Fixes to several github issues

.github/workflows/ci.yml

@@ -48,8 +48,8 @@ jobs:
  shell: bash
  - name: Build
  run: |
- python setup.py install
- python setup.py sdist bdist_wheel
+ python -m pip install --upgrade pip
+ python -m pip install .
  - name: Test with PyTest
  run: |
  pytest

.github/workflows/release-test.yml

@@ -0,0 +1,35 @@
+name: release-test
+
+on:
+ release:
+ types: [published]
+
+jobs:
+ test-release:
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, windows-latest, macos-latest]
+ python-version: ["3.9", "3.10", "3.11", "3.12"]
+ steps:
+ - uses: actions/checkout@v4
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v5
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Install bionetgen from PyPI
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install bionetgen
+
+ - name: Smoke test bionetgen command
+ run: |
+ bionetgen -h
+ python -c "import bionetgen; print('bionetgen', bionetgen.__version__)"
+
+ - name: Run unit tests
+ run: |
+ python -m pip install pytest
+ pytest

bionetgen/__main__.py

@@ -0,0 +1,4 @@
+from .main import main
+
+if __name__ == "__main__":
+ main()

bionetgen/core/tools/info.py

@@ -64,6 +64,50 @@ def gatherInfo(self):
  # Save version info
  self.info["Perl version"] = text[num_start:num_end] + " (used to run BNG2.pl)"
 
+ # Get NFsim version (if available on PATH or adjacent to BNG2.pl)
+ self.logger.debug("NFsim info", loc=f"{__file__} : BNGInfo.gatherInfo()")
+ nf_version_text = "not found"
+ try:
+ # Try the standard PATH lookup first
+ result = subprocess.run(
+ ["NFsim", "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ else:
+ nf_version_text = f"exit {result.returncode}"
+ except FileNotFoundError:
+ # If NFsim isn't on PATH, attempt to locate it relative to BNG2.pl
+ try:
+ bng2_path = self.config.get("bionetgen", "bngpath")
+ bng2_dir = os.path.dirname(bng2_path)
+ candidates = [
+ os.path.join(bng2_dir, "bin", "NFsim"),
+ os.path.join(bng2_dir, "bin", "NFsim.exe"),
+ ]
+ for cmd in candidates:
+ if os.path.isfile(cmd):
+ result = subprocess.run(
+ [cmd, "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ break
+ except Exception:
+ pass
+ except Exception as e:
+ nf_version_text = f"error: {e}"
+
+ self.info["NFsim version"] = nf_version_text
+
  self.logger.debug("PyBNG info", loc=f"{__file__} : BNGInfo.gatherInfo()")
  # Get CLI version
  with open(

bionetgen/core/utils/utils.py

@@ -1,6 +1,7 @@
-import os, subprocess
+import os
+import shutil
+import subprocess
 from bionetgen.core.exc import BNGPerlError
-from distutils import spawn
 
 from bionetgen.core.utils.logging import BNGLogger
 
@@ -589,7 +590,7 @@ def _try_path(candidate_path):
  return hit
 
  # 3) On PATH
- bng_on_path = spawn.find_executable("BNG2.pl")
+ bng_on_path = shutil.which("BNG2.pl")
  if bng_on_path:
  tried.append(bng_on_path)
  hit = _try_path(bng_on_path)
@@ -616,7 +617,7 @@ def test_perl(app=None, perl_path=None):
  logger.debug("Checking if perl is installed.", loc=f"{__file__} : test_perl()")
  # find path to perl binary
  if perl_path is None:
- perl_path = spawn.find_executable("perl")
+ perl_path = shutil.which("perl")
  if perl_path is None:
  raise BNGPerlError
  # check if perl is actually working

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,11 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
- # All Delete operations in rule must have DeleteMolecules attribute or
- # it does not apply to the whole rule
- if all(dmvals) == 1:
+
+ # Use get() to avoid KeyError if the attribute is missing.
+ dmvals = [op.get("@DeleteMolecules") for op in del_op]
+ # All Delete operations in rule must have DeleteMolecules attribute set to "1".
+ if all(dmvals) and all(str(v) == "1" for v in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +732,22 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ # @totalrate comes as a string in the XML
+ if rate_type == "Function" and str(ratelaw.get("@totalrate")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate")
 
  # TODO: add support for include/exclude reactants/products
  if (

bionetgen/simulator/csimulator.py

@@ -1,7 +1,13 @@
 import ctypes, os, tempfile, bionetgen
 import numpy as np
 
-from distutils import ccompiler
+# distutils is deprecated in Python 3.12+. setuptools still provides the
+# equivalent via setuptools._distutils for backwards compatibility.
+try:
+ from setuptools._distutils import ccompiler
+except ImportError:
+ from distutils import ccompiler
+
 from .bngsimulator import BNGSimulator
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGCompileError

setup.py

@@ -14,7 +14,9 @@ def get_folder(arch):
  return fname
 
 
-subprocess.check_call([sys.executable, "-m", "pip", "install", "numpy"])
+# Note: don't run pip install at import time; in PEP 517 builds pip isn't available
+# and running subprocesses during import breaks isolated build environments.
+# numpy is declared in install_requires and will be installed by pip.
 import urllib.request
 import itertools as itt
 
@@ -186,6 +188,7 @@ def get_folder(arch):
  [console_scripts]
  bionetgen = bionetgen.main:main
  """,
+ python_requires=">=3.8",
  install_requires=[
  "cement",
  "nbopen",
@@ -201,6 +204,9 @@ def get_folder(arch):
  "python-libsbml",
  "pylru",
  "pyparsing",
+ "pyyed",
+ "matplotlib",
+ "pandas",
  "packaging",
  ],
 )

tests/test_action_parsing.py

@@ -0,0 +1,16 @@
+import pytest
+
+from bionetgen.core.utils.utils import ActionList
+
+
+def test_action_parser_rejects_unclosed_brace():
+ """Ensure malformed actions (missing closing brace) raise a parsing error."""
+
+ alist = ActionList()
+ alist.define_parser()
+
+ # Missing closing '}' should cause pyparsing to raise an exception
+ malformed = "simulate_ssa({t_start=>0,t_end=>10" # missing closing '}' and ')'
+
+ with pytest.raises(Exception):
+ alist.action_parser.parseString(malformed)

tests/test_rule_modifiers.py

@@ -0,0 +1,84 @@
+import pytest
+
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def _rule_block_parser():
+ # Create a RuleBlockXML instance without running __init__ (which expects full rule XML)
+ return RuleBlockXML.__new__(RuleBlockXML)
+
+
+def test_get_rule_mod_total_rate_string_true():
+ xml = {
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "r1",
+ "@name": "foo",
+ },
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "TotalRate"
+ assert mod.id == "r1"
+ assert mod.call == "1"
+
+
+def test_get_rule_mod_delete_molecules_all_operations():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {"@DeleteMolecules": "1"},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "DeleteMolecules"
+
+
+def test_get_rule_mod_delete_molecules_missing_attribute_does_not_apply():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type is None
+
+
+def test_get_rule_mod_move_connected_list_uses_each_element():
+ xml = {
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "a",
+ "@source": "s",
+ "@destination": "d",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "b",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "MoveConnected"
+ assert mod.id == ["a", "b"]
+ assert mod.source == ["s", "s2"]
+ assert mod.destination == ["d", "d2"]
+ assert mod.flip == ["0", "1"]
+ assert mod.call == ["1", "1"]

