Merge pull request #165 from ModECI/to_031

Move to v0.3.1 of package
ModECI · Oct 18, 2021 · d4ca950 · d4ca950
2 parents 452b77e + e8ed0ef
commit d4ca950
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diff --git a/docs/MDF_function_specifications.json b/docs/MDF_function_specifications.json
@@ -1327,7 +1327,7 @@
             "pattern",
             "curr_goal"
         ],
-        "expression_string": "actr_functions.change_goal(pattern, curr_goal)"
+        "expression_string": "actr.change_goal(pattern, curr_goal)"
     },
     "retrieve_chunk": {
         "description": "ACT-R retrieve chunk function",
@@ -1336,7 +1336,7 @@
             "dm_chunks",
             "types"
         ],
-        "expression_string": "actr_functions.retrieve_chunk(pattern, dm_chunks, types)"
+        "expression_string": "actr.retrieve_chunk(pattern, dm_chunks, types)"
     },
     "pattern_matching_function": {
         "description": "ACT-R pattern matching function",
@@ -1345,34 +1345,34 @@
             "goal",
             "retrieval"
         ],
-        "expression_string": "actr_functions.pattern_matching_function(productions, goal, retrieval)"
+        "expression_string": "actr.pattern_matching_function(productions, goal, retrieval)"
     },
     "conflict_resolution_function": {
         "description": "ACT-R conflict resolution function",
         "arguments": [
             "productions"
         ],
-        "expression_string": "actr_functions.conflict_resolution_function(productions)"
+        "expression_string": "actr.conflict_resolution_function(productions)"
     },
     "update_goal": {
         "description": "ACT-R update goal buffer function",
         "arguments": [
             "production"
         ],
-        "expression_string": "actr_functions.update_goal(production)"
+        "expression_string": "actr.update_goal(production)"
     },
     "update_retrieval": {
         "description": "ACT-R update retrieval buffer function",
         "arguments": [
             "production"
         ],
-        "expression_string": "actr_functions.update_retrieval(production)"
+        "expression_string": "actr.update_retrieval(production)"
     },
     "check_termination": {
         "description": "check_termination",
         "arguments": [
             "production"
         ],
-        "expression_string": "actr_functions.check_termination(production)"
+        "expression_string": "actr.check_termination(production)"
     }
 }
diff --git a/docs/MDF_function_specifications.yaml b/docs/MDF_function_specifications.yaml
@@ -3258,8 +3258,7 @@ pattern_matching_function:
     - productions
     - goal
     - retrieval
-    expression_string: actr.pattern_matching_function(productions, goal,
-        retrieval)
+    expression_string: actr.pattern_matching_function(productions, goal, retrieval)
 conflict_resolution_function:
     description: ACT-R conflict resolution function
     arguments:

diff --git a/docs/MDF_specification.json b/docs/MDF_specification.json
@@ -1,5 +1,5 @@
 {
-    "version": "ModECI MDF v0.2",
+    "version": "ModECI MDF v0.3",
     "comment": "**Note: the ModECI MDF specification is still in development! Subject to change without (much) notice. See [here](https://github.com/ModECI/MDF/issues?q=is%3Aissue+is%3Aopen+label%3Aspecification) for ongoing discussions.**",
     "specification": {
         "Model": {

diff --git a/docs/MDF_specification.yaml b/docs/MDF_specification.yaml
@@ -1,4 +1,4 @@
-version: ModECI MDF v0.2
+version: ModECI MDF v0.3
 comment: '**Note: the ModECI MDF specification is still in development! Subject to
     change without (much) notice. See [here](https://github.com/ModECI/MDF/issues?q=is%3Aissue+is%3Aopen+label%3Aspecification)
     for ongoing discussions.**'

diff --git a/docs/README.md b/docs/README.md
@@ -1,4 +1,4 @@
-# Specification of ModECI v0.2
+# Specification of ModECI v0.3
 **Note: the ModECI MDF specification is still in development! Subject to change without (much) notice. See [here](https://github.com/ModECI/MDF/issues?q=is%3Aissue+is%3Aopen+label%3Aspecification) for ongoing discussions.**
 ## Model
 The top level Model containing <a href="#graph">Graph</a>s consisting of <a href="#node">Node</a>s connected via <a href="#edge">Edge</a>s.

