
 - name: Install dependencies
 run: |
 if [ "$RUNNER_OS" == "Linux" ]; then
 sudo apt-get -y install libncurses5-dev libncursesw5-dev libncurses5
sudo apt-get update && sudo apt-get -y install libncurses-dev
 fi
 python -m pip install --upgrade pip
 pip install -r requirements-dev.txt
Expand DownExpand Up@@ -73,7 +73,7 @@ jobs:
 uses: docker/login-action@v2
 with:
 registry: ghcr.io
 username: ${{ secrets.GHCR_USER }}
 username: ${{ github.actor }}
 password: ${{ secrets.GITHUB_TOKEN }}

 - name: Extract metadata (tags, labels) for Docker
Expand All@@ -86,7 +86,7 @@ jobs:
 uses: docker/build-push-action@v4.0.0
 with:
 context: .
 push: true
 push: ${{ github.event_name != 'pull_request' }}
 tags: ${{ steps.meta.outputs.tags }}
 labels: ${{ steps.meta.outputs.labels }}

Expand Down

4 changes: 1 addition & 3 deletions
Dockerfile

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,7 @@ LABEL org.opencontainers.image.source=https://github.com/RuleWorld/PyBioNetGen
LABEL org.opencontainers.image.description="PyBNG container"
LABEL org.opencontainers.image.licenses=MIT
RUN apt-get update && apt-get install -y \
 libncurses5-dev \
 libncursesw5-dev \
 libncurses5
 libncurses-dev
WORKDIR /src
COPY . /src
RUN pip install --no-cache-dir -r requirements.txt 
Expand Down

4 changes: 2 additions & 2 deletions
Issues/parameter_init/parameter_init.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
import bionetgen
import bionetgen

parameter = bionetgen.modelapi.structs.Parameter("A0", "10")
print(parameter.gen_string())
print(parameter.gen_string())

4 changes: 2 additions & 2 deletions
Issues/rule_keywords/run_pybng.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import bionetgen

mname="test_deleteMolecules"
model= bionetgen.bngmodel(mname+".bngl")
mname = "test_deleteMolecules"
model= bionetgen.bngmodel(mname + ".bngl")
print(model)

20 changes: 20 additions & 0 deletions
bionetgen/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,3 +2,23 @@
from .modelapi import bngmodel
from .modelapi.runner import run
from .simulator import sim_getter

# sympy is an expensive dependency to import. We delay importing the
# SympyOdes helpers until they are actually accessed.

__all__ = [
 "defaults",
 "bngmodel",
 "run",
 "sim_getter",
 "SympyOdes",
 "export_sympy_odes",
]


def __getattr__(name):
 if name in {"SympyOdes", "export_sympy_odes"}:
 from .modelapi.sympy_odes import SympyOdes, export_sympy_odes

 return locals()[name]
 raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizeTool.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,6 @@

from bionetgen.core.utils.logging import BNGLogger, log_level


d = BNGDefaults()


Expand Down

7 changes: 3 additions & 4 deletions
bionetgen/atomizer/atomizer/analyzeSBML.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,7 +6,6 @@
"""

import enum
import imp
from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore
import numpy as np
import json
Expand DownExpand Up@@ -820,9 +819,9 @@ def loadConfigFiles(self, fileName):
 # deal with modifications
 if "modificationDefinition" in reactionDefinition_new:
 # TODO: Change file format to be nicer?
 reactionDefinition[
 "modificationDefinition"
] = reactionDefinition_new["modificationDefinition"]
 reactionDefinition["modificationDefinition"] = (
reactionDefinition_new["modificationDefinition"]
)
 # convert new JSON format to old data format
 else:
 reactionDefinition["modificationDefinition"] = {}
Expand Down

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizer/atomizationAux.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,6 @@


class CycleError(Exception):

 """Exception raised for errors in the input.

