reorganized main packages

Makefile

@@ -8,13 +8,15 @@ CMD_UPDATE_VERSION = sed -i -E 's/^__version__ = \"[0-9]+\.[0-9]+\.[0-9]+((a|b|r
 
 USING_PODMAN := $(shell docker --version | grep -q podman && echo 1 || echo 0)
 
+.PHONY: docs
+
 venv:
 	test -d .venv || python -m venv .venv
 	source .venv/bin/activate && pip install -Ur requirements-dev.txt
 	source .venv/bin/activate && pip install -Ur requirements-dev-extras.txt
 
 docs:
-	sphinx-apidoc -f -o ./docs/source ./src/funman -t ./docs/apidoc_templates --no-toc --module-first
+	sphinx-apidoc -f -o ./docs/source ./src/funman -t ./docs/apidoc_templates --no-toc --module-first 
 	mkdir -p ./docs/source/_static
 	mkdir -p ./docs/source/_templates
 	pyreverse \

auxiliary_packages/funman_demo/src/funman_demo/box_plotter.py

@@ -10,8 +10,8 @@
 from matplotlib.lines import Line2D
 
 from funman.model import Parameter
-from funman.search_episode import BoxSearchEpisode, SearchEpisode
-from funman.utils.search_utils import Box, Interval, Point
+from funman.search import SearchEpisode
+from funman.search.representation import Box, Interval, Point
 
 l = logging.getLogger(__file__)
 l.setLevel(logging.INFO)

auxiliary_packages/funman_demo/src/funman_demo/example/__init__.py

@@ -10,7 +10,7 @@
     ParameterSynthesisScenario,
     ParameterSynthesisScenarioResult,
 )
-from funman.utils.search_utils import ResultCombinedHandler, SearchConfig
+from funman.search.representation import ResultCombinedHandler, SearchConfig
 
 from ..plot import plot_parameter_space
 

auxiliary_packages/funman_demo/src/funman_demo/example/bilayer.py

@@ -9,14 +9,14 @@
 
 from funman import Funman
 from funman.model import Parameter, QueryLE, QueryTrue
-from funman.model2smtlib.bilayer.translate import (
-    BilayerEncoder,
-    BilayerEncodingOptions,
-)
 from funman.model.bilayer import Bilayer, BilayerMeasurement, BilayerModel
 from funman.scenario.consistency import ConsistencyScenario
 from funman.scenario.parameter_synthesis import ParameterSynthesisScenario
-from funman.utils.search_utils import ResultCombinedHandler, SearchConfig
+from funman.search.representation import ResultCombinedHandler, SearchConfig
+from funman.translate.bilayer.bilayer import (
+    BilayerEncoder,
+    BilayerEncodingOptions,
+)
 
 
 def run_chime_bilayer_example(output_path):

auxiliary_packages/funman_demo/src/funman_demo/example/demo120822.py

@@ -13,20 +13,20 @@
 
 from funman import Funman
 from funman.model import Parameter, QueryLE, QueryTrue
-from funman.model2smtlib.bilayer.translate import (
-    BilayerEncoder,
-    BilayerEncodingOptions,
-)
 from funman.model.bilayer import Bilayer, BilayerMeasurement, BilayerModel
 from funman.scenario.consistency import ConsistencyScenario
 from funman.scenario.parameter_synthesis import ParameterSynthesisScenario
 from funman.search import BoxSearch, SMTCheck
-from funman.search_episode import DRealSearchEpisode
-from funman.utils.search_utils import (
+from funman.search.representation import (
     Point,
     ResultCombinedHandler,
     SearchConfig,
 )
+from funman.search.search_episode import DRealSearchEpisode
+from funman.translate.bilayer.bilayer import (
+    BilayerEncoder,
+    BilayerEncodingOptions,
+)
 
 
 class Scenario1(object):

auxiliary_packages/funman_demo/src/funman_demo/handlers.py

@@ -7,7 +7,7 @@
 from IPython.display import Image, display
 
 from funman.model import Parameter
-from funman.utils.search_utils import (
+from funman.search.representation import (
     Box,
     Point,
     ResultHandler,

