From eb831c2ad5ea271a5358915a2340d641e2866631 Mon Sep 17 00:00:00 2001
From: "R. Bernstein" <rocky@users.noreply.github.com>
Date: Sun, 20 Oct 2024 20:35:25 -0400
Subject: [PATCH 1/4] Simplify & inference fns moved under mathics.eval (#1140)

---
 mathics/builtin/arithmetic.py            |  2 +-
 mathics/builtin/numbers/algebra.py       | 71 ++++--------------------
 mathics/builtin/numeric.py               |  7 ++-
 mathics/{builtin => eval}/inference.py   | 33 +++++++----
 mathics/eval/numbers/algebra/simplify.py | 63 +++++++++++++++++++++
 5 files changed, 100 insertions(+), 76 deletions(-)
 rename mathics/{builtin => eval}/inference.py (95%)

diff --git a/mathics/builtin/arithmetic.py b/mathics/builtin/arithmetic.py
index bd42e7e74..0313ceb94 100644
--- a/mathics/builtin/arithmetic.py
+++ b/mathics/builtin/arithmetic.py
@@ -10,7 +10,6 @@
 
 import sympy
 
-from mathics.builtin.inference import get_assumptions_list
 from mathics.builtin.numeric import Abs
 from mathics.builtin.scoping import dynamic_scoping
 from mathics.core.atoms import (
@@ -72,6 +71,7 @@
     SymbolUndefined,
 )
 from mathics.eval.arithmetic import eval_Sign
+from mathics.eval.inference import get_assumptions_list
 from mathics.eval.nevaluator import eval_N
 
 # This tells documentation how to sort this module
diff --git a/mathics/builtin/numbers/algebra.py b/mathics/builtin/numbers/algebra.py
index 6fb082bcf..51c0a0591 100644
--- a/mathics/builtin/numbers/algebra.py
+++ b/mathics/builtin/numbers/algebra.py
@@ -17,7 +17,6 @@
 
 import sympy
 
-from mathics.builtin.inference import evaluate_predicate
 from mathics.builtin.options import options_to_rules
 from mathics.builtin.scoping import dynamic_scoping
 from mathics.core.atoms import Integer, Integer0, Integer1, Number, RationalOneHalf
@@ -63,7 +62,10 @@
     SymbolTable,
     SymbolTanh,
 )
-from mathics.eval.numbers.algebra.simplify import default_complexity_function
+from mathics.eval.numbers.algebra.simplify import (
+    default_complexity_function,
+    eval_Simplify,
+)
 from mathics.eval.numbers.numbers import cancel, sympy_factor
 from mathics.eval.parts import walk_parts
 from mathics.eval.patterns import match
@@ -1496,7 +1498,10 @@ def eval_list(self, expr, vars, evaluation):
 # FullSimplify
 class Simplify(Builtin):
     r"""
-    <url>:WMA link:
+    <url>:SymPy:
+    https://docs.sympy.org/latest/modules/simplify
+    /simplify.html</url>, <url>
+    :WMA:
     https://reference.wolfram.com/language/ref/Simplify.html</url>
 
     <dl>
@@ -1605,65 +1610,9 @@ def eval(self, expr, evaluation, options={}):
                 {"System`$Assumptions": assumptions},
                 evaluation,
             )
-        return self.do_apply(expr, evaluation, options)
-
-    def do_apply(self, expr, evaluation, options={}):
-        # Check first if we are dealing with a logic expression...
-        if expr in (SymbolTrue, SymbolFalse, SymbolList):
-            return expr
-
-        # ``evaluate_predicate`` tries to reduce expr taking into account
-        # the assumptions established in ``$Assumptions``.
-        expr = evaluate_predicate(expr, evaluation)
-
-        # If we get an atom, return it.
-        if isinstance(expr, Atom):
-            return expr
-
-        # Now, try to simplify the elements.
-        # TODO:  Consider to move this step inside ``evaluate_predicate``.
-        # Notice that here we want to pass through the full evaluation process
-        # to use all the defined rules...
-        name = self.get_name()
-        symbol_name = Symbol(name)
-        elements = [
-            Expression(symbol_name, element).evaluate(evaluation)
-            for element in expr._elements
-        ]
-        head = Expression(symbol_name, expr.get_head()).evaluate(evaluation)
-        expr = Expression(head, *elements)
 
-        # At this point, we used all the tools available in Mathics.
-        # If the expression has a sympy form, try to use it.
-        # Now, convert the expression to sympy
-        sympy_expr = expr.to_sympy()
-        # If the expression cannot be handled by Sympy, just return it.
-        if sympy_expr is None:
-            return expr
-        # Now, try to simplify using sympy
-        complexity_function = options.get("System`ComplexityFunction", None)
-        if complexity_function is None or complexity_function is SymbolAutomatic:
-
-            def _default_complexity_function(x):
-                return default_complexity_function(from_sympy(x))
-
-            complexity_function = _default_complexity_function
-        else:
-            if isinstance(complexity_function, (Expression, Symbol)):
-                _complexity_function = complexity_function
-                complexity_function = (
-                    lambda x: Expression(_complexity_function, from_sympy(x))
-                    .evaluate(evaluation)
-                    .to_python()
-                )
-
-        # At this point, ``complexity_function`` is a function that takes a
-        # sympy expression and returns an integer.
-        sympy_result = sympy.simplify(sympy_expr, measure=complexity_function)
-
-        # and bring it back
-        result = from_sympy(sympy_result).evaluate(evaluation)
-        return result
+        symbol_name = Symbol(self.get_name())
+        return eval_Simplify(symbol_name, expr, evaluation, options)
 
 
 class FullSimplify(Simplify):
diff --git a/mathics/builtin/numeric.py b/mathics/builtin/numeric.py
index 1d5a65d32..27f283f69 100644
--- a/mathics/builtin/numeric.py
+++ b/mathics/builtin/numeric.py
@@ -15,7 +15,6 @@
 
 import sympy
 
-from mathics.builtin.inference import evaluate_predicate
 from mathics.core.atoms import (
     Complex,
     Integer,
@@ -52,6 +51,7 @@
     eval_RealSign,
     eval_Sign,
 )
+from mathics.eval.inference import evaluate_predicate
 from mathics.eval.nevaluator import eval_NValues
 
 
@@ -319,7 +319,10 @@ def eval_N(self, expr, evaluation: Evaluation):
 
 class Piecewise(SympyFunction):
     """
-    <url>:WMA link:https://reference.wolfram.com/language/ref/Piecewise.html</url>
+    <url>:SymPy:
+    https://docs.sympy.org/latest/modules/functions
+    /elementary.html#piecewise</url>, <url>
+    :WMA:https://reference.wolfram.com/language/ref/Piecewise.html</url>
 
     <dl>
       <dt>'Piecewise[{{expr1, cond1}, ...}]'
diff --git a/mathics/builtin/inference.py b/mathics/eval/inference.py
similarity index 95%
rename from mathics/builtin/inference.py
rename to mathics/eval/inference.py
index b34beb384..1f1e10eab 100644
--- a/mathics/builtin/inference.py
+++ b/mathics/eval/inference.py
@@ -3,8 +3,7 @@
 Inference Functions
 """
 
-no_doc = "no doc"
-
+from mathics.core.evaluation import Evaluation
 from mathics.core.expression import Expression
 from mathics.core.parser import parse_builtin_rule
 from mathics.core.parser.util import SystemDefinitions
@@ -14,11 +13,21 @@
 
 # TODO: Extend these rules?
 
+no_doc = "no doc"
+
+
+def debug_logical_expr(pref, expr, evaluation: Evaluation):
+    print(
+        pref, expr
+    )  # expr.format(evaluation,"OutputForm").boxes_to_text(evaluation=evaluation))
+
+
+def null_debug_logical_expr(pref, expr, evaluation: Evaluation):
+    return
+
 
-def debug_logical_expr(pref, expr, evaluation):
-    pass
-    # return
-    # print(pref , expr) #expr.format(evaluation,"OutputForm").boxes_to_text(evaluation=evaluation))
+# Tracing can redefine this to provide trace information
+DEBUG_LOGICAL_EXPR = null_debug_logical_expr
 
 
 logical_algebraic_rules_spec = {
@@ -105,7 +114,7 @@ def remove_nots_when_unnecesary(pred, evaluation):
     cc = True
     while cc:
         pred, cc = pred.do_apply_rules(remove_not_rules, evaluation)
-        debug_logical_expr("->  ", pred, evaluation)
+        DEBUG_LOGICAL_EXPR("->  ", pred, evaluation)
         if pred is SymbolTrue or pred is SymbolFalse:
             return pred
     return pred
@@ -362,14 +371,14 @@ def evaluate_predicate(pred, evaluation):
             *[evaluate_predicate(subp, evaluation) for subp in pred.elements],
         )
 
-    debug_logical_expr("reducing ", pred, evaluation)
+    DEBUG_LOGICAL_EXPR("reducing ", pred, evaluation)
     ensure_logical_algebraic_rules()
     pred = pred.evaluate(evaluation)
-    debug_logical_expr("->  ", pred, evaluation)
+    DEBUG_LOGICAL_EXPR("->  ", pred, evaluation)
     cc = True
     while cc:
         pred, cc = pred.do_apply_rules(logical_algebraic_rules, evaluation)
-        debug_logical_expr("->  ", pred, evaluation)
+        DEBUG_LOGICAL_EXPR("->  ", pred, evaluation)
         if pred is SymbolTrue or pred is SymbolFalse:
             return pred
 
@@ -378,11 +387,11 @@ def evaluate_predicate(pred, evaluation):
         return remove_nots_when_unnecesary(pred, evaluation).evaluate(evaluation)
 
     if assumption_rules is not None:
-        debug_logical_expr(" Now, using the assumptions over ", pred, evaluation)
+        DEBUG_LOGICAL_EXPR(" Now, using the assumptions over ", pred, evaluation)
         changed = True
         while changed:
             pred, changed = pred.do_apply_rules(assumption_rules, evaluation)
-            debug_logical_expr(" -> ", pred, evaluation)
+            DEBUG_LOGICAL_EXPR(" -> ", pred, evaluation)
 
     pred = remove_nots_when_unnecesary(pred, evaluation).evaluate(evaluation)
     return pred
diff --git a/mathics/eval/numbers/algebra/simplify.py b/mathics/eval/numbers/algebra/simplify.py
index 5cf158515..fb2a40e97 100644
--- a/mathics/eval/numbers/algebra/simplify.py
+++ b/mathics/eval/numbers/algebra/simplify.py
@@ -4,8 +4,14 @@
 Algorithms for simplifying expressions and evaluate complexity.
 """
 
+from sympy import simplify
+
 from mathics.core.atoms import Number
+from mathics.core.convert.sympy import from_sympy
 from mathics.core.expression import Expression
+from mathics.core.symbols import Atom, Symbol, SymbolFalse, SymbolList, SymbolTrue
+from mathics.core.systemsymbols import SymbolAutomatic
+from mathics.eval.inference import evaluate_predicate
 
 
 def default_complexity_function(expr: Expression) -> int:
@@ -24,3 +30,60 @@ def default_complexity_function(expr: Expression) -> int:
         )
     else:
         return 1
+
+
+def eval_Simplify(symbol_name: Symbol, expr, evaluation, options: dict):
+    # Check first if we are dealing with a logic expression...
+    if expr in (SymbolTrue, SymbolFalse, SymbolList):
+        return expr
+
+    # ``evaluate_predicate`` tries to reduce expr taking into account
+    # the assumptions established in ``$Assumptions``.
+    expr = evaluate_predicate(expr, evaluation)
+
+    # If we get an atom, return it.
+    if isinstance(expr, Atom):
+        return expr
+
+    # Now, try to simplify the elements.
+    # TODO:  Consider to move this step inside ``evaluate_predicate``.
+    # Notice that here we want to pass through the full evaluation process
+    # to use all the defined rules...
+    elements = [
+        Expression(symbol_name, element).evaluate(evaluation)
+        for element in expr._elements
+    ]
+    head = Expression(symbol_name, expr.get_head()).evaluate(evaluation)
+    expr = Expression(head, *elements)
+
+    # At this point, we used all the tools available in Mathics.
+    # If the expression has a sympy form, try to use it.
+    # Now, convert the expression to sympy
+    sympy_expr = expr.to_sympy()
+    # If the expression cannot be handled by Sympy, just return it.
+    if sympy_expr is None:
+        return expr
+    # Now, try to simplify using sympy
+    complexity_function = options.get("System`ComplexityFunction", None)
+    if complexity_function is None or complexity_function is SymbolAutomatic:
+
+        def _default_complexity_function(x):
+            return default_complexity_function(from_sympy(x))
+
+        complexity_function = _default_complexity_function
+    else:
+        if isinstance(complexity_function, (Expression, Symbol)):
+            _complexity_function = complexity_function
+            complexity_function = (
+                lambda x: Expression(_complexity_function, from_sympy(x))
+                .evaluate(evaluation)
+                .to_python()
+            )
+
+    # At this point, ``complexity_function`` is a function that takes a
+    # sympy expression and returns an integer.
+    sympy_result = simplify(sympy_expr, measure=complexity_function)
+
+    # and bring it back
+    result = from_sympy(sympy_result).evaluate(evaluation)
+    return result

From e7ca02646d741cc6dd97579e51f65bba5e3db92b Mon Sep 17 00:00:00 2001
From: "R. Bernstein" <rocky@users.noreply.github.com>
Date: Sun, 20 Oct 2024 22:26:17 -0400
Subject: [PATCH 2/4] We can tolerate PyPy now... (#1139)

Fixes #661

---------

Co-authored-by: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
---
 mathics/builtin/drawing/plot.py            | 2 +-
 mathics/builtin/scipy_utils/integrators.py | 3 +--
 mathics/builtin/scipy_utils/optimizers.py  | 3 +--
 mathics/eval/drawing/plot.py               | 3 ++-
 mathics/eval/nevaluator.py                 | 2 +-
 5 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/mathics/builtin/drawing/plot.py b/mathics/builtin/drawing/plot.py
index 3069a9cae..e08af31f6 100644
--- a/mathics/builtin/drawing/plot.py
+++ b/mathics/builtin/drawing/plot.py
@@ -316,7 +316,7 @@ def eval(self, points, evaluation: Evaluation, options: dict):
         all_points = (
             points.value
             if hasattr(points, "value") and points.value is not None
-            else eval_N(points, evaluation).to_python()
+            else eval_N(points, evaluation).to_python()  # TODO: force tuple-ness?
         )
 
         # FIXME: arrange for self to have a .symbolname property or attribute
diff --git a/mathics/builtin/scipy_utils/integrators.py b/mathics/builtin/scipy_utils/integrators.py
index 82db83667..39b4c078e 100644
--- a/mathics/builtin/scipy_utils/integrators.py
+++ b/mathics/builtin/scipy_utils/integrators.py
@@ -1,9 +1,8 @@
 # -*- coding: utf-8 -*-
 
 from mathics.core.builtin import check_requires_list
-from mathics.core.util import IS_PYPY
 
-if IS_PYPY or not check_requires_list(["scipy", "numpy"]):
+if not check_requires_list(["scipy", "numpy"]):
     raise ImportError
 
 import numpy as np
diff --git a/mathics/builtin/scipy_utils/optimizers.py b/mathics/builtin/scipy_utils/optimizers.py
index dcc52b47a..fe76eca3c 100644
--- a/mathics/builtin/scipy_utils/optimizers.py
+++ b/mathics/builtin/scipy_utils/optimizers.py
@@ -5,10 +5,9 @@
 from mathics.core.evaluation import Evaluation
 from mathics.core.expression import Expression
 from mathics.core.systemsymbols import SymbolAutomatic, SymbolFailed, SymbolInfinity
-from mathics.core.util import IS_PYPY
 from mathics.eval.nevaluator import eval_N
 
-if IS_PYPY or not check_requires_list(["scipy", "numpy"]):
+if not check_requires_list(["scipy", "numpy"]):
     raise ImportError
 
 
diff --git a/mathics/eval/drawing/plot.py b/mathics/eval/drawing/plot.py
index cc279fe40..3d34424c7 100644
--- a/mathics/eval/drawing/plot.py
+++ b/mathics/eval/drawing/plot.py
@@ -134,7 +134,8 @@ def quiet_f(*args):
 
 
 def eval_ListPlot(
-    plot_groups: list,
+    # TODO: plot_groups should be a tuple only?
+    plot_groups: Union[list, tuple],
     x_range: list,
     y_range: list,
     is_discrete_plot: bool,
diff --git a/mathics/eval/nevaluator.py b/mathics/eval/nevaluator.py
index 05751dd64..4dbe16674 100644
--- a/mathics/eval/nevaluator.py
+++ b/mathics/eval/nevaluator.py
@@ -29,7 +29,7 @@ def eval_N(
     expression: BaseElement,
     evaluation: Evaluation,
     prec: BaseElement = SymbolMachinePrecision,
-) -> BaseElement:
+) -> Optional[BaseElement]:
     """
     Equivalent to Expression(SymbolN, expression).evaluate(evaluation)
     """