 Attributes:
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/atomizer/detectOntology.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

import pprint
import difflib
from collections import Counter
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/atomizer/resolveSCT.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -113,9 +113,9 @@ def createSpeciesCompositionGraph(
 # lexicalDependencyGraph[element], oldDependency))
 """
 if self.database.dependencyGraph[element] != []:
 self.database.alternativeDependencyGraph[
 element
] = lexicalDependencyGraph[element]
 self.database.alternativeDependencyGraph[element] = (
lexicalDependencyGraph[element]
)
 else:
 logMess(
 "INFO:LAE009",
Expand DownExpand Up@@ -1464,9 +1464,9 @@ def selectBestCandidate(

 tmpCandidates = namingTmpCandidates
 if loginformation:
 self.database.alternativeDependencyGraph[
reactant
] = tmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
tmpCandidates
)
 elif all(
 sorted(x) == sorted(originalTmpCandidates[0])
 for x in originalTmpCandidates
Expand DownExpand Up@@ -1568,9 +1568,9 @@ def selectBestCandidate(
 namingTmpCandidates = tmpCandidates

 else:
 self.database.alternativeDependencyGraph[
reactant
] = namingtmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
namingtmpCandidates
)
 logMess(
 "WARNING:SCT111",
 "{0}:stoichiometry analysis:{1}:conflicts with and naming conventions:{2}:Selecting lexical analysis".format(
Expand Down

1 change: 1 addition & 0 deletions
bionetgen/atomizer/contactMap.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

# import sys
# sys.path.insert(0, '../utils/')
import utils.consoleCommands as console
Expand Down

25 changes: 12 additions & 13 deletions
bionetgen/atomizer/libsbml2bngl.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@

#!/usr/bin/env python
from collections import OrderedDict
from telnetlib import IP
import time
import libsbml
import bionetgen.atomizer.writer.bnglWriter as writer
Expand DownExpand Up@@ -438,9 +437,9 @@ def extractCompartmentStatistics(
 for element in compartmentPairs:
 if element[0][0] not in finalCompartmentPairs:
 finalCompartmentPairs[element[0][0]] = {}
 finalCompartmentPairs[element[0][0]][
tuple([element[0][1], element[1][1]])
] = compartmentPairs[element]
 finalCompartmentPairs[element[0][0]][tuple([element[0][1], element[1][1]])] = (
compartmentPairs[element]
)
 return finalCompartmentPairs


Expand DownExpand Up@@ -1457,16 +1456,16 @@ def analyzeHelper(
 param = ["__epsilon__ 1e-100"] + param

 if atomize:
 commentDictionary[
 "notes"
] = "'This is an atomized translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is an atomized translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 else:
 commentDictionary[
 "notes"
] = "'This is a plain translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is a plain translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 commentDictionary[
 "notes"
Expand DownExpand Up@@ -1652,7 +1651,7 @@ def main():
 metavar="FILE",
 )

(options, _) = parser.parse_args()
 options, _ = parser.parse_args()
 # 144
 rdfArray = []
 # classificationArray = []
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/componentGroups.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -681,9 +681,9 @@ def getContextRequirements(
 requirementDependencies[molecule][
 "doubleActivation"
 ].append(relationship)
 processNodes[molecule]["doubleActivation"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleActivation"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 elif not combination[0] and combination[1]:
 if motif in ["ordering"]:
 requirementDependencies[molecule][motif].remove(
Expand All@@ -700,14 +700,14 @@ def getContextRequirements(
 requirementDependencies[molecule]["reprordering"].append(
 relationship
 )
 processNodes[molecule]["reprordering"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["reprordering"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )

 elif not combination[0] and not combination[1]:
 processNodes[molecule]["doubleRepression"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleRepression"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 if motif == "repression":
 requirementDependencies[molecule][motif].remove(
 relationship
Expand Down

43 changes: 23 additions & 20 deletions
bionetgen/atomizer/rulifier/postAnalysis.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -128,11 +128,11 @@ def getParticipatingReactions(self, molecule, componentPair, reactionDictionary)
 for x in reactionDictionary[moleculeName][component]
 if x in componentPair
 ]:
 correlationList[
(component[0], componentComplement)
] = reactionDictionary[moleculeName][component][
componentComplement
]
 correlationList[(component[0], componentComplement)] = (
reactionDictionary[moleculeName][component][
 componentComplement
]
)
 return correlationList

 def getPairsFromMotif(self, motif1, motif2, excludedComponents):
Expand All@@ -146,10 +146,10 @@ def getPairsFromMotif(self, motif1, motif2, excludedComponents):
 if len(self.motifMoleculeDict[element][molecule]) > 0:
 for componentPair in self.motifMoleculeDict[element][molecule]:
 if not any(x in excludedComponents for x in componentPair):
 correlationList[
componentPair
] = self.getParticipatingReactions(
molecule, componentPair, self.patternXreactions
 correlationList[componentPair] = (
self.getParticipatingReactions(
 molecule, componentPair, self.patternXreactions
)
 )
 moleculeCorrelationList[molecule].update(correlationList)
 return dict(moleculeCorrelationList)
Expand DownExpand Up@@ -283,10 +283,13 @@ def getClassification(keys, translator):
 localAnalysisFlag = True
 if not any(
 [
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x]) > 0
 else molecule in x
 (
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x])
 > 0
 else molecule in x
 )
 for x in difference
 ]
 ):
Expand DownExpand Up@@ -372,9 +375,9 @@ def getContextMotifInformation(self):
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
frozenset([requirementClass, requirementClass])
] = self.getPairsFromMotif(requirementClass, requirementClass, [])
 motifDictionary[frozenset([requirementClass, requirementClass])] = (
self.getPairsFromMotif(requirementClass, requirementClass, [])
 )
 return motifDictionary

 def getComplexReactions(self, threshold=2):
Expand DownExpand Up@@ -548,10 +551,10 @@ def runTests():
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
(requirementClass, requirementClass)
] = modelLearning.getPairsFromMotif(
requirementClass, requirementClass, ["imod"]
 motifDictionary[(requirementClass, requirementClass)] = (
modelLearning.getPairsFromMotif(
 requirementClass, requirementClass, ["imod"]
)
 )
 if len(motifDictionary[(requirementClass, requirementClass)]) > 0:
 print(
Expand Down

18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/stateTransitionDiagram.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -138,9 +138,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -158,9 +158,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -179,9 +179,9 @@ def isActive(state):
 for species in productUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in destinationCounter:
 destinationCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 destinationCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand Down
Loading
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
sympy: lazy import sympy + SBML getSize compatibility fix#63

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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 Merged

jrfaeder
merged 5 commits into

from

Mar 17, 2026
 Merged


sympy: lazy import sympy + SBML getSize compatibility fix
#63
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Commits

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5 commits


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46aeffa

sympy: lazy import sympy + SBML getSize compatibility fix


akutuva21 Mar 17, 2026
6a93f10

Refactor code to improve compatibility and maintainability:


akutuva21 Mar 17, 2026
c392f2b

CI fixes


akutuva21 Mar 17, 2026
9b7bd7a

CI and Black lint fixes


akutuva21 Mar 17, 2026
e3b7a2a

Black lint changes to match version used by CI


akutuva21 Mar 17, 2026

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Filter by extension
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14 changes: 7 additions & 7 deletions
.github/workflows/ci.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,17 +21,17 @@ jobs:
 fail-fast: false
 matrix:
 os: [ubuntu-latest, windows-latest, macos-latest]
 python-version: [3.7, 3.8]
 python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 steps:
 - uses: actions/checkout@v2
 - uses: actions/checkout@v4
 with:
 fetch-depth: 0
 - name: Set up Python ${{ matrix.python-version }}
 uses: actions/setup-python@v2
 uses: actions/setup-python@v5
 with:
 python-version: ${{ matrix.python-version }}
 - name: Cache pip
 uses: actions/cache@v2
 uses: actions/cache@v4
 with:
 path: ~/.cache/pip
 key: ${{ runner.os }}-pip-${{ hashFiles('requirements-dev.txt') }}
Expand All@@ -41,7 +41,7 @@ jobs:
 - name: Install dependencies
 run: |
 if [ "$RUNNER_OS" == "Linux" ]; then
 sudo apt-get -y install libncurses5-dev libncursesw5-dev libncurses5
sudo apt-get update && sudo apt-get -y install libncurses-dev
 fi
 python -m pip install --upgrade pip
 pip install -r requirements-dev.txt
Expand DownExpand Up@@ -73,7 +73,7 @@ jobs:
 uses: docker/login-action@v2
 with:
 registry: ghcr.io
 username: ${{ secrets.GHCR_USER }}
 username: ${{ github.actor }}
 password: ${{ secrets.GITHUB_TOKEN }}