diff --git a/docs/sphinx/source/api/MDF_function_specifications.md b/docs/sphinx/source/api/MDF_function_specifications.md
@@ -1,4 +1,4 @@
-# Specification of standard functions in ModECI v0.2
+# Specification of standard functions in ModECI v0.3
 **Note: the ModECI MDF specification is still in development! Subject to change without (much) notice. See [here](https://github.com/ModECI/MDF/issues?q=is%3Aissue+is%3Aopen+label%3Aspecification) for ongoing discussions.**
 These functions are defined in https://github.com/ModECI/MDF/blob/main/src/modeci_mdf/standard_functions.py
 ## All functions:
@@ -2973,35 +2973,35 @@ This operator has **optional** inputs/outputs. See [the doc](IR.md) for more det
 
 ## change_goal
  <p><i>ACT-R change goal buffer function</i></p>
-<p><b>change_goal(pattern, curr_goal)</b> = actr_functions.change_goal(pattern, curr_goal)</p>
-<p>Python version: actr_functions.change_goal(pattern, curr_goal)</p>
+<p><b>change_goal(pattern, curr_goal)</b> = actr.change_goal(pattern, curr_goal)</p>
+<p>Python version: actr.change_goal(pattern, curr_goal)</p>
 
 ## retrieve_chunk
  <p><i>ACT-R retrieve chunk function</i></p>
-<p><b>retrieve_chunk(pattern, dm_chunks, types)</b> = actr_functions.retrieve_chunk(pattern, dm_chunks, types)</p>
-<p>Python version: actr_functions.retrieve_chunk(pattern, dm_chunks, types)</p>
+<p><b>retrieve_chunk(pattern, dm_chunks, types)</b> = actr.retrieve_chunk(pattern, dm_chunks, types)</p>
+<p>Python version: actr.retrieve_chunk(pattern, dm_chunks, types)</p>
 
 ## pattern_matching_function
  <p><i>ACT-R pattern matching function</i></p>
-<p><b>pattern_matching_function(productions, goal, retrieval)</b> = actr_functions.pattern_matching_function(productions, goal, retrieval)</p>
-<p>Python version: actr_functions.pattern_matching_function(productions, goal, retrieval)</p>
+<p><b>pattern_matching_function(productions, goal, retrieval)</b> = actr.pattern_matching_function(productions, goal, retrieval)</p>
+<p>Python version: actr.pattern_matching_function(productions, goal, retrieval)</p>
 
 ## conflict_resolution_function
  <p><i>ACT-R conflict resolution function</i></p>
-<p><b>conflict_resolution_function(productions)</b> = actr_functions.conflict_resolution_function(productions)</p>
-<p>Python version: actr_functions.conflict_resolution_function(productions)</p>
+<p><b>conflict_resolution_function(productions)</b> = actr.conflict_resolution_function(productions)</p>
+<p>Python version: actr.conflict_resolution_function(productions)</p>
 
 ## update_goal
  <p><i>ACT-R update goal buffer function</i></p>
-<p><b>update_goal(production)</b> = actr_functions.update_goal(production)</p>
-<p>Python version: actr_functions.update_goal(production)</p>
+<p><b>update_goal(production)</b> = actr.update_goal(production)</p>
+<p>Python version: actr.update_goal(production)</p>
 
 ## update_retrieval
  <p><i>ACT-R update retrieval buffer function</i></p>
-<p><b>update_retrieval(production)</b> = actr_functions.update_retrieval(production)</p>
-<p>Python version: actr_functions.update_retrieval(production)</p>
+<p><b>update_retrieval(production)</b> = actr.update_retrieval(production)</p>
+<p>Python version: actr.update_retrieval(production)</p>
 
 ## check_termination
  <p><i>check_termination</i></p>
-<p><b>check_termination(production)</b> = actr_functions.check_termination(production)</p>
-<p>Python version: actr_functions.check_termination(production)</p>
+<p><b>check_termination(production)</b> = actr.check_termination(production)</p>
+<p>Python version: actr.check_termination(production)</p>
diff --git a/docs/sphinx/source/api/Specification.md b/docs/sphinx/source/api/Specification.md
@@ -1,4 +1,4 @@
-# Specification of ModECI v0.2
+# Specification of ModECI v0.3
 **Note: the ModECI MDF specification is still in development! Subject to change without (much) notice. See [here](https://github.com/ModECI/MDF/issues?q=is%3Aissue+is%3Aopen+label%3Aspecification) for ongoing discussions.**
 ## Model
 The top level Model containing <a href="#graph">Graph</a>s consisting of <a href="#node">Node</a>s connected via <a href="#edge">Edge</a>s.

diff --git a/examples/ACT-R/addition.json b/examples/ACT-R/addition.json
@@ -1,7 +1,7 @@
 {
     "addition": {
-        "format": "ModECI MDF v0.2",
-        "generating_application": "Python modeci-mdf v0.2.1",
+        "format": "ModECI MDF v0.3",
+        "generating_application": "Python modeci-mdf v0.3.1",
         "graphs": {
             "addition_graph": {
                 "conditions": {

diff --git a/examples/ACT-R/addition.yaml b/examples/ACT-R/addition.yaml
@@ -1,6 +1,6 @@
 addition:
-    format: ModECI MDF v0.2
-    generating_application: Python modeci-mdf v0.2.1
+    format: ModECI MDF v0.3
+    generating_application: Python modeci-mdf v0.3.1
     graphs:
         addition_graph:
             conditions:

diff --git a/examples/ACT-R/count.json b/examples/ACT-R/count.json
@@ -1,7 +1,7 @@
 {
     "count": {
-        "format": "ModECI MDF v0.2",
-        "generating_application": "Python modeci-mdf v0.2.1",
+        "format": "ModECI MDF v0.3",
+        "generating_application": "Python modeci-mdf v0.3.1",
         "graphs": {
             "count_graph": {
                 "conditions": {

diff --git a/examples/ACT-R/count.yaml b/examples/ACT-R/count.yaml
@@ -1,6 +1,6 @@
 count:
-    format: ModECI MDF v0.2
-    generating_application: Python modeci-mdf v0.2.1
+    format: ModECI MDF v0.3
+    generating_application: Python modeci-mdf v0.3.1
     graphs:
         count_graph:
             conditions:

diff --git a/examples/MDF/ABCD.json b/examples/MDF/ABCD.json
@@ -1,7 +1,7 @@
 {
     "ABCD": {
-        "format": "ModECI MDF v0.2",
-        "generating_application": "Python modeci-mdf v0.2.1",
+        "format": "ModECI MDF v0.3",
+        "generating_application": "Python modeci-mdf v0.3.1",
         "graphs": {
             "abcd_example": {
                 "nodes": {

diff --git a/examples/MDF/ABCD.yaml b/examples/MDF/ABCD.yaml
@@ -1,6 +1,6 @@
 ABCD:
-    format: ModECI MDF v0.2
-    generating_application: Python modeci-mdf v0.2.1
+    format: ModECI MDF v0.3
+    generating_application: Python modeci-mdf v0.3.1
     graphs:
         abcd_example:
             nodes:

diff --git a/examples/MDF/Arrays.json b/examples/MDF/Arrays.json
@@ -1,7 +1,7 @@
 {
     "Arrays": {
-        "format": "ModECI MDF v0.2",
-        "generating_application": "Python modeci-mdf v0.2.1",
+        "format": "ModECI MDF v0.3",
+        "generating_application": "Python modeci-mdf v0.3.1",
         "graphs": {
             "array_example": {
                 "nodes": {

diff --git a/examples/MDF/Arrays.yaml b/examples/MDF/Arrays.yaml
@@ -1,6 +1,6 @@
 Arrays:
-    format: ModECI MDF v0.2
-    generating_application: Python modeci-mdf v0.2.1
+    format: ModECI MDF v0.3
+    generating_application: Python modeci-mdf v0.3.1
     graphs:
         array_example:
             nodes:

diff --git a/examples/MDF/Simple.json b/examples/MDF/Simple.json
@@ -1,7 +1,7 @@
 {
     "Simple": {
-        "format": "ModECI MDF v0.2",
-        "generating_application": "Python modeci-mdf v0.2.1",
+        "format": "ModECI MDF v0.3",
+        "generating_application": "Python modeci-mdf v0.3.1",
         "graphs": {
             "simple_example": {
                 "nodes": {

diff --git a/examples/MDF/Simple.yaml b/examples/MDF/Simple.yaml
@@ -1,6 +1,6 @@
 Simple:
-    format: ModECI MDF v0.2
-    generating_application: Python modeci-mdf v0.2.1
+    format: ModECI MDF v0.3
+    generating_application: Python modeci-mdf v0.3.1
     graphs:
         simple_example:
             nodes:

diff --git a/examples/MDF/States.json b/examples/MDF/States.json
@@ -1,7 +1,7 @@
 {
     "States": {
-        "format": "ModECI MDF v0.2",
-        "generating_application": "Python modeci-mdf v0.2.1",
+        "format": "ModECI MDF v0.3",
+        "generating_application": "Python modeci-mdf v0.3.1",
         "graphs": {
             "state_example": {
                 "nodes": {

diff --git a/examples/MDF/States.yaml b/examples/MDF/States.yaml
@@ -1,6 +1,6 @@
 States:
-    format: ModECI MDF v0.2
-    generating_application: Python modeci-mdf v0.2.1
+    format: ModECI MDF v0.3
+    generating_application: Python modeci-mdf v0.3.1
     graphs:
         state_example:
             nodes:

diff --git a/examples/MDF/abc_conditions.json b/examples/MDF/abc_conditions.json
@@ -1,7 +1,7 @@
 {
     "abc_conditions": {
-        "format": "ModECI MDF v0.2",
-        "generating_application": "Python modeci-mdf v0.2.1",
+        "format": "ModECI MDF v0.3",
+        "generating_application": "Python modeci-mdf v0.3.1",
         "graphs": {
             "abc_conditions_example": {
                 "conditions": {

diff --git a/examples/MDF/abc_conditions.yaml b/examples/MDF/abc_conditions.yaml
@@ -1,6 +1,6 @@
 abc_conditions:
-    format: ModECI MDF v0.2
-    generating_application: Python modeci-mdf v0.2.1
+    format: ModECI MDF v0.3
+    generating_application: Python modeci-mdf v0.3.1
     graphs:
         abc_conditions_example:
             conditions:

diff --git a/examples/NeuroML/ABCD.mdf.json b/examples/NeuroML/ABCD.mdf.json
@@ -1,6 +1,6 @@
 {
     "ABCD": {
-        "format": "ModECI MDF v0.2",
+        "format": "ModECI MDF v0.3",
         "graphs": {
             "ABCD": {
                 "notes": "Example of a simplified network",

diff --git a/examples/NeuroML/ABCD.mdf.yaml b/examples/NeuroML/ABCD.mdf.yaml
@@ -1,5 +1,5 @@
 ABCD:
-    format: ModECI MDF v0.2
+    format: ModECI MDF v0.3
     graphs:
         ABCD:
             notes: Example of a simplified network

diff --git a/examples/NeuroML/FN.mdf.json b/examples/NeuroML/FN.mdf.json
@@ -1,6 +1,6 @@
 {
     "FN": {
-        "format": "ModECI MDF v0.2",
+        "format": "ModECI MDF v0.3",
         "graphs": {
             "FN": {
                 "notes": "FitzHugh Nagumo cell model - originally specified in NeuroML/LEMS",

diff --git a/examples/NeuroML/FN.mdf.yaml b/examples/NeuroML/FN.mdf.yaml
@@ -1,5 +1,5 @@
 FN:
-    format: ModECI MDF v0.2
+    format: ModECI MDF v0.3
     graphs:
         FN:
             notes: FitzHugh Nagumo cell model - originally specified in NeuroML/LEMS

diff --git a/examples/NeuroML/regenerateAndTest.sh b/examples/NeuroML/regenerateAndTest.sh
@@ -26,7 +26,7 @@ pynml LEMS_SimABCD.xml -nogui
 python ABCD.py -mdf
 