auxiliary_packages/funman_demo/src/funman_demo/plot.py

@@ -6,7 +6,7 @@
 from matplotlib.lines import Line2D
 
 from funman.parameter_space import ParameterSpace
-from funman.utils.search_utils import Box, Point, decode_labeled_object
+from funman.search.representation import Box, Point, decode_labeled_object
 
 from .box_plotter import BoxPlotter
 

auxiliary_packages/funman_demo/test/test_chime_param_synth.py

@@ -30,7 +30,7 @@
 from funman.model.encoded import EncodedModel
 from funman.scenario.parameter_synthesis import ParameterSynthesisScenario
 from funman.search import BoxSearch
-from funman.utils.search_utils import SearchConfig
+from funman.search.representation import SearchConfig
 
 l = logging.getLogger(__file__)
 l.setLevel(logging.INFO)

auxiliary_packages/funman_dreal/test/test_chime_bilayer_solve.py

@@ -31,21 +31,21 @@
 
 from funman import Funman
 from funman.model import Model, Parameter, QueryLE
-from funman.model2smtlib.bilayer.translate import (
-    Bilayer,
-    BilayerEncoder,
-    BilayerEncodingOptions,
-    BilayerMeasurement,
-    BilayerModel,
-)
 from funman.scenario.consistency import ConsistencyScenario
 from funman.scenario.parameter_synthesis import ParameterSynthesisScenario
 from funman.search import BoxSearch, SMTCheck
-from funman.utils.search_utils import (
+from funman.search.representation import (
     Point,
     ResultCombinedHandler,
     SearchConfig,
 )
+from funman.translate.bilayer.bilayer import (
+    Bilayer,
+    BilayerEncoder,
+    BilayerEncodingOptions,
+    BilayerMeasurement,
+    BilayerModel,
+)
 from funman.utils.smtlib_utils import smtlibscript_from_formula
 
 l = logging.getLogger(__file__)

docs/apidoc_templates/package.rst_t

@@ -5,7 +5,7 @@
 {%- endfor %}
 {%- endmacro %}
 
-{%- macro toctree(docnames) -%}
+{%- macro toctree(docnames, maxdepth) -%}
 .. toctree::
    :maxdepth: {{ maxdepth }}
 {% for docname in docnames %}
@@ -31,8 +31,12 @@
 Subpackages
 -----------
 
-{{ toctree(subpackages) }}
-{% endif %}
+{{ toctree(subpackages, maxdepth=2) }}
+{% for subpackage in subpackages %}
+{{- subpackage | e | heading(3) }}
+{{ automodule(subpackage, automodule_options)  }}
+{% endfor %}
+{%- endif %}
 
 {%- if submodules %}
 Submodules

docs/source/funman.model.rst

@@ -28,3 +28,13 @@ funman.model.encoded
    :members:
    :undoc-members:
    :show-inheritance:
+
+funman.model.query
+------------------
+.. inheritance-diagram:: funman.model.query
+   :parts: 1
+
+.. automodule:: funman.model.query
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/funman.model2smtlib.rst

@@ -10,10 +10,22 @@ Subpackages
 -----------
 
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 2
 
    funman.model2smtlib.bilayer
    funman.model2smtlib.gromet
+funman.model2smtlib.bilayer
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: funman.model2smtlib.bilayer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+funman.model2smtlib.gromet
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: funman.model2smtlib.gromet
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 Submodules
 ----------

scratch/CHIME/test_CHIME_SIR.py

@@ -3,7 +3,7 @@
 
 from funman_demo.sim.CHIME.CHIME_SIR import main as run_CHIME_SIR
 
-from funman.model2smtlib.gromet.translate import QueryableGromet
+from funman.translate.gromet.gromet import QueryableGromet
 
 RESOURCES = os.path.join("resources")
 GROMET_FILE = os.path.join(

scratch/CHIME/test_CHIME_parameter_synthesis.py

@@ -2,8 +2,8 @@
 import unittest
 from multiprocessing.heap import Arena
 
-from funman.model2smtlib.gromet.translate import QueryableGromet
 from funman.parameter_space import ParameterSpace
+from funman.translate.gromet.gromet import QueryableGromet
 
