Make typing-extensions and sympy required dependencies to fix PyB…

…aMM import (pybamm-team#3848) * import `typing_extensions` as optional_dependency * Make `typing-extensions` a required dependency * Try forward referencing for `sympy` in `IndependentVariable` * Make `sympy` a required dependency * Update docs for SymPy * Import `sympy` without `have_optional_dependency` * Import `sympy` without `TYPE_CHECKING` * Changelog * Update CHANGELOG.md Co-authored-by: Agriya Khetarpal <[email protected]> * Rearrange position in changelog --------- Co-authored-by: Agriya Khetarpal <[email protected]> Co-authored-by: Eric G. Kratz <[email protected]>
lorenzofavaro · Mar 13, 2024 · 4a5c6eb · 4a5c6eb
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,7 @@
 
 ## Breaking changes
 
+- Integrated the `[latexify]` extra into the core PyBaMM package, deprecating the `pybamm[latexify]` set of optional dependencies. SymPy is now a required dependency and will be installed upon installing PyBaMM ([#3848](https://github.com/pybamm-team/PyBaMM/pull/3848))
 - Renamed "testing" argument for plots to "show_plot" and flipped its meaning (show_plot=True is now the default and shows the plot) ([#3842](https://github.com/pybamm-team/PyBaMM/pull/3842))
 - Dropped support for BPX version 0.3.0 and below ([#3414](https://github.com/pybamm-team/PyBaMM/pull/3414))
 

diff --git a/docs/source/user_guide/installation/index.rst b/docs/source/user_guide/installation/index.rst
@@ -59,15 +59,17 @@ Required dependencies
 
 PyBaMM requires the following dependencies.
 
-================================================================ ==========================
-Package                                                          Minimum supported version
-================================================================ ==========================
-`NumPy <https://numpy.org>`__                                    1.23.5
-`SciPy <https://docs.scipy.org/doc/scipy/>`__                    1.9.3
-`CasADi <https://web.casadi.org/docs/>`__                        3.6.3
-`Xarray <https://docs.xarray.dev/en/stable/>`__                  2022.6.0
-`Anytree <https://anytree.readthedocs.io/en/stable/>`__          2.8.0
-================================================================ ==========================
+=================================================================== ==========================
+Package                                                             Minimum supported version
+=================================================================== ==========================
+`NumPy <https://numpy.org>`__                                       1.23.5
+`SciPy <https://docs.scipy.org/doc/scipy/>`__                       1.9.3
+`CasADi <https://web.casadi.org/docs/>`__                           3.6.3
+`Xarray <https://docs.xarray.dev/en/stable/>`__                     2022.6.0
+`Anytree <https://anytree.readthedocs.io/en/stable/>`__             2.8.0
+`SymPy <https://docs.sympy.org/latest/index.html>`__                1.9.3
+`typing-extensions <https://pypi.org/project/typing-extensions/>`__ 4.10.0
+=================================================================== ==========================
 
 .. _install.optional_dependencies:
 
@@ -174,19 +176,6 @@ Dependency                                                  Minimum Version    p
 `pybtex <https://docs.pybtex.org/>`__                       0.24.0             cite               BibTeX-compatible bibliography processor.
 =========================================================== ================== ================== =========================================
 
-.. _install.latexify_dependencies:
-
-Latexify dependencies
-^^^^^^^^^^^^^^^^^^^^^
-
-Installable with ``pip install "pybamm[latexify]"``
-
-=========================================================== ================== ================== =========================
-Dependency                                                  Minimum Version    pip extra          Notes
-=========================================================== ================== ================== =========================
-`sympy <https://docs.sympy.org/latest/index.html>`__        1.9.3              latexify           For symbolic mathematics.
-=========================================================== ================== ================== =========================
-
 .. _install.bpx_dependencies:
 
 bpx dependencies

diff --git a/pybamm/expression_tree/array.py b/pybamm/expression_tree/array.py
@@ -4,14 +4,10 @@
 from __future__ import annotations
 import numpy as np
 from scipy.sparse import csr_matrix, issparse
-from typing import TYPE_CHECKING
 
