implementing API

tests/test_api.py

@@ -0,0 +1,22 @@
+""" Tests API
+
+:Author: Jonathan Karr <jonrkarr@gmail.com>
+:Date: 2018-03-12
+:Copyright: 2018, Karr Lab
+:License: MIT
+"""
+
+import wc_lang
+import types
+import unittest
+
+
+class ApiTestCase(unittest.TestCase):
+    def test(self):
+        self.assertIsInstance(wc_lang, types.ModuleType)
+        self.assertIsInstance(wc_lang.Model, type)
+        self.assertIsInstance(wc_lang.io, types.ModuleType)
+        self.assertIsInstance(wc_lang.config, types.ModuleType)
+        self.assertIsInstance(wc_lang.config.get_config, types.FunctionType)
+        self.assertIsInstance(wc_lang.sbml, types.ModuleType)
+        self.assertIsInstance(wc_lang.sbml.io, types.ModuleType)

wc_lang/__init__.py

@@ -3,3 +3,19 @@
 with open(pkg_resources.resource_filename('wc_lang', 'VERSION'), 'r') as file:
     __version__ = file.read().strip()
 # :obj:`str`: version
+
+# API
+from .core import (TaxonRank, SubmodelAlgorithm, SpeciesTypeType, RateLawDirection, ReferenceType,
+                   Model, Taxon, Submodel, ObjectiveFunction, Compartment,
+                   SpeciesType, Species, Concentration,
+                   Reaction, ReactionParticipant, RateLaw, RateLawEquation,
+                   BiomassComponent, BiomassReaction, Parameter, Reference,
+                   DatabaseReference)
+from . import config
+from . import io
+from . import model_gen
+from . import prepare
+from . import rate_law_utils
+from . import sbml
+from . import transform
+from . import util

wc_lang/config/__init__.py

@@ -1 +1 @@
-__version__ = '0.0.2'
+from .core import get_config, get_debug_logs_config

wc_lang/core.py

@@ -40,6 +40,7 @@
 from math import ceil, floor, exp, log, log10, isnan
 from natsort import natsorted, ns
 from six import with_metaclass, string_types
+import pkg_resources
 import re
 import sys
 from obj_model.core import (Model as BaseModel,
@@ -53,7 +54,9 @@
 from wc_lang.sbml.util import (wrap_libsbml, str_to_xmlstr, LibSBMLError,
                                init_sbml_model, create_sbml_parameter, add_sbml_unit, UNIT_KIND_DIMENSIONLESS)
 from wc_lang.rate_law_utils import RateLawUtils
-import wc_lang
+
+with open(pkg_resources.resource_filename('wc_lang', 'VERSION'), 'r') as file:
+    wc_lang_version = file.read().strip()
 
 # wc_lang generates obj_model SchemaWarning warnings because some Models lack primary attributes.
 # These models include RateLaw, ReactionParticipant, RateLawEquation, and Species.
@@ -471,7 +474,7 @@ class Model(BaseModel):
     name = StringAttribute()
     version = RegexAttribute(min_length=1, pattern='^[0-9]+\.[0-9+]\.[0-9]+', flags=re.I)
     wc_lang_version = RegexAttribute(min_length=1, pattern='^[0-9]+\.[0-9+]\.[0-9]+', flags=re.I,
-                                     default=wc_lang.__version__, verbose_name='wc_lang version')
+                                     default=wc_lang_version, verbose_name='wc_lang version')
     comments = LongStringAttribute()
 
     class Meta(BaseModel.Meta):

wc_lang/sbml/__init__.py

@@ -0,0 +1,2 @@
+from . import io
+from . import util

wc_lang/sbml/io.py

@@ -18,10 +18,8 @@
 from six import iteritems
 
 from obj_model.core import Validator
-from wc_lang.core import (Model, Taxon, Submodel, ObjectiveFunction, Compartment, SpeciesType,
-    Species, Concentration, Reaction, ReactionParticipant, RateLaw, RateLawEquation,
-    BiomassComponent, BiomassReaction, Parameter, Reference, DatabaseReference, SubmodelAlgorithm)
 from wc_lang.sbml.util import (init_sbml_model, SBML_LEVEL, SBML_VERSION, create_sbml_doc_w_fbc)
+import wc_lang.core
 
 '''
 wc_lang to SBML mapping to support FBA modeling
@@ -106,7 +104,7 @@ def run(model, algorithms=None, path=None):
                 otherwise a list of SBML file(s) created
         """
         if algorithms is None:
-            algorithms = [SubmodelAlgorithm.dfba]
+            algorithms = [wc_lang.core.SubmodelAlgorithm.dfba]
         sbml_documents = {}
         for submodel in model.get_submodels():
             if submodel.algorithm in algorithms:
@@ -188,8 +186,15 @@ def write(objects):
         #     Reaction must precede ObjectiveFunction
         #     BiomassReaction must precede ObjectiveFunction
         # This partial order is satisfied by this sequence:
-        model_order = [Submodel, Compartment, Parameter, Species,
-            Reaction, BiomassReaction, ObjectiveFunction]
+        model_order = [
+            wc_lang.core.Submodel, 
+            wc_lang.core.Compartment, 
+            wc_lang.core.Parameter, 
+            wc_lang.core.Species,
+            wc_lang.core.Reaction, 
+            wc_lang.core.BiomassReaction, 
+            wc_lang.core.ObjectiveFunction,
+            ]
 
         # add objects into libsbml.SBMLDocument
         for model in model_order: