From 45c302b6c929b2d698b25186a27f99d2f12d837c Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Thu, 4 Dec 2025 10:09:58 -0300
Subject: [PATCH 01/15] adding `evaluate_without_side_effects` for helping
 compile expressions.

---
 mathics/builtin/assignments/assignment.py |  5 ++--
 mathics/builtin/attributes.py             |  5 +++-
 mathics/builtin/procedural.py             | 14 +++++++----
 mathics/builtin/scoping.py                | 12 ++++++----
 mathics/core/builtin.py                   | 13 ++++++++++
 mathics/core/convert/function.py          | 29 +++++++++++++++++++++++
 mathics/core/definitions.py               |  6 +++++
 mathics/eval/drawing/plot_compile.py      |  3 ++-
 8 files changed, 73 insertions(+), 14 deletions(-)

diff --git a/mathics/builtin/assignments/assignment.py b/mathics/builtin/assignments/assignment.py
index cc85e83ca..f7aaae725 100644
--- a/mathics/builtin/assignments/assignment.py
+++ b/mathics/builtin/assignments/assignment.py
@@ -134,7 +134,7 @@ class Set(InfixOperator):
         "setraw": "Cannot assign to raw object `1`.",
         "shape": "Lists `1` and `2` are not the same shape.",
     }
-
+    has_side_effects = True
     summary_text = "assign a value"
 
     def eval(self, lhs, rhs, evaluation):
@@ -258,7 +258,7 @@ class TagSet(Builtin):
     """
 
     attributes = A_HOLD_ALL | A_PROTECTED | A_SEQUENCE_HOLD
-
+    has_side_effects = True
     messages = {
         "tagnfd": "Tag `1` not found or too deep for an assigned rule.",
     }
@@ -353,6 +353,7 @@ class UpSet(InfixOperator):
     """
 
     attributes = A_HOLD_FIRST | A_PROTECTED | A_SEQUENCE_HOLD
+    has_side_effects = True
     grouping = "Right"
 
     summary_text = (
diff --git a/mathics/builtin/attributes.py b/mathics/builtin/attributes.py
index a4dc27382..2bdfc40d3 100644
--- a/mathics/builtin/attributes.py
+++ b/mathics/builtin/attributes.py
@@ -126,6 +126,7 @@ class ClearAttributes(Builtin):
     """
 
     attributes = A_HOLD_FIRST | A_PROTECTED
+    has_side_effects = True
     summary_text = "clear the attributes of a symbol"
 
     def eval(self, symbols, attributes, evaluation):
@@ -526,6 +527,7 @@ class Protect(Builtin):
     """
 
     attributes = A_HOLD_ALL | A_PROTECTED
+    has_side_effects = True
     summary_text = "protect a symbol against redefinitions"
 
     def eval(self, symbols, evaluation):
@@ -696,7 +698,7 @@ class SetAttributes(Builtin):
     """
 
     attributes = A_HOLD_FIRST | A_PROTECTED
-
+    has_side_effects = True
     messages = {
         "unknownattr": f"`1` should be one of {', '.join(attribute_string_to_number.keys())}"
     }
@@ -752,6 +754,7 @@ class Unprotect(Builtin):
     """
 
     attributes = A_HOLD_ALL | A_PROTECTED
+    has_side_effects = True
     summary_text = "remove protection against redefinitions"
 
     def eval(self, symbols, evaluation):
diff --git a/mathics/builtin/procedural.py b/mathics/builtin/procedural.py
index 6d4841c88..4d0efefcf 100644
--- a/mathics/builtin/procedural.py
+++ b/mathics/builtin/procedural.py
@@ -219,7 +219,7 @@ class CompoundExpression(InfixOperator):
     """
 
     attributes = A_HOLD_ALL | A_PROTECTED | A_READ_PROTECTED
-
+    has_side_effects = True
     summary_text = "execute expressions in sequence"
 
     def eval(self, expr, evaluation):
@@ -346,6 +346,7 @@ class For(Builtin):
     """
 
     attributes = A_HOLD_REST | A_PROTECTED
+    has_side_effects = True
     rules = {
         "For[start_, test_, incr_]": "For[start, test, incr, Null]",
     }
@@ -486,6 +487,7 @@ class Interrupt(Builtin):
      | a
      = $Aborted
     """
+    has_side_effects = True
 
     # Set checking that the no arguments are allowed.
     # eval_error = Builtin.generic_argument_error
@@ -511,6 +513,7 @@ class Pause(Builtin):
     >> Pause[0.5]
     """
 
+    has_side_effects = True
     messages = {
         "numnm": (
             "Non-negative machine-sized number expected at " "position 1 in `1`."
@@ -563,7 +566,7 @@ class Return(Builtin):
     rules = {
         "Return[]": "Return[Null]",
     }
-
+    has_side_effects = True
     summary_text = "return from a function"
 
     def eval(self, expr, evaluation: Evaluation):  # pylint: disable=unused-argument
@@ -604,7 +607,7 @@ class Switch(Builtin):
 
     summary_text = "switch based on a value, with patterns allowed"
     attributes = A_HOLD_REST | A_PROTECTED
-
+    has_side_effects = True
     messages = {
         "argct": (
             "Switch called with `2` arguments. "
@@ -659,7 +662,7 @@ class Throw(Builtin):
     # Set checking that the number of arguments required is one or two. WMA uses 1..3.
     eval_error = Builtin.generic_argument_error
     expected_args = (1, 2)
-
+    has_side_effects = True
     messages = {
         "nocatch": "Uncaught `1` returned to top level.",
     }
@@ -714,6 +717,7 @@ class Which(SympyFunction):
     """
 
     attributes = A_HOLD_ALL | A_PROTECTED
+    has_side_effects = True
     summary_text = "test which of a sequence of conditions are true"
 
     def eval(self, items, evaluation):
@@ -773,7 +777,7 @@ class While(Builtin):
     # Set checking that the number of arguments required is one.
     eval_error = Builtin.generic_argument_error
     expected_args = (1, 2)
-
+    has_side_effects = True
     rules = {
         "While[test_]": "While[test, Null]",
     }
diff --git a/mathics/builtin/scoping.py b/mathics/builtin/scoping.py
index 6063788ca..2d7202a5f 100644
--- a/mathics/builtin/scoping.py
+++ b/mathics/builtin/scoping.py
@@ -99,6 +99,7 @@ class Begin(Builtin):
     ##  = Global`test`
     """
 
+    has_side_effects = True
     rules = {
         "Begin[context_String]": """
              Unprotect[System`Private`$ContextStack];
@@ -128,7 +129,7 @@ class BeginPackage(Builtin):
     ## >> BeginPackage["test`"]
     ##  = test`
     """
-
+    has_side_effects = True
     messages = {"unimpl": "The second argument to BeginPackage is not yet implemented."}
 
     rules = {
@@ -187,7 +188,7 @@ class Block(Builtin):
     """
 
     attributes = A_HOLD_ALL | A_PROTECTED
-
+    has_side_effects = True
     messages = {
         "lvsym": (
             "Local variable specification contains `1`, "
@@ -351,6 +352,7 @@ class End(Builtin):
     </dl>
     """
 
+    has_side_effects = True
     messages = {
         "noctx": "No previous context defined.",
     }
@@ -385,7 +387,7 @@ class EndPackage(Builtin):
     After 'EndPackage', the values of '\$Context' and '\$ContextPath' at the \
     time of the 'BeginPackage' call are restored, with the new package\'s context prepended to '\$ContextPath'.
     """
-
+    has_side_effects = True
     messages = {
         "noctx": "No previous context defined.",
     }
@@ -450,7 +452,7 @@ class Module(Builtin):
     """
 
     attributes = A_HOLD_ALL | A_PROTECTED
-
+    has_side_effects = True
     messages = {
         "lvsym": (
             "Local variable specification contains `1`, "
@@ -710,7 +712,7 @@ class With(Builtin):
     """
 
     attributes = A_HOLD_ALL | A_PROTECTED
-
+    has_side_effects = True
     messages = {
         "lvsym": (
             "Local variable specification contains `1`, "
diff --git a/mathics/core/builtin.py b/mathics/core/builtin.py
index f91e4ea76..ad371d499 100644
--- a/mathics/core/builtin.py
+++ b/mathics/core/builtin.py
@@ -207,6 +207,11 @@ def eval_with_options(x, evaluation: Evaluation, options: dict):
     expected_args: Union[int, Tuple[int, int], range] = -1
 
     formats: Dict[str, Any] = {}
+
+    # If the symbol include rules involving loops,
+    # setting values, or creating/changing contexts.
+    has_side_effects: bool = False
+
     messages: Dict[str, Any] = {}
     name: Optional[str] = None
     options: Dict[str, Any] = {}
@@ -434,6 +439,13 @@ def contextify_form_name(f):
         else:
             definitions.builtin[name] = definition
 
