Defer BioNetGen app setup in library imports

bionetgen/modelapi/bngfile.py

@@ -4,17 +4,11 @@
 import tempfile
 from typing import NoReturn
 
-from bionetgen.main import BioNetGen
+from bionetgen.main import get_default_bng_path
 from bionetgen.core.exc import BNGFileError
 from bionetgen.core.utils.logging import BNGLogger
 from bionetgen.core.utils.utils import find_BNG_path, run_command, ActionList
 
-# This allows access to the CLIs config setup
-app = BioNetGen()
-app.setup()
-conf = app.config["bionetgen"]
-def_bng_path = conf["bngpath"]
-
 
 class BNGFile:
     """
@@ -45,14 +39,16 @@ class BNGFile:
     """
 
     def __init__(
-        self, path, BNGPATH=def_bng_path, generate_network=False, suppress=True
+        self, path, BNGPATH=None, generate_network=False, suppress=True
     ) -> None:
         self.path = path
         self.logger = BNGLogger()
         self.generate_network = generate_network
         self.suppress = suppress
         AList = ActionList()
         self._action_list = [i + "(" for i in AList.possible_types]
+        if BNGPATH is None:
+            BNGPATH = get_default_bng_path()
         BNGPATH, bngexec = find_BNG_path(BNGPATH)
         self.BNGPATH = BNGPATH
         self.bngexec = bngexec

bionetgen/modelapi/bngparser.py

@@ -1,6 +1,5 @@
 import xmltodict
 
-from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGFileError, BNGParseError, BNGModelError
 from tempfile import TemporaryFile
 
@@ -11,12 +10,6 @@
 from .blocks import ActionBlock, ProtocolBlock
 from bionetgen.core.utils.utils import ActionList
 
-# This allows access to the CLIs config setup
-app = BioNetGen()
-app.setup()
-conf = app.config["bionetgen"]
-def_bng_path = conf["bngpath"]
-
 
 def _normalize_action_text(action: str) -> str:
     """Strip BNGL comments and unquoted whitespace, keep quoted spans intact.
@@ -188,13 +181,15 @@ class BNGParser:
     def __init__(
         self,
         path,
-        BNGPATH=def_bng_path,
+        BNGPATH=None,
         parse_actions=True,
         generate_network=False,
         suppress=True,
     ) -> None:
         self.to_parse_actions = parse_actions
-        self.bngfile = BNGFile(path, generate_network=generate_network, suppress=True)
+        self.bngfile = BNGFile(
+            path, BNGPATH=BNGPATH, generate_network=generate_network, suppress=suppress
+        )
         self.alist = ActionList()
         self.alist.define_parser()
 

bionetgen/modelapi/model.py

@@ -1,6 +1,5 @@
 import copy, tempfile, shutil
 
-from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGFileError, BNGModelError
 
 from .bngparser import BNGParser
@@ -18,12 +17,6 @@
     PopulationMapBlock,
 )
 
-# This allows access to the CLIs config setup
-app = BioNetGen()
-app.setup()
-conf = app.config["bionetgen"]
-def_bng_path = conf["bngpath"]
-
 
 ###### CORE OBJECT AND PARSING FRONT-END ######
 class bngmodel:
@@ -73,9 +66,7 @@ class bngmodel:
         "population_maps", "rules", "reaction_rules", "actions".
     """
 
-    def __init__(
-        self, bngl_model, BNGPATH=def_bng_path, generate_network=False, suppress=True
-    ):
+    def __init__(self, bngl_model, BNGPATH=None, generate_network=False, suppress=True):
         self.active_blocks = []
         # We want blocks to be printed in the same order every time
         self._block_order = [
@@ -94,7 +85,10 @@ def __init__(
         self.model_name = ""
         self.model_path = bngl_model
         self.bngparser = BNGParser(
-            bngl_model, generate_network=generate_network, suppress=True
+            bngl_model,
+            BNGPATH=BNGPATH,
+            generate_network=generate_network,
+            suppress=suppress,
         )
         self.bngparser.parse_model(self)
         for block in self._block_order:

bionetgen/network/network.py

@@ -1,4 +1,3 @@
-from bionetgen.main import BioNetGen
 from bionetgen.network.networkparser import BNGNetworkParser
 from bionetgen.network.blocks import (
     NetworkGroupBlock,
@@ -11,12 +10,6 @@
     NetworkPopulationMapBlock,
 )
 
