gotranx 2.0.0__tar.gz → 2.2.0__tar.gz

{gotranx-2.0.0/src/gotranx.egg-info → gotranx-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gotranx
-Version: 2.0.0
+Version: 2.2.0
 Summary: A declarative language describing ordinary differential equations
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -47,6 +47,7 @@ Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
 Requires-Dist: jax; extra == "test"
 Requires-Dist: cmake; extra == "test"
+Requires-Dist: fenics-ufl; extra == "test"
 Requires-Dist: gotranx[formatters]; extra == "test"
 Provides-Extra: benchmark
 Requires-Dist: pytest-benchmark>=4.0.0; extra == "benchmark"

{gotranx-2.0.0 → gotranx-2.2.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gotranx"
-version = "2.0.0"
+version = "2.2.0"
 description = "A declarative language describing ordinary differential equations"
 authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
 license = {text = "MIT"}
@@ -62,6 +62,7 @@ test = [
     "pytest-cov",
     "jax",
     "cmake",
+    "fenics-ufl",
     "gotranx[formatters]",
 ]
 benchmark = [
@@ -171,7 +172,7 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "2.0.0"
+current_version = "2.2.0"
 
 
 [[tool.bumpversion.files]]

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/atoms.py

@@ -192,53 +192,6 @@ class Expression:
         return build_expression(self.tree, symbols=symbols)
 
 
-@attr.s(frozen=True, kw_only=True, slots=True)
-class Singularity:
-    symbol: sp.Symbol = attr.ib()
-    value: float | sp.core.Number = attr.ib()
-    replacement: sp.Expr = attr.ib()
-
-    @property
-    def is_infinite(self):
-        """Return True if the replacement is potentially infinite"""
-        return self.replacement.has(sp.oo) or self.replacement.has(-sp.oo)
-
-
-def remove_singularities(expr: sp.Expr, singularities: frozenset[Singularity]) -> sp.Expr:
-    """Remove singularities from an expression recursively using Conditionals
-
-    Parameters
-    ----------
-    expr : sp.Expr
-        The expression
-    singularities : frozenset[Singularity]
-        The singularities
-
-    Returns
-    -------
-    sp.Expr
-        The expression with singularities removed
-    """
-    from .sympytools import Conditional
-
-    exprs = [
-        Conditional(
-            cond=sp.Eq(singularity.symbol, singularity.value),
-            true_value=singularity.replacement,
-            false_value=expr,
-        )
-        for singularity in singularities
-        if not singularity.is_infinite
-    ]
-    if len(exprs) == 0:
-        logger.debug("No singularities to remove")
-        return expr
-
-    new_expr = sp.piecewise_fold(sum(exprs))
-    logger.debug("Removing singularities", new_expr=new_expr)
-    return new_expr
-
-
 @attr.s(frozen=True, kw_only=True, slots=True)
 class Assignment(Atom):
     """Assignments are object of the form `name = value`."""
@@ -266,79 +219,6 @@ class Assignment(Atom):
                 return True
         return False
 
-    def singularities(self, lookup: dict[str, Atom]) -> frozenset[Singularity]:
-        """Check if the expression has any singularities
-        and return a list of singularities"""
-        from sympy import singularities, limit
-
-        singularity_list: set[Singularity] = set()
-        if self.value is None:
-            return frozenset(singularity_list)
-        if self.expr == 0:
-            logger.warning(
-                f"Expression {self.name} is zero. Maybe you forgot to resolve the expression?"
-            )
-            return frozenset(singularity_list)
-
-        for dep in self.value.dependencies:
-            try:
-                var = lookup[dep]
-            except KeyError:
-                continue
-
-            if not var.is_stateful(lookup):
-                continue
-
-            values = singularities(self.expr, var.symbol)
-
-            if not values:
-                continue
-
-            if not isinstance(values, sp.sets.sets.FiniteSet):
-                continue
-
-            for value in values:
-                singularity_list.add(
-                    Singularity(
-                        symbol=var.symbol,
-                        value=value,
-                        replacement=limit(self.expr, var.symbol, value),
-                    )
-                )
-        return frozenset(singularity_list)
-
-    def remove_singularities(self, lookup: dict[str, Atom]) -> Assignment:
-        """Remove singularities from the assignment
-
-        Parameters
-        ----------
-        lookup : dict[str, Atom]
-            A lookup table for atoms
-
-        Returns
-        -------
-        Assignment
-            A new assignment with singularities removed
-        """
-        logger.debug("Removing singularities")
-        if singularities := self.singularities(lookup):
-            logger.debug("Singularities found", singularities=singularities)
-            new_expr = remove_singularities(self.expr, singularities)
-            return type(self)(
-                name=self.name,
-                value=self.value,
-                components=self.components,
-                unit_str=self.unit_str,
-                unit=self.unit,
-                expr=new_expr,
-                symbol=self.symbol,
-                description=self.description,
-                comment=self.comment,
-            )
-
-        # Do not make a copy if no singularities
-        return self
-
     def resolve_expression(self, symbols: dict[str, sp.Symbol]) -> Assignment:
         """Resolve the expression of the assignment by
         building the sympy expression from the expression tree