+        # If the definition has side effects, store it in a
+        # dictionary.
+        if self.has_side_effects:
+            from mathics.core.definitions import SIDE_EFFECT_BUILTINS
+
+            SIDE_EFFECT_BUILTINS[name] = definition
+
         makeboxes_def = definitions.builtin["System`MakeBoxes"]
         for rule in box_rules:
             makeboxes_def.add_rule(rule)
@@ -1024,6 +1036,7 @@ def get_name(cls, short=False) -> str:
 class IterationFunction(Builtin, ABC):
     attributes = A_HOLD_ALL | A_PROTECTED
     allow_loopcontrol = False
+    has_side_effects = True
     throw_iterb = True
 
     def get_result(self, elements, is_uniform=False) -> Expression:
diff --git a/mathics/core/convert/function.py b/mathics/core/convert/function.py
index 0250b04c6..62f0b4e0a 100644
--- a/mathics/core/convert/function.py
+++ b/mathics/core/convert/function.py
@@ -2,6 +2,8 @@
 
 from typing import Callable, Optional, Tuple
 
+from mathics.core.definitions import SIDE_EFFECT_BUILTINS, Definition
+from mathics.core.element import BaseElement
 from mathics.core.evaluation import Evaluation
 from mathics.core.expression import Expression, from_python
 from mathics.core.symbols import Symbol, SymbolFalse, SymbolTrue
@@ -44,6 +46,32 @@ def __init__(self, var):
         self.var = var
 
 
+def evaluate_without_side_effects(
+    expr: BaseElement, evaluation: Evaluation
+) -> BaseElement:
+    """
+    Evaluate an expression leaving unevaluated subexpressions
+    related with side-effects (assignments, loops).
+    """
+    definitions = evaluation.definitions
+    # Temporarily remove the builtin definitions
+    # of symbols with side effects
+    for name, defin in SIDE_EFFECT_BUILTINS.items():
+        # Change the definition by a temporal definition setting
+        # just the name and the attributes.
+        definitions.builtin[name] = Definition(
+            name, attributes=defin.attributes, builtin=defin.builtin
+        )
+        definitions.clear_cache(name)
+    try:
+        result = expr.evaluate(evaluation)
+    finally:
+        # Restore the definitions
+        for name, defin in SIDE_EFFECT_BUILTINS.items():
+            definitions.builtin[name] = defin
+    return result
+
+
 def expression_to_callable(
     expr: Expression,
     args: Optional[list] = None,
@@ -56,6 +84,7 @@ def expression_to_callable(
     args: a list of CompileArg elements
     evaluation: an Evaluation object used if the llvm compilation fails
     """
+    expr = evaluate_without_side_effects(expr, evaluation)
     try:
         cfunc = _compile(expr, args) if (use_llvm and args is not None) else None
     except CompileError:
diff --git a/mathics/core/definitions.py b/mathics/core/definitions.py
index b66f6e735..87f0bdeb9 100644
--- a/mathics/core/definitions.py
+++ b/mathics/core/definitions.py
@@ -121,6 +121,12 @@ def __repr__(self) -> str:
         return repr_str
 
 
+# Dictionary of builtin definitions involving side effects
+# like setting values, changing contexts or running loops:
+
+SIDE_EFFECT_BUILTINS: Dict[str, Definition] = {}
+
+
 class Definitions:
     """The state of one instance of the Mathics3 interpreter is stored in this object.
 
diff --git a/mathics/eval/drawing/plot_compile.py b/mathics/eval/drawing/plot_compile.py
index 1cfaf2066..09f2a6c62 100644
--- a/mathics/eval/drawing/plot_compile.py
+++ b/mathics/eval/drawing/plot_compile.py
@@ -18,6 +18,7 @@
 import scipy
 import sympy
 
+from mathics.core.convert.function import evaluate_without_side_effects
 from mathics.core.convert.sympy import SympyExpression
 from mathics.core.symbols import strip_context
 from mathics.core.util import print_expression_tree, print_sympy_tree
@@ -54,7 +55,7 @@ def plot_compile(evaluation, expr, names, debug=0):
     # because some functions are not themselves sympy-enabled
     # if they always get rewritten to one that is.
     try:
-        new_expr = expr.evaluate(evaluation)
+        new_expr = eval_without_side_effects(expr, evaluation)
         if new_expr:
             expr = new_expr
     except Exception:

From 36837e4cdf71b74ed281530012f7139fac0a3d20 Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Thu, 4 Dec 2025 11:02:16 -0300
Subject: [PATCH 02/15] mypy fix. typo in function call. remove
 has_side_effects for `Which`

---
 mathics/builtin/procedural.py        |  1 -
 mathics/core/convert/function.py     | 11 ++++++-----
 mathics/eval/drawing/plot_compile.py |  2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/mathics/builtin/procedural.py b/mathics/builtin/procedural.py
index 4d0efefcf..fc0e6e712 100644
--- a/mathics/builtin/procedural.py
+++ b/mathics/builtin/procedural.py
@@ -717,7 +717,6 @@ class Which(SympyFunction):
     """
 
     attributes = A_HOLD_ALL | A_PROTECTED
-    has_side_effects = True
     summary_text = "test which of a sequence of conditions are true"
 
     def eval(self, items, evaluation):
diff --git a/mathics/core/convert/function.py b/mathics/core/convert/function.py
index 62f0b4e0a..94887381b 100644
--- a/mathics/core/convert/function.py
+++ b/mathics/core/convert/function.py
@@ -3,7 +3,7 @@
 from typing import Callable, Optional, Tuple
 
 from mathics.core.definitions import SIDE_EFFECT_BUILTINS, Definition
-from mathics.core.element import BaseElement
+from mathics.core.element import BaseElement, EvalMixin
 from mathics.core.evaluation import Evaluation
 from mathics.core.expression import Expression, from_python
 from mathics.core.symbols import Symbol, SymbolFalse, SymbolTrue
@@ -47,8 +47,8 @@ def __init__(self, var):
 
 
 def evaluate_without_side_effects(
-    expr: BaseElement, evaluation: Evaluation
-) -> BaseElement:
+    expr: Expression, evaluation: Evaluation
+) -> Expression:
     """
     Evaluate an expression leaving unevaluated subexpressions
     related with side-effects (assignments, loops).
@@ -69,7 +69,7 @@ def evaluate_without_side_effects(
         # Restore the definitions
         for name, defin in SIDE_EFFECT_BUILTINS.items():
             definitions.builtin[name] = defin
-    return result
+    return result if result is not None else expr
 
 
 def expression_to_callable(
@@ -84,7 +84,8 @@ def expression_to_callable(
     args: a list of CompileArg elements
     evaluation: an Evaluation object used if the llvm compilation fails
     """
-    expr = evaluate_without_side_effects(expr, evaluation)
+    if evaluation is not None:
+        expr = evaluate_without_side_effects(expr, evaluation)
     try:
         cfunc = _compile(expr, args) if (use_llvm and args is not None) else None
     except CompileError:
diff --git a/mathics/eval/drawing/plot_compile.py b/mathics/eval/drawing/plot_compile.py
index 09f2a6c62..2eac8d579 100644
--- a/mathics/eval/drawing/plot_compile.py
+++ b/mathics/eval/drawing/plot_compile.py
@@ -55,7 +55,7 @@ def plot_compile(evaluation, expr, names, debug=0):
     # because some functions are not themselves sympy-enabled
     # if they always get rewritten to one that is.
     try:
-        new_expr = eval_without_side_effects(expr, evaluation)
+        new_expr = evaluate_without_side_effects(expr, evaluation)
         if new_expr:
             expr = new_expr
     except Exception:

From 969a2322aea91e7c6d8f796697a775017c8166e2 Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Thu, 4 Dec 2025 11:49:16 -0300
Subject: [PATCH 03/15] improve implementation of pythonized code. Fix test
 case

---
 mathics/builtin/compilation.py   |  4 ++--
 mathics/core/convert/function.py | 12 +++++++-----
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/mathics/builtin/compilation.py b/mathics/builtin/compilation.py
index 09b56fa3e..fbf3ed20b 100644
--- a/mathics/builtin/compilation.py
+++ b/mathics/builtin/compilation.py
@@ -65,9 +65,9 @@ class Compile(Builtin):
     >> cf[3.5, 2]
      = 2.18888
 
-    Loops and variable assignments are supported usinv Python builtin "compile" function:
+    Loops and variable assignments are supported using Python builtin "compile" function:
     >> Compile[{{a, _Integer}, {b, _Integer}}, While[b != 0, {a, b} = {b, Mod[a, b]}]; a]       (* GCD of a, b *)
-     =  CompiledFunction[{a, b}, a, -PythonizedCode-]
+     =  CompiledFunction[{a, b}, While[b != 0, {a, b} = {b, Mod[a, b]}] ; a, -PythonizedCode-]
     """
 
     attributes = A_HOLD_ALL | A_PROTECTED
diff --git a/mathics/core/convert/function.py b/mathics/core/convert/function.py
index 94887381b..09e9e9e4c 100644
--- a/mathics/core/convert/function.py
+++ b/mathics/core/convert/function.py
@@ -69,6 +69,7 @@ def evaluate_without_side_effects(
         # Restore the definitions
         for name, defin in SIDE_EFFECT_BUILTINS.items():
             definitions.builtin[name] = defin
+            definitions.clear_cache(name)
     return result if result is not None else expr
 