 ####  Generate graph from MDF version
-python -m modeci_mdf.interfaces.graphviz.importer ABCD.mdf.yaml 1 -noview
+python -m modeci_mdf.interfaces.graphviz.exporter ABCD.mdf.yaml 1 -noview
 
 ####  Test evaluating MDF version
 python -m modeci_mdf.execution_engine ABCD.mdf.json
@@ -53,7 +53,7 @@ pynml LEMS_SimFN.xml -lems-graph
 python FN.py -mdf
 
 ####  Generate graph from MDF version
-python -m modeci_mdf.interfaces.graphviz.importer FN.mdf.yaml 3 -noview
+python -m modeci_mdf.interfaces.graphviz.exporter FN.mdf.yaml 3 -noview
 
 ####  Test evaluating MDF version
 python -m modeci_mdf.execution_engine FN.mdf.json

diff --git a/examples/ONNX/ab.json b/examples/ONNX/ab.json
@@ -1,7 +1,7 @@
 {
     "ONNX Model": {
-        "format": "ModECI MDF v0.2",
-        "generating_application": "Python modeci-mdf v0.2.1",
+        "format": "ModECI MDF v0.3",
+        "generating_application": "Python modeci-mdf v0.3.1",
         "graphs": {
             "torch-jit-export": {
                 "nodes": {

diff --git a/examples/ONNX/ab.png b/examples/ONNX/ab.png
diff --git a/examples/ONNX/ab.yaml b/examples/ONNX/ab.yaml
@@ -1,6 +1,6 @@
 ONNX Model:
-    format: ModECI MDF v0.2
-    generating_application: Python modeci-mdf v0.2.1
+    format: ModECI MDF v0.3
+    generating_application: Python modeci-mdf v0.3.1
     graphs:
         torch-jit-export:
             nodes:

diff --git a/examples/ONNX/abc.json b/examples/ONNX/abc.json
@@ -1,7 +1,7 @@
 {
     "ONNX Model": {
-        "format": "ModECI MDF v0.2",
-        "generating_application": "Python modeci-mdf v0.2.1",
+        "format": "ModECI MDF v0.3",
+        "generating_application": "Python modeci-mdf v0.3.1",
         "graphs": {
             "torch-jit-export": {
                 "nodes": {

diff --git a/examples/ONNX/abc.png b/examples/ONNX/abc.png
diff --git a/examples/ONNX/abc.yaml b/examples/ONNX/abc.yaml
@@ -1,6 +1,6 @@
 ONNX Model:
-    format: ModECI MDF v0.2
-    generating_application: Python modeci-mdf v0.2.1
+    format: ModECI MDF v0.3
+    generating_application: Python modeci-mdf v0.3.1
     graphs:
         torch-jit-export:
             nodes:

diff --git a/examples/ONNX/abcd.json b/examples/ONNX/abcd.json
@@ -1,7 +1,7 @@
 {
     "ONNX Model": {
-        "format": "ModECI MDF v0.2",
-        "generating_application": "Python modeci-mdf v0.2.1",
+        "format": "ModECI MDF v0.3",
+        "generating_application": "Python modeci-mdf v0.3.1",
         "graphs": {
             "torch-jit-export": {
                 "nodes": {

diff --git a/examples/ONNX/abcd.yaml b/examples/ONNX/abcd.yaml
@@ -1,6 +1,6 @@
 ONNX Model:
-    format: ModECI MDF v0.2
-    generating_application: Python modeci-mdf v0.2.1
+    format: ModECI MDF v0.3
+    generating_application: Python modeci-mdf v0.3.1
     graphs:
         torch-jit-export:
             nodes:

diff --git a/src/modeci_mdf/__init__.py b/src/modeci_mdf/__init__.py
@@ -10,7 +10,7 @@
 """
 
 # Version of the specification for MDF
-MODECI_MDF_VERSION = "0.2"
+MODECI_MDF_VERSION = "0.3"
 
 # Version of the python module. Use MDF version here and just change minor version
 __version__ = "%s.1" % MODECI_MDF_VERSION