-# This allows access to the CLIs config setup
-app = BioNetGen()
-app.setup()
-conf = app.config["bionetgen"]
-def_bng_path = conf["bngpath"]
-
 
 ###### CORE OBJECT AND PARSING FRONT-END ######
 class Network:
@@ -46,7 +39,7 @@ class Network:
         type of simulator is libRR for libRoadRunner simulator.
     """
 
-    def __init__(self, bngl_model, BNGPATH=def_bng_path):
+    def __init__(self, bngl_model, BNGPATH=None):
         self.active_blocks = []
         # We want blocks to be printed in the same order every time
         self.block_order = [

bionetgen/network/networkparser.py

@@ -1,7 +1,6 @@
 import re, os
 from bionetgen.core.exc import BNGParseError
 from bionetgen.core.utils.logging import BNGLogger
-from bionetgen.main import BioNetGen
 from bionetgen.network.blocks import (
     NetworkGroupBlock,
     NetworkParameterBlock,
@@ -13,11 +12,6 @@
     NetworkPopulationMapBlock,
 )
 
-# This allows access to the CLIs config setup
-app = BioNetGen()
-app.setup()
-conf = app.config["bionetgen"]
-def_bng_path = conf["bngpath"]
 logger = BNGLogger()
 
 

bionetgen/simulator/csimulator.py

@@ -2,7 +2,7 @@
 import numpy as np
 
 from .bngsimulator import BNGSimulator
-from bionetgen.main import BioNetGen
+from bionetgen.main import get_conf
 from bionetgen.core.exc import BNGCompileError, BNGFormatError, BNGSimError
 from bionetgen.core.utils.logging import BNGLogger
 
@@ -27,11 +27,6 @@ def _new_ccompiler():
     return ccompiler.new_compiler()
 
 
-# This allows access to the CLIs config setup
-app = BioNetGen()
-app.setup()
-conf = app.config["bionetgen"]
-def_bng_path = conf["bngpath"]
 logger = BNGLogger()
 
 
@@ -161,6 +156,7 @@ class CSimulator(BNGSimulator):
     """
 
     def __init__(self, model_file, generate_network=False):
+        conf = get_conf()
         # check cvode library paths
         if (conf.get("cvode_include") is None) or (conf.get("cvode_lib") is None):
             logger.warning(

tests/test_csimulator_errors.py

@@ -12,11 +12,15 @@ def test_csimulator_init_logs_missing_cvode_paths():
     fake_model.species = {}
     fake_compiler = mock.MagicMock()
     mock_conf_get = mock.MagicMock(side_effect=lambda key: None)
+    fake_conf = mock.MagicMock()
+    fake_conf.get = mock_conf_get
 
     def fake_compile(self):
         self.lib_file = "/tmp/fake/libcsim.so"
 
-    with mock.patch.object(csim_module.conf, "get", mock_conf_get), mock.patch.object(
+    with mock.patch.object(
+        csim_module, "get_conf", return_value=fake_conf
+    ) as mock_get_conf, mock.patch.object(
         csim_module, "logger"
     ) as mock_logger, mock.patch.object(
         csim_module.bionetgen, "bngmodel", return_value=fake_model
@@ -29,6 +33,7 @@ def fake_compile(self):
     ) as mock_wrapper:
         csim_module.CSimulator("/fake/model.bngl")
 
+    mock_get_conf.assert_called_once_with()
     mock_logger.warning.assert_called_once()
     warning_args, warning_kwargs = mock_logger.warning.call_args
     assert "CVODE include and library paths are not set" in warning_args[0]
@@ -55,16 +60,19 @@ def test_csimulator_init_invalid_model_type_raises_bng_format_error():
             "cvode_lib": "/tmp/lib",
         }[key]
     )
+    fake_conf = mock.MagicMock()
+    fake_conf.get = mock_conf_get
 
-    with mock.patch.object(csim_module.conf, "get", mock_conf_get), mock.patch.object(
-        csim_module, "logger"
-    ) as mock_logger:
+    with mock.patch.object(
+        csim_module, "get_conf", return_value=fake_conf
+    ) as mock_get_conf, mock.patch.object(csim_module, "logger") as mock_logger:
         with pytest.raises(
             BNGFormatError,
             match="CSimulator model input must be a BNGL path or bngmodel instance",
         ):
             csim_module.CSimulator(123)
 