 
@@ -86,6 +87,7 @@ def expression_to_callable(
     """
     if evaluation is not None:
         expr = evaluate_without_side_effects(expr, evaluation)
+
     try:
         cfunc = _compile(expr, args) if (use_llvm and args is not None) else None
     except CompileError:
@@ -97,11 +99,11 @@ def expression_to_callable(
         try:
 
             def _pythonized_mathics_expr(*x):
-                inner_evaluation = Evaluation(definitions=evaluation.definitions)
-                x_mathics = (from_python(u) for u in x[: len(args)])
-                vars = dict(list(zip([a.name for a in args], x_mathics)))
-                pyexpr = expr.replace_vars(vars)
-                pyexpr = eval_N(pyexpr, inner_evaluation)
+                from mathics.eval.scoping import dynamic_scoping
+
+                vars = {a.name: from_python(u) for a, u in zip(args, x[: len(args)])}
+                pyexpr = dynamic_scoping(lambda ev: expr.evaluate(ev), vars, evaluation)
+                pyexpr = eval_N(pyexpr, evaluation)
                 res = pyexpr.to_python()
                 return res
 

From abe1bbd31532c15fb22e1a03fb9e57380f93356c Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Thu, 4 Dec 2025 13:21:47 -0300
Subject: [PATCH 04/15] improve doctest. use a fresh evaluation object for the
 compiled function

---
 mathics/builtin/compilation.py   | 32 ++++++++++++++++++++++++++++----
 mathics/core/convert/function.py |  7 +++++--
 mathics/eval/scoping.py          |  1 +
 3 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/mathics/builtin/compilation.py b/mathics/builtin/compilation.py
index fbf3ed20b..df342e24f 100644
--- a/mathics/builtin/compilation.py
+++ b/mathics/builtin/compilation.py
@@ -12,7 +12,12 @@
 
 from mathics.builtin.box.compilation import CompiledCodeBox
 from mathics.core.atoms import Integer, String
-from mathics.core.attributes import A_HOLD_ALL, A_PROTECTED
+from mathics.core.attributes import (
+    A_HOLD_ALL,
+    A_N_HOLD_ALL,
+    A_PROTECTED,
+    A_READ_PROTECTED,
+)
 from mathics.core.builtin import Builtin
 from mathics.core.convert.expression import to_mathics_list
 from mathics.core.convert.function import (
@@ -66,8 +71,10 @@ class Compile(Builtin):
      = 2.18888
 
     Loops and variable assignments are supported using Python builtin "compile" function:
-    >> Compile[{{a, _Integer}, {b, _Integer}}, While[b != 0, {a, b} = {b, Mod[a, b]}]; a]       (* GCD of a, b *)
-     =  CompiledFunction[{a, b}, While[b != 0, {a, b} = {b, Mod[a, b]}] ; a, -PythonizedCode-]
+    >> gdc = Compile[{{a, _Integer}, {b, _Integer}}, Module[{x=a, y=b}, While[y != 0, {x, y} = {y, Mod[x, y]}]; x]] (* GCD of a, b *)
+     =  CompiledFunction[{a, b}, Module[{x = a, y = b}, While[y != 0, {x, y} = {y, Mod[x, y]}] ; x], -PythonizedCode-]
+    >> gdc[18, 81]
+     = 9.
     """
 
     attributes = A_HOLD_ALL | A_PROTECTED
@@ -167,7 +174,23 @@ def to_sympy(self, *args, **kwargs):
         raise NotImplementedError
 
     def __hash__(self):
-        return hash(("CompiledCode", ctypes.addressof(self.cfunc)))  # XXX hack
+        cfunc = self.cfunc
+        if cfunc is None:
+            hash(
+                (
+                    "CompiledCode",
+                    None,
+                )
+            )  # XXX hack
+        try:
+            return hash(("CompiledCode", ctypes.addressof(cfunc)))  # XXX hack
+        except TypeError:
+            return hash(
+                (
+                    "Pythonized-function",
+                    cfunc,
+                )
+            )
 
     def atom_to_boxes(self, f, evaluation: Evaluation):
         return CompiledCodeBox(String(self.__str__()), evaluation=evaluation)
@@ -191,6 +214,7 @@ class CompiledFunction(Builtin):
 
     """
 
+    attributes = A_HOLD_ALL | A_PROTECTED | A_N_HOLD_ALL | A_READ_PROTECTED
     messages = {"argerr": "Invalid argument `1` should be Integer, Real or boolean."}
     summary_text = "A CompiledFunction object."
 
diff --git a/mathics/core/convert/function.py b/mathics/core/convert/function.py
index 09e9e9e4c..de282d2f2 100644
--- a/mathics/core/convert/function.py
+++ b/mathics/core/convert/function.py
@@ -101,9 +101,12 @@ def expression_to_callable(
             def _pythonized_mathics_expr(*x):
                 from mathics.eval.scoping import dynamic_scoping
 
+                inner_evaluation = Evaluation(definitions=evaluation.definitions)
                 vars = {a.name: from_python(u) for a, u in zip(args, x[: len(args)])}
-                pyexpr = dynamic_scoping(lambda ev: expr.evaluate(ev), vars, evaluation)
-                pyexpr = eval_N(pyexpr, evaluation)
+                pyexpr = dynamic_scoping(
+                    lambda ev: expr.evaluate(ev), vars, inner_evaluation
+                )
+                pyexpr = eval_N(pyexpr, inner_evaluation)
                 res = pyexpr.to_python()
                 return res
 
diff --git a/mathics/eval/scoping.py b/mathics/eval/scoping.py
index 6579c24de..eba2bb63b 100644
--- a/mathics/eval/scoping.py
+++ b/mathics/eval/scoping.py
@@ -16,6 +16,7 @@ def dynamic_scoping(func, vars, evaluation: Evaluation):
     and evaluates func(evaluation)
     """
     original_definitions = {}
+
     for var_name, new_def in vars.items():
         assert fully_qualified_symbol_name(var_name)
         original_definitions[var_name] = evaluation.definitions.get_user_definition(

From 66c6c6a4463e83162c1447f2ba8dbdcabf6998ef Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Thu, 4 Dec 2025 13:35:23 -0300
Subject: [PATCH 05/15] another fix on doctests

---
 mathics/builtin/compilation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mathics/builtin/compilation.py b/mathics/builtin/compilation.py
index df342e24f..1bd493f2e 100644
--- a/mathics/builtin/compilation.py
+++ b/mathics/builtin/compilation.py
@@ -206,7 +206,7 @@ class CompiledFunction(Builtin):
     </dl>
 
     >> sqr = Compile[{x}, x x]
-     = CompiledFunction[{x}, x ^ 2, ...]
+     = CompiledFunction[{x}, x x, ...]
     >> Head[sqr]
      = CompiledFunction
     >> sqr[2]

From d4696d01064847b3e5bdbf83da7b7da1568f1bcc Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Sun, 14 Dec 2025 01:02:36 -0300
Subject: [PATCH 06/15] add test

---
 test/core/convert/test_function.py | 32 ++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 test/core/convert/test_function.py

diff --git a/test/core/convert/test_function.py b/test/core/convert/test_function.py
new file mode 100644
index 000000000..6c9f7d6bd
--- /dev/null
+++ b/test/core/convert/test_function.py
@@ -0,0 +1,32 @@
+"""
+Conversion from expressions to functions
+"""
+
+from test.helper import check_evaluation, session
+
+from mathics.core.convert.function import evaluate_without_side_effects
+
+
+def test_evaluate_without_side_effects():
+    session.reset()
+    session.evaluate(
+        """
+    F[x_]:=G[x];
+    G[x_]:=(a=2^2*x;Do[a=x+2^2,{3}];a); 
+    Q[x_]:=(a=2^2*x);
+    """
+    )
+    expr = session.parse("F[x]")
+    # Notice that since `CompoundExpression` has the attribute "HoldAll",
+    # subelements are not evaluated (`2^2`->`2^2`)
+    expect = session.parse("(a=2^2*x; Do[a=x+2^2,{3}];a)")
+    result = evaluate_without_side_effects(expr, session.evaluation)
+    assert result.sameQ(expect)
+
+    expr = session.parse("Q[x]")
+    # If the head of the expression does not have the attribute "HoldAll",
+    # subelements are evaluated (`2^2`->`4`)
+    expect = session.parse("a=4*x")
+    result = evaluate_without_side_effects(expr, session.evaluation)
+
+    assert result.sameQ(expect)

From 0102928b2aee8d0de3818a839c84990cba78857a Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Sun, 14 Dec 2025 22:37:56 -0300
Subject: [PATCH 07/15] black