 import pybamm
-from pybamm.util import have_optional_dependency
 from pybamm.type_definitions import DomainType, AuxiliaryDomainType, DomainsType
-
-if TYPE_CHECKING:  # pragma: no cover
-    import sympy
+import sympy
 
 
 class Array(pybamm.Symbol):
@@ -157,7 +153,6 @@ def is_constant(self):
 
     def to_equation(self) -> sympy.Array:
         """Returns the value returned by the node when evaluated."""
-        sympy = have_optional_dependency("sympy")
         entries_list = self.entries.tolist()
         return sympy.Array(entries_list)
 

diff --git a/pybamm/expression_tree/binary_operators.py b/pybamm/expression_tree/binary_operators.py
@@ -5,11 +5,11 @@
 import numbers
 
 import numpy as np
+import sympy
 from scipy.sparse import csr_matrix, issparse
 import functools
 
 import pybamm
-from pybamm.util import have_optional_dependency
 
 from typing import Callable, cast
 
@@ -180,7 +180,6 @@ def _sympy_operator(self, left, right):
 
     def to_equation(self):
         """Convert the node and its subtree into a SymPy equation."""
-        sympy = have_optional_dependency("sympy")
         if self.print_name is not None:
             return sympy.Symbol(self.print_name)
         else:
@@ -388,7 +387,6 @@ def _binary_evaluate(self, left, right):
 
     def _sympy_operator(self, left, right):
         """Override :meth:`pybamm.BinaryOperator._sympy_operator`"""
-        sympy = have_optional_dependency("sympy")
         left = sympy.Matrix(left)
         right = sympy.Matrix(right)
         return left * right
@@ -737,7 +735,6 @@ def _binary_new_copy(
 
     def _sympy_operator(self, left, right):
         """Override :meth:`pybamm.BinaryOperator._sympy_operator`"""
-        sympy = have_optional_dependency("sympy")
         return sympy.Min(left, right)
 
 
@@ -782,7 +779,6 @@ def _binary_new_copy(
 
     def _sympy_operator(self, left, right):
         """Override :meth:`pybamm.BinaryOperator._sympy_operator`"""
-        sympy = have_optional_dependency("sympy")
         return sympy.Max(left, right)
 
 

diff --git a/pybamm/expression_tree/concatenations.py b/pybamm/expression_tree/concatenations.py
@@ -6,11 +6,11 @@
 from collections import defaultdict
 
 import numpy as np
+import sympy
 from scipy.sparse import issparse, vstack
 from typing import Sequence
 
 import pybamm
-from pybamm.util import have_optional_dependency
 
 
 class Concatenation(pybamm.Symbol):
@@ -159,7 +159,6 @@ def is_constant(self):
 
     def _sympy_operator(self, *children):
         """Apply appropriate SymPy operators."""
-        sympy = have_optional_dependency("sympy")
         self.concat_latex = tuple(map(sympy.latex, children))
 
         if self.print_name is not None:

diff --git a/pybamm/expression_tree/functions.py b/pybamm/expression_tree/functions.py
@@ -5,6 +5,7 @@
 
 import numpy as np
 from scipy import special
+import sympy
 from typing import Sequence, Callable
 from typing_extensions import TypeVar
 
@@ -210,7 +211,6 @@ def _sympy_operator(self, child):
 
     def to_equation(self):
         """Convert the node and its subtree into a SymPy equation."""
-        sympy = have_optional_dependency("sympy")
         if self.print_name is not None:
             return sympy.Symbol(self.print_name)
         else:
@@ -275,7 +275,6 @@ def _function_new_copy(self, children):
 
     def _sympy_operator(self, child):
         """Apply appropriate SymPy operators."""
-        sympy = have_optional_dependency("sympy")
         class_name = self.__class__.__name__.lower()
         sympy_function = getattr(sympy, class_name)
         return sympy_function(child)
@@ -332,7 +331,6 @@ def _function_diff(self, children, idx):
 
     def _sympy_operator(self, child):
         """Override :meth:`pybamm.Function._sympy_operator`"""
-        sympy = have_optional_dependency("sympy")
         return sympy.asinh(child)
 