+    mock_get_conf.assert_called_once_with()
     mock_logger.error.assert_called_once()
     error_args, error_kwargs = mock_logger.error.call_args
     assert "got int" in error_args[0]

tests/test_deferred_app_setup.py

@@ -0,0 +1,71 @@
+import subprocess
+import sys
+import textwrap
+from pathlib import Path
+from unittest.mock import patch
+
+REPO_ROOT = Path(__file__).resolve().parents[1]
+
+
+def test_library_imports_do_not_setup_default_app():
+    script = textwrap.dedent("""
+        import importlib
+        from unittest.mock import patch
+
+        modules = [
+            "bionetgen.modelapi.bngfile",
+            "bionetgen.modelapi.bngparser",
+            "bionetgen.modelapi.model",
+            "bionetgen.network.network",
+            "bionetgen.network.networkparser",
+            "bionetgen.simulator.csimulator",
+        ]
+
+        with patch("cement.core.foundation.App.setup") as setup:
+            for module in modules:
+                importlib.import_module(module)
+
+        if setup.called:
+            raise SystemExit(f"App.setup() called during import: {setup.call_args!r}")
+        """)
+    result = subprocess.run(
+        [sys.executable, "-c", script],
+        cwd=REPO_ROOT,
+        capture_output=True,
+        text=True,
+        check=False,
+    )
+
+    assert result.returncode == 0, result.stdout + result.stderr
+
+
+def test_bngfile_resolves_default_bngpath_lazily():
+    from bionetgen.modelapi import bngfile as bngfile_module
+
+    with patch.object(
+        bngfile_module, "get_default_bng_path", return_value="/default/bng"
+    ) as mock_default, patch.object(
+        bngfile_module,
+        "find_BNG_path",
+        return_value=("/resolved/bng", "/resolved/bng/BNG2.pl"),
+    ) as mock_find:
+        bngfile_module.BNGFile("/some/model.bngl")
+
+    mock_default.assert_called_once_with()
+    mock_find.assert_called_once_with("/default/bng")
+
+
+def test_bngfile_explicit_bngpath_skips_default_lookup():
+    from bionetgen.modelapi import bngfile as bngfile_module
+
+    with patch.object(
+        bngfile_module, "get_default_bng_path"
+    ) as mock_default, patch.object(
+        bngfile_module,
+        "find_BNG_path",
+        return_value=("/custom/bng", "/custom/bng/BNG2.pl"),
+    ) as mock_find:
+        bngfile_module.BNGFile("/some/model.bngl", BNGPATH="/custom/bng")
+
+    mock_default.assert_not_called()
+    mock_find.assert_called_once_with("/custom/bng")

tests/test_modelapi_export_errors.py

@@ -202,6 +202,48 @@ def test_parse_model_xml_generation_failure_wraps_bngfile_error(mock_bngfile_cls
         parser.parse_model(MagicMock())
 
 
+@patch("bionetgen.modelapi.bngparser.BNGFile")
+def test_bngparser_passes_path_options_to_bngfile(mock_bngfile_cls):
+    from bionetgen.modelapi.bngparser import BNGParser
+
+    BNGParser(
+        "/some/model.bngl",
+        BNGPATH="/custom/bng",
+        generate_network=True,
+        suppress=False,
+    )
+
+    mock_bngfile_cls.assert_called_once_with(
+        "/some/model.bngl",
+        BNGPATH="/custom/bng",
+        generate_network=True,
+        suppress=False,
+    )
+
+
+@patch("bionetgen.modelapi.model.BNGParser")
+def test_bngmodel_passes_path_options_to_bngparser(mock_parser_cls):
+    from bionetgen.modelapi.model import bngmodel
+
+    parser = MagicMock()
+    mock_parser_cls.return_value = parser
+
+    bngmodel(
+        "/some/model.bngl",
+        BNGPATH="/custom/bng",
+        generate_network=True,
+        suppress=False,
+    )
+
+    mock_parser_cls.assert_called_once_with(
+        "/some/model.bngl",
+        BNGPATH="/custom/bng",
+        generate_network=True,
+        suppress=False,
+    )
+    parser.parse_model.assert_called_once()
+
+
 def test_setup_simulator_write_xml_failure_raises_bngmodel_error_and_restores_actions(
     tmp_path, monkeypatch
 ):