---
 mathics/core/convert/function.py   | 3 ++-
 mathics/core/convert/lambdify.py   | 8 ++++----
 mathics/core/definitions.py        | 2 +-
 test/core/convert/test_function.py | 2 +-
 4 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/mathics/core/convert/function.py b/mathics/core/convert/function.py
index 34e988740..42668f2f0 100644
--- a/mathics/core/convert/function.py
+++ b/mathics/core/convert/function.py
@@ -5,7 +5,6 @@
 
 
 from mathics.core.definitions import SIDE_EFFECT_BUILTINS, Definition
-from mathics.core.element import BaseElement, EvalMixin
 from mathics.core.evaluation import Evaluation
 from mathics.core.expression import Expression, from_python
 from mathics.core.symbols import Symbol, SymbolFalse, SymbolTrue
@@ -193,6 +192,8 @@ def expression_to_callable_and_args(
     expr: A Mathics Expression object
     vars: a list of Symbols or Mathics Lists of the form {Symbol, Type}
     """
+    from mathics.core.convert.lambdify import LambdifyCompileError, lambdify_compile
+    
     args = collect_args(vars)
 
     # If vectorize is requested, first, try to lambdify the expression:
diff --git a/mathics/core/convert/lambdify.py b/mathics/core/convert/lambdify.py
index 9a633a15e..8b6c27284 100644
--- a/mathics/core/convert/lambdify.py
+++ b/mathics/core/convert/lambdify.py
@@ -42,7 +42,7 @@ def hyppfq(p, q, x):
 # mappings = [dict(AdditionalMappings.__dict__), "numpy"]
 
 
-class CompileError(Exception):
+class LambdifyCompileError(Exception):
     pass
 
 
@@ -85,9 +85,9 @@ def lambdify_compile(evaluation, expr, names, debug=0):
         print("post-eval", expr)
 
     # Ask the expr Expression to generate a sympy expression and handle errors
-    sympy_expr = expr.to_sympy(raise_on_error=CompileError)
+    sympy_expr = expr.to_sympy(raise_on_error=LambdifyCompileError)
     if isinstance(sympy_expr, SympyExpression):
-        raise CompileError(f"{expr.head}.to_sympy returns invalid sympy expr.")
+        raise LambdifyCompileError(f"{expr.head}.to_sympy returns invalid sympy expr.")
 
     # Strip symbols in sympy expression of context.
     subs = {
@@ -110,7 +110,7 @@ def lambdify_compile(evaluation, expr, names, debug=0):
             symbols, sympy_expr, modules=["numpy", "scipy"]
         )
     except Exception as oops:
-        raise CompileError(f"error compiling sympy expr {sympy_expr}: {oops}")
+        raise LambdifyCompileError(f"error compiling sympy expr {sympy_expr}: {oops}")
 
     if debug >= 2:
         print("=== compiled python")
diff --git a/mathics/core/definitions.py b/mathics/core/definitions.py
index 87f0bdeb9..413e80d98 100644
--- a/mathics/core/definitions.py
+++ b/mathics/core/definitions.py
@@ -1099,7 +1099,7 @@ def load_builtin_definitions(
         mathics3_builtins_modules,
     )
     from mathics.eval.files_io.files import get_file_time
-    from mathics.eval.pymathics import PyMathicsLoadException, load_pymathics_module
+    from mathics.eval.pymathics import load_pymathics_module
     from mathics.session import autoload_files
 
     loaded = False
diff --git a/test/core/convert/test_function.py b/test/core/convert/test_function.py
index 6c9f7d6bd..37a9df658 100644
--- a/test/core/convert/test_function.py
+++ b/test/core/convert/test_function.py
@@ -2,7 +2,7 @@
 Conversion from expressions to functions
 """
 
-from test.helper import check_evaluation, session
+from test.helper import session
 
 from mathics.core.convert.function import evaluate_without_side_effects
 

From 64d7790a51fa7797185589b0027ed3321a5ddbba Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Sun, 14 Dec 2025 23:01:04 -0300
Subject: [PATCH 08/15] merge

---
 mathics/core/convert/function.py | 9 ++++++---
 mathics/core/convert/lambdify.py | 8 ++++----
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/mathics/core/convert/function.py b/mathics/core/convert/function.py
index 42668f2f0..d75b3e301 100644
--- a/mathics/core/convert/function.py
+++ b/mathics/core/convert/function.py
@@ -78,7 +78,7 @@ def evaluate_without_side_effects(
     return result if result is not None else expr
 
 
-def expression_to_callable(
+def expression_to_llvm(
     expr: Expression,
     args: Optional[list] = None,
     evaluation: Optional[Evaluation] = None,
@@ -192,7 +192,10 @@ def expression_to_callable_and_args(
     expr: A Mathics Expression object
     vars: a list of Symbols or Mathics Lists of the form {Symbol, Type}
     """
-    from mathics.core.convert.lambdify import LambdifyCompileError, lambdify_compile
+    from mathics.core.convert.lambdify import (
+        CompileError as LambdifyCompileError,
+        lambdify_compile,
+    )
     
     args = collect_args(vars)
 
@@ -222,7 +225,7 @@ def expression_to_callable_and_args(
                     for compile_arg in args
                 ]
             )
-            cfunc = expression_to_callable(expr, llvm_args, evaluation)
+            cfunc = expression_to_llvm(expr, llvm_args, evaluation)
             if cfunc is not None:
                 if vectorize:
                     cfunc = numpy.vectorize(cfunc)
diff --git a/mathics/core/convert/lambdify.py b/mathics/core/convert/lambdify.py
index 8b6c27284..9a633a15e 100644
--- a/mathics/core/convert/lambdify.py
+++ b/mathics/core/convert/lambdify.py
@@ -42,7 +42,7 @@ def hyppfq(p, q, x):
 # mappings = [dict(AdditionalMappings.__dict__), "numpy"]
 
 
-class LambdifyCompileError(Exception):
+class CompileError(Exception):
     pass
 
 
@@ -85,9 +85,9 @@ def lambdify_compile(evaluation, expr, names, debug=0):
         print("post-eval", expr)
 
     # Ask the expr Expression to generate a sympy expression and handle errors
-    sympy_expr = expr.to_sympy(raise_on_error=LambdifyCompileError)
+    sympy_expr = expr.to_sympy(raise_on_error=CompileError)
     if isinstance(sympy_expr, SympyExpression):
-        raise LambdifyCompileError(f"{expr.head}.to_sympy returns invalid sympy expr.")
+        raise CompileError(f"{expr.head}.to_sympy returns invalid sympy expr.")
 
     # Strip symbols in sympy expression of context.
     subs = {
@@ -110,7 +110,7 @@ def lambdify_compile(evaluation, expr, names, debug=0):
             symbols, sympy_expr, modules=["numpy", "scipy"]
         )
     except Exception as oops:
-        raise LambdifyCompileError(f"error compiling sympy expr {sympy_expr}: {oops}")
+        raise CompileError(f"error compiling sympy expr {sympy_expr}: {oops}")
 
     if debug >= 2:
         print("=== compiled python")

From 8f50b4e33af05d64fe8c1823a795bee4ab30f0d0 Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Mon, 15 Dec 2025 00:03:34 -0300
Subject: [PATCH 09/15] black

---
 mathics/builtin/box/__init__.py                          | 1 +
 mathics/builtin/compilation.py                           | 2 --
 mathics/builtin/directories/__init__.py                  | 1 +
 mathics/builtin/drawing/graphics3d.py                    | 9 ++++-----
 mathics/builtin/exp_structure/size_and_sig.py            | 1 +
 mathics/builtin/file_operations/__init__.py              | 1 +
 mathics/builtin/files_io/__init__.py                     | 1 +
 mathics/builtin/image/base.py                            | 1 +
 mathics/builtin/image/composition.py                     | 1 +
 mathics/builtin/image/pixel.py                           | 1 +
 mathics/builtin/image/structure.py                       | 1 +
 mathics/builtin/image/test.py                            | 1 +
 mathics/builtin/list/math.py                             | 1 +
 mathics/builtin/procedural.py                            | 1 +
 mathics/builtin/scoping.py                               | 2 ++
 mathics/builtin/specialfns/orthogonal.py                 | 1 -
 mathics/builtin/statistics/base.py                       | 1 +
 mathics/builtin/string/__init__.py                       | 1 +
 mathics/builtin/string/patterns.py                       | 3 +++
 mathics/builtin/symbolic_history/__init__.py             | 1 +
 mathics/builtin/testing_expressions/expression_tests.py  | 1 +
 .../builtin/testing_expressions/numerical_properties.py  | 1 +
 mathics/core/convert/function.py                         | 2 +-
 mathics/core/convert/regex.py                            | 1 +
 24 files changed, 28 insertions(+), 9 deletions(-)

diff --git a/mathics/builtin/box/__init__.py b/mathics/builtin/box/__init__.py
index 5d2777e44..8275c12be 100644
--- a/mathics/builtin/box/__init__.py
+++ b/mathics/builtin/box/__init__.py
@@ -6,5 +6,6 @@
 Boxing information like bounding-box width and size makes it easier for formatters to do
 layout without having to know the intricacies of what is inside the box.
 """
+
 # Docs are not yet ready for prime time. Maybe after release 6.0.0.
 no_doc = True
diff --git a/mathics/builtin/compilation.py b/mathics/builtin/compilation.py
index d21b56b39..1d7b4255c 100644
--- a/mathics/builtin/compilation.py
+++ b/mathics/builtin/compilation.py
@@ -200,7 +200,6 @@ def __hash__(self):
                 )
             )
 
-
     def atom_to_boxes(self, f, evaluation: Evaluation):
         return CompiledCodeBox(String(self.__str__()), evaluation=evaluation)
 
@@ -223,7 +222,6 @@ class CompiledFunction(Builtin):
 
     """
 
-
     attributes = A_HOLD_ALL | A_PROTECTED | A_N_HOLD_ALL | A_READ_PROTECTED
     messages = {
         "argerr": "Invalid argument `1` should be Integer, Real, Complex or boolean.",
diff --git a/mathics/builtin/directories/__init__.py b/mathics/builtin/directories/__init__.py
index b7bf1f9e4..a17fc9441 100644
--- a/mathics/builtin/directories/__init__.py
+++ b/mathics/builtin/directories/__init__.py
@@ -1,6 +1,7 @@
 """
 Directories and Directory Operations
 """
+
 # Note: everything in this module is not loaded if environment
 # variable ENABLE_FILES_MODULE is False.  Here we do not want to
 # include any built-in commands that can write to the filesytesm.
diff --git a/mathics/builtin/drawing/graphics3d.py b/mathics/builtin/drawing/graphics3d.py
index 5caa0b1c3..52daa2dc3 100644
--- a/mathics/builtin/drawing/graphics3d.py
+++ b/mathics/builtin/drawing/graphics3d.py
@@ -107,6 +107,7 @@ class Graphics3D(Graphics):
          . draw(((1,1,-1)--(1,1,1)), rgb(0.4, 0.4, 0.4)+linewidth(1));
          . \end{asy}
     """
+
     summary_text = "a three-dimensional graphics image wrapper"
     options = Graphics.options.copy()
     options.update(
@@ -172,11 +173,9 @@ class Graphics3DElements(_GraphicsElements):
     def __init__(self, content, evaluation, neg_y=False):
         super(Graphics3DElements, self).__init__(content, evaluation)
         self.neg_y = neg_y
-        self.xmin = (
-            self.ymin
-        ) = (
-            self.pixel_width
-        ) = self.pixel_height = self.extent_width = self.extent_height = None
+        self.xmin = self.ymin = self.pixel_width = self.pixel_height = (
+            self.extent_width
+        ) = self.extent_height = None
         self.view_width = None
         self.content = content
 
diff --git a/mathics/builtin/exp_structure/size_and_sig.py b/mathics/builtin/exp_structure/size_and_sig.py
index b06cede7f..075499752 100644
--- a/mathics/builtin/exp_structure/size_and_sig.py
+++ b/mathics/builtin/exp_structure/size_and_sig.py
@@ -1,6 +1,7 @@
 """
 Expression Sizes and Signatures
 """
+
 import hashlib
 import platform
 import zlib
diff --git a/mathics/builtin/file_operations/__init__.py b/mathics/builtin/file_operations/__init__.py
index c69d15343..5d05c229f 100644
--- a/mathics/builtin/file_operations/__init__.py
+++ b/mathics/builtin/file_operations/__init__.py
@@ -1,6 +1,7 @@
 """
 File Operations
 """
+
 # Note: everything in this module is not loaded if environment
 # variable ENABLE_FILES_MODULE is False.  Here we do not want to
 # include any built-in commands that can write to the filesytesm.
diff --git a/mathics/builtin/files_io/__init__.py b/mathics/builtin/files_io/__init__.py
index 82b851411..c06a44c84 100644
--- a/mathics/builtin/files_io/__init__.py
+++ b/mathics/builtin/files_io/__init__.py
@@ -2,6 +2,7 @@
 Input/Output, Files, and Filesystem
 
 """
+
 # Note: everything in this module is not loaded if environment
 # variable ENABLE_FILES_MODULE is False.  Here we do not want to
 # include any built-in commands that can write to the filesystem.
diff --git a/mathics/builtin/image/base.py b/mathics/builtin/image/base.py
index 2d8ce7756..6274f7e27 100644
--- a/mathics/builtin/image/base.py
+++ b/mathics/builtin/image/base.py
@@ -1,6 +1,7 @@
 """
 Base classes for Image Manipulation
 """
+
 from typing import Tuple
 
 import numpy
diff --git a/mathics/builtin/image/composition.py b/mathics/builtin/image/composition.py
index b5051425e..7aedb542f 100644
--- a/mathics/builtin/image/composition.py
+++ b/mathics/builtin/image/composition.py
@@ -1,6 +1,7 @@
 """
 Image Compositions
 """
+
 import os.path as osp
 from collections import defaultdict
 
diff --git a/mathics/builtin/image/pixel.py b/mathics/builtin/image/pixel.py
index b7b58573b..1fdd330fa 100644
--- a/mathics/builtin/image/pixel.py
+++ b/mathics/builtin/image/pixel.py
@@ -1,6 +1,7 @@
 """
 Pixel Operations
 """
+
 import numpy
 
 from mathics.builtin.image.base import Image
diff --git a/mathics/builtin/image/structure.py b/mathics/builtin/image/structure.py
index 95cd65548..fe9faaa91 100644
--- a/mathics/builtin/image/structure.py
+++ b/mathics/builtin/image/structure.py
@@ -1,6 +1,7 @@
 """
 Operations on Image Structure
 """
+
 import numpy
 
 from mathics.builtin.image.base import Image
diff --git a/mathics/builtin/image/test.py b/mathics/builtin/image/test.py
index 62945df64..f5b60d53d 100644
--- a/mathics/builtin/image/test.py
+++ b/mathics/builtin/image/test.py
@@ -1,6 +1,7 @@
 """
 Image testing
 """
+
 from mathics.builtin.image.base import Image, skimage_requires
 from mathics.core.builtin import Test
 
diff --git a/mathics/builtin/list/math.py b/mathics/builtin/list/math.py
index 8f1d84c10..b6a27a711 100644
--- a/mathics/builtin/list/math.py
+++ b/mathics/builtin/list/math.py
@@ -1,6 +1,7 @@
 """
 Math & Counting Operations on Lists
 """
+
 import heapq
 
 from mathics.core.builtin import Builtin, CountableInteger, NegativeIntegerException
diff --git a/mathics/builtin/procedural.py b/mathics/builtin/procedural.py
index fc0e6e712..be420bfbd 100644
--- a/mathics/builtin/procedural.py
+++ b/mathics/builtin/procedural.py
@@ -487,6 +487,7 @@ class Interrupt(Builtin):
      | a
      = $Aborted
     """
+
     has_side_effects = True
 
     # Set checking that the no arguments are allowed.
diff --git a/mathics/builtin/scoping.py b/mathics/builtin/scoping.py
index 2d7202a5f..1b50f9aeb 100644
--- a/mathics/builtin/scoping.py
+++ b/mathics/builtin/scoping.py
@@ -129,6 +129,7 @@ class BeginPackage(Builtin):
     ## >> BeginPackage["test`"]
     ##  = test`
     """
+
     has_side_effects = True
     messages = {"unimpl": "The second argument to BeginPackage is not yet implemented."}
 
@@ -387,6 +388,7 @@ class EndPackage(Builtin):
     After 'EndPackage', the values of '\$Context' and '\$ContextPath' at the \
     time of the 'BeginPackage' call are restored, with the new package\'s context prepended to '\$ContextPath'.
     """
+
     has_side_effects = True
     messages = {
         "noctx": "No previous context defined.",
diff --git a/mathics/builtin/specialfns/orthogonal.py b/mathics/builtin/specialfns/orthogonal.py
index 4925a2f09..ef0354a48 100644
--- a/mathics/builtin/specialfns/orthogonal.py
+++ b/mathics/builtin/specialfns/orthogonal.py
@@ -6,7 +6,6 @@
 https://dlmf.nist.gov/18.3</url>.
 """
 
-
 from mathics.core.atoms import Integer0
 from mathics.core.builtin import MPMathFunction
 
diff --git a/mathics/builtin/statistics/base.py b/mathics/builtin/statistics/base.py
index 8ab72cd74..baf0c94c1 100644
--- a/mathics/builtin/statistics/base.py
+++ b/mathics/builtin/statistics/base.py
@@ -1,6 +1,7 @@
 """
 Base classes for Descriptive Statistics
 """
+
 from mathics.core.builtin import Builtin
 from mathics.core.expression import Expression
 from mathics.core.list import ListExpression
diff --git a/mathics/builtin/string/__init__.py b/mathics/builtin/string/__init__.py
index d9abdaad9..c49df12e1 100644
--- a/mathics/builtin/string/__init__.py
+++ b/mathics/builtin/string/__init__.py
@@ -2,4 +2,5 @@
 Strings and Characters
 