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/cli/__init__.py

@@ -78,6 +78,14 @@ def convert(
         "--remove-unused",
         help="Remove unused variables",
     ),
+    remove_singularities: bool = typer.Option(
+        True,
+        "--remove-singularities/--no-remove-singularities",
+        help=(
+            "Replace a small neighborhood of every removable singularity "
+            "(e.g. x/(exp(x) - 1) at x = 0) with a truncated Taylor series"
+        ),
+    ),
     jax: bool = typer.Option(
         False,
         "--jax",
@@ -148,6 +156,7 @@ def convert(
             outname=outname,
             scheme=scheme,
             remove_unused=remove_unused,
+            remove_singularities=remove_singularities,
             verbose=verbose,
             stiff_states=stiff_states,
             delta=delta,
@@ -160,6 +169,7 @@ def convert(
             outname=outname,
             scheme=scheme,
             remove_unused=remove_unused,
+            remove_singularities=remove_singularities,
             verbose=verbose,
             stiff_states=stiff_states,
             delta=delta,
@@ -302,6 +312,14 @@ def ode2py(
         "--remove-unused",
         help="Remove unused variables",
     ),
+    remove_singularities: bool = typer.Option(
+        True,
+        "--remove-singularities/--no-remove-singularities",
+        help=(
+            "Replace a small neighborhood of every removable singularity "
+            "(e.g. x/(exp(x) - 1) at x = 0) with a truncated Taylor series"
+        ),
+    ),
     version: bool = typer.Option(
         None,
         "--version",
@@ -376,6 +394,9 @@ def ode2py(
     delta = config_data.get("delta", delta)
     stiff_states = config_data.get("stiff_states", stiff_states)
     cse = utils.validate_cse(config_data.get("cse", cse))
+    remove_singularities = utils.validate_remove_singularities(
+        config_data.get("remove_singularities", remove_singularities)
+    )
     scheme = config_data.get("scheme", scheme)
     shape = Shape(config_data.get("shape", shape))
     scheme = utils.validate_scheme(scheme)
@@ -388,6 +409,7 @@ def ode2py(
         outname=outname,
         scheme=scheme,
         remove_unused=remove_unused,
+        remove_singularities=remove_singularities,
         verbose=verbose,
         stiff_states=stiff_states,
         delta=delta,
@@ -425,6 +447,14 @@ def ode2c(
         "--remove-unused",
         help="Remove unused variables",
     ),
+    remove_singularities: bool = typer.Option(
+        True,
+        "--remove-singularities/--no-remove-singularities",
+        help=(
+            "Replace a small neighborhood of every removable singularity "
+            "(e.g. x/(exp(x) - 1) at x = 0) with a truncated Taylor series"
+        ),
+    ),
     version: bool = typer.Option(
         None,
         "--version",
@@ -487,6 +517,9 @@ def ode2c(
     delta = config_data.get("delta", delta)
     stiff_states = config_data.get("stiff_states", stiff_states)
     cse = utils.validate_cse(config_data.get("cse", cse))
+    remove_singularities = utils.validate_remove_singularities(
+        config_data.get("remove_singularities", remove_singularities)
+    )
     scheme = config_data.get("scheme", scheme)
     scheme = utils.validate_scheme(scheme)
     c_config = config_data.get("c", {})
@@ -499,6 +532,7 @@ def ode2c(
         outname=outname,
         scheme=scheme,
         remove_unused=remove_unused,
+        remove_singularities=remove_singularities,
         verbose=verbose,
         stiff_states=stiff_states,
         delta=delta,
@@ -528,6 +562,14 @@ def ode2julia(
         "--remove-unused",
         help="Remove unused variables",
     ),
+    remove_singularities: bool = typer.Option(
+        True,
+        "--remove-singularities/--no-remove-singularities",
+        help=(
+            "Replace a small neighborhood of every removable singularity "
+            "(e.g. x/(exp(x) - 1) at x = 0) with a truncated Taylor series"
+        ),
+    ),
     version: bool = typer.Option(
         None,
         "--version",
@@ -595,6 +637,9 @@ def ode2julia(
     delta = config_data.get("delta", delta)
     stiff_states = config_data.get("stiff_states", stiff_states)
     cse = utils.validate_cse(config_data.get("cse", cse))
+    remove_singularities = utils.validate_remove_singularities(
+        config_data.get("remove_singularities", remove_singularities)
+    )
     scheme = config_data.get("scheme", scheme)
     scheme = utils.validate_scheme(scheme)
     # c_config = config_data.get("c", {})
@@ -605,6 +650,7 @@ def ode2julia(
         outname=outname,
         scheme=scheme,
         remove_unused=remove_unused,
+        remove_singularities=remove_singularities,
         verbose=verbose,
         stiff_states=stiff_states,
         delta=delta,
@@ -635,6 +681,14 @@ def ode2mtk(
         "--remove-unused",
         help="Remove unused variables",
     ),
+    remove_singularities: bool = typer.Option(
+        True,
+        "--remove-singularities/--no-remove-singularities",
+        help=(
+            "Replace a small neighborhood of every removable singularity "
+            "(e.g. x/(exp(x) - 1) at x = 0) with a truncated Taylor series"
+        ),
+    ),
     version: bool = typer.Option(
         None,
         "--version",
@@ -668,10 +722,14 @@ def ode2mtk(
     config_data = utils.read_config(config)
     verbose = config_data.get("verbose", verbose)
     remove_unused = config_data.get("remove_unused", remove_unused)
+    remove_singularities = utils.validate_remove_singularities(
+        config_data.get("remove_singularities", remove_singularities)
+    )
     gotran2mtk.main(
         fname=fname,
         outname=outname,
         remove_unused=remove_unused,
+        remove_singularities=remove_singularities,
         verbose=verbose,
     )
 