From 712337b4fc7eaa0c50bd0c37ee506406a166dd28 Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Mon, 21 Oct 2024 09:38:43 -0300
Subject: [PATCH 3/4] fixing check manifest (#1142)

This PR just fixes and reinstall the SYMBOL_MANIFEST consistency check,
to avoid erase/ duplicate symbols.
---
 .github/workflows/consistency-checks.yml |  1 +
 SYMBOLS_MANIFEST.txt                     | 30 +++++++++++--
 admin-tools/build_and_check_manifest.py  |  4 +-
 mathics/builtin/atomic/strings.py        |  8 ++--
 mathics/builtin/files_io/filesystem.py   | 57 ------------------------
 mathics/builtin/numbers/constants.py     |  5 +++
 6 files changed, 39 insertions(+), 66 deletions(-)

diff --git a/.github/workflows/consistency-checks.yml b/.github/workflows/consistency-checks.yml
index ea3742c34..0cbf4dc4c 100644
--- a/.github/workflows/consistency-checks.yml
+++ b/.github/workflows/consistency-checks.yml
@@ -35,3 +35,4 @@ jobs:
     - name: Test Mathics Consistency and Style
       run: |
         make check-consistency-and-style
+        make check-builtin-manifest
diff --git a/SYMBOLS_MANIFEST.txt b/SYMBOLS_MANIFEST.txt
index 43c6e2162..47d30dde6 100644
--- a/SYMBOLS_MANIFEST.txt
+++ b/SYMBOLS_MANIFEST.txt
@@ -1,4 +1,3 @@
-CombinatoricaOld`BinarySearch
 HTML`DataImport
 HTML`FullDataImport
 HTML`HyperlinksImport
@@ -40,6 +39,7 @@ System`$Machine
 System`$MachineEpsilon
 System`$MachineName
 System`$MachinePrecision
+System`$MaxLengthIntStringConversion
 System`$MaxMachineNumber
 System`$MaxPrecision
 System`$MinMachineNumber
@@ -105,7 +105,6 @@ System`Apart
 System`Append
 System`AppendTo
 System`Apply
-System`ApplyLevel
 System`ArcCos
 System`ArcCosh
 System`ArcCot
@@ -134,10 +133,12 @@ System`Attributes
 System`Automatic
 System`Axes
 System`Axis
+System`Background
 System`BarChart
 System`BaseForm
 System`Begin
 System`BeginPackage
+System`BellB
 System`BernoulliB
 System`BernsteinBasis
 System`BesselI
@@ -197,6 +198,7 @@ System`ChartLegends
 System`ChebyshevT
 System`ChebyshevU
 System`Check
+System`CheckAbort
 System`ChessboardDistance
 System`Chop
 System`Circle
@@ -238,6 +240,7 @@ System`ConditionalExpression
 System`Cone
 System`Cone3DBox
 System`Conjugate
+System`ConjugateTranspose
 System`Constant
 System`ConstantArray
 System`ContainsOnly
@@ -322,6 +325,8 @@ System`Dispatch
 System`Divide
 System`DivideBy
 System`Divisible
+System`DivisorSigma
+System`DivisorSum
 System`Divisors
 System`Do
 System`Dodecahedron
@@ -355,12 +360,14 @@ System`Erf
 System`Erfc
 System`Erosion
 System`EuclideanDistance
+System`EulerE
 System`EulerGamma
 System`EulerPhi
 System`Evaluate
 System`EvenQ
 System`ExactNumberQ
 System`Except
+System`Exit
 System`Exp
 System`ExpIntegralE
 System`ExpIntegralEi
@@ -526,6 +533,8 @@ System`Integer
 System`IntegerDigits
 System`IntegerExponent
 System`IntegerLength
+System`IntegerPart
+System`IntegerPartitions
 System`IntegerQ
 System`IntegerReverse
 System`IntegerString
@@ -543,6 +552,7 @@ System`InverseGudermannian
 System`InverseHaversine
 System`JaccardDissimilarity
 System`JacobiP
+System`JacobiSymbol
 System`Join
 System`Joined
 System`KelvinBei
@@ -554,6 +564,7 @@ System`Keys
 System`Khinchin
 System`KnownUnitQ
 System`KroneckerProduct
+System`KroneckerSymbol
 System`Kurtosis
 System`LABColor
 System`LCHColor