 """
+
 # FIXME: Redo. This is a Tech note, not a Guide Section.
diff --git a/mathics/builtin/string/patterns.py b/mathics/builtin/string/patterns.py
index 648caf6ce..92bf302db 100644
--- a/mathics/builtin/string/patterns.py
+++ b/mathics/builtin/string/patterns.py
@@ -57,6 +57,7 @@ class EndOfLine(Builtin):
      . def,
      . hij}
     """
+
     summary_text = "a string pattern matching EOF"
 
 
@@ -146,6 +147,7 @@ class StartOfString(Builtin):
      = cba
      . abb
     """
+
     summary_text = "start of a whole string"
 
 
@@ -312,4 +314,5 @@ class WordCharacter(Builtin):
     >> StringMatchQ["$b;123", WordCharacter..]
      = False
     """
+
     summary_text = "letter or digit"
diff --git a/mathics/builtin/symbolic_history/__init__.py b/mathics/builtin/symbolic_history/__init__.py
index afc5a13bd..b8c63d722 100644
--- a/mathics/builtin/symbolic_history/__init__.py
+++ b/mathics/builtin/symbolic_history/__init__.py
@@ -3,4 +3,5 @@
 
 In order to debug and understand program execution, the execution history can be saved.
 """
+
 sort_order = "mathics.builtin.symbolic-execution-history"
diff --git a/mathics/builtin/testing_expressions/expression_tests.py b/mathics/builtin/testing_expressions/expression_tests.py
index bee098e46..7cead39ee 100644
--- a/mathics/builtin/testing_expressions/expression_tests.py
+++ b/mathics/builtin/testing_expressions/expression_tests.py
@@ -1,6 +1,7 @@
 """
 Expression Tests
 """
+
 from mathics.core.atoms import Integer0, Integer1, IntegerM1
 from mathics.core.builtin import Builtin, PatternError, Test
 from mathics.core.evaluation import Evaluation
diff --git a/mathics/builtin/testing_expressions/numerical_properties.py b/mathics/builtin/testing_expressions/numerical_properties.py
index 0cb3fd8a7..7c9356822 100644
--- a/mathics/builtin/testing_expressions/numerical_properties.py
+++ b/mathics/builtin/testing_expressions/numerical_properties.py
@@ -1,6 +1,7 @@
 """
 Numerical Properties
 """
+
 from itertools import combinations
 
 import sympy
diff --git a/mathics/core/convert/function.py b/mathics/core/convert/function.py
index d75b3e301..5d249f784 100644
--- a/mathics/core/convert/function.py
+++ b/mathics/core/convert/function.py
@@ -196,7 +196,7 @@ def expression_to_callable_and_args(
         CompileError as LambdifyCompileError,
         lambdify_compile,
     )
-    
+
     args = collect_args(vars)
 
     # If vectorize is requested, first, try to lambdify the expression:
diff --git a/mathics/core/convert/regex.py b/mathics/core/convert/regex.py
index 0e468961e..2987f3e27 100644
--- a/mathics/core/convert/regex.py
+++ b/mathics/core/convert/regex.py
@@ -1,6 +1,7 @@
 """
 Convert expressions to Python regular expressions
 """
+
 import re
 from binascii import hexlify
 from typing import Callable, Optional

From dc91eedc94203fb026300aff5406768e58600aab Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Mon, 15 Dec 2025 00:05:41 -0300
Subject: [PATCH 10/15] isort

---
 mathics/builtin/compilation.py   | 1 -
 mathics/core/convert/function.py | 1 -
 mathics/core/convert/lambdify.py | 2 --
 3 files changed, 4 deletions(-)

diff --git a/mathics/builtin/compilation.py b/mathics/builtin/compilation.py
index 1d7b4255c..ac8ad3aca 100644
--- a/mathics/builtin/compilation.py
+++ b/mathics/builtin/compilation.py
@@ -18,7 +18,6 @@
     A_PROTECTED,
     A_READ_PROTECTED,
 )
-
 from mathics.core.builtin import Builtin
 from mathics.core.convert.expression import to_mathics_list
 from mathics.core.convert.function import (
diff --git a/mathics/core/convert/function.py b/mathics/core/convert/function.py
index 5d249f784..c64b028c8 100644
--- a/mathics/core/convert/function.py
+++ b/mathics/core/convert/function.py
@@ -3,7 +3,6 @@
 
 import numpy
 
-
 from mathics.core.definitions import SIDE_EFFECT_BUILTINS, Definition
 from mathics.core.evaluation import Evaluation
 from mathics.core.expression import Expression, from_python
diff --git a/mathics/core/convert/lambdify.py b/mathics/core/convert/lambdify.py
index 9a633a15e..82db5a109 100644
--- a/mathics/core/convert/lambdify.py
+++ b/mathics/core/convert/lambdify.py
@@ -18,11 +18,9 @@
 import scipy
 import sympy
 
-
 from mathics.core.convert.function import evaluate_without_side_effects
 from mathics.core.convert.sympy import SympyExpression
 from mathics.core.symbols import strip_context, sympy_strip_context
-
 from mathics.core.util import print_expression_tree, print_sympy_tree
 
 

From af8fb0a2b695922b3add9fe6168357773a732c66 Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Mon, 15 Dec 2025 00:06:53 -0300
Subject: [PATCH 11/15] more black

---
 test/builtin/test-optimization.py | 1 +
 test/core/test_pattern.py         | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/builtin/test-optimization.py b/test/builtin/test-optimization.py
index 8d2d68d32..66e0ace34 100644
--- a/test/builtin/test-optimization.py
+++ b/test/builtin/test-optimization.py
@@ -7,6 +7,7 @@
 
 
 """
+
 from test.helper import check_evaluation
 
 import pytest
diff --git a/test/core/test_pattern.py b/test/core/test_pattern.py
index 75997b493..46847a2ce 100644
--- a/test/core/test_pattern.py
+++ b/test/core/test_pattern.py
@@ -5,7 +5,6 @@
 expressions.
 """
 
-
 from test.helper import check_evaluation, session
 
 import pytest

From 88d07dae5543eaf86e0ae478d64a451cef1533f0 Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Mon, 15 Dec 2025 07:46:17 -0300
Subject: [PATCH 12/15] black

---
 mathics/doc/gather.py                       |  6 +++---
 mathics/eval/assignments/assign_binaryop.py |  1 +
 mathics/eval/drawing/util.py                |  2 --
 mathics/eval/scoping.py                     |  1 +
 mathics/eval/strings.py                     |  1 +
 mathics/format/text.py                      | 16 +++++++++-------
 6 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/mathics/doc/gather.py b/mathics/doc/gather.py
index 7da4ed0e1..319c82dbe 100644
--- a/mathics/doc/gather.py
+++ b/mathics/doc/gather.py
@@ -357,7 +357,7 @@ def sorted_modules(modules) -> list:
     exists, or the module's name if not."""
     return sorted(
         modules,
-        key=lambda module: module.sort_order
-        if hasattr(module, "sort_order")
-        else module.__name__,
+        key=lambda module: (
+            module.sort_order if hasattr(module, "sort_order") else module.__name__
+        ),
     )
diff --git a/mathics/eval/assignments/assign_binaryop.py b/mathics/eval/assignments/assign_binaryop.py
index 318e187c7..9b3be0565 100644
--- a/mathics/eval/assignments/assign_binaryop.py
+++ b/mathics/eval/assignments/assign_binaryop.py
@@ -2,6 +2,7 @@
 evaluation functions associated with the mathics.builtin.assign_binary_op
 module.
 """
+
 from mathics.core.evaluation import Evaluation
 from mathics.core.expression import Expression
 from mathics.core.systemsymbols import SymbolSet
diff --git a/mathics/eval/drawing/util.py b/mathics/eval/drawing/util.py
index d6e5c8ec4..99ab780bb 100644
--- a/mathics/eval/drawing/util.py
+++ b/mathics/eval/drawing/util.py
@@ -2,7 +2,6 @@
 Common utilities for plotting
 """
 
-
 from mathics.core.atoms import NumericArray
 from mathics.core.convert.expression import to_expression, to_mathics_list
 from mathics.core.expression import Expression
@@ -23,7 +22,6 @@
 # TODO: this will be extended with support for GraphicsComplex in a
 # subsequent PR, which may involve a little more refactoring
 class GraphicsGenerator:
-
     """
     Support for generating Graphics and Graphics3D expressions
     """
diff --git a/mathics/eval/scoping.py b/mathics/eval/scoping.py
index eba2bb63b..bc63393f6 100644
--- a/mathics/eval/scoping.py
+++ b/mathics/eval/scoping.py
@@ -1,6 +1,7 @@
 """
 Evaluation module corresponding to builtin functions in mathics.builtins.scoping.
 """
+
 import re
 
 from mathics.core.atoms import String
diff --git a/mathics/eval/strings.py b/mathics/eval/strings.py
index 96a73a2c4..c17b84e3e 100644
--- a/mathics/eval/strings.py
+++ b/mathics/eval/strings.py
@@ -1,6 +1,7 @@
 """
 String-related evaluation functions.
 """
+
 import re
 
 from mathics.core.atoms import Integer1, Integer3, String
diff --git a/mathics/format/text.py b/mathics/format/text.py
index 422ce940a..0f51b5eb8 100644
--- a/mathics/format/text.py
+++ b/mathics/format/text.py
@@ -72,13 +72,15 @@ def gridbox(self, elements=None, **box_options) -> str:
         widths = [0]
 
     cells = [
-        [
-            # TODO: check if this evaluation is necessary.
-            boxes_to_text(item, **box_options).splitlines()
-            for item in row
-        ]
-        if isinstance(row, tuple)
-        else [boxes_to_text(row, **box_options).splitlines()]
+        (
+            [
+                # TODO: check if this evaluation is necessary.
+                boxes_to_text(item, **box_options).splitlines()
+                for item in row
+            ]
+            if isinstance(row, tuple)
+            else [boxes_to_text(row, **box_options).splitlines()]
+        )
         for row in items
     ]
 