@@ -750,11 +808,25 @@ def ode2md(
         "--pdf",
         help="Generate PDF output",
     ),
+    remove_singularities: bool = typer.Option(
+        True,
+        "--remove-singularities/--no-remove-singularities",
+        help=(
+            "Replace a small neighborhood of every removable singularity "
+            "(e.g. x/(exp(x) - 1) at x = 0) with a truncated Taylor series"
+        ),
+    ),
 ):
     if fname is None:
         return typer.echo("No file specified")
 
-    gotran2md.main(fname=fname, outname=outname, verbose=verbose, pdf=pdf)
+    gotran2md.main(
+        fname=fname,
+        outname=outname,
+        verbose=verbose,
+        pdf=pdf,
+        remove_singularities=remove_singularities,
+    )
 
 
 @app.command()
@@ -779,6 +851,14 @@ def ode2ufl(
         "--remove-unused",
         help="Remove unused variables",
     ),
+    remove_singularities: bool = typer.Option(
+        True,
+        "--remove-singularities/--no-remove-singularities",
+        help=(
+            "Replace a small neighborhood of every removable singularity "
+            "(e.g. x/(exp(x) - 1) at x = 0) with a truncated Taylor series"
+        ),
+    ),
     version: bool = typer.Option(
         None,
         "--version",
@@ -847,6 +927,9 @@ def ode2ufl(
     delta = config_data.get("delta", delta)
     stiff_states = config_data.get("stiff_states", stiff_states)
     cse = utils.validate_cse(config_data.get("cse", cse))
+    remove_singularities = utils.validate_remove_singularities(
+        config_data.get("remove_singularities", remove_singularities)
+    )
     scheme = config_data.get("scheme", scheme)
     shape = Shape(config_data.get("shape", shape))
     scheme = utils.validate_scheme(scheme)
@@ -858,6 +941,7 @@ def ode2ufl(
         outname=outname,
         scheme=scheme,
         remove_unused=remove_unused,
+        remove_singularities=remove_singularities,
         verbose=verbose,
         stiff_states=stiff_states,
         delta=delta,