@@ -574,9 +585,9 @@ System`LessEqual
 System`LetterCharacter
 System`LetterNumber
 System`LetterQ
-System`LeviCivitaTensor
 System`Level
 System`LevelQ
+System`LeviCivitaTensor
 System`LightBlue
 System`LightBrown
 System`LightCyan
@@ -600,6 +611,7 @@ System`ListLinePlot
 System`ListLogPlot
 System`ListPlot
 System`ListQ
+System`ListStepPlot
 System`Listable
 System`LoadModule
 System`Locked
@@ -612,6 +624,7 @@ System`LogisticSigmoid
 System`Longest
 System`Lookup
 System`LowerCaseQ
+System`LucasL
 System`MachineNumberQ
 System`MachinePrecision
 System`Magenta
@@ -619,6 +632,7 @@ System`MakeBoxes
 System`ManhattanDistance
 System`MantissaExponent
 System`Map
+System`MapApply
 System`MapAt
 System`MapIndexed
 System`MapThread
@@ -642,6 +656,7 @@ System`Medium
 System`MemberQ
 System`MemoryAvailable
 System`MemoryInUse
+System`MersennePrimeExponent
 System`Mesh
 System`Message
 System`MessageName
@@ -655,6 +670,7 @@ System`Missing
 System`Mod
 System`ModularInverse
 System`Module
+System`MoebiusMu
 System`MorphologicalComponents
 System`Most
 System`Multinomial
@@ -760,6 +776,7 @@ System`PolyGamma
 System`Polygon
 System`Polygon3DBox
 System`PolygonBox
+System`PolygonalNumber
 System`PolynomialQ
 System`Position
 System`Positive
@@ -768,6 +785,7 @@ System`Postfix
 System`Power
 System`PowerExpand
 System`PowerMod
+System`PowersRepresentations
 System`PreDecrement
 System`PreIncrement
 System`Precedence
@@ -793,6 +811,7 @@ System`PseudoInverse
 System`Purple
 System`Put
 System`PutAppend
+System`PythonCProfileEvaluation
 System`PythonForm
 System`QRDecomposition
 System`Quantile
@@ -827,8 +846,8 @@ System`ReadProtected
 System`Real
 System`RealAbs
 System`RealDigits
-System`RealNumberQ
 System`RealSign
+System`RealValuedNumberQ
 System`Reals
 System`Reap
 System`Record
@@ -855,6 +874,7 @@ System`ResetDirectory
 System`Rest
 System`Return
 System`Reverse
+System`ReverseSort
 System`Riffle
 System`Right
 System`RogersTanimotoDissimilarity
@@ -886,6 +906,7 @@ System`Set
 System`SetAttributes
 System`SetDelayed
 System`SetDirectory
+System`SetEnvironment
 System`SetFileDate
 System`SetOptions
 System`SetStreamPosition
@@ -925,6 +946,7 @@ System`SplitBy
 System`Sqrt
 System`SqrtBox
 System`SquaredEuclideanDistance
+System`SquaresR
 System`StandardDeviation
 System`StandardForm
 System`StartOfLine
diff --git a/admin-tools/build_and_check_manifest.py b/admin-tools/build_and_check_manifest.py
index 9a8400068..2a1c33fdb 100755
--- a/admin-tools/build_and_check_manifest.py
+++ b/admin-tools/build_and_check_manifest.py
@@ -5,7 +5,7 @@
 from mathics.core.builtin import Builtin
 from mathics.core.load_builtin import (
     import_and_load_builtins,
-    modules,
+    mathics3_builtins_modules,
     name_is_builtin_symbol,
 )
 
@@ -15,7 +15,7 @@
 def generate_available_builtins_names():
     msg = ""
     builtins_by_name = {}
-    for module in modules:
+    for module in mathics3_builtins_modules:
         vars = dir(module)
         for name in vars:
             var = name_is_builtin_symbol(module, name)
diff --git a/mathics/builtin/atomic/strings.py b/mathics/builtin/atomic/strings.py
index 72326d7b7..22291b7ec 100644
--- a/mathics/builtin/atomic/strings.py
+++ b/mathics/builtin/atomic/strings.py
@@ -411,14 +411,16 @@ class HexadecimalCharacter(Builtin):
 
 # This isn't your normal Box class. We'll keep this here rather than
 # in mathics.builtin.box for now.
-class InterpretationBox(PrefixOperator):
+# mmatera commenct: This does not even exist in WMA. \! should be associated
+# to `ToExpression`, but it was not  properly implemented by now...
+class InterpretedBox(PrefixOperator):
     r"""
     <url>
     :WMA link:
     https://reference.wolfram.com/language/ref/InterpretationBox.html</url>
 
     <dl>
-      <dt>'InterpretationBox[$box$]'
+      <dt>'InterpretedBox[$box$]'
       <dd>is the ad hoc fullform for \! $box$. just for internal use...
     </dl>
 
@@ -430,7 +432,7 @@ class InterpretationBox(PrefixOperator):
     summary_text = "interpret boxes as an expression"
 
     def eval(self, boxes, evaluation: Evaluation):
-        """InterpretationBox[boxes_]"""
+        """InterpretedBox[boxes_]"""
         # TODO: the following is a very raw and dummy way to
         # handle these expressions.
         # In the first place, this should handle different kind
diff --git a/mathics/builtin/files_io/filesystem.py b/mathics/builtin/files_io/filesystem.py
index f0faf505e..59a7fea58 100644
--- a/mathics/builtin/files_io/filesystem.py
+++ b/mathics/builtin/files_io/filesystem.py
@@ -346,63 +346,6 @@ def eval(self, evaluation: Evaluation):
         return String(result)
 
 
-class DirectoryName(Builtin):
-    """
-    <url>:WMA link:https://reference.wolfram.com/language/ref/DirectoryName.html</url>
-
-    <dl>
-      <dt>'DirectoryName["$name$"]'
-      <dd>extracts the directory name from a filename.
-    </dl>
-
-    >> DirectoryName["a/b/c"]
-     = a/b
-
-    >> DirectoryName["a/b/c", 2]
-     = a
-    """
-
-    messages = {
-        "string": "String expected at position 1 in `1`.",
-        "intpm": ("Positive machine-sized integer expected at " "position 2 in `1`."),
-    }
-
-    options = {
-        "OperatingSystem": "$OperatingSystem",
-    }
-    summary_text = "directory part of a filename"
-
-    def eval_with_n(self, name, n, evaluation: Evaluation, options: dict):
-        "DirectoryName[name_, n_, OptionsPattern[DirectoryName]]"
-
-        if n is None:
-            expr = to_expression("DirectoryName", name)
-            py_n = 1
-        else:
-            expr = to_expression("DirectoryName", name, n)
-            py_n = n.to_python()
-
-        if not (isinstance(py_n, int) and py_n > 0):
-            evaluation.message("DirectoryName", "intpm", expr)
-            return
-
-        py_name = name.to_python()
-        if not (isinstance(py_name, str) and py_name[0] == py_name[-1] == '"'):
-            evaluation.message("DirectoryName", "string", expr)
-            return
-        py_name = py_name[1:-1]
-
-        result = py_name
-        for i in range(py_n):
-            (result, tmp) = osp.split(result)
-
-        return String(result)
-
-    def eval(self, name, evaluation: Evaluation, options: dict):
-        "DirectoryName[name_, OptionsPattern[DirectoryName]]"
-        return self.eval_with_n(name, None, evaluation, options)
-
-
 class DirectoryStack(Builtin):
     """
     <url>:WMA link:https://reference.wolfram.com/language/ref/DirectoryStack.html</url>
diff --git a/mathics/builtin/numbers/constants.py b/mathics/builtin/numbers/constants.py
index fc9067197..2f4e4a1d6 100644
--- a/mathics/builtin/numbers/constants.py
+++ b/mathics/builtin/numbers/constants.py
@@ -756,3 +756,8 @@ class Underflow(Builtin):
     instance = cls(expression=False)
     val = instance.get_constant()
     NUMERICAL_CONSTANTS[instance.symbol] = MachineReal(val.value)
+
+# Remove these variables to prevent errors in the SYMBOL_MANIFEST check.
+del cls
+del instance
+del val

From 8c472bd199573f8500813da55a215f4be1e5278b Mon Sep 17 00:00:00 2001
From: "R. Bernstein" <rocky@users.noreply.github.com>
Date: Tue, 22 Oct 2024 06:47:11 -0400
Subject: [PATCH 4/4] Romberg is deprecated... (#1131)

and will be removed by SciPyi 1.15
---
 CHANGES.rst                                |  1 +
 mathics/builtin/scipy_utils/integrators.py | 18 +++---------------
 test/builtin/numbers/test_nintegrate.py    |  4 ++--
 test/core/__init__.py                      |  0
 4 files changed, 6 insertions(+), 17 deletions(-)
 create mode 100644 test/core/__init__.py

diff --git a/CHANGES.rst b/CHANGES.rst
index 0bedb26bc..41dd4d21c 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -33,6 +33,7 @@ API incompatibility
 -------------------
 
 * ``Matcher`` now requires an additional ``evaluation`` parameter
+* ``Romberg`` removed as an ``NIntegrate[]`` method. It is depcrecated in SciPy and is to be removed by SciPy 1.15.
 
 
 Bugs
diff --git a/mathics/builtin/scipy_utils/integrators.py b/mathics/builtin/scipy_utils/integrators.py
index 39b4c078e..bca1ec473 100644
--- a/mathics/builtin/scipy_utils/integrators.py
+++ b/mathics/builtin/scipy_utils/integrators.py
@@ -5,8 +5,6 @@
 if not check_requires_list(["scipy", "numpy"]):
     raise ImportError
 
-import numpy as np
-
 
 def _scipy_interface(integrator, options_map, mandatory=None, adapt_func=None):
     """
@@ -24,7 +22,8 @@ def _scipy_proxy_func_filter(fun, a, b, **opts):
                 if native_opt[1]:
                     val = native_opt[1](val)
                 native_opts[native_opt[0]] = val
-        return adapt_func(integrator(fun, a, b, **native_opts))
+        if adapt_func is not None:
+            return adapt_func(integrator(fun, a, b, **native_opts))
 
     def _scipy_proxy_func(fun, a, b, **opts):
         native_opts = {}
@@ -42,7 +41,7 @@ def _scipy_proxy_func(fun, a, b, **opts):
 
 
 try:
-    from scipy.integrate import nquad, quad, romberg
+    from scipy.integrate import nquad, quad
 except Exception:
     scipy_nintegrate_methods = {}
 else:
@@ -69,17 +68,6 @@ def _scipy_proxy_func(fun, a, b, **opts):
                 False,
             )
         ),
-        "Romberg": tuple(
-            (
-                _scipy_interface(
-                    romberg,
-                    {"tol": ("tol", None), "maxrec": ("divmax", None)},
-                    None,
-                    lambda x: (x, np.nan),
-                ),
-                False,
-            )
-        ),
     }
 
 scipy_nintegrate_methods["Automatic"] = scipy_nintegrate_methods["Quadrature"]
diff --git a/test/builtin/numbers/test_nintegrate.py b/test/builtin/numbers/test_nintegrate.py
index cfe1e2b05..b3d9443a0 100644
--- a/test/builtin/numbers/test_nintegrate.py
+++ b/test/builtin/numbers/test_nintegrate.py
@@ -13,7 +13,7 @@
 from mathics.core.builtin import check_requires_list
 
 if check_requires_list(["scipy", "scipy.integrate"]):
-    methods = ["Automatic", "Romberg", "Internal", "NQuadrature"]
+    methods = ["Automatic", "Internal", "NQuadrature"]
 
     generic_tests_for_nintegrate = [
         (r"NIntegrate[x^2, {x,0,1}, {method} ]", r"1/3.", ""),
@@ -46,7 +46,7 @@
                 "1.",
                 None,
                 [
-                    r"The Method option should be a built-in method name in {`Automatic`, `Internal`, `Simpson`, `NQuadrature`, `Quadrature`, `Romberg`}. Using `Automatic`"
+                    r"The Method option should be a built-in method name in {`Automatic`, `Internal`, `Simpson`, `NQuadrature`, `Quadrature`}. Using `Automatic`"
                 ],
             ),
         ],
diff --git a/test/core/__init__.py b/test/core/__init__.py
new file mode 100644
index 000000000..e69de29bb