.github/workflows/ci.yml

@@ -48,8 +48,8 @@ jobs:
  shell: bash
  - name: Build
  run: |
- python setup.py install
- python setup.py sdist bdist_wheel
+ python -m pip install --upgrade pip
+ python -m pip install .
  - name: Test with PyTest
  run: |
  pytest

.github/workflows/release-test.yml

@@ -0,0 +1,35 @@
+name: release-test
+
+on:
+ release:
+ types: [published]
+
+jobs:
+ test-release:
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, windows-latest, macos-latest]
+ python-version: ["3.9", "3.10", "3.11", "3.12"]
+ steps:
+ - uses: actions/checkout@v4
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v5
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Install bionetgen from PyPI
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install bionetgen
+
+ - name: Smoke test bionetgen command
+ run: |
+ bionetgen -h
+ python -c "import bionetgen; print('bionetgen', bionetgen.__version__)"
+
+ - name: Run unit tests
+ run: |
+ python -m pip install pytest
+ pytest

bionetgen/__main__.py

@@ -0,0 +1,4 @@
+from .main import main
+
+if __name__ == "__main__":
+ main()

bionetgen/core/tools/info.py

@@ -64,6 +64,50 @@ def gatherInfo(self):
  # Save version info
  self.info["Perl version"] = text[num_start:num_end] + " (used to run BNG2.pl)"
 
+ # Get NFsim version (if available on PATH or adjacent to BNG2.pl)
+ self.logger.debug("NFsim info", loc=f"{__file__} : BNGInfo.gatherInfo()")
+ nf_version_text = "not found"
+ try:
+ # Try the standard PATH lookup first
+ result = subprocess.run(
+ ["NFsim", "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ else:
+ nf_version_text = f"exit {result.returncode}"
+ except FileNotFoundError:
+ # If NFsim isn't on PATH, attempt to locate it relative to BNG2.pl
+ try:
+ bng2_path = self.config.get("bionetgen", "bngpath")
+ bng2_dir = os.path.dirname(bng2_path)
+ candidates = [
+ os.path.join(bng2_dir, "bin", "NFsim"),
+ os.path.join(bng2_dir, "bin", "NFsim.exe"),
+ ]
+ for cmd in candidates:
+ if os.path.isfile(cmd):
+ result = subprocess.run(
+ [cmd, "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ break
+ except Exception:
+ pass
+ except Exception as e:
+ nf_version_text = f"error: {e}"
+
+ self.info["NFsim version"] = nf_version_text
+
  self.logger.debug("PyBNG info", loc=f"{__file__} : BNGInfo.gatherInfo()")
  # Get CLI version
  with open(

bionetgen/core/utils/utils.py

@@ -1,6 +1,7 @@
-import os, subprocess
+import os
+import shutil
+import subprocess
 from bionetgen.core.exc import BNGPerlError
-from distutils import spawn
 
 from bionetgen.core.utils.logging import BNGLogger
 
@@ -589,7 +590,7 @@ def _try_path(candidate_path):
  return hit
 
  # 3) On PATH
- bng_on_path = spawn.find_executable("BNG2.pl")
+ bng_on_path = shutil.which("BNG2.pl")
  if bng_on_path:
  tried.append(bng_on_path)
  hit = _try_path(bng_on_path)
@@ -616,7 +617,7 @@ def test_perl(app=None, perl_path=None):
  logger.debug("Checking if perl is installed.", loc=f"{__file__} : test_perl()")
  # find path to perl binary
  if perl_path is None:
- perl_path = spawn.find_executable("perl")
+ perl_path = shutil.which("perl")
  if perl_path is None:
  raise BNGPerlError
  # check if perl is actually working

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,11 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
- # All Delete operations in rule must have DeleteMolecules attribute or
- # it does not apply to the whole rule
- if all(dmvals) == 1:
+
+ # Use get() to avoid KeyError if the attribute is missing.
+ dmvals = [op.get("@DeleteMolecules") for op in del_op]
+ # All Delete operations in rule must have DeleteMolecules attribute set to "1".
+ if all(dmvals) and all(str(v) == "1" for v in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +732,22 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ # @totalrate comes as a string in the XML
+ if rate_type == "Function" and str(ratelaw.get("@totalrate")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate")
 
  # TODO: add support for include/exclude reactants/products
  if (

bionetgen/simulator/csimulator.py

@@ -1,7 +1,13 @@
 import ctypes, os, tempfile, bionetgen
 import numpy as np
 
-from distutils import ccompiler
+# distutils is deprecated in Python 3.12+. setuptools still provides the
+# equivalent via setuptools._distutils for backwards compatibility.
+try:
+ from setuptools._distutils import ccompiler
+except ImportError:
+ from distutils import ccompiler
+
 from .bngsimulator import BNGSimulator
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGCompileError

setup.py

@@ -14,7 +14,9 @@ def get_folder(arch):
  return fname
 
 
-subprocess.check_call([sys.executable, "-m", "pip", "install", "numpy"])
+# Note: don't run pip install at import time; in PEP 517 builds pip isn't available
+# and running subprocesses during import breaks isolated build environments.
+# numpy is declared in install_requires and will be installed by pip.
 import urllib.request
 import itertools as itt
 
@@ -186,6 +188,7 @@ def get_folder(arch):
  [console_scripts]
  bionetgen = bionetgen.main:main
  """,
+ python_requires=">=3.8",
  install_requires=[
  "cement",
  "nbopen",
@@ -201,6 +204,9 @@ def get_folder(arch):
  "python-libsbml",
  "pylru",
  "pyparsing",
+ "pyyed",
+ "matplotlib",
+ "pandas",
  "packaging",
  ],
 )

tests/test_action_parsing.py

@@ -0,0 +1,16 @@
+import pytest
+
+from bionetgen.core.utils.utils import ActionList
+
+
+def test_action_parser_rejects_unclosed_brace():
+ """Ensure malformed actions (missing closing brace) raise a parsing error."""
+
+ alist = ActionList()
+ alist.define_parser()
+
+ # Missing closing '}' should cause pyparsing to raise an exception
+ malformed = "simulate_ssa({t_start=>0,t_end=>10" # missing closing '}' and ')'
+
+ with pytest.raises(Exception):
+ alist.action_parser.parseString(malformed)

tests/test_rule_modifiers.py

@@ -0,0 +1,84 @@
+import pytest
+
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def _rule_block_parser():
+ # Create a RuleBlockXML instance without running __init__ (which expects full rule XML)
+ return RuleBlockXML.__new__(RuleBlockXML)
+
+
+def test_get_rule_mod_total_rate_string_true():
+ xml = {
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "r1",
+ "@name": "foo",
+ },
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "TotalRate"
+ assert mod.id == "r1"
+ assert mod.call == "1"
+
+
+def test_get_rule_mod_delete_molecules_all_operations():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {"@DeleteMolecules": "1"},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "DeleteMolecules"
+
+
+def test_get_rule_mod_delete_molecules_missing_attribute_does_not_apply():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type is None
+
+
+def test_get_rule_mod_move_connected_list_uses_each_element():
+ xml = {
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "a",
+ "@source": "s",
+ "@destination": "d",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "b",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "MoveConnected"
+ assert mod.id == ["a", "b"]
+ assert mod.source == ["s", "s2"]
+ assert mod.destination == ["d", "d2"]
+ assert mod.flip == ["0", "1"]
+ assert mod.call == ["1", "1"]