 - name: Extract metadata (tags, labels) for Docker
Expand All@@ -86,7 +86,7 @@ jobs:
 uses: docker/build-push-action@v4.0.0
 with:
 context: .
 push: true
 push: ${{ github.event_name != 'pull_request' }}
 tags: ${{ steps.meta.outputs.tags }}
 labels: ${{ steps.meta.outputs.labels }}

Expand Down

4 changes: 1 addition & 3 deletions
Dockerfile

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,7 @@ LABEL org.opencontainers.image.source=https://github.com/RuleWorld/PyBioNetGen
LABEL org.opencontainers.image.description="PyBNG container"
LABEL org.opencontainers.image.licenses=MIT
RUN apt-get update && apt-get install -y \
 libncurses5-dev \
 libncursesw5-dev \
 libncurses5
 libncurses-dev
WORKDIR /src
COPY . /src
RUN pip install --no-cache-dir -r requirements.txt 
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4 changes: 2 additions & 2 deletions
Issues/parameter_init/parameter_init.py

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@@ -1,4 +1,4 @@
import bionetgen
import bionetgen

parameter = bionetgen.modelapi.structs.Parameter("A0", "10")
print(parameter.gen_string())
print(parameter.gen_string())

4 changes: 2 additions & 2 deletions
Issues/rule_keywords/run_pybng.py

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@@ -1,5 +1,5 @@
import bionetgen

mname="test_deleteMolecules"
model= bionetgen.bngmodel(mname+".bngl")
mname = "test_deleteMolecules"
model= bionetgen.bngmodel(mname + ".bngl")
print(model)

20 changes: 20 additions & 0 deletions
bionetgen/__init__.py

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Expand Up@@ -2,3 +2,23 @@
from .modelapi import bngmodel
from .modelapi.runner import run
from .simulator import sim_getter

# sympy is an expensive dependency to import. We delay importing the
# SympyOdes helpers until they are actually accessed.

__all__ = [
 "defaults",
 "bngmodel",
 "run",
 "sim_getter",
 "SympyOdes",
 "export_sympy_odes",
]


def __getattr__(name):
 if name in {"SympyOdes", "export_sympy_odes"}:
 from .modelapi.sympy_odes import SympyOdes, export_sympy_odes

 return locals()[name]
 raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizeTool.py

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Expand Up@@ -4,7 +4,6 @@

from bionetgen.core.utils.logging import BNGLogger, log_level


d = BNGDefaults()


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7 changes: 3 additions & 4 deletions
bionetgen/atomizer/atomizer/analyzeSBML.py

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Expand Up@@ -6,7 +6,6 @@
"""

import enum
import imp
from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore
import numpy as np
import json
Expand DownExpand Up@@ -820,9 +819,9 @@ def loadConfigFiles(self, fileName):
 # deal with modifications
 if "modificationDefinition" in reactionDefinition_new:
 # TODO: Change file format to be nicer?
 reactionDefinition[
 "modificationDefinition"
] = reactionDefinition_new["modificationDefinition"]
 reactionDefinition["modificationDefinition"] = (
reactionDefinition_new["modificationDefinition"]
)
 # convert new JSON format to old data format
 else:
 reactionDefinition["modificationDefinition"] = {}
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1 change: 0 additions & 1 deletion
bionetgen/atomizer/atomizer/atomizationAux.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,6 @@


class CycleError(Exception):

 """Exception raised for errors in the input.