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/cli/gotran2c.py

@@ -97,6 +97,7 @@ def main(
     outname: Path | str | None = None,
     scheme: list[Scheme] | None = None,
     remove_unused: bool = False,
+    remove_singularities: bool = True,
     format: Format = Format.clang_format,
     verbose: bool = False,
     missing_values: dict[str, int] | None = None,
@@ -108,7 +109,7 @@ def main(
     structlog.configure(
         wrapper_class=structlog.make_filtering_bound_logger(loglevel),
     )
-    ode = load_ode(fname)
+    ode = load_ode(fname, remove_singularities=remove_singularities)
     code = get_code(
         ode,
         scheme=scheme,

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/cli/gotran2julia.py

@@ -97,6 +97,7 @@ def main(
     outname: Path | str | None = None,
     scheme: list[Scheme] | None = None,
     remove_unused: bool = False,
+    remove_singularities: bool = True,
     verbose: bool = False,
     missing_values: dict[str, int] | None = None,
     delta: float = 1e-8,
@@ -108,7 +109,7 @@ def main(
     structlog.configure(
         wrapper_class=structlog.make_filtering_bound_logger(loglevel),
     )
-    ode = load_ode(fname)
+    ode = load_ode(fname, remove_singularities=remove_singularities)
     code = get_code(
         ode,
         scheme=scheme,

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/cli/gotran2md.py

@@ -14,13 +14,14 @@ def main(
     outname: Path | str | None = None,
     verbose: bool = False,
     pdf: bool = False,
+    remove_singularities: bool = True,
 ) -> None:
     loglevel = logging.DEBUG if verbose else logging.INFO
     structlog.configure(
         wrapper_class=structlog.make_filtering_bound_logger(loglevel),
     )
 
-    ode = load_ode(fname)
+    ode = load_ode(fname, remove_singularities=remove_singularities)
     generator = MarkdownGenerator(ode)
     code = generator.generate()
 

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/cli/gotran2mtk.py

@@ -24,13 +24,14 @@ def main(
     fname: Path,
     outname: Path | str | None = None,
     remove_unused: bool = False,
+    remove_singularities: bool = True,
     verbose: bool = False,
 ) -> None:
     loglevel = logging.DEBUG if verbose else logging.INFO
     structlog.configure(
         wrapper_class=structlog.make_filtering_bound_logger(loglevel),
     )
-    ode = load_ode(fname)
+    ode = load_ode(fname, remove_singularities=remove_singularities)
     code = get_code(
         ode,
         remove_unused=remove_unused,

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/cli/gotran2py.py

@@ -119,6 +119,7 @@ def main(
     format: Format = Format.black,
     scheme: list[Scheme] | None = None,
     remove_unused: bool = False,
+    remove_singularities: bool = True,
     verbose: bool = True,
     stiff_states: list[str] | None = None,
     cse: bool = True,
@@ -132,7 +133,7 @@ def main(
         wrapper_class=structlog.make_filtering_bound_logger(loglevel),
     )
 
-    ode = load_ode(fname)
+    ode = load_ode(fname, remove_singularities=remove_singularities)
 
     code = get_code(
         ode,

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/cli/gotran2ufl.py

@@ -72,6 +72,7 @@ def main(
     format: Format = Format.black,
     scheme: list[Scheme] | None = None,
     remove_unused: bool = False,
+    remove_singularities: bool = True,
     verbose: bool = True,
     stiff_states: list[str] | None = None,
     cse: bool = True,
@@ -84,7 +85,7 @@ def main(
         wrapper_class=structlog.make_filtering_bound_logger(loglevel),
     )
 
-    ode = load_ode(fname)
+    ode = load_ode(fname, remove_singularities=remove_singularities)
 
     code = get_code(
         ode,

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/cli/ode2cellml.py

@@ -20,7 +20,10 @@ def main(
     )
     assert fname.suffix == ".ode", f"File {fname} must be an ode file"
     assert fname.exists(), f"File {fname} does not exist"
-    ode = load_ode(fname)
+    # A model export, not code generation: writing gotranx's float guard
+    # windows into an interchange format would bake a numerical artifact
+    # into someone else's model.
+    ode = load_ode(fname, remove_singularities=False)
     logger.info(f"Converting {fname} to CellML")
     cellml_file = fname.with_suffix(".cellml") if outname is None else Path(outname)
     gotran_to_cellml(ode, filename=cellml_file)