.github/workflows/ci.yml

@@ -48,8 +48,8 @@ jobs:
  shell: bash
  - name: Build
  run: |
- python setup.py install
- python setup.py sdist bdist_wheel
+ python -m pip install --upgrade pip
+ python -m pip install .
  - name: Test with PyTest
  run: |
  pytest

.github/workflows/release-test.yml

@@ -0,0 +1,35 @@
+name: release-test
+
+on:
+ release:
+ types: [published]
+
+jobs:
+ test-release:
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, windows-latest, macos-latest]
+ python-version: ["3.9", "3.10", "3.11", "3.12"]
+ steps:
+ - uses: actions/checkout@v4
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v5
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Install bionetgen from PyPI
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install bionetgen
+
+ - name: Smoke test bionetgen command
+ run: |
+ bionetgen -h
+ python -c "import bionetgen; print('bionetgen', bionetgen.__version__)"
+
+ - name: Run unit tests
+ run: |
+ python -m pip install pytest
+ pytest

bionetgen/__main__.py

@@ -0,0 +1,4 @@
+from .main import main
+
+if __name__ == "__main__":
+ main()

bionetgen/core/tools/info.py

@@ -64,6 +64,50 @@ def gatherInfo(self):
  # Save version info
  self.info["Perl version"] = text[num_start:num_end] + " (used to run BNG2.pl)"
 
+ # Get NFsim version (if available on PATH or adjacent to BNG2.pl)
+ self.logger.debug("NFsim info", loc=f"{__file__} : BNGInfo.gatherInfo()")
+ nf_version_text = "not found"
+ try:
+ # Try the standard PATH lookup first
+ result = subprocess.run(
+ ["NFsim", "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ else:
+ nf_version_text = f"exit {result.returncode}"
+ except FileNotFoundError:
+ # If NFsim isn't on PATH, attempt to locate it relative to BNG2.pl
+ try:
+ bng2_path = self.config.get("bionetgen", "bngpath")
+ bng2_dir = os.path.dirname(bng2_path)
+ candidates = [
+ os.path.join(bng2_dir, "bin", "NFsim"),
+ os.path.join(bng2_dir, "bin", "NFsim.exe"),
+ ]
+ for cmd in candidates:
+ if os.path.isfile(cmd):
+ result = subprocess.run(
+ [cmd, "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ break
+ except Exception:
+ pass
+ except Exception as e:
+ nf_version_text = f"error: {e}"
+
+ self.info["NFsim version"] = nf_version_text
+
  self.logger.debug("PyBNG info", loc=f"{__file__} : BNGInfo.gatherInfo()")
  # Get CLI version
  with open(

bionetgen/core/utils/utils.py

@@ -1,6 +1,7 @@
-import os, subprocess
+import os
+import shutil
+import subprocess
 from bionetgen.core.exc import BNGPerlError
-from distutils import spawn
 
 from bionetgen.core.utils.logging import BNGLogger
 
@@ -589,7 +590,7 @@ def _try_path(candidate_path):
  return hit
 
  # 3) On PATH
- bng_on_path = spawn.find_executable("BNG2.pl")
+ bng_on_path = shutil.which("BNG2.pl")
  if bng_on_path:
  tried.append(bng_on_path)
  hit = _try_path(bng_on_path)
@@ -616,7 +617,7 @@ def test_perl(app=None, perl_path=None):
  logger.debug("Checking if perl is installed.", loc=f"{__file__} : test_perl()")
  # find path to perl binary
  if perl_path is None:
- perl_path = spawn.find_executable("perl")
+ perl_path = shutil.which("perl")
  if perl_path is None:
  raise BNGPerlError
  # check if perl is actually working

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,11 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
- # All Delete operations in rule must have DeleteMolecules attribute or
- # it does not apply to the whole rule
- if all(dmvals) == 1:
+
+ # Use get() to avoid KeyError if the attribute is missing.
+ dmvals = [op.get("@DeleteMolecules") for op in del_op]
+ # All Delete operations in rule must have DeleteMolecules attribute set to "1".
+ if all(dmvals) and all(str(v) == "1" for v in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +732,22 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ # @totalrate comes as a string in the XML
+ if rate_type == "Function" and str(ratelaw.get("@totalrate")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate")
 
  # TODO: add support for include/exclude reactants/products
  if (

bionetgen/simulator/csimulator.py

@@ -1,7 +1,13 @@
 import ctypes, os, tempfile, bionetgen
 import numpy as np
 
-from distutils import ccompiler
+# distutils is deprecated in Python 3.12+. setuptools still provides the
+# equivalent via setuptools._distutils for backwards compatibility.
+try:
+ from setuptools._distutils import ccompiler
+except ImportError:
+ from distutils import ccompiler
+
 from .bngsimulator import BNGSimulator
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGCompileError

setup.py

@@ -14,7 +14,9 @@ def get_folder(arch):
  return fname
 
 
-subprocess.check_call([sys.executable, "-m", "pip", "install", "numpy"])
+# Note: don't run pip install at import time; in PEP 517 builds pip isn't available
+# and running subprocesses during import breaks isolated build environments.
+# numpy is declared in install_requires and will be installed by pip.
 import urllib.request
 import itertools as itt
 
@@ -186,6 +188,7 @@ def get_folder(arch):
  [console_scripts]
  bionetgen = bionetgen.main:main
  """,
+ python_requires=">=3.8",
  install_requires=[
  "cement",
  "nbopen",
@@ -201,6 +204,9 @@ def get_folder(arch):
  "python-libsbml",
  "pylru",
  "pyparsing",
+ "pyyed",
+ "matplotlib",
+ "pandas",
  "packaging",
  ],
 )

tests/test_action_parsing.py

@@ -0,0 +1,16 @@
+import pytest
+
+from bionetgen.core.utils.utils import ActionList
+
+
+def test_action_parser_rejects_unclosed_brace():
+ """Ensure malformed actions (missing closing brace) raise a parsing error."""
+
+ alist = ActionList()
+ alist.define_parser()
+
+ # Missing closing '}' should cause pyparsing to raise an exception
+ malformed = "simulate_ssa({t_start=>0,t_end=>10" # missing closing '}' and ')'
+
+ with pytest.raises(Exception):
+ alist.action_parser.parseString(malformed)

tests/test_rule_modifiers.py

@@ -0,0 +1,84 @@
+import pytest
+
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def _rule_block_parser():
+ # Create a RuleBlockXML instance without running __init__ (which expects full rule XML)
+ return RuleBlockXML.__new__(RuleBlockXML)
+
+
+def test_get_rule_mod_total_rate_string_true():
+ xml = {
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "r1",
+ "@name": "foo",
+ },
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "TotalRate"
+ assert mod.id == "r1"
+ assert mod.call == "1"
+
+
+def test_get_rule_mod_delete_molecules_all_operations():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {"@DeleteMolecules": "1"},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "DeleteMolecules"
+
+
+def test_get_rule_mod_delete_molecules_missing_attribute_does_not_apply():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type is None
+
+
+def test_get_rule_mod_move_connected_list_uses_each_element():
+ xml = {
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "a",
+ "@source": "s",
+ "@destination": "d",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "b",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "MoveConnected"
+ assert mod.id == ["a", "b"]
+ assert mod.source == ["s", "s2"]
+ assert mod.destination == ["d", "d2"]
+ assert mod.flip == ["0", "1"]
+ assert mod.call == ["1", "1"]