From a95b65f463939cd20a8881ac5b77bffb51088bae Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Mon, 15 Dec 2025 07:55:40 -0300
Subject: [PATCH 13/15] revert trivial changes

---
 mathics/builtin/directories/__init__.py                     | 1 -
 mathics/builtin/exp_structure/size_and_sig.py               | 1 -
 mathics/builtin/file_operations/__init__.py                 | 1 -
 mathics/builtin/files_io/__init__.py                        | 1 -
 mathics/builtin/image/base.py                               | 1 -
 mathics/builtin/image/composition.py                        | 1 -
 mathics/builtin/image/pixel.py                              | 1 -
 mathics/builtin/image/structure.py                          | 1 -
 mathics/builtin/image/test.py                               | 1 -
 mathics/builtin/list/math.py                                | 1 -
 mathics/builtin/specialfns/orthogonal.py                    | 1 +
 mathics/builtin/statistics/base.py                          | 1 -
 mathics/builtin/string/__init__.py                          | 1 -
 mathics/builtin/string/patterns.py                          | 3 ---
 mathics/builtin/symbolic_history/__init__.py                | 1 -
 mathics/builtin/testing_expressions/expression_tests.py     | 1 -
 mathics/builtin/testing_expressions/numerical_properties.py | 1 -
 mathics/core/convert/regex.py                               | 1 -
 mathics/eval/assignments/assign_binaryop.py                 | 1 -
 mathics/eval/drawing/util.py                                | 2 ++
 mathics/eval/scoping.py                                     | 2 --
 mathics/eval/strings.py                                     | 1 -
 22 files changed, 3 insertions(+), 23 deletions(-)

diff --git a/mathics/builtin/directories/__init__.py b/mathics/builtin/directories/__init__.py
index a17fc9441..b7bf1f9e4 100644
--- a/mathics/builtin/directories/__init__.py
+++ b/mathics/builtin/directories/__init__.py
@@ -1,7 +1,6 @@
 """
 Directories and Directory Operations
 """
-
 # Note: everything in this module is not loaded if environment
 # variable ENABLE_FILES_MODULE is False.  Here we do not want to
 # include any built-in commands that can write to the filesytesm.
diff --git a/mathics/builtin/exp_structure/size_and_sig.py b/mathics/builtin/exp_structure/size_and_sig.py
index 075499752..b06cede7f 100644
--- a/mathics/builtin/exp_structure/size_and_sig.py
+++ b/mathics/builtin/exp_structure/size_and_sig.py
@@ -1,7 +1,6 @@
 """
 Expression Sizes and Signatures
 """
-
 import hashlib
 import platform
 import zlib
diff --git a/mathics/builtin/file_operations/__init__.py b/mathics/builtin/file_operations/__init__.py
index 5d05c229f..c69d15343 100644
--- a/mathics/builtin/file_operations/__init__.py
+++ b/mathics/builtin/file_operations/__init__.py
@@ -1,7 +1,6 @@
 """
 File Operations
 """
-
 # Note: everything in this module is not loaded if environment
 # variable ENABLE_FILES_MODULE is False.  Here we do not want to
 # include any built-in commands that can write to the filesytesm.
diff --git a/mathics/builtin/files_io/__init__.py b/mathics/builtin/files_io/__init__.py
index c06a44c84..82b851411 100644
--- a/mathics/builtin/files_io/__init__.py
+++ b/mathics/builtin/files_io/__init__.py
@@ -2,7 +2,6 @@
 Input/Output, Files, and Filesystem
 
 """
-
 # Note: everything in this module is not loaded if environment
 # variable ENABLE_FILES_MODULE is False.  Here we do not want to
 # include any built-in commands that can write to the filesystem.
diff --git a/mathics/builtin/image/base.py b/mathics/builtin/image/base.py
index 6274f7e27..2d8ce7756 100644
--- a/mathics/builtin/image/base.py
+++ b/mathics/builtin/image/base.py
@@ -1,7 +1,6 @@
 """
 Base classes for Image Manipulation
 """
-
 from typing import Tuple
 
 import numpy
diff --git a/mathics/builtin/image/composition.py b/mathics/builtin/image/composition.py
index 7aedb542f..b5051425e 100644
--- a/mathics/builtin/image/composition.py
+++ b/mathics/builtin/image/composition.py
@@ -1,7 +1,6 @@
 """
 Image Compositions
 """
-
 import os.path as osp
 from collections import defaultdict
 
diff --git a/mathics/builtin/image/pixel.py b/mathics/builtin/image/pixel.py
index 1fdd330fa..b7b58573b 100644
--- a/mathics/builtin/image/pixel.py
+++ b/mathics/builtin/image/pixel.py
@@ -1,7 +1,6 @@
 """
 Pixel Operations
 """
-
 import numpy
 
 from mathics.builtin.image.base import Image
diff --git a/mathics/builtin/image/structure.py b/mathics/builtin/image/structure.py
index fe9faaa91..95cd65548 100644
--- a/mathics/builtin/image/structure.py
+++ b/mathics/builtin/image/structure.py
@@ -1,7 +1,6 @@
 """
 Operations on Image Structure
 """
-
 import numpy
 
 from mathics.builtin.image.base import Image
diff --git a/mathics/builtin/image/test.py b/mathics/builtin/image/test.py
index f5b60d53d..62945df64 100644
--- a/mathics/builtin/image/test.py
+++ b/mathics/builtin/image/test.py
@@ -1,7 +1,6 @@
 """
 Image testing
 """
-
 from mathics.builtin.image.base import Image, skimage_requires
 from mathics.core.builtin import Test
 
diff --git a/mathics/builtin/list/math.py b/mathics/builtin/list/math.py
index b6a27a711..8f1d84c10 100644
--- a/mathics/builtin/list/math.py
+++ b/mathics/builtin/list/math.py
@@ -1,7 +1,6 @@
 """
 Math & Counting Operations on Lists
 """
-
 import heapq
 
 from mathics.core.builtin import Builtin, CountableInteger, NegativeIntegerException
diff --git a/mathics/builtin/specialfns/orthogonal.py b/mathics/builtin/specialfns/orthogonal.py
index ef0354a48..4925a2f09 100644
--- a/mathics/builtin/specialfns/orthogonal.py
+++ b/mathics/builtin/specialfns/orthogonal.py
@@ -6,6 +6,7 @@
 https://dlmf.nist.gov/18.3</url>.
 """
 
+
 from mathics.core.atoms import Integer0
 from mathics.core.builtin import MPMathFunction
 
diff --git a/mathics/builtin/statistics/base.py b/mathics/builtin/statistics/base.py
index baf0c94c1..8ab72cd74 100644
--- a/mathics/builtin/statistics/base.py
+++ b/mathics/builtin/statistics/base.py
@@ -1,7 +1,6 @@
 """
 Base classes for Descriptive Statistics
 """
-
 from mathics.core.builtin import Builtin
 from mathics.core.expression import Expression
 from mathics.core.list import ListExpression
diff --git a/mathics/builtin/string/__init__.py b/mathics/builtin/string/__init__.py
index c49df12e1..d9abdaad9 100644
--- a/mathics/builtin/string/__init__.py
+++ b/mathics/builtin/string/__init__.py
@@ -2,5 +2,4 @@
 Strings and Characters
 
 """
-
 # FIXME: Redo. This is a Tech note, not a Guide Section.
diff --git a/mathics/builtin/string/patterns.py b/mathics/builtin/string/patterns.py
index 92bf302db..648caf6ce 100644
--- a/mathics/builtin/string/patterns.py
+++ b/mathics/builtin/string/patterns.py
@@ -57,7 +57,6 @@ class EndOfLine(Builtin):
      . def,
      . hij}
     """
-
     summary_text = "a string pattern matching EOF"
 
 
@@ -147,7 +146,6 @@ class StartOfString(Builtin):
      = cba
      . abb
     """
-
     summary_text = "start of a whole string"
 
