[code2fn] Various bug fixes and documentation updates (#878)

## Summary of Changes
- Adds unit testing for Fortran compound-conditional
- Adds missing files for consumer mode model coverage reports
- Fixes circular dependency issue between model coverage reports and
img2mml
- Pins code2fn related libraries in pyproject.toml
- Pins all tree-sitter grammar versions to prevent a breaking change in
the future.

### Related issues

Resolves #663
Resolves #876

.github/workflows/tests-and-docs.yml

@@ -83,12 +83,12 @@ jobs:
         # retrieve latest model for img2mml component
         curl -L https://artifacts.askem.lum.ai/skema/img2mml/models/cnn_xfmer_arxiv_im2mml_with_fonts_boldface_best.pt > skema/img2mml/trained_models/cnn_xfmer_arxiv_im2mml_with_fonts_boldface_best.pt
         pip install ".[all]"
+
     # Install tree-sitter parser (for Python component unit tests)
     - name: Install tree-sitter parsers
       working-directory: .
       run: python skema/program_analysis/tree_sitter_parsers/build_parsers.py --ci --all
 
-
     # docs (API)
     # generate python docs using pdoc
     - name: "Create documentation for Python components (API docs)"

pyproject.toml

@@ -15,19 +15,19 @@ dependencies=[
     "numpy",
     "dill==0.3.7",
     "networkx==2.8.8",
-    "PyYAML",
+    "PyYAML==6.*",
     "tree-sitter==0.20.4",
     "neo4j==5.14.1",
     "requests",
-    "beautifulsoup4", # used to remove comments etc from pMML before sending to MORAE
+    "beautifulsoup4==4.12.*", # used to remove comments etc from pMML before sending to MORAE
     "typing_extensions", # see https://github.com/pydantic/pydantic/issues/5821#issuecomment-1559196859
     "fastapi~=0.100.0",
     "starlette",
     "httpx",
     "pydantic>=2.0.0",
     "uvicorn",
     "python-multipart",
-    "func_timeout"
+    "func_timeout==4.3.5"
 ]
 # The Python program analysis pipeline does not currently work with Python 3.9
 # or 3.10. This may change in the future.
@@ -110,7 +110,7 @@ all = ["skema[core]", "skema[dev]", "skema[doc]", "skema[demo]", "skema[annotati
 
 [tool.setuptools.package-data]
 # needed to ensure models are included in package/discoverable
-"*" = ["*.json", "vocab.txt", "*.pt", "*.png", "*.html", "*.yml", "*.yaml"]
+"*" = ["*.json", "*vocab.txt", "*.pt", "*.png", "*.html", "*.yml", "*.yaml"]
 
 [tool.setuptools.dynamic]
 readme = {file = ["README.md"], content-type = "text/markdown"}

skema/program_analysis/CAST/fortran/tests/test_compound_conditional_cast_fortran.py

@@ -0,0 +1,101 @@
+import pytest
+from tempfile import TemporaryDirectory
+from pathlib import Path 
+
+from skema.program_analysis.CAST.fortran.ts2cast import TS2CAST
+from skema.program_analysis.CAST2FN.model.cast import (
+    Assignment,
+    Var,
+    Name,
+    CASTLiteralValue,
+    ModelIf,
+    Operator,
+    ScalarType
+)
+
+def cond_compound1():
+    return """
+program cond_compound1
+integer :: a = 3
+if (a .gt. 1 .and. a .lt. 10) then
+    a = 40
+end if
+end program cond_compound1
+    """
+
+
+def generate_cast(test_file_string):
+    with TemporaryDirectory() as temp:
+        source_path = Path(temp) / "source.f95"
+        source_path.write_text(test_file_string)
+        out_cast = TS2CAST(str(source_path)).out_cast
+
+    return out_cast[0]
+
+def test_cond_compound1():
+    exp_cast = generate_cast(cond_compound1())
+
+    asg_node = exp_cast.nodes[0].body[0]
+
+    assert isinstance(asg_node, Assignment)
+    assert isinstance(asg_node.left, Var)
+    assert isinstance(asg_node.left.val, Name)
+    assert asg_node.left.val.name == "a"
+    assert asg_node.left.val.id == 0
+
+    assert isinstance(asg_node.right, CASTLiteralValue)
+    assert asg_node.right.value_type == ScalarType.INTEGER
+    assert asg_node.right.value == '3'
+
+    cond_node = exp_cast.nodes[0].body[1]
+    cond_expr = cond_node.expr
+    assert isinstance(cond_node, ModelIf)
+    assert isinstance(cond_expr, ModelIf)
+
+    if_node = cond_expr
+    assert isinstance(if_node, ModelIf)
+
+    expr = if_node.expr
+    assert isinstance(expr, Operator)
+    assert expr.op == ".gt."
+    assert len(expr.operands) == 2
+    assert isinstance(expr.operands[1], CASTLiteralValue)
+    assert expr.operands[1].value_type == ScalarType.INTEGER
+    assert expr.operands[1].value == "1"
+
+    assert isinstance(expr.operands[0], Name)
+    assert expr.operands[0].name == "a"
+    assert expr.operands[0].id == 0
+
+    assert len(if_node.body) == 1
+    body = if_node.body[0]
+    assert isinstance(body, Operator)
+    assert body.op == ".lt."
+    assert len(body.operands) == 2
+    assert isinstance(body.operands[0], Name)
+    assert body.operands[0].name == "a"
+    assert body.operands[0].id == 0
+
+    assert isinstance(body.operands[1], CASTLiteralValue)
+    assert body.operands[1].value_type == ScalarType.INTEGER
+    assert body.operands[1].value == "10"
+
+    assert len(if_node.orelse) == 1
+    orelse = if_node.orelse[0]
+    assert isinstance(orelse, CASTLiteralValue)
+    assert orelse.value_type == ScalarType.BOOLEAN
+    assert orelse.value == False
+
+    cond_body = cond_node.body
+    assert len(cond_body) == 1
+    assert isinstance(cond_body[0], Assignment)
+    assert isinstance(cond_body[0].left, Var)
+    assert cond_body[0].left.val.name == "a"
+    assert cond_body[0].left.val.id == 0
+
+    assert isinstance(cond_body[0].right, CASTLiteralValue)
+    assert cond_body[0].right.value_type == ScalarType.INTEGER
+    assert cond_body[0].right.value == '40'
+
+    cond_else = cond_node.orelse
+    assert len(cond_else) == 0

skema/program_analysis/CAST/fortran/tests/test_conditional_cast_fortran.py

@@ -9,7 +9,8 @@
     Name,
     CASTLiteralValue,
     ModelIf,
-    Operator
+    Operator,
+    ScalarType
 )
 
 def cond1():
@@ -63,7 +64,7 @@ def test_cond1():
     assert asg_node.left.val.name == "x"
 
     assert isinstance(asg_node.right, CASTLiteralValue)
-    assert asg_node.right.value_type == "Integer"
+    assert asg_node.right.value_type == ScalarType.INTEGER
     assert asg_node.right.value == '2'
 
     assert isinstance(cond_node, ModelIf)
@@ -103,7 +104,7 @@ def test_cond2():
     assert asg_node.left.val.id == 0
 
     assert isinstance(asg_node.right, CASTLiteralValue)
-    assert asg_node.right.value_type == "Integer"
+    assert asg_node.right.value_type == ScalarType.INTEGER
     assert asg_node.right.value == '2'
 
     asg_node = exp_cast.nodes[0].body[1]
@@ -114,7 +115,7 @@ def test_cond2():
     assert asg_node.left.val.id == 1
 
     assert isinstance(asg_node.right, CASTLiteralValue)
-    assert asg_node.right.value_type == "Integer"
+    assert asg_node.right.value_type == ScalarType.INTEGER
     assert asg_node.right.value == '3'
 
     assert isinstance(cond_node, ModelIf)
@@ -127,7 +128,7 @@ def test_cond2():
     assert isinstance(cond_expr.operands[0], Name)
     assert cond_expr.operands[0].name == "x"
     assert isinstance(cond_expr.operands[1], CASTLiteralValue)
-    assert cond_expr.operands[1].value_type == "Integer"
+    assert cond_expr.operands[1].value_type == ScalarType.INTEGER
     assert cond_expr.operands[1].value == "5"
 
     assert len(cond_body) == 3

skema/program_analysis/CAST/fortran/tests/test_expression_cast_fortran.py

@@ -7,7 +7,8 @@
     Assignment,
     Var,
     Name,
-    CASTLiteralValue
+    CASTLiteralValue, 
+    ScalarType
 )
 
 def exp0():
@@ -44,7 +45,7 @@ def test_exp0():
     assert asg_node.left.val.name == "x"
 
     assert isinstance(asg_node.right, CASTLiteralValue)
-    assert asg_node.right.value_type == "Integer"
+    assert asg_node.right.value_type == ScalarType.INTEGER
     assert asg_node.right.value == '2'
 
 
@@ -60,7 +61,7 @@ def test_exp1():
     assert asg_node.left.val.id == 0
 
     assert isinstance(asg_node.right, CASTLiteralValue)
-    assert asg_node.right.value_type == "Integer"
+    assert asg_node.right.value_type == ScalarType.INTEGER
     assert asg_node.right.value == '2'
 
     # ------
@@ -72,7 +73,7 @@ def test_exp1():
     assert asg_node.left.val.id == 1
 
     assert isinstance(asg_node.right, CASTLiteralValue)
-    assert asg_node.right.value_type == "Integer"
+    assert asg_node.right.value_type == ScalarType.INTEGER
     assert asg_node.right.value == '3'
 
 if __name__ == "__main__": 

skema/program_analysis/CAST/fortran/tests/test_for_cast_fortran.py

@@ -11,7 +11,9 @@
     CASTLiteralValue,
     ModelIf,
     Loop,
-    Operator
+    Operator,
+    ScalarType,
+    StructureType
 )
 
 def for1():
@@ -48,7 +50,7 @@ def test_for1():
     assert asg_node.left.val.name == "x"
 
     assert isinstance(asg_node.right, CASTLiteralValue)
-    assert asg_node.right.value_type == "Integer"
+    assert asg_node.right.value_type == ScalarType.INTEGER
     assert asg_node.right.value == '7'
 
     assert isinstance(loop_node, Loop)
@@ -79,7 +81,7 @@ def test_for1():
 
     assert isinstance(loop_pre[1], Assignment)
     assert isinstance(loop_pre[1].left, CASTLiteralValue)
-    assert loop_pre[1].left.value_type == "Tuple"
+    assert loop_pre[1].left.value_type == StructureType.TUPLE
 
     assert isinstance(loop_pre[1].left.value[0], Var)
     assert loop_pre[1].left.value[0].val.name == "i"
@@ -101,7 +103,7 @@ def test_for1():
     assert loop_test.operands[0].name == "sc_0"
 
     assert isinstance(loop_test.operands[1], CASTLiteralValue)
-    assert loop_test.operands[1].value_type == "Boolean"
+    assert loop_test.operands[1].value_type == ScalarType.BOOLEAN
 
     # Loop Body
     loop_body = loop_node.body

skema/program_analysis/CAST/fortran/tests/test_identifier_cast_fortran.py

@@ -10,7 +10,8 @@
     CASTLiteralValue,
     ModelIf,
     Loop,
-    Operator
+    Operator,
+    ScalarType
 )
 
 def identifier1():
@@ -41,6 +42,6 @@ def test_identifier1():
     assert asg_node.left.val.name == "x"
 
     assert isinstance(asg_node.right, CASTLiteralValue)
-    assert asg_node.right.value_type == "Integer"
+    assert asg_node.right.value_type == ScalarType.INTEGER
     assert asg_node.right.value == '2'
 

skema/program_analysis/CAST/fortran/tests/test_operation_cast_fortran.py

@@ -8,7 +8,8 @@
     Var,
     Name,
     Operator,
-    CASTLiteralValue
+    CASTLiteralValue,
+    ScalarType
 )
 
 def binop1():
@@ -74,11 +75,11 @@ def test_binop1():
 
     assert isinstance(binop_node.right.operands[0], CASTLiteralValue)
     assert binop_node.right.operands[0].value == '2'
-    assert binop_node.right.operands[0].value_type == 'Integer'
+    assert binop_node.right.operands[0].value_type == ScalarType.INTEGER
 
     assert isinstance(binop_node.right.operands[1], CASTLiteralValue)
     assert binop_node.right.operands[1].value == '3'
-    assert binop_node.right.operands[1].value_type == 'Integer'
+    assert binop_node.right.operands[1].value_type == ScalarType.INTEGER
 
 def test_binop2():
     exp_cast = generate_cast(binop2())
@@ -92,7 +93,7 @@ def test_binop2():
     assert binop_node.left.val.id == 0
 
     assert isinstance(binop_node.right, CASTLiteralValue)
-    assert binop_node.right.value_type == "Integer"
+    assert binop_node.right.value_type == ScalarType.INTEGER
     assert binop_node.right.value == '2'
 
     # ------
@@ -112,7 +113,7 @@ def test_binop2():
 
     assert isinstance(binop_node.right.operands[1], CASTLiteralValue)
     assert binop_node.right.operands[1].value == '3'
-    assert binop_node.right.operands[1].value_type == 'Integer'
+    assert binop_node.right.operands[1].value_type == ScalarType.INTEGER
 
 def test_binop3():
     exp_cast = generate_cast(binop3())
@@ -126,7 +127,7 @@ def test_binop3():
     assert binop_node.left.val.id == 0
 
     assert isinstance(binop_node.right, CASTLiteralValue)
-    assert binop_node.right.value_type == "Integer"
+    assert binop_node.right.value_type == ScalarType.INTEGER
     assert binop_node.right.value == '1'
 
     # ------
@@ -138,7 +139,7 @@ def test_binop3():
     assert binop_node.left.val.id == 1
 
     assert isinstance(binop_node.right, CASTLiteralValue)
-    assert binop_node.right.value_type == "Integer"
+    assert binop_node.right.value_type == ScalarType.INTEGER
     assert binop_node.right.value == '2'
 
     # ------
@@ -198,7 +199,7 @@ def test_unary1():
 
     assert isinstance(unary_node.right.operands[0], CASTLiteralValue)
     assert unary_node.right.operands[0].value == '1'
-    assert unary_node.right.operands[0].value_type == 'Integer'
+    assert unary_node.right.operands[0].value_type == ScalarType.INTEGER
 
 def test_unary2():
     exp_cast = generate_cast(unary2())
@@ -213,7 +214,7 @@ def test_unary2():
 
     assert isinstance(unary_node.right, CASTLiteralValue)
     assert unary_node.right.value == '1'
-    assert unary_node.right.value_type == 'Integer'
+    assert unary_node.right.value_type == ScalarType.INTEGER
 
     unary_node = exp_cast.nodes[0].body[1]