.github/workflows/ci.yml

@@ -48,8 +48,8 @@ jobs:
  shell: bash
  - name: Build
  run: |
- python setup.py install
- python setup.py sdist bdist_wheel
+ python -m pip install --upgrade pip
+ python -m pip install .
  - name: Test with PyTest
  run: |
  pytest

.github/workflows/release-test.yml

@@ -0,0 +1,35 @@
+name: release-test
+
+on:
+ release:
+ types: [published]
+
+jobs:
+ test-release:
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, windows-latest, macos-latest]
+ python-version: ["3.9", "3.10", "3.11", "3.12"]
+ steps:
+ - uses: actions/checkout@v4
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v5
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Install bionetgen from PyPI
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install bionetgen
+
+ - name: Smoke test bionetgen command
+ run: |
+ bionetgen -h
+ python -c "import bionetgen; print('bionetgen', bionetgen.__version__)"
+
+ - name: Run unit tests
+ run: |
+ python -m pip install pytest
+ pytest

bionetgen/__main__.py

@@ -0,0 +1,4 @@
+from .main import main
+
+if __name__ == "__main__":
+ main()

bionetgen/core/tools/info.py

@@ -64,6 +64,50 @@ def gatherInfo(self):
  # Save version info
  self.info["Perl version"] = text[num_start:num_end] + " (used to run BNG2.pl)"
 
+ # Get NFsim version (if available on PATH or adjacent to BNG2.pl)
+ self.logger.debug("NFsim info", loc=f"{__file__} : BNGInfo.gatherInfo()")
+ nf_version_text = "not found"
+ try:
+ # Try the standard PATH lookup first
+ result = subprocess.run(
+ ["NFsim", "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ else:
+ nf_version_text = f"exit {result.returncode}"
+ except FileNotFoundError:
+ # If NFsim isn't on PATH, attempt to locate it relative to BNG2.pl
+ try:
+ bng2_path = self.config.get("bionetgen", "bngpath")
+ bng2_dir = os.path.dirname(bng2_path)
+ candidates = [
+ os.path.join(bng2_dir, "bin", "NFsim"),
+ os.path.join(bng2_dir, "bin", "NFsim.exe"),
+ ]
+ for cmd in candidates:
+ if os.path.isfile(cmd):
+ result = subprocess.run(
+ [cmd, "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ break
+ except Exception:
+ pass
+ except Exception as e:
+ nf_version_text = f"error: {e}"
+
+ self.info["NFsim version"] = nf_version_text
+
  self.logger.debug("PyBNG info", loc=f"{__file__} : BNGInfo.gatherInfo()")
  # Get CLI version
  with open(

bionetgen/core/utils/utils.py

@@ -1,6 +1,7 @@
-import os, subprocess
+import os
+import shutil
+import subprocess
 from bionetgen.core.exc import BNGPerlError
-from distutils import spawn
 
 from bionetgen.core.utils.logging import BNGLogger
 
@@ -589,7 +590,7 @@ def _try_path(candidate_path):
  return hit
 
  # 3) On PATH
- bng_on_path = spawn.find_executable("BNG2.pl")
+ bng_on_path = shutil.which("BNG2.pl")
  if bng_on_path:
  tried.append(bng_on_path)
  hit = _try_path(bng_on_path)
@@ -616,7 +617,7 @@ def test_perl(app=None, perl_path=None):
  logger.debug("Checking if perl is installed.", loc=f"{__file__} : test_perl()")
  # find path to perl binary
  if perl_path is None:
- perl_path = spawn.find_executable("perl")
+ perl_path = shutil.which("perl")
  if perl_path is None:
  raise BNGPerlError
  # check if perl is actually working

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,11 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
- # All Delete operations in rule must have DeleteMolecules attribute or
- # it does not apply to the whole rule
- if all(dmvals) == 1:
+
+ # Use get() to avoid KeyError if the attribute is missing.
+ dmvals = [op.get("@DeleteMolecules") for op in del_op]
+ # All Delete operations in rule must have DeleteMolecules attribute set to "1".
+ if all(dmvals) and all(str(v) == "1" for v in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +732,22 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ # @totalrate comes as a string in the XML
+ if rate_type == "Function" and str(ratelaw.get("@totalrate")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate")
 
  # TODO: add support for include/exclude reactants/products
  if (

bionetgen/simulator/csimulator.py

@@ -1,7 +1,13 @@
 import ctypes, os, tempfile, bionetgen
 import numpy as np
 
-from distutils import ccompiler
+# distutils is deprecated in Python 3.12+. setuptools still provides the
+# equivalent via setuptools._distutils for backwards compatibility.
+try:
+ from setuptools._distutils import ccompiler
+except ImportError:
+ from distutils import ccompiler
+
 from .bngsimulator import BNGSimulator
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGCompileError

setup.py

@@ -14,7 +14,9 @@ def get_folder(arch):
  return fname
 
 
-subprocess.check_call([sys.executable, "-m", "pip", "install", "numpy"])
+# Note: don't run pip install at import time; in PEP 517 builds pip isn't available
+# and running subprocesses during import breaks isolated build environments.
+# numpy is declared in install_requires and will be installed by pip.
 import urllib.request
 import itertools as itt
 
@@ -186,6 +188,7 @@ def get_folder(arch):
  [console_scripts]
  bionetgen = bionetgen.main:main
  """,
+ python_requires=">=3.8",
  install_requires=[
  "cement",
  "nbopen",
@@ -201,6 +204,9 @@ def get_folder(arch):
  "python-libsbml",
  "pylru",
  "pyparsing",
+ "pyyed",
+ "matplotlib",
+ "pandas",
  "packaging",
  ],
 )

tests/test_action_parsing.py

@@ -0,0 +1,16 @@
+import pytest
+
+from bionetgen.core.utils.utils import ActionList
+
+
+def test_action_parser_rejects_unclosed_brace():
+ """Ensure malformed actions (missing closing brace) raise a parsing error."""
+
+ alist = ActionList()
+ alist.define_parser()
+
+ # Missing closing '}' should cause pyparsing to raise an exception
+ malformed = "simulate_ssa({t_start=>0,t_end=>10" # missing closing '}' and ')'
+
+ with pytest.raises(Exception):
+ alist.action_parser.parseString(malformed)

tests/test_rule_modifiers.py

@@ -0,0 +1,84 @@
+import pytest
+
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def _rule_block_parser():
+ # Create a RuleBlockXML instance without running __init__ (which expects full rule XML)
+ return RuleBlockXML.__new__(RuleBlockXML)
+
+
+def test_get_rule_mod_total_rate_string_true():
+ xml = {
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "r1",
+ "@name": "foo",
+ },
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "TotalRate"
+ assert mod.id == "r1"
+ assert mod.call == "1"
+
+
+def test_get_rule_mod_delete_molecules_all_operations():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {"@DeleteMolecules": "1"},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "DeleteMolecules"
+
+
+def test_get_rule_mod_delete_molecules_missing_attribute_does_not_apply():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type is None
+
+
+def test_get_rule_mod_move_connected_list_uses_each_element():
+ xml = {
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "a",
+ "@source": "s",
+ "@destination": "d",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "b",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "MoveConnected"
+ assert mod.id == ["a", "b"]
+ assert mod.source == ["s", "s2"]
+ assert mod.destination == ["d", "d2"]
+ assert mod.flip == ["0", "1"]
+ assert mod.call == ["1", "1"]

.github/workflows/ci.yml

@@ -48,8 +48,8 @@ jobs:
  shell: bash
  - name: Build
  run: |
- python setup.py install
- python setup.py sdist bdist_wheel
+ python -m pip install --upgrade pip
+ python -m pip install .
  - name: Test with PyTest
  run: |
  pytest