 
@@ -360,7 +358,6 @@ def _function_diff(self, children, idx):
 
     def _sympy_operator(self, child):
         """Override :meth:`pybamm.Function._sympy_operator`"""
-        sympy = have_optional_dependency("sympy")
         return sympy.atan(child)
 
 

diff --git a/pybamm/expression_tree/independent_variable.py b/pybamm/expression_tree/independent_variable.py
@@ -6,7 +6,6 @@
 import numpy as np
 
 import pybamm
-from pybamm.util import have_optional_dependency
 from pybamm.type_definitions import DomainType, AuxiliaryDomainType, DomainsType
 
 KNOWN_COORD_SYS = ["cartesian", "cylindrical polar", "spherical polar"]
@@ -58,7 +57,6 @@ def _jac(self, variable) -> pybamm.Scalar:
 
     def to_equation(self) -> sympy.Symbol:
         """Convert the node and its subtree into a SymPy equation."""
-        sympy = have_optional_dependency("sympy")
         if self.print_name is not None:
             return sympy.Symbol(self.print_name)
         else:
@@ -102,7 +100,6 @@ def _evaluate_for_shape(self):
 
     def to_equation(self):
         """Convert the node and its subtree into a SymPy equation."""
-        sympy = have_optional_dependency("sympy")
         return sympy.Symbol("t")
 
 

diff --git a/pybamm/expression_tree/operations/latexify.py b/pybamm/expression_tree/operations/latexify.py
@@ -9,7 +9,7 @@
 
 import pybamm
 from pybamm.expression_tree.printing.sympy_overrides import custom_print_func
-from pybamm.util import have_optional_dependency
+import sympy
 
 
 def get_rng_min_max_name(rng, min_or_max):
@@ -89,7 +89,6 @@ def _get_bcs_displays(self, var):
         Returns a list of boundary condition equations with ranges in front of
         the equations.
         """
-        sympy = have_optional_dependency("sympy")
         bcs_eqn_list = []
         bcs = self.model.boundary_conditions.get(var, None)
 
@@ -120,7 +119,6 @@ def _get_bcs_displays(self, var):
 
     def _get_param_var(self, node):
         """Returns a list of parameters and a list of variables."""
-        sympy = have_optional_dependency("sympy")
         param_list = []
         var_list = []
         dfs_nodes = [node]
@@ -163,7 +161,6 @@ def _get_param_var(self, node):
         return param_list, var_list
 
     def latexify(self, output_variables=None):
-        sympy = have_optional_dependency("sympy")
         # Voltage is the default output variable if it exists
         if output_variables is None:
             if "Voltage [V]" in self.model.variables:

diff --git a/pybamm/expression_tree/parameter.py b/pybamm/expression_tree/parameter.py
@@ -5,13 +5,11 @@
 import sys
 
 import numpy as np
-from typing import TYPE_CHECKING, Literal
+from typing import Literal
 
-if TYPE_CHECKING:  # pragma: no cover
-    import sympy
+import sympy
 
 import pybamm
-from pybamm.util import have_optional_dependency
 
 
 class Parameter(pybamm.Symbol):
@@ -48,7 +46,6 @@ def is_constant(self) -> Literal[False]:
 
     def to_equation(self) -> sympy.Symbol:
         """Convert the node and its subtree into a SymPy equation."""
-        sympy = have_optional_dependency("sympy")
         if self.print_name is not None:
             return sympy.Symbol(self.print_name)
         else:
@@ -244,7 +241,6 @@ def _evaluate_for_shape(self):
 
     def to_equation(self) -> sympy.Symbol:
         """Convert the node and its subtree into a SymPy equation."""
-        sympy = have_optional_dependency("sympy")
         if self.print_name is not None:
             return sympy.Symbol(self.print_name)
         else:

diff --git a/pybamm/expression_tree/scalar.py b/pybamm/expression_tree/scalar.py
@@ -3,10 +3,10 @@
 #
 from __future__ import annotations
 import numpy as np
+import sympy
 from typing import Literal
 
 import pybamm
-from pybamm.util import have_optional_dependency
 from pybamm.type_definitions import Numeric
 
