Bringing testing branch up to date with main

CHANGELOG.md

@@ -112,4 +112,20 @@ Small bugfix to ensure the model file is opened with UTF-8 encoding which caused
 Removing numpy dependency from setup.py, action reading off of BNGL file. 
 
 ## 0.3.8
-Moving imports around, removing unnecessary ones to speed up CLI performance. 
+Moving imports around, removing unnecessary ones to speed up CLI performance. 
+
+## 0.3.9
+A couple bugfixes to plotting, running the CLI on a model can now generate a log file with the option
+-l/--log. Failing to run now raises a ValueError (will be changed with custom errors in the future). Added some input and output file checks to notebook subcommand. 
+
+## 0.4.0 
+Fixed a but where "0" species was being printed as "0()". Action block is now a list and not a dictionary which was disallowing multiple actions of the same type. 
+
+## 0.4.1
+Changed `bionetgen.run` behavior when called with a `bngmodel` object. Now the model file is saved and if it exists, it's overwritten with a warning. Slightly better error reporting when the `run` call fails. 
+
+## 0.4.2
+Changed `bionetgen.run` behavior again, how calling the method with an `out` argument doesn't leave you in the output folder when it's done executing and it will return you back to the folder you started with. Bugfix where parsing a model without actions failed. 
+
+## 0.4.3
+Bugfix where the libroadrunner simulator object was not handled correctly. 

README.md

@@ -52,10 +52,10 @@ with open("new_model.bngl", "w") as f:
     f.write(str(model)) # writes the changed model to new_model file
 
 # this will give you a libRoadRunner instance of the model
-librr_sim = model.setup_simulator()._simulator
+librr_sim = model.setup_simulator()
 ```
 
-More documentation and tutorials are in progress.
+You can find more tutorials [here](https://pybionetgen.readthedocs.io/en/latest/tutorials.html).
 
 ### Environment Setup
 

bionetgen/assets/VERSION

@@ -1 +1 @@
-0 3 8 alpha 0
+0 4 3 alpha 0

bionetgen/core/main.py

@@ -145,6 +145,9 @@ def _set_output(self, output):
             os.chdir(output)
 
     def run(self):
+        import ipdb
+
+        ipdb.set_trace()
         try:
             stdout_loc = getattr(subprocess, self.stdout)
         except:
@@ -198,7 +201,7 @@ def run(self):
         #     print(rc.stdout.decode('utf-8'))
         # if rc.stderr is not None:
         #     print(rc.stderr.decode('utf-8'))
-        import ipdb;ipdb.set_trace()
+        # import ipdb;ipdb.set_trace()
         if rc == 0:
             # load in the result
             self.result = BNGResult(os.getcwd())
@@ -213,4 +216,4 @@ def run(self):
                 os.environ["BNGPATH"] = self.old_bngpath
             raise ValueError(
                 "Failed to run your BNGL file, there might be an issue with your model!"
-            )
+            )

bionetgen/core/plot.py

@@ -83,8 +83,11 @@ def _datplot(self):
         ymin = self.kwargs.get("ymin", False) or oymin
         ymax = self.kwargs.get("ymax", False) or oymax
 
-        fax.set_xlim(xmin, xmax)
-        fax.set_ylim(ymin, ymax)
+        assert xmax > xmin, "--xmin is bigger than --xmax!"
+        assert ymax > ymin, "--ymin is bigger than --ymax!"
+
+        fax.set_xlim(left=xmin, right=xmax)
+        fax.set_ylim(bottom=ymin, top=ymax)
         # labels and title
         _ = plt.xlabel(self.kwargs.get("xlabel") or x_name)
         _ = plt.ylabel(self.kwargs.get("ylabel") or "concentration")

bionetgen/main.py

@@ -1,6 +1,6 @@
 from bionetgen.modelapi.utils import run_command
 import cement
-import subprocess
+import subprocess, os
 import bionetgen as bng
 from cement.core.exc import CaughtSignal
 from .core.exc import BioNetGenError
@@ -74,6 +74,15 @@ class Meta:
                     "type": str,
                 },
             ),
+            (
+                ["-l", "--log"],
+                {
+                    "help": "saves BNG2.pl log to a file given (default: None)",
+                    "default": None,
+                    "type": str,
+                    "dest": "log_file",
+                },
+            ),
         ],
     )
     def run(self):
@@ -132,6 +141,16 @@ def notebook(self):
         args = self.app.pargs
         if args.input is not None:
             # we want to use the template to write a custom notebok
+            assert args.input.endswith(
+                ".bngl"
+            ), f"File {args.input} doesn't have bngl extension!"
+            try:
+                import bionetgen
+
+                m = bionetgen.bngmodel(args.input)
+                str(m)
+            except:
+                raise RuntimeError(f"Couldn't import given model: {args.input}!")
             notebook = BNGNotebook(
                 CONFIG["bionetgen"]["notebook"]["template"], INPUT_ARG=args.input
             )
@@ -144,13 +163,22 @@ def notebook(self):
         else:
             fname = args.output
         # write the notebook out
+        if os.path.isdir(fname):
+            if args.input is not None:
+                basename = os.path.basename(args.input)
+                mname = basename.replace(".bngl", "")
+                fname = mname + ".ipynb"
+            else:
+                mname = CONFIG["bionetgen"]["notebook"]["name"]
+                fname = os.path.join(args.output, mname)
+
         notebook.write(fname)
         # open the notebook with nbopen
         stdout = getattr(subprocess, CONFIG["bionetgen"]["stdout"])
         stderr = getattr(subprocess, CONFIG["bionetgen"]["stderr"])
         if args.open:
             command = ["nbopen", fname]
-            rc = run_command(command)
+            rc, _ = run_command(command)
 
     @cement.ex(
         help="Rudimentary plotting of gdat/cdat/scan files",
@@ -186,27 +214,31 @@ def notebook(self):
                 {
                     "help": "x-axis minimum (default: determined from data)",
                     "default": None,
+                    "type": float,
                 },
             ),
             (
                 ["--xmax"],
                 {
                     "help": "x-axis maximum (default: determined from data)",
                     "default": False,
+                    "type": float,
                 },
             ),
             (
                 ["--ymin"],
                 {
                     "help": "y-axis minimum (default: determined from data)",
                     "default": False,
+                    "type": float,
                 },
             ),
             (
                 ["--ymax"],
                 {
                     "help": "y-axis maximum (default: determined from data)",
                     "default": False,
+                    "type": float,
                 },
             ),
             (["--xlabel"], {"help": "x-axis label (default: time)", "default": False}),

bionetgen/modelapi/blocks.py

@@ -543,10 +543,44 @@ def __init__(self) -> None:
         self.name = "actions"
         AList = ActionList()
         self._action_list = AList.possible_types
+        self.items = []
 
     def __setattr__(self, name, value) -> None:
         self.__dict__[name] = value
 
+    def add_item(self, item_tpl) -> None:
+        name, value = item_tpl
+        # set the line
+        self.items.append(value)
+
+    def __repr__(self) -> str:
+        # overwrites what the class representation
+        # shows the items in the model block in
+        # say ipython
+        repr_str = "{} block with {} item(s): {}".format(
+            self.name, len(self.items), self.items
+        )
+        return repr_str
+
+    def __getitem__(self, key):
+        return self.items[key]
+
+    def __setitem__(self, key, value) -> None:
+        self.items[key] = value
+
+    def __delitem__(self, key) -> None:
+        try:
+            return self.items.pop(key)
+        # TODO: more specific except statements
+        except:
+            print("Item {} not found".format(key))
+
+    def __iter__(self):
+        return self.items.__iter__()
+
+    def __contains__(self, key) -> bool:
+        return key in self.items
+
     def add_action(self, action_type, action_args) -> None:
         """
         adds action, needs type as string and args as list of tuples
@@ -564,7 +598,7 @@ def clear_actions(self) -> None:
     def gen_string(self) -> str:
         block_lines = []
         # we just loop over lines for actions
-        for item in self.items.keys():
-            block_lines.append(self.items[item].print_line())