.github/workflows/release-test.yml

@@ -0,0 +1,35 @@
+name: release-test
+
+on:
+ release:
+ types: [published]
+
+jobs:
+ test-release:
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, windows-latest, macos-latest]
+ python-version: ["3.9", "3.10", "3.11", "3.12"]
+ steps:
+ - uses: actions/checkout@v4
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v5
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Install bionetgen from PyPI
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install bionetgen
+
+ - name: Smoke test bionetgen command
+ run: |
+ bionetgen -h
+ python -c "import bionetgen; print('bionetgen', bionetgen.__version__)"
+
+ - name: Run unit tests
+ run: |
+ python -m pip install pytest
+ pytest

bionetgen/__main__.py

@@ -0,0 +1,4 @@
+from .main import main
+
+if __name__ == "__main__":
+ main()

bionetgen/core/tools/info.py

@@ -64,6 +64,50 @@ def gatherInfo(self):
  # Save version info
  self.info["Perl version"] = text[num_start:num_end] + " (used to run BNG2.pl)"
 
+ # Get NFsim version (if available on PATH or adjacent to BNG2.pl)
+ self.logger.debug("NFsim info", loc=f"{__file__} : BNGInfo.gatherInfo()")
+ nf_version_text = "not found"
+ try:
+ # Try the standard PATH lookup first
+ result = subprocess.run(
+ ["NFsim", "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ else:
+ nf_version_text = f"exit {result.returncode}"
+ except FileNotFoundError:
+ # If NFsim isn't on PATH, attempt to locate it relative to BNG2.pl
+ try:
+ bng2_path = self.config.get("bionetgen", "bngpath")
+ bng2_dir = os.path.dirname(bng2_path)
+ candidates = [
+ os.path.join(bng2_dir, "bin", "NFsim"),
+ os.path.join(bng2_dir, "bin", "NFsim.exe"),
+ ]
+ for cmd in candidates:
+ if os.path.isfile(cmd):
+ result = subprocess.run(
+ [cmd, "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ break
+ except Exception:
+ pass
+ except Exception as e:
+ nf_version_text = f"error: {e}"
+
+ self.info["NFsim version"] = nf_version_text
+
  self.logger.debug("PyBNG info", loc=f"{__file__} : BNGInfo.gatherInfo()")
  # Get CLI version
  with open(

bionetgen/core/utils/utils.py

@@ -1,6 +1,7 @@
-import os, subprocess
+import os
+import shutil
+import subprocess
 from bionetgen.core.exc import BNGPerlError
-from distutils import spawn
 
 from bionetgen.core.utils.logging import BNGLogger
 
@@ -589,7 +590,7 @@ def _try_path(candidate_path):
  return hit
 
  # 3) On PATH
- bng_on_path = spawn.find_executable("BNG2.pl")
+ bng_on_path = shutil.which("BNG2.pl")
  if bng_on_path:
  tried.append(bng_on_path)
  hit = _try_path(bng_on_path)
@@ -616,7 +617,7 @@ def test_perl(app=None, perl_path=None):
  logger.debug("Checking if perl is installed.", loc=f"{__file__} : test_perl()")
  # find path to perl binary
  if perl_path is None:
- perl_path = spawn.find_executable("perl")
+ perl_path = shutil.which("perl")
  if perl_path is None:
  raise BNGPerlError
  # check if perl is actually working

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,11 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
- # All Delete operations in rule must have DeleteMolecules attribute or
- # it does not apply to the whole rule
- if all(dmvals) == 1:
+
+ # Use get() to avoid KeyError if the attribute is missing.
+ dmvals = [op.get("@DeleteMolecules") for op in del_op]
+ # All Delete operations in rule must have DeleteMolecules attribute set to "1".
+ if all(dmvals) and all(str(v) == "1" for v in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +732,22 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ # @totalrate comes as a string in the XML
+ if rate_type == "Function" and str(ratelaw.get("@totalrate")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate")
 
  # TODO: add support for include/exclude reactants/products
  if (

bionetgen/simulator/csimulator.py

@@ -1,7 +1,13 @@
 import ctypes, os, tempfile, bionetgen
 import numpy as np
 
-from distutils import ccompiler
+# distutils is deprecated in Python 3.12+. setuptools still provides the
+# equivalent via setuptools._distutils for backwards compatibility.
+try:
+ from setuptools._distutils import ccompiler
+except ImportError:
+ from distutils import ccompiler
+
 from .bngsimulator import BNGSimulator
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGCompileError

setup.py

@@ -14,7 +14,9 @@ def get_folder(arch):
  return fname
 
 
-subprocess.check_call([sys.executable, "-m", "pip", "install", "numpy"])
+# Note: don't run pip install at import time; in PEP 517 builds pip isn't available
+# and running subprocesses during import breaks isolated build environments.
+# numpy is declared in install_requires and will be installed by pip.
 import urllib.request
 import itertools as itt
 
@@ -186,6 +188,7 @@ def get_folder(arch):
  [console_scripts]
  bionetgen = bionetgen.main:main
  """,
+ python_requires=">=3.8",
  install_requires=[
  "cement",
  "nbopen",
@@ -201,6 +204,9 @@ def get_folder(arch):
  "python-libsbml",
  "pylru",
  "pyparsing",
+ "pyyed",
+ "matplotlib",
+ "pandas",
  "packaging",
  ],
 )

tests/test_action_parsing.py

@@ -0,0 +1,16 @@
+import pytest
+
+from bionetgen.core.utils.utils import ActionList
+
+
+def test_action_parser_rejects_unclosed_brace():
+ """Ensure malformed actions (missing closing brace) raise a parsing error."""
+
+ alist = ActionList()
+ alist.define_parser()
+
+ # Missing closing '}' should cause pyparsing to raise an exception
+ malformed = "simulate_ssa({t_start=>0,t_end=>10" # missing closing '}' and ')'
+
+ with pytest.raises(Exception):
+ alist.action_parser.parseString(malformed)

tests/test_rule_modifiers.py

@@ -0,0 +1,84 @@
+import pytest
+
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def _rule_block_parser():
+ # Create a RuleBlockXML instance without running __init__ (which expects full rule XML)
+ return RuleBlockXML.__new__(RuleBlockXML)
+
+
+def test_get_rule_mod_total_rate_string_true():
+ xml = {
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "r1",
+ "@name": "foo",
+ },
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "TotalRate"
+ assert mod.id == "r1"
+ assert mod.call == "1"
+
+
+def test_get_rule_mod_delete_molecules_all_operations():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {"@DeleteMolecules": "1"},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "DeleteMolecules"
+
+
+def test_get_rule_mod_delete_molecules_missing_attribute_does_not_apply():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type is None
+
+
+def test_get_rule_mod_move_connected_list_uses_each_element():
+ xml = {
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "a",
+ "@source": "s",
+ "@destination": "d",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "b",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "MoveConnected"
+ assert mod.id == ["a", "b"]
+ assert mod.source == ["s", "s2"]
+ assert mod.destination == ["d", "d2"]
+ assert mod.flip == ["0", "1"]
+ assert mod.call == ["1", "1"]

.github/workflows/ci.yml

@@ -48,8 +48,8 @@ jobs:
  shell: bash
  - name: Build
  run: |
- python setup.py install
- python setup.py sdist bdist_wheel
+ python -m pip install --upgrade pip
+ python -m pip install .
  - name: Test with PyTest
  run: |
  pytest