 Attributes:
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1 change: 1 addition & 0 deletions
bionetgen/atomizer/atomizer/detectOntology.py

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Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

import pprint
import difflib
from collections import Counter
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18 changes: 9 additions & 9 deletions
bionetgen/atomizer/atomizer/resolveSCT.py

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Expand Up@@ -113,9 +113,9 @@ def createSpeciesCompositionGraph(
 # lexicalDependencyGraph[element], oldDependency))
 """
 if self.database.dependencyGraph[element] != []:
 self.database.alternativeDependencyGraph[
 element
] = lexicalDependencyGraph[element]
 self.database.alternativeDependencyGraph[element] = (
lexicalDependencyGraph[element]
)
 else:
 logMess(
 "INFO:LAE009",
Expand DownExpand Up@@ -1464,9 +1464,9 @@ def selectBestCandidate(

 tmpCandidates = namingTmpCandidates
 if loginformation:
 self.database.alternativeDependencyGraph[
reactant
] = tmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
tmpCandidates
)
 elif all(
 sorted(x) == sorted(originalTmpCandidates[0])
 for x in originalTmpCandidates
Expand DownExpand Up@@ -1568,9 +1568,9 @@ def selectBestCandidate(
 namingTmpCandidates = tmpCandidates

 else:
 self.database.alternativeDependencyGraph[
reactant
] = namingtmpCandidates
 self.database.alternativeDependencyGraph[reactant] = (
namingtmpCandidates
)
 logMess(
 "WARNING:SCT111",
 "{0}:stoichiometry analysis:{1}:conflicts with and naming conventions:{2}:Selecting lexical analysis".format(
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1 change: 1 addition & 0 deletions
bionetgen/atomizer/contactMap.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@

@author: proto
"""

# import sys
# sys.path.insert(0, '../utils/')
import utils.consoleCommands as console
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25 changes: 12 additions & 13 deletions
bionetgen/atomizer/libsbml2bngl.py

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Expand Up@@ -7,7 +7,6 @@

#!/usr/bin/env python
from collections import OrderedDict
from telnetlib import IP
import time
import libsbml
import bionetgen.atomizer.writer.bnglWriter as writer
Expand DownExpand Up@@ -438,9 +437,9 @@ def extractCompartmentStatistics(
 for element in compartmentPairs:
 if element[0][0] not in finalCompartmentPairs:
 finalCompartmentPairs[element[0][0]] = {}
 finalCompartmentPairs[element[0][0]][
tuple([element[0][1], element[1][1]])
] = compartmentPairs[element]
 finalCompartmentPairs[element[0][0]][tuple([element[0][1], element[1][1]])] = (
compartmentPairs[element]
)
 return finalCompartmentPairs


Expand DownExpand Up@@ -1457,16 +1456,16 @@ def analyzeHelper(
 param = ["__epsilon__ 1e-100"] + param

 if atomize:
 commentDictionary[
 "notes"
] = "'This is an atomized translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is an atomized translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 else:
 commentDictionary[
 "notes"
] = "'This is a plain translation of an SBML model created on {0}.".format(
time.strftime("%d/%m/%Y")
 commentDictionary["notes"] = (
 "'This is a plain translation of an SBML model created on {0}.".format(
 time.strftime("%d/%m/%Y")
 )
 )
 commentDictionary[
 "notes"
Expand DownExpand Up@@ -1652,7 +1651,7 @@ def main():
 metavar="FILE",
 )

(options, _) = parser.parse_args()
 options, _ = parser.parse_args()
 # 144
 rdfArray = []
 # classificationArray = []
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18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/componentGroups.py