+        for item in self.items:
+            block_lines.append(item.print_line())
         # join everything with new lines
         return "\n".join(block_lines)

bionetgen/modelapi/bngfile.py

@@ -67,8 +67,7 @@ def generate_xml(self, xml_file, model_file=None) -> bool:
             # run with --xml
             os.chdir(temp_folder)
             # TODO: take stdout option from app instead
-            # rc = subprocess.run(["perl",self.bngexec, "--xml", stripped_bngl], stdout=bng.defaults.stdout)
-            rc = run_command(["perl", self.bngexec, "--xml", stripped_bngl])
+            rc, _ = run_command(["perl", self.bngexec, "--xml", stripped_bngl])
             if rc == 1:
                 # if we fail, print out what we have to
                 # let the user know what BNG2.pl says
@@ -145,7 +144,7 @@ def write_xml(self, open_file, xml_type="bngxml", bngl_str=None) -> bool:
             # run with --xml
             # TODO: Make output supression an option somewhere
             if xml_type == "bngxml":
-                rc = run_command(["perl", self.bngexec, "--xml", "temp.bngl"])
+                rc, _ = run_command(["perl", self.bngexec, "--xml", "temp.bngl"])
                 if rc == 1:
                     print("XML generation failed")
                     # go back to our original location
@@ -162,7 +161,7 @@ def write_xml(self, open_file, xml_type="bngxml", bngl_str=None) -> bool:
                     return True
             elif xml_type == "sbml":
                 command = ["perl", self.bngexec, "temp.bngl"]
-                rc = run_command(command)
+                rc, _ = run_command(command)
                 if rc == 1:
                     print("SBML generation failed")
                     # go back to our original location
@@ -179,4 +178,3 @@ def write_xml(self, open_file, xml_type="bngxml", bngl_str=None) -> bool:
             else:
                 print("XML type {} not recognized".format(xml_type))
                 return False
-            return False

bionetgen/modelapi/bngparser.py

@@ -121,7 +121,7 @@ def parse_actions(self, model_obj):
                         ablock.add_action(atype, arg_tuples)
                     else:
                         ablock.add_action(atype, [])
-        model_obj.add_block(ablock)
+            model_obj.add_block(ablock)
 
     def parse_xml(self, xml_str, model_obj) -> None:
         xml_dict = xmltodict.parse(xml_str)

bionetgen/modelapi/model.py

@@ -256,9 +256,12 @@ def setup_simulator(self, sim_type="libRR"):
             # temporary file
             with TemporaryFile(mode="w+") as tpath:
                 # write the sbml
-                self.bngparser.bngfile.write_xml(
-                    tpath, xml_type="sbml", bngl_str=str(self)
-                )
+                if not (
+                    self.bngparser.bngfile.write_xml(
+                        tpath, xml_type="sbml", bngl_str=str(self)
+                    )
+                ):
+                    raise ValueError("SBML couldn't be generated for libRR simulator")
                 # TODO: Only clear the writeSBML action
                 # by adding a mechanism to do so
                 self.actions.clear_actions()
@@ -279,7 +282,8 @@ def setup_simulator(self, sim_type="libRR"):
                 )
             )
             return None
-        return self.simulator
+        # for now we return the underlying simulator
+        return self.simulator.simulator
 
 
 ###### CORE OBJECT AND PARSING FRONT-END ######

bionetgen/modelapi/pattern.py

@@ -131,13 +131,20 @@ def __str__(self):
         mol_str = self.name
         if self.label is not None:
             mol_str += "%{}".format(self.label)
-        mol_str += "("
+        # we have a null species
+        if not self.name == "0":
+            mol_str += "("
+        # we _could_ just not do () if components
+        # don't exist but that has other issues,
+        # especially for extension highlighting
         if len(self.components) > 0:
             for icomp, comp in enumerate(self.components):
                 if icomp > 0:
                     mol_str += ","
                 mol_str += str(comp)
-        mol_str += ")"
+        # we have a null species
+        if not self.name == "0":
+            mol_str += ")"
         if self.compartment is not None:
             mol_str += "@{}".format(self.compartment)
         return mol_str

bionetgen/modelapi/runner.py

@@ -24,8 +24,8 @@ def run(inp, out=None, suppress=False):
         into. If it doesn't exist, it will be created.
     """
     # if out is None we make a temp directory
+    cur_dir = os.getcwd()
     if out is None:
-        cur_dir = os.getcwd()
         with TemporaryDirectory() as out:
             # instantiate a CLI object with the info
             cli = BNGCLI(inp, out, conf["bngpath"], suppress=suppress)

bionetgen/modelapi/utils.py

@@ -100,7 +100,7 @@ def test_bngexec(bngexec):
         path to BNG2.pl to test
     """
     command = ["perl", bngexec]
-    rc = run_command(command, suppress=True)
+    rc, _ = run_command(command, suppress=True)
     if rc == 0:
         return True
     else:
@@ -112,14 +112,17 @@ def run_command(command, suppress=False):
         process = subprocess.Popen(
             command, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL, bufsize=-1
         )
-        return process.poll()
+        return process.poll(), None
     else:
         process = subprocess.Popen(command, stdout=subprocess.PIPE, encoding="utf8")
+        out = []
         while True:
             output = process.stdout.readline()
             if output == "" and process.poll() is not None:
                 break
             if output:
-                print(output.strip())
+                o = output.strip()
+                out.append(o)
+                print(o)
         rc = process.poll()
-        return rc
+        return rc, out

bionetgen/simulator/simulators.py

@@ -26,12 +26,12 @@ def sim_getter(model_file=None, model_str=None, sim_type="libRR"):
     """
     if model_file is not None:
         if sim_type == "libRR":
-            return libRRSimulator(model_file=model_file).simulator
+            return libRRSimulator(model_file=model_file)
         else:
             print("simulator type {} not supported".format(sim_type))
     elif model_str is not None:
         if sim_type == "libRR":
-            return libRRSimulator(model_str=model_str).simulator
+            return libRRSimulator(model_str=model_str)
         else:
             print("simulator type {} not supported".format(sim_type))
 

docs/source/index.rst

@@ -30,8 +30,8 @@ Indices and Tables:
 * :ref:`modindex`
 * :ref:`search`
 
-BioNetGen Home & GitHub Links
-=============================
+BioNetGen Home & GitHub Links:
+==============================
 
 * `BioNetGen <https://bionetgen.org/>`_
 * `BNG VSCode Extension GitHub <https://github.com/RuleWorld/BNG_vscode_extension>`_