.github/workflows/release-test.yml

@@ -0,0 +1,35 @@
+name: release-test
+
+on:
+ release:
+ types: [published]
+
+jobs:
+ test-release:
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, windows-latest, macos-latest]
+ python-version: ["3.9", "3.10", "3.11", "3.12"]
+ steps:
+ - uses: actions/checkout@v4
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v5
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Install bionetgen from PyPI
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install bionetgen
+
+ - name: Smoke test bionetgen command
+ run: |
+ bionetgen -h
+ python -c "import bionetgen; print('bionetgen', bionetgen.__version__)"
+
+ - name: Run unit tests
+ run: |
+ python -m pip install pytest
+ pytest

bionetgen/__main__.py

@@ -0,0 +1,4 @@
+from .main import main
+
+if __name__ == "__main__":
+ main()

bionetgen/core/tools/info.py

@@ -64,6 +64,50 @@ def gatherInfo(self):
  # Save version info
  self.info["Perl version"] = text[num_start:num_end] + " (used to run BNG2.pl)"
 
+ # Get NFsim version (if available on PATH or adjacent to BNG2.pl)
+ self.logger.debug("NFsim info", loc=f"{__file__} : BNGInfo.gatherInfo()")
+ nf_version_text = "not found"
+ try:
+ # Try the standard PATH lookup first
+ result = subprocess.run(
+ ["NFsim", "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ else:
+ nf_version_text = f"exit {result.returncode}"
+ except FileNotFoundError:
+ # If NFsim isn't on PATH, attempt to locate it relative to BNG2.pl
+ try:
+ bng2_path = self.config.get("bionetgen", "bngpath")
+ bng2_dir = os.path.dirname(bng2_path)
+ candidates = [
+ os.path.join(bng2_dir, "bin", "NFsim"),
+ os.path.join(bng2_dir, "bin", "NFsim.exe"),
+ ]
+ for cmd in candidates:
+ if os.path.isfile(cmd):
+ result = subprocess.run(
+ [cmd, "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ break
+ except Exception:
+ pass
+ except Exception as e:
+ nf_version_text = f"error: {e}"
+
+ self.info["NFsim version"] = nf_version_text
+
  self.logger.debug("PyBNG info", loc=f"{__file__} : BNGInfo.gatherInfo()")
  # Get CLI version
  with open(

bionetgen/core/utils/utils.py

@@ -1,6 +1,7 @@
-import os, subprocess
+import os
+import shutil
+import subprocess
 from bionetgen.core.exc import BNGPerlError
-from distutils import spawn
 
 from bionetgen.core.utils.logging import BNGLogger
 
@@ -589,7 +590,7 @@ def _try_path(candidate_path):
  return hit
 
  # 3) On PATH
- bng_on_path = spawn.find_executable("BNG2.pl")
+ bng_on_path = shutil.which("BNG2.pl")
  if bng_on_path:
  tried.append(bng_on_path)
  hit = _try_path(bng_on_path)
@@ -616,7 +617,7 @@ def test_perl(app=None, perl_path=None):
  logger.debug("Checking if perl is installed.", loc=f"{__file__} : test_perl()")
  # find path to perl binary
  if perl_path is None:
- perl_path = spawn.find_executable("perl")
+ perl_path = shutil.which("perl")
  if perl_path is None:
  raise BNGPerlError
  # check if perl is actually working

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,11 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
- # All Delete operations in rule must have DeleteMolecules attribute or
- # it does not apply to the whole rule
- if all(dmvals) == 1:
+
+ # Use get() to avoid KeyError if the attribute is missing.
+ dmvals = [op.get("@DeleteMolecules") for op in del_op]
+ # All Delete operations in rule must have DeleteMolecules attribute set to "1".
+ if all(dmvals) and all(str(v) == "1" for v in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +732,22 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ # @totalrate comes as a string in the XML
+ if rate_type == "Function" and str(ratelaw.get("@totalrate")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate")
 
  # TODO: add support for include/exclude reactants/products
  if (

bionetgen/simulator/csimulator.py

@@ -1,7 +1,13 @@
 import ctypes, os, tempfile, bionetgen
 import numpy as np
 
-from distutils import ccompiler
+# distutils is deprecated in Python 3.12+. setuptools still provides the
+# equivalent via setuptools._distutils for backwards compatibility.
+try:
+ from setuptools._distutils import ccompiler
+except ImportError:
+ from distutils import ccompiler
+
 from .bngsimulator import BNGSimulator
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGCompileError

setup.py

@@ -14,7 +14,9 @@ def get_folder(arch):
  return fname
 
 
-subprocess.check_call([sys.executable, "-m", "pip", "install", "numpy"])
+# Note: don't run pip install at import time; in PEP 517 builds pip isn't available
+# and running subprocesses during import breaks isolated build environments.
+# numpy is declared in install_requires and will be installed by pip.
 import urllib.request
 import itertools as itt
 
@@ -186,6 +188,7 @@ def get_folder(arch):
  [console_scripts]
  bionetgen = bionetgen.main:main
  """,
+ python_requires=">=3.8",
  install_requires=[
  "cement",
  "nbopen",
@@ -201,6 +204,9 @@ def get_folder(arch):
  "python-libsbml",
  "pylru",
  "pyparsing",
+ "pyyed",
+ "matplotlib",
+ "pandas",
  "packaging",
  ],
 )

tests/test_action_parsing.py

@@ -0,0 +1,16 @@
+import pytest
+
+from bionetgen.core.utils.utils import ActionList
+
+
+def test_action_parser_rejects_unclosed_brace():
+ """Ensure malformed actions (missing closing brace) raise a parsing error."""
+
+ alist = ActionList()
+ alist.define_parser()
+
+ # Missing closing '}' should cause pyparsing to raise an exception
+ malformed = "simulate_ssa({t_start=>0,t_end=>10" # missing closing '}' and ')'
+
+ with pytest.raises(Exception):
+ alist.action_parser.parseString(malformed)

tests/test_rule_modifiers.py

@@ -0,0 +1,84 @@
+import pytest
+
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def _rule_block_parser():
+ # Create a RuleBlockXML instance without running __init__ (which expects full rule XML)
+ return RuleBlockXML.__new__(RuleBlockXML)
+
+
+def test_get_rule_mod_total_rate_string_true():
+ xml = {
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "r1",
+ "@name": "foo",
+ },
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "TotalRate"
+ assert mod.id == "r1"
+ assert mod.call == "1"
+
+
+def test_get_rule_mod_delete_molecules_all_operations():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {"@DeleteMolecules": "1"},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "DeleteMolecules"
+
+
+def test_get_rule_mod_delete_molecules_missing_attribute_does_not_apply():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type is None
+
+
+def test_get_rule_mod_move_connected_list_uses_each_element():
+ xml = {
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "a",
+ "@source": "s",
+ "@destination": "d",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "b",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "MoveConnected"
+ assert mod.id == ["a", "b"]
+ assert mod.source == ["s", "s2"]
+ assert mod.destination == ["d", "d2"]
+ assert mod.flip == ["0", "1"]
+ assert mod.call == ["1", "1"]

.github/workflows/ci.yml

@@ -48,8 +48,8 @@ jobs:
  shell: bash
  - name: Build
  run: |
- python setup.py install
- python setup.py sdist bdist_wheel
+ python -m pip install --upgrade pip
+ python -m pip install .
  - name: Test with PyTest
  run: |
  pytest