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Expand Up@@ -681,9 +681,9 @@ def getContextRequirements(
 requirementDependencies[molecule][
 "doubleActivation"
 ].append(relationship)
 processNodes[molecule]["doubleActivation"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleActivation"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 elif not combination[0] and combination[1]:
 if motif in ["ordering"]:
 requirementDependencies[molecule][motif].remove(
Expand All@@ -700,14 +700,14 @@ def getContextRequirements(
 requirementDependencies[molecule]["reprordering"].append(
 relationship
 )
 processNodes[molecule]["reprordering"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["reprordering"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )

 elif not combination[0] and not combination[1]:
 processNodes[molecule]["doubleRepression"][
relationship
] = "{0}_{1}".format(molecule, "_".join(label))
 processNodes[molecule]["doubleRepression"][relationship] = (
"{0}_{1}".format(molecule, "_".join(label))
 )
 if motif == "repression":
 requirementDependencies[molecule][motif].remove(
 relationship
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43 changes: 23 additions & 20 deletions
bionetgen/atomizer/rulifier/postAnalysis.py

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Expand Up@@ -128,11 +128,11 @@ def getParticipatingReactions(self, molecule, componentPair, reactionDictionary)
 for x in reactionDictionary[moleculeName][component]
 if x in componentPair
 ]:
 correlationList[
(component[0], componentComplement)
] = reactionDictionary[moleculeName][component][
componentComplement
]
 correlationList[(component[0], componentComplement)] = (
reactionDictionary[moleculeName][component][
 componentComplement
]
)
 return correlationList

 def getPairsFromMotif(self, motif1, motif2, excludedComponents):
Expand All@@ -146,10 +146,10 @@ def getPairsFromMotif(self, motif1, motif2, excludedComponents):
 if len(self.motifMoleculeDict[element][molecule]) > 0:
 for componentPair in self.motifMoleculeDict[element][molecule]:
 if not any(x in excludedComponents for x in componentPair):
 correlationList[
componentPair
] = self.getParticipatingReactions(
molecule, componentPair, self.patternXreactions
 correlationList[componentPair] = (
self.getParticipatingReactions(
 molecule, componentPair, self.patternXreactions
)
 )
 moleculeCorrelationList[molecule].update(correlationList)
 return dict(moleculeCorrelationList)
Expand DownExpand Up@@ -283,10 +283,13 @@ def getClassification(keys, translator):
 localAnalysisFlag = True
 if not any(
 [
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x]) > 0
 else molecule in x
 (
 molecule
 in database.prunnedDependencyGraph[x][0]
 if len(database.prunnedDependencyGraph[x])
 > 0
 else molecule in x
 )
 for x in difference
 ]
 ):
Expand DownExpand Up@@ -372,9 +375,9 @@ def getContextMotifInformation(self):
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
frozenset([requirementClass, requirementClass])
] = self.getPairsFromMotif(requirementClass, requirementClass, [])
 motifDictionary[frozenset([requirementClass, requirementClass])] = (
self.getPairsFromMotif(requirementClass, requirementClass, [])
 )
 return motifDictionary

 def getComplexReactions(self, threshold=2):
Expand DownExpand Up@@ -548,10 +551,10 @@ def runTests():
 "nullrequirement",
 "exclusion",
 ]:
 motifDictionary[
(requirementClass, requirementClass)
] = modelLearning.getPairsFromMotif(
requirementClass, requirementClass, ["imod"]
 motifDictionary[(requirementClass, requirementClass)] = (
modelLearning.getPairsFromMotif(
 requirementClass, requirementClass, ["imod"]
)
 )
 if len(motifDictionary[(requirementClass, requirementClass)]) > 0:
 print(
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18 changes: 9 additions & 9 deletions
bionetgen/atomizer/rulifier/stateTransitionDiagram.py

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Expand Up@@ -138,9 +138,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -158,9 +158,9 @@ def isActive(state):
 for species in centerUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in sourceCounter:
 sourceCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 sourceCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
Expand All@@ -179,9 +179,9 @@ def isActive(state):
 for species in productUnit:
 for element in species.split("."):
 if element.split("(")[0].split("%")[0] not in destinationCounter:
 destinationCounter[
element.split("(")[0].split("%")[0]
] = Counter()
 destinationCounter[element.split("(")[0].split("%")[0]] = (
Counter()
 )
 for component in moleculeDict[
 element.split("(")[0].split("%")[0]
 ]:
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