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/cli/utils.py

@@ -89,6 +89,18 @@ def validate_cse(cse: Any) -> bool:
     return cse
 
 
+def validate_remove_singularities(remove_singularities: Any) -> bool:
+    """Reject a non-boolean `remove_singularities`, which can only reach here
+    from a config file -- where a string such as "false" is truthy and would
+    silently do the opposite of what it says."""
+    if not isinstance(remove_singularities, bool):
+        raise typer.BadParameter(
+            f"remove_singularities must be true or false, got {remove_singularities!r}",
+            param_hint="remove_singularities",
+        )
+    return remove_singularities
+
+
 def validate_scheme(scheme: list[Scheme] | list[str]) -> list[Scheme]:
     lst = []
     for s in scheme:

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/codegen/ufl.py

@@ -74,6 +74,28 @@ class UFLPrinter(GotranPythonCodePrinter):
 
         return "".join(result)
 
+    # Comparisons are printed as calls to the ufl functions, not as Python
+    # operators. With two numbers as operands (say a parameter passed as a
+    # float) an operator gives a Python bool, which ufl.conditional, ufl.And
+    # and ufl.Or refuse; the functions convert both operands with ufl.as_ufl.
+    # `==` and `!=` never give a condition: UFL keeps them for structural
+    # equality of expressions.
+    _comparisons = {
+        "==": "ufl.eq",
+        "!=": "ufl.ne",
+        "<": "ufl.lt",
+        "<=": "ufl.le",
+        ">": "ufl.gt",
+        ">=": "ufl.ge",
+    }
+
+    def _print_Relational(self, expr):
+        func = self._comparisons[expr.rel_op]
+        return f"{func}({self._print(expr.lhs)}, {self._print(expr.rhs)})"
+
+    # The Python printer's own _print_Equality would otherwise take precedence
+    _print_Equality = _print_Relational
+
     def _print_And(self, expr):
         args = [self._print(arg) for arg in expr.args]
         return functools.reduce(lambda x, y: f"ufl.And({x}, {y})", args)

{gotranx-2.0.0 → gotranx-2.2.0}/src/gotranx/load.py

@@ -12,7 +12,7 @@ from .transformer import TreeToODE, LarkODE
 logger = get_logger()
 
 
-def ode_from_string(text: str, name="ode") -> ODE:
+def ode_from_string(text: str, name="ode", *, remove_singularities: bool = True) -> ODE:
     """Create an ODE from a string
 
     Parameters
@@ -21,6 +21,13 @@ def ode_from_string(text: str, name="ode") -> ODE:
         The string to parse
     name : str, optional
         Name of the ODE, by default "ode"
+    remove_singularities : bool, optional
+        Replace a neighborhood of every removable singularity with a
+        truncated Taylor series, by default True. Pass False to get the
+        expressions exactly as written, which will divide by zero wherever the
+        model has a removable pole -- numpy warns and returns nan there, numba
+        crashes -- and whose derivative, which the Rush-Larsen schemes form, is
+        wrong by an O(1) amount with a possibly wrong sign well before that.
 
     Returns
     -------
@@ -37,18 +44,24 @@ def ode_from_string(text: str, name="ode") -> ODE:
         name=name,
         comments=result.comments,
     )
+    if remove_singularities:
+        ode = ode.remove_singularities()
     logger.info(f"Num states {ode.num_states}")
     logger.info(f"Num parameters {ode.num_parameters}")
     return ode
 
 
-def load_ode(path: str | Path) -> ODE:
+def load_ode(path: str | Path, *, remove_singularities: bool = True) -> ODE:
     """Load an ODE from a file
 
     Parameters
     ----------
     path : str | Path
         Path to the file
+    remove_singularities : bool, optional
+        Replace a neighborhood of every removable singularity with a
+        truncated Taylor series, by default True. See
+        :func:`ode_from_string`.
 
     Returns
     -------
@@ -67,4 +80,6 @@ def load_ode(path: str | Path) -> ODE:
     if not fname.is_file():
         raise exceptions.ODEFileNotFound(fname)
 
-    return ode_from_string(fname.read_text(), name=fname.stem)
+    return ode_from_string(
+        fname.read_text(), name=fname.stem, remove_singularities=remove_singularities
+    )