.github/workflows/release-test.yml

@@ -0,0 +1,35 @@
+name: release-test
+
+on:
+ release:
+ types: [published]
+
+jobs:
+ test-release:
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, windows-latest, macos-latest]
+ python-version: ["3.9", "3.10", "3.11", "3.12"]
+ steps:
+ - uses: actions/checkout@v4
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v5
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Install bionetgen from PyPI
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install bionetgen
+
+ - name: Smoke test bionetgen command
+ run: |
+ bionetgen -h
+ python -c "import bionetgen; print('bionetgen', bionetgen.__version__)"
+
+ - name: Run unit tests
+ run: |
+ python -m pip install pytest
+ pytest

bionetgen/__main__.py

@@ -0,0 +1,4 @@
+from .main import main
+
+if __name__ == "__main__":
+ main()

bionetgen/core/tools/info.py

@@ -64,6 +64,50 @@ def gatherInfo(self):
  # Save version info
  self.info["Perl version"] = text[num_start:num_end] + " (used to run BNG2.pl)"
 
+ # Get NFsim version (if available on PATH or adjacent to BNG2.pl)
+ self.logger.debug("NFsim info", loc=f"{__file__} : BNGInfo.gatherInfo()")
+ nf_version_text = "not found"
+ try:
+ # Try the standard PATH lookup first
+ result = subprocess.run(
+ ["NFsim", "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ else:
+ nf_version_text = f"exit {result.returncode}"
+ except FileNotFoundError:
+ # If NFsim isn't on PATH, attempt to locate it relative to BNG2.pl
+ try:
+ bng2_path = self.config.get("bionetgen", "bngpath")
+ bng2_dir = os.path.dirname(bng2_path)
+ candidates = [
+ os.path.join(bng2_dir, "bin", "NFsim"),
+ os.path.join(bng2_dir, "bin", "NFsim.exe"),
+ ]
+ for cmd in candidates:
+ if os.path.isfile(cmd):
+ result = subprocess.run(
+ [cmd, "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ break
+ except Exception:
+ pass
+ except Exception as e:
+ nf_version_text = f"error: {e}"
+
+ self.info["NFsim version"] = nf_version_text
+
  self.logger.debug("PyBNG info", loc=f"{__file__} : BNGInfo.gatherInfo()")
  # Get CLI version
  with open(

bionetgen/core/utils/utils.py

@@ -1,6 +1,7 @@
-import os, subprocess
+import os
+import shutil
+import subprocess
 from bionetgen.core.exc import BNGPerlError
-from distutils import spawn
 
 from bionetgen.core.utils.logging import BNGLogger
 
@@ -589,7 +590,7 @@ def _try_path(candidate_path):
  return hit
 
  # 3) On PATH
- bng_on_path = spawn.find_executable("BNG2.pl")
+ bng_on_path = shutil.which("BNG2.pl")
  if bng_on_path:
  tried.append(bng_on_path)
  hit = _try_path(bng_on_path)
@@ -616,7 +617,7 @@ def test_perl(app=None, perl_path=None):
  logger.debug("Checking if perl is installed.", loc=f"{__file__} : test_perl()")
  # find path to perl binary
  if perl_path is None:
- perl_path = spawn.find_executable("perl")
+ perl_path = shutil.which("perl")
  if perl_path is None:
  raise BNGPerlError
  # check if perl is actually working

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,11 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
- # All Delete operations in rule must have DeleteMolecules attribute or
- # it does not apply to the whole rule
- if all(dmvals) == 1:
+
+ # Use get() to avoid KeyError if the attribute is missing.
+ dmvals = [op.get("@DeleteMolecules") for op in del_op]
+ # All Delete operations in rule must have DeleteMolecules attribute set to "1".
+ if all(dmvals) and all(str(v) == "1" for v in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +732,22 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ # @totalrate comes as a string in the XML
+ if rate_type == "Function" and str(ratelaw.get("@totalrate")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate")
 
  # TODO: add support for include/exclude reactants/products
  if (

bionetgen/simulator/csimulator.py

@@ -1,7 +1,13 @@
 import ctypes, os, tempfile, bionetgen
 import numpy as np
 
-from distutils import ccompiler
+# distutils is deprecated in Python 3.12+. setuptools still provides the
+# equivalent via setuptools._distutils for backwards compatibility.
+try:
+ from setuptools._distutils import ccompiler
+except ImportError:
+ from distutils import ccompiler
+
 from .bngsimulator import BNGSimulator
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGCompileError

setup.py

@@ -14,7 +14,9 @@ def get_folder(arch):
  return fname
 
 
-subprocess.check_call([sys.executable, "-m", "pip", "install", "numpy"])
+# Note: don't run pip install at import time; in PEP 517 builds pip isn't available
+# and running subprocesses during import breaks isolated build environments.
+# numpy is declared in install_requires and will be installed by pip.
 import urllib.request
 import itertools as itt
 
@@ -186,6 +188,7 @@ def get_folder(arch):
  [console_scripts]
  bionetgen = bionetgen.main:main
  """,
+ python_requires=">=3.8",
  install_requires=[
  "cement",
  "nbopen",
@@ -201,6 +204,9 @@ def get_folder(arch):
  "python-libsbml",
  "pylru",
  "pyparsing",
+ "pyyed",
+ "matplotlib",
+ "pandas",
  "packaging",
  ],
 )

tests/test_action_parsing.py

@@ -0,0 +1,16 @@
+import pytest
+
+from bionetgen.core.utils.utils import ActionList
+
+
+def test_action_parser_rejects_unclosed_brace():
+ """Ensure malformed actions (missing closing brace) raise a parsing error."""
+
+ alist = ActionList()
+ alist.define_parser()
+
+ # Missing closing '}' should cause pyparsing to raise an exception
+ malformed = "simulate_ssa({t_start=>0,t_end=>10" # missing closing '}' and ')'
+
+ with pytest.raises(Exception):
+ alist.action_parser.parseString(malformed)

tests/test_rule_modifiers.py

@@ -0,0 +1,84 @@
+import pytest
+
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def _rule_block_parser():
+ # Create a RuleBlockXML instance without running __init__ (which expects full rule XML)
+ return RuleBlockXML.__new__(RuleBlockXML)
+
+
+def test_get_rule_mod_total_rate_string_true():
+ xml = {
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "r1",
+ "@name": "foo",
+ },
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "TotalRate"
+ assert mod.id == "r1"
+ assert mod.call == "1"
+
+
+def test_get_rule_mod_delete_molecules_all_operations():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {"@DeleteMolecules": "1"},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "DeleteMolecules"
+
+
+def test_get_rule_mod_delete_molecules_missing_attribute_does_not_apply():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type is None
+
+
+def test_get_rule_mod_move_connected_list_uses_each_element():
+ xml = {
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "a",
+ "@source": "s",
+ "@destination": "d",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "b",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "MoveConnected"
+ assert mod.id == ["a", "b"]
+ assert mod.source == ["s", "s2"]
+ assert mod.destination == ["d", "d2"]
+ assert mod.flip == ["0", "1"]
+ assert mod.call == ["1", "1"]

.github/workflows/ci.yml

@@ -48,8 +48,8 @@ jobs:
  shell: bash
  - name: Build
  run: |
- python setup.py install
- python setup.py sdist bdist_wheel
+ python -m pip install --upgrade pip
+ python -m pip install .
  - name: Test with PyTest
  run: |
  pytest