 
@@ -87,7 +87,6 @@ def is_constant(self) -> Literal[True]:
 
     def to_equation(self):
         """Returns the value returned by the node when evaluated."""
-        sympy = have_optional_dependency("sympy")
         if self.print_name is not None:
             return sympy.Symbol(self.print_name)
         else:

diff --git a/pybamm/expression_tree/symbol.py b/pybamm/expression_tree/symbol.py
@@ -5,6 +5,7 @@
 import numbers
 
 import numpy as np
+import sympy
 from scipy.sparse import csr_matrix, issparse
 from functools import cached_property
 from typing import TYPE_CHECKING, Sequence, cast
@@ -1058,7 +1059,6 @@ def print_name(self, name):
         self._print_name = prettify_print_name(name)
 
     def to_equation(self):
-        sympy = have_optional_dependency("sympy")
         return sympy.Symbol(str(self.name))
 
     def to_json(self):

diff --git a/pybamm/expression_tree/unary_operators.py b/pybamm/expression_tree/unary_operators.py
@@ -5,6 +5,7 @@
 
 import numpy as np
 from scipy.sparse import csr_matrix, issparse
+import sympy
 import pybamm
 from pybamm.util import have_optional_dependency
 from pybamm.type_definitions import DomainsType
@@ -108,7 +109,6 @@ def _sympy_operator(self, child):
 
     def to_equation(self):
         """Convert the node and its subtree into a SymPy equation."""
-        sympy = have_optional_dependency("sympy")
         if self.print_name is not None:
             return sympy.Symbol(self.print_name)
         else:
@@ -672,7 +672,6 @@ def _evaluates_on_edges(self, dimension: str) -> bool:
 
     def _sympy_operator(self, child):
         """Override :meth:`pybamm.UnaryOperator._sympy_operator`"""
-        sympy = have_optional_dependency("sympy")
         return sympy.Integral(child, sympy.Symbol("xn"))
 
 
@@ -996,7 +995,6 @@ def _unary_new_copy(self, child):
 
     def _sympy_operator(self, child):
         """Override :meth:`pybamm.UnaryOperator._sympy_operator`"""
-        sympy = have_optional_dependency("sympy")
         if (
             self.child.domain[0] in ["negative particle", "positive particle"]
             and self.side == "right"

diff --git a/pybamm/expression_tree/variable.py b/pybamm/expression_tree/variable.py
@@ -5,7 +5,7 @@
 import numpy as np
 import numbers
 import pybamm
-from pybamm.util import have_optional_dependency
+import sympy
 from pybamm.type_definitions import (
     DomainType,
     AuxiliaryDomainType,
@@ -135,7 +135,6 @@ def _evaluate_for_shape(self):
 
     def to_equation(self):
         """Convert the node and its subtree into a SymPy equation."""
-        sympy = have_optional_dependency("sympy")
         if self.print_name is not None:
             return sympy.Symbol(self.print_name)
         else:

diff --git a/pybamm/models/base_model.py b/pybamm/models/base_model.py
@@ -13,7 +13,7 @@
 
 import pybamm
 from pybamm.expression_tree.operations.serialise import Serialise
-from pybamm.util import have_optional_dependency
+import sympy
 
 
 class BaseModel:
@@ -1185,7 +1185,6 @@ def latexify(self, filename=None, newline=True, output_variables=None):
         This will return first five model equations
         >>> model.latexify(newline=False)[1:5]
         """
-        sympy = have_optional_dependency("sympy")
         if sympy:
             from pybamm.expression_tree.operations.latexify import Latexify
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -41,6 +41,8 @@ dependencies = [
     "casadi>=3.6.3",
     "xarray>=2022.6.0",
     "anytree>=2.8.0",
+    "sympy>=1.12",
+    "typing-extensions>=4.10.0",
 ]
 
 [project.urls]
@@ -86,10 +88,6 @@ plot = [
 cite = [
     "pybtex>=0.24.0",
 ]
-# To generate LaTeX strings
-latexify = [
-    "sympy>=1.12",
-]
 # Battery Parameter eXchange format
 bpx = [
     "bpx>=0.4.0",