 RESOURCES = os.path.join("resources")
 GROMET_FILE_1 = os.path.join(

scratch/CHIME/test_cached_parameter_space.py

@@ -10,7 +10,7 @@
 from funman.model.encoded import EncodedModel
 from funman.scenario.parameter_synthesis import ParameterSynthesisScenario
 from funman.search import BoxSearch
-from funman.utils.search_utils import ResultCombinedHandler, SearchConfig
+from funman.search.representation import ResultCombinedHandler, SearchConfig
 
 l = logging.getLogger(__file__)
 l.setLevel(logging.ERROR)

scratch/model2smtlib/test_fn2smt.py

@@ -4,7 +4,7 @@
 from pysmt.shortcuts import Symbol, get_model
 from pysmt.typing import INT
 
-from funman.model2smtlib.gromet.translate import QueryableGromet
+from funman.translate.gromet.gromet import QueryableGromet
 
 RESOURCES = os.path.join(
     os.path.dirname(os.path.abspath(__file__)), "../resources"

scratch/model2smtlib/test_parseGroMEtJSON.py

@@ -1,7 +1,7 @@
 import os
 import unittest
 
-from funman.model2smtlib.gromet.translate import QueryableGromet
+from funman.translate.gromet.gromet import QueryableGromet
 
 RESOURCES = os.path.join(
     os.path.dirname(os.path.abspath(__file__)), "../resources"

src/funman/__init__.py

@@ -6,52 +6,6 @@
 - Parameter Synthesis: Generating feasible values for model parameters.
 """
 
-import logging
 
-import funman
-from funman._version import __version__
-from funman.config import Config
-from funman.scenario import AnalysisScenario, AnalysisScenarioResult
-
-l = logging.getLogger(__file__)
-l.setLevel(logging.ERROR)
-
-
-class Funman(object):
-    """
-    The Funman FUNctional Model ANalysis class is the main entry point for
-    performing analysis on models.  The main entry point Funman.solve() performs
-    analysis of an funman.scenario.AnalysisScenario, subject to a set of configuration
-    options in the funman.search.SearchConfig class.
-    """
-
-    def solve(
-        self, problem: AnalysisScenario, config: Config = None
-    ) -> AnalysisScenarioResult:
-        """
-        This method is the main entry point for Funman analysis.  Its inputs
-        describe an AnalysisScenario and SearchConfig that setup the problem and
-        analysis technique.  The return value is an AnalysisScenarioResult,
-        which comprises all relevant output pertaining to the AnalysisScenario.
-
-        Parameters
-        ----------
-        problem : AnalysisScenario
-            The problem is a description of the analysis to be performed, and typically describes a Model and a Query.
-        config : SearchConfig, optional
-            The configuration for the search algorithm applied to analyze the problem, by default SearchConfig()
-
-        Returns
-        -------
-        AnalysisScenarioResult
-            The resulting data, statistics, and other relevant information produced by the analysis.
-        """
-        return problem.solve(config)
-
-
-def main():
-    return funman.Funman()
-
-
-if __name__ == "main":
-    main()
+from ._version import __version__
+from .funman import *

src/funman/funman.py

@@ -0,0 +1,38 @@
+import logging
+
+from funman.scenario import AnalysisScenario, AnalysisScenarioResult, Config
+
+l = logging.getLogger(__file__)
+l.setLevel(logging.ERROR)
+
+
+class Funman(object):
+    """
+    The Funman FUNctional Model ANalysis class is the main entry point for
+    performing analysis on models.  The main entry point Funman.solve() performs
+    analysis of an funman.scenario.AnalysisScenario, subject to a set of configuration
+    options in the funman.search.SearchConfig class.
+    """
+
+    def solve(
+        self, problem: AnalysisScenario, config: Config = None
+    ) -> AnalysisScenarioResult:
+        """
+        This method is the main entry point for Funman analysis.  Its inputs
+        describe an AnalysisScenario and SearchConfig that setup the problem and
+        analysis technique.  The return value is an AnalysisScenarioResult,
+        which comprises all relevant output pertaining to the AnalysisScenario.
+
+        Parameters
+        ----------
+        problem : AnalysisScenario
+            The problem is a description of the analysis to be performed, and typically describes a Model and a Query.
+        config : SearchConfig, optional
+            The configuration for the search algorithm applied to analyze the problem, by default SearchConfig()
+
+        Returns
+        -------
+        AnalysisScenarioResult
+            The resulting data, statistics, and other relevant information produced by the analysis.
+        """
+        return problem.solve(config)