.github/workflows/release-test.yml

@@ -0,0 +1,35 @@
+name: release-test
+
+on:
+ release:
+ types: [published]
+
+jobs:
+ test-release:
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, windows-latest, macos-latest]
+ python-version: ["3.9", "3.10", "3.11", "3.12"]
+ steps:
+ - uses: actions/checkout@v4
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v5
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Install bionetgen from PyPI
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install bionetgen
+
+ - name: Smoke test bionetgen command
+ run: |
+ bionetgen -h
+ python -c "import bionetgen; print('bionetgen', bionetgen.__version__)"
+
+ - name: Run unit tests
+ run: |
+ python -m pip install pytest
+ pytest

bionetgen/__main__.py

@@ -0,0 +1,4 @@
+from .main import main
+
+if __name__ == "__main__":
+ main()

bionetgen/core/tools/info.py

@@ -64,6 +64,50 @@ def gatherInfo(self):
  # Save version info
  self.info["Perl version"] = text[num_start:num_end] + " (used to run BNG2.pl)"
 
+ # Get NFsim version (if available on PATH or adjacent to BNG2.pl)
+ self.logger.debug("NFsim info", loc=f"{__file__} : BNGInfo.gatherInfo()")
+ nf_version_text = "not found"
+ try:
+ # Try the standard PATH lookup first
+ result = subprocess.run(
+ ["NFsim", "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ else:
+ nf_version_text = f"exit {result.returncode}"
+ except FileNotFoundError:
+ # If NFsim isn't on PATH, attempt to locate it relative to BNG2.pl
+ try:
+ bng2_path = self.config.get("bionetgen", "bngpath")
+ bng2_dir = os.path.dirname(bng2_path)
+ candidates = [
+ os.path.join(bng2_dir, "bin", "NFsim"),
+ os.path.join(bng2_dir, "bin", "NFsim.exe"),
+ ]
+ for cmd in candidates:
+ if os.path.isfile(cmd):
+ result = subprocess.run(
+ [cmd, "--version"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=10,
+ )
+ if result.returncode == 0:
+ nf_version_text = result.stdout.strip().splitlines()[0]
+ break
+ except Exception:
+ pass
+ except Exception as e:
+ nf_version_text = f"error: {e}"
+
+ self.info["NFsim version"] = nf_version_text
+
  self.logger.debug("PyBNG info", loc=f"{__file__} : BNGInfo.gatherInfo()")
  # Get CLI version
  with open(

bionetgen/core/utils/utils.py

@@ -1,6 +1,7 @@
-import os, subprocess
+import os
+import shutil
+import subprocess
 from bionetgen.core.exc import BNGPerlError
-from distutils import spawn
 
 from bionetgen.core.utils.logging import BNGLogger
 
@@ -589,7 +590,7 @@ def _try_path(candidate_path):
  return hit
 
  # 3) On PATH
- bng_on_path = spawn.find_executable("BNG2.pl")
+ bng_on_path = shutil.which("BNG2.pl")
  if bng_on_path:
  tried.append(bng_on_path)
  hit = _try_path(bng_on_path)
@@ -616,7 +617,7 @@ def test_perl(app=None, perl_path=None):
  logger.debug("Checking if perl is installed.", loc=f"{__file__} : test_perl()")
  # find path to perl binary
  if perl_path is None:
- perl_path = spawn.find_executable("perl")
+ perl_path = shutil.which("perl")
  if perl_path is None:
  raise BNGPerlError
  # check if perl is actually working

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,11 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
- # All Delete operations in rule must have DeleteMolecules attribute or
- # it does not apply to the whole rule
- if all(dmvals) == 1:
+
+ # Use get() to avoid KeyError if the attribute is missing.
+ dmvals = [op.get("@DeleteMolecules") for op in del_op]
+ # All Delete operations in rule must have DeleteMolecules attribute set to "1".
+ if all(dmvals) and all(str(v) == "1" for v in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +732,22 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ # @totalrate comes as a string in the XML
+ if rate_type == "Function" and str(ratelaw.get("@totalrate")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate")
 
  # TODO: add support for include/exclude reactants/products
  if (

bionetgen/simulator/csimulator.py

@@ -1,7 +1,13 @@
 import ctypes, os, tempfile, bionetgen
 import numpy as np
 
-from distutils import ccompiler
+# distutils is deprecated in Python 3.12+. setuptools still provides the
+# equivalent via setuptools._distutils for backwards compatibility.
+try:
+ from setuptools._distutils import ccompiler
+except ImportError:
+ from distutils import ccompiler
+
 from .bngsimulator import BNGSimulator
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGCompileError

setup.py

@@ -14,7 +14,9 @@ def get_folder(arch):
  return fname
 
 
-subprocess.check_call([sys.executable, "-m", "pip", "install", "numpy"])
+# Note: don't run pip install at import time; in PEP 517 builds pip isn't available
+# and running subprocesses during import breaks isolated build environments.
+# numpy is declared in install_requires and will be installed by pip.
 import urllib.request
 import itertools as itt
 
@@ -186,6 +188,7 @@ def get_folder(arch):
  [console_scripts]
  bionetgen = bionetgen.main:main
  """,
+ python_requires=">=3.8",
  install_requires=[
  "cement",
  "nbopen",
@@ -201,6 +204,9 @@ def get_folder(arch):
  "python-libsbml",
  "pylru",
  "pyparsing",
+ "pyyed",
+ "matplotlib",
+ "pandas",
  "packaging",
  ],
 )

tests/test_action_parsing.py

@@ -0,0 +1,16 @@
+import pytest
+
+from bionetgen.core.utils.utils import ActionList
+
+
+def test_action_parser_rejects_unclosed_brace():
+ """Ensure malformed actions (missing closing brace) raise a parsing error."""
+
+ alist = ActionList()
+ alist.define_parser()
+
+ # Missing closing '}' should cause pyparsing to raise an exception
+ malformed = "simulate_ssa({t_start=>0,t_end=>10" # missing closing '}' and ')'
+
+ with pytest.raises(Exception):
+ alist.action_parser.parseString(malformed)

tests/test_rule_modifiers.py

@@ -0,0 +1,84 @@
+import pytest
+
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def _rule_block_parser():
+ # Create a RuleBlockXML instance without running __init__ (which expects full rule XML)
+ return RuleBlockXML.__new__(RuleBlockXML)
+
+
+def test_get_rule_mod_total_rate_string_true():
+ xml = {
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "r1",
+ "@name": "foo",
+ },
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "TotalRate"
+ assert mod.id == "r1"
+ assert mod.call == "1"
+
+
+def test_get_rule_mod_delete_molecules_all_operations():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {"@DeleteMolecules": "1"},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "DeleteMolecules"
+
+
+def test_get_rule_mod_delete_molecules_missing_attribute_does_not_apply():
+ xml = {
+ "ListOfOperations": {
+ "Delete": [
+ {"@DeleteMolecules": "1"},
+ {},
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type is None
+
+
+def test_get_rule_mod_move_connected_list_uses_each_element():
+ xml = {
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "a",
+ "@source": "s",
+ "@destination": "d",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "b",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ }
+ }
+
+ mod = _rule_block_parser().get_rule_mod(xml)
+ assert mod.type == "MoveConnected"
+ assert mod.id == ["a", "b"]
+ assert mod.source == ["s", "s2"]
+ assert mod.destination == ["d", "d2"]
+ assert mod.flip == ["0", "1"]
+ assert mod.call == ["1", "1"]