 
@@ -314,5 +312,4 @@ class WordCharacter(Builtin):
     >> StringMatchQ["$b;123", WordCharacter..]
      = False
     """
-
     summary_text = "letter or digit"
diff --git a/mathics/builtin/symbolic_history/__init__.py b/mathics/builtin/symbolic_history/__init__.py
index b8c63d722..afc5a13bd 100644
--- a/mathics/builtin/symbolic_history/__init__.py
+++ b/mathics/builtin/symbolic_history/__init__.py
@@ -3,5 +3,4 @@
 
 In order to debug and understand program execution, the execution history can be saved.
 """
-
 sort_order = "mathics.builtin.symbolic-execution-history"
diff --git a/mathics/builtin/testing_expressions/expression_tests.py b/mathics/builtin/testing_expressions/expression_tests.py
index 7cead39ee..bee098e46 100644
--- a/mathics/builtin/testing_expressions/expression_tests.py
+++ b/mathics/builtin/testing_expressions/expression_tests.py
@@ -1,7 +1,6 @@
 """
 Expression Tests
 """
-
 from mathics.core.atoms import Integer0, Integer1, IntegerM1
 from mathics.core.builtin import Builtin, PatternError, Test
 from mathics.core.evaluation import Evaluation
diff --git a/mathics/builtin/testing_expressions/numerical_properties.py b/mathics/builtin/testing_expressions/numerical_properties.py
index 7c9356822..0cb3fd8a7 100644
--- a/mathics/builtin/testing_expressions/numerical_properties.py
+++ b/mathics/builtin/testing_expressions/numerical_properties.py
@@ -1,7 +1,6 @@
 """
 Numerical Properties
 """
-
 from itertools import combinations
 
 import sympy
diff --git a/mathics/core/convert/regex.py b/mathics/core/convert/regex.py
index 2987f3e27..0e468961e 100644
--- a/mathics/core/convert/regex.py
+++ b/mathics/core/convert/regex.py
@@ -1,7 +1,6 @@
 """
 Convert expressions to Python regular expressions
 """
-
 import re
 from binascii import hexlify
 from typing import Callable, Optional
diff --git a/mathics/eval/assignments/assign_binaryop.py b/mathics/eval/assignments/assign_binaryop.py
index 9b3be0565..318e187c7 100644
--- a/mathics/eval/assignments/assign_binaryop.py
+++ b/mathics/eval/assignments/assign_binaryop.py
@@ -2,7 +2,6 @@
 evaluation functions associated with the mathics.builtin.assign_binary_op
 module.
 """
-
 from mathics.core.evaluation import Evaluation
 from mathics.core.expression import Expression
 from mathics.core.systemsymbols import SymbolSet
diff --git a/mathics/eval/drawing/util.py b/mathics/eval/drawing/util.py
index 99ab780bb..d6e5c8ec4 100644
--- a/mathics/eval/drawing/util.py
+++ b/mathics/eval/drawing/util.py
@@ -2,6 +2,7 @@
 Common utilities for plotting
 """
 
+
 from mathics.core.atoms import NumericArray
 from mathics.core.convert.expression import to_expression, to_mathics_list
 from mathics.core.expression import Expression
@@ -22,6 +23,7 @@
 # TODO: this will be extended with support for GraphicsComplex in a
 # subsequent PR, which may involve a little more refactoring
 class GraphicsGenerator:
+
     """
     Support for generating Graphics and Graphics3D expressions
     """
diff --git a/mathics/eval/scoping.py b/mathics/eval/scoping.py
index bc63393f6..6579c24de 100644
--- a/mathics/eval/scoping.py
+++ b/mathics/eval/scoping.py
@@ -1,7 +1,6 @@
 """
 Evaluation module corresponding to builtin functions in mathics.builtins.scoping.
 """
-
 import re
 
 from mathics.core.atoms import String
@@ -17,7 +16,6 @@ def dynamic_scoping(func, vars, evaluation: Evaluation):
     and evaluates func(evaluation)
     """
     original_definitions = {}
-
     for var_name, new_def in vars.items():
         assert fully_qualified_symbol_name(var_name)
         original_definitions[var_name] = evaluation.definitions.get_user_definition(
diff --git a/mathics/eval/strings.py b/mathics/eval/strings.py
index c17b84e3e..96a73a2c4 100644
--- a/mathics/eval/strings.py
+++ b/mathics/eval/strings.py
@@ -1,7 +1,6 @@
 """
 String-related evaluation functions.
 """
-
 import re
 
 from mathics.core.atoms import Integer1, Integer3, String

From 2ebd8efcc9fed5b57a2e674964494d11a2a5d736 Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Mon, 15 Dec 2025 08:04:56 -0300
Subject: [PATCH 14/15] restore graphics3d.py

---
 mathics/builtin/drawing/graphics3d.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/mathics/builtin/drawing/graphics3d.py b/mathics/builtin/drawing/graphics3d.py
index 52daa2dc3..5caa0b1c3 100644
--- a/mathics/builtin/drawing/graphics3d.py
+++ b/mathics/builtin/drawing/graphics3d.py
@@ -107,7 +107,6 @@ class Graphics3D(Graphics):
          . draw(((1,1,-1)--(1,1,1)), rgb(0.4, 0.4, 0.4)+linewidth(1));
          . \end{asy}
     """
-
     summary_text = "a three-dimensional graphics image wrapper"
     options = Graphics.options.copy()
     options.update(
@@ -173,9 +172,11 @@ class Graphics3DElements(_GraphicsElements):
     def __init__(self, content, evaluation, neg_y=False):
         super(Graphics3DElements, self).__init__(content, evaluation)
         self.neg_y = neg_y
-        self.xmin = self.ymin = self.pixel_width = self.pixel_height = (
-            self.extent_width
-        ) = self.extent_height = None
+        self.xmin = (
+            self.ymin
+        ) = (
+            self.pixel_width
+        ) = self.pixel_height = self.extent_width = self.extent_height = None
         self.view_width = None
         self.content = content
 

From 1e1e02bc13a37bc0f44f2e244095cab09f2d00d6 Mon Sep 17 00:00:00 2001
From: Juan Mauricio Matera <matera@fisica.unlp.edu.ar>
Date: Mon, 15 Dec 2025 08:06:32 -0300
Subject: [PATCH 15/15] more on restoring trivial changes

---
 mathics/builtin/box/__init__.py   |  1 -
 mathics/doc/gather.py             |  6 +++---
 mathics/format/text.py            | 16 +++++++---------
 test/builtin/test-optimization.py |  1 -
 test/core/test_pattern.py         |  1 +
 5 files changed, 11 insertions(+), 14 deletions(-)

diff --git a/mathics/builtin/box/__init__.py b/mathics/builtin/box/__init__.py
index 8275c12be..5d2777e44 100644
--- a/mathics/builtin/box/__init__.py
+++ b/mathics/builtin/box/__init__.py
@@ -6,6 +6,5 @@
 Boxing information like bounding-box width and size makes it easier for formatters to do
 layout without having to know the intricacies of what is inside the box.
 """
-
 # Docs are not yet ready for prime time. Maybe after release 6.0.0.
 no_doc = True
diff --git a/mathics/doc/gather.py b/mathics/doc/gather.py
index 319c82dbe..7da4ed0e1 100644
--- a/mathics/doc/gather.py
+++ b/mathics/doc/gather.py
@@ -357,7 +357,7 @@ def sorted_modules(modules) -> list:
     exists, or the module's name if not."""
     return sorted(
         modules,
-        key=lambda module: (
-            module.sort_order if hasattr(module, "sort_order") else module.__name__
-        ),
+        key=lambda module: module.sort_order
+        if hasattr(module, "sort_order")
+        else module.__name__,
     )
diff --git a/mathics/format/text.py b/mathics/format/text.py
index 0f51b5eb8..422ce940a 100644
--- a/mathics/format/text.py
+++ b/mathics/format/text.py
@@ -72,15 +72,13 @@ def gridbox(self, elements=None, **box_options) -> str:
         widths = [0]
 
     cells = [
-        (
-            [
-                # TODO: check if this evaluation is necessary.
-                boxes_to_text(item, **box_options).splitlines()
-                for item in row
-            ]
-            if isinstance(row, tuple)
-            else [boxes_to_text(row, **box_options).splitlines()]
-        )
+        [
+            # TODO: check if this evaluation is necessary.
+            boxes_to_text(item, **box_options).splitlines()
+            for item in row
+        ]
+        if isinstance(row, tuple)
+        else [boxes_to_text(row, **box_options).splitlines()]
         for row in items
     ]
 
diff --git a/test/builtin/test-optimization.py b/test/builtin/test-optimization.py
index 66e0ace34..8d2d68d32 100644
--- a/test/builtin/test-optimization.py
+++ b/test/builtin/test-optimization.py
@@ -7,7 +7,6 @@
 
 
 """
-
 from test.helper import check_evaluation
 
 import pytest
diff --git a/test/core/test_pattern.py b/test/core/test_pattern.py
index 46847a2ce..75997b493 100644
--- a/test/core/test_pattern.py
+++ b/test/core/test_pattern.py
@@ -5,6 +5,7 @@
 expressions.
 """
 
+
 from test.helper import check_evaluation, session
 
 import pytest