sympy: lazy import sympy + SBML getSize compatibility fix

.github/workflows/ci.yml

@@ -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') }}
@@ -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
@@ -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
@@ -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 }}
 

Dockerfile

@@ -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 

Issues/parameter_init/parameter_init.py

@@ -1,4 +1,4 @@
-import  bionetgen
+import bionetgen
 
 parameter = bionetgen.modelapi.structs.Parameter("A0", "10")
-print(parameter.gen_string())
+print(parameter.gen_string())

Issues/rule_keywords/run_pybng.py

@@ -1,5 +1,5 @@
 import bionetgen
 
-mname="test_deleteMolecules"
-model= bionetgen.bngmodel(mname+".bngl")
+mname = "test_deleteMolecules"
+model = bionetgen.bngmodel(mname + ".bngl")
 print(model)

bionetgen/__init__.py

@@ -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}")

bionetgen/atomizer/atomizeTool.py

@@ -4,7 +4,6 @@
 
 from bionetgen.core.utils.logging import BNGLogger, log_level
 
-
 d = BNGDefaults()
 
 

bionetgen/atomizer/atomizer/analyzeSBML.py

@@ -6,7 +6,6 @@
 """
 
 import enum
-import imp
 from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore
 import numpy as np
 import json
@@ -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"] = {}

bionetgen/atomizer/atomizer/atomizationAux.py

@@ -3,7 +3,6 @@
 
 
 class CycleError(Exception):
-
     """Exception raised for errors in the input.
 
     Attributes:

bionetgen/atomizer/atomizer/detectOntology.py

@@ -4,6 +4,7 @@
 
 @author: proto
 """
+
 import pprint
 import difflib
 from collections import Counter

bionetgen/atomizer/atomizer/resolveSCT.py

@@ -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",
@@ -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
@@ -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(

bionetgen/atomizer/contactMap.py

@@ -4,6 +4,7 @@
 
 @author: proto
 """
+
 # import sys
 # sys.path.insert(0, '../utils/')
 import utils.consoleCommands as console

bionetgen/atomizer/libsbml2bngl.py

@@ -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
@@ -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
 
 
@@ -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"
@@ -1652,7 +1651,7 @@ def main():
         metavar="FILE",
     )
 
-    (options, _) = parser.parse_args()
+    options, _ = parser.parse_args()
     # 144
     rdfArray = []
     # classificationArray = []

bionetgen/atomizer/rulifier/componentGroups.py

@@ -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(
@@ -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

bionetgen/atomizer/rulifier/postAnalysis.py

@@ -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):
@@ -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)
@@ -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
                                     ]
                                 ):
@@ -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):
@@ -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(

bionetgen/atomizer/rulifier/stateTransitionDiagram.py

@@ -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]
                             ]:
@@ -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]
                             ]:
@@ -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]
                         ]: