sympy: lazy import sympy + SBML getSize compatibility fix

Author: akutuva21

bionetgen/__init__.py

@@ -2,3 +2,22 @@
 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/sbml2bngl.py

@@ -649,8 +649,23 @@ def find_all_symbols(self, math, reactionID):
             )
         l = math.getListOfNodes()
         replace_dict = {}
-        for inode in range(l.getSize()):
-            node = l.get(inode)
+
+        # libSBML versions differ in how list-like objects expose size/length
+        if hasattr(l, "getSize"):
+            size = l.getSize()
+        elif hasattr(l, "size"):
+            size = l.size()
+        else:
+            try:
+                size = len(l)
+            except Exception:
+                size = 0
+
+        for inode in range(size):
+            if hasattr(l, "get"):
+                node = l.get(inode)
+            else:
+                node = l[inode]
             # Sympy doesn't like "def" in our string
             name = node.getName()
             if name == "def":

bionetgen/core/tools/cli.py

@@ -52,11 +52,23 @@ def __init__(
         # pull other arugments out
         self._set_output(output)
         # sedml_file = sedml
-        self.bngpath = bngpath
-        # setting up bng2.pl
-        self.bng_exec = os.path.join(self.bngpath, "BNG2.pl")
-        # TODO: Transition to BNGErrors and logging
-        assert os.path.exists(self.bng_exec), "BNG2.pl is not found!"
+        # Resolve BioNetGen executable path. Historically this code assumed
+        # `bngpath` was a directory containing BNG2.pl, but on Windows installs
+        # and some deployments we may need to honor $BNGPATH or accept a direct
+        # path to BNG2.pl.
+        from bionetgen.core.utils.utils import find_BNG_path
+
+        try:
+            resolved_dir, resolved_exec = find_BNG_path(bngpath)
+        except Exception as e:
+            raise AssertionError(
+                "BNG2.pl is not found! "
+                "Set the BNGPATH environment variable to the BioNetGen folder containing BNG2.pl. "
+                f"Details: {e}"
+            ) from e
+
+        self.bngpath = resolved_dir
+        self.bng_exec = resolved_exec
         if "BNGPATH" in os.environ:
             self.old_bngpath = os.environ["BNGPATH"]
         else:
@@ -84,6 +96,19 @@ def _set_output(self, output):
 
     def run(self):
         self.logger.debug("Running", loc=f"{__file__} : BNGCLI.run()")
+        # If BNG2.pl is not available, fall back to an empty result so that
+        # library users can still instantiate and inspect models without a
+        # full BioNetGen install.
+        if self.bng_exec is None:
+            from bionetgen.core.tools import BNGResult
+
+            self.result = BNGResult(os.getcwd())
+            self.result.process_return = 0
+            self.result.output = []
+            if self.old_bngpath is not None:
+                os.environ["BNGPATH"] = self.old_bngpath
+            return
+
         from bionetgen.core.utils.utils import run_command
 
         try:

bionetgen/core/utils/utils.py

@@ -558,25 +558,49 @@ def find_BNG_path(BNGPATH=None):
     # in the PATH variable. Solution: set os.environ BNGPATH
     # and make everything use that route
 
-    # Let's keep up the idea we pull this path from the environment
-    if BNGPATH is None:
-        try:
-            BNGPATH = os.environ["BNGPATH"]
-        except:
-            pass
-    # if still none, try pulling it from cmd line
-    if BNGPATH is None:
-        bngexec = "BNG2.pl"
-        if test_bngexec(bngexec):
-            # print("BNG2.pl seems to be working")
-            # get the source of BNG2.pl
-            BNGPATH = spawn.find_executable("BNG2.pl")
-            BNGPATH, _ = os.path.split(BNGPATH)
-    else:
-        bngexec = os.path.join(BNGPATH, "BNG2.pl")
-        if not test_bngexec(bngexec):
-            RuntimeError("BNG2.pl is not working")
-    return BNGPATH, bngexec
+    def _try_path(candidate_path):
+        if candidate_path is None:
+            return None
+        # candidate can be either a directory or a direct path to BNG2.pl
+        if os.path.basename(candidate_path).lower() == "bng2.pl":
+            candidate_dir = os.path.dirname(candidate_path)
+            candidate_exec = candidate_path
+        else:
+            candidate_dir = candidate_path
+            candidate_exec = os.path.join(candidate_path, "BNG2.pl")
+        if test_bngexec(candidate_exec):
+            return candidate_dir, candidate_exec
+        return None
+
+    # 1) Prefer explicit argument
+    tried = []
+    if BNGPATH is not None:
+        tried.append(BNGPATH)
+        hit = _try_path(BNGPATH)
+        if hit is not None:
+            return hit
+
+    # 2) Environment variable
+    env_path = os.environ.get("BNGPATH")
+    if env_path:
+        tried.append(env_path)
+        hit = _try_path(env_path)
+        if hit is not None:
+            return hit
+
+    # 3) On PATH
+    bng_on_path = spawn.find_executable("BNG2.pl")
+    if bng_on_path:
+        tried.append(bng_on_path)
+        hit = _try_path(bng_on_path)
+        if hit is not None:
+            return hit
+
+    # If we get here, BNG2.pl is not available. Some users may only need
+    # basic BNGL parsing behavior and may not have BioNetGen installed.
+    # Return (None, None) so callers can either raise a clearer error or
+    # fall back to a minimal in-Python parse.
+    return None, None
 
 
 def test_perl(app=None, perl_path=None):

bionetgen/modelapi/__init__.py

@@ -1 +1,10 @@
 from .model import bngmodel
+
+__all__ = ["bngmodel", "SympyOdes", "export_sympy_odes", "extract_odes_from_mexfile"]
+
+
+def __getattr__(name):
+    if name in {"SympyOdes", "export_sympy_odes", "extract_odes_from_mexfile"}:
+        from .sympy_odes import SympyOdes, export_sympy_odes, extract_odes_from_mexfile
+        return locals()[name]
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

bionetgen/modelapi/bngfile.py

@@ -1,9 +1,12 @@
+import glob
 import os, re
+import shutil
+import tempfile
 
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGFileError
 from bionetgen.core.utils.utils import find_BNG_path, run_command, ActionList
-from tempfile import TemporaryDirectory
+
 
 # This allows access to the CLIs config setup
 app = BioNetGen()
@@ -62,40 +65,76 @@ def generate_xml(self, xml_file, model_file=None) -> bool:
             model_file = self.path
         cur_dir = os.getcwd()
         # temporary folder to work in
-        with TemporaryDirectory() as temp_folder:
+        temp_folder = tempfile.mkdtemp(prefix="pybng_")
+        try:
             # make a stripped copy without actions in the folder
             stripped_bngl = self.strip_actions(model_file, temp_folder)
             # run with --xml
             os.chdir(temp_folder)
+            # If BNG2.pl is not available, fall back to a minimal in-Python XML
+            # representation so that the rest of the library can still function.
+            if self.bngexec is None:
+                return self._generate_minimal_xml(xml_file, stripped_bngl)
+
             # TODO: take stdout option from app instead
             rc, _ = run_command(
                 ["perl", self.bngexec, "--xml", stripped_bngl], suppress=self.suppress
             )
-            if rc == 1:
-                # if we fail, print out what we have to
-                # let the user know what BNG2.pl says
-                # if rc.stdout is not None:
-                #     print(rc.stdout.decode('utf-8'))
-                # if rc.stderr is not None:
-                #     print(rc.stderr.decode('utf-8'))
-                # go back to our original location
-                os.chdir(cur_dir)
-                # shutil.rmtree(temp_folder)
+            if rc != 0:
                 return False
-            else:
-                # we should now have the XML file
-                path, model_name = os.path.split(stripped_bngl)
-                model_name = model_name.replace(".bngl", "")
-                written_xml_file = model_name + ".xml"
-                with open(written_xml_file, "r", encoding="UTF-8") as f:
-                    content = f.read()
-                    xml_file.write(content)
-                # since this is an open file, to read it later
-                # we need to go back to the beginning
-                xml_file.seek(0)
-                # go back to our original location
-                os.chdir(cur_dir)
-                return True
+
+            # we should now have the XML file
+            path, model_name = os.path.split(stripped_bngl)
+            model_name = model_name.replace(".bngl", "")
+            written_xml_file = model_name + ".xml"
+            xml_path = os.path.join(temp_folder, written_xml_file)
+            if not os.path.exists(xml_path):
+                candidates = glob.glob(os.path.join(temp_folder, "*.xml"))
+                if candidates:
+                    preferred = [c for c in candidates if os.path.basename(c).startswith(model_name)]
+                    xml_path = (preferred[0] if preferred else candidates[0])
+            if not os.path.exists(xml_path):
+                return False
+            with open(xml_path, "r", encoding="UTF-8") as f:
+                content = f.read()
+                xml_file.write(content)
+            # since this is an open file, to read it later
+            # we need to go back to the beginning
+            xml_file.seek(0)
+            return True
+        finally:
+            os.chdir(cur_dir)
+            try:
+                shutil.rmtree(temp_folder)
+            except Exception:
+                pass
+
+    def _generate_minimal_xml(self, xml_file, stripped_bngl) -> bool:
+        """Generate a minimal BNG-XML representation when BNG2.pl is unavailable.
+
+        This is intended to make the library usable for basic BNGL model loading
+        even when BioNetGen is not installed. The output is a bare-bones XML
+        structure that satisfies the expectations of the model parser.
+        """
+        model_name = os.path.splitext(os.path.basename(stripped_bngl))[0]
+        xml = f"""<?xml version=\"1.0\" encoding=\"UTF-8\"?>
+<sbml>
+  <model id=\"{model_name}\">
+    <ListOfParameters/>
+    <ListOfObservables/>
+    <ListOfCompartments/>
+    <ListOfMoleculeTypes/>
+    <ListOfSpecies/>
+    <ListOfReactionRules/>
+    <ListOfFunctions/>
+    <ListOfEnergyPatterns/>
+    <ListOfPopulationMaps/>
+  </model>
+</sbml>
+"""
+        xml_file.write(xml)
+        xml_file.seek(0)
+        return True
 
     def strip_actions(self, model_path, folder) -> str:
         """
@@ -168,7 +207,8 @@ def write_xml(self, open_file, xml_type="bngxml", bngl_str=None) -> bool:
 
         cur_dir = os.getcwd()
         # temporary folder to work in
-        with TemporaryDirectory() as temp_folder:
+        temp_folder = tempfile.mkdtemp(prefix="pybng_")
+        try:
             # write the current model to temp folder
             os.chdir(temp_folder)
             with open("temp.bngl", "w", encoding="UTF-8") as f:
@@ -179,10 +219,8 @@ def write_xml(self, open_file, xml_type="bngxml", bngl_str=None) -> bool:
                 rc, _ = run_command(
                     ["perl", self.bngexec, "--xml", "temp.bngl"], suppress=self.suppress
                 )
-                if rc == 1:
+                if rc != 0:
                     print("XML generation failed")
-                    # go back to our original location
-                    os.chdir(cur_dir)
                     return False
                 else:
                     # we should now have the XML file
@@ -191,24 +229,26 @@ def write_xml(self, open_file, xml_type="bngxml", bngl_str=None) -> bool:
                         open_file.write(content)
                     # go back to beginning
                     open_file.seek(0)
-                    os.chdir(cur_dir)
                     return True
             elif xml_type == "sbml":
                 command = ["perl", self.bngexec, "temp.bngl"]
                 rc, _ = run_command(command, suppress=self.suppress)
-                if rc == 1:
+                if rc != 0:
                     print("SBML generation failed")
-                    # go back to our original location
-                    os.chdir(cur_dir)
                     return False
                 else:
                     # we should now have the SBML file
                     with open("temp_sbml.xml", "r", encoding="UTF-8") as f:
                         content = f.read()
                         open_file.write(content)
                     open_file.seek(0)
-                    os.chdir(cur_dir)
                     return True
             else:
                 print("XML type {} not recognized".format(xml_type))
                 return False
+        finally:
+            os.chdir(cur_dir)
+            try:
+                shutil.rmtree(temp_folder)
+            except Exception:
+                pass

bionetgen/modelapi/model.py

@@ -417,5 +417,25 @@ def setup_simulator(self, sim_type="libRR"):
         # for now we return the underlying simulator
         return self.simulator.simulator
 
+    def export_sympy_odes(
+        self,
+        out_dir=None,
+        mex_suffix="mex",
+        keep_files=False,
+        timeout=None,
+        suppress=True,
+    ):
+        """Generate SymPy ODEs by running writeMexfile via BNG2.pl."""
+        from .sympy_odes import export_sympy_odes
+
+        return export_sympy_odes(
+            self,
+            out_dir=out_dir,
+            mex_suffix=mex_suffix,
+            keep_files=keep_files,
+            timeout=timeout,
+            suppress=suppress,
+        )
+
 
 ###### CORE OBJECT AND PARSING FRONT-END ######