Rename have_optional_dependency (#3866)

* Rename have_optional_dependency

* Change log

* Fix import

* style: pre-commit fixes

* Update pybamm/util.py

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Arjun Verma <[email protected]>

CHANGELOG.md

@@ -18,6 +18,7 @@
 
 ## Breaking changes
 
+- Renamed "have_optional_dependency" to "import_optional_dependency" ([#3866](https://github.com/pybamm-team/PyBaMM/pull/3866))
 - 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))

CONTRIBUTING.md

@@ -104,21 +104,21 @@ Only 'core pybamm' is installed by default. The others have to be specified expl
 
 PyBaMM utilizes optional dependencies to allow users to choose which additional libraries they want to use. Managing these optional dependencies and their imports is essential to provide flexibility to PyBaMM users.
 
-PyBaMM provides a utility function `have_optional_dependency`, to check for the availability of optional dependencies within methods. This function can be used to conditionally import optional dependencies only if they are available. Here's how to use it:
+PyBaMM provides a utility function `import_optional_dependency`, to check for the availability of optional dependencies within methods. This function can be used to conditionally import optional dependencies only if they are available. Here's how to use it:
 
 Optional dependencies should never be imported at the module level, but always inside methods. For example:
 
 ```
 def use_pybtex(x,y,z):
-    pybtex = have_optional_dependency("pybtex")
+    pybtex = import_optional_dependency("pybtex")
     ...
 ```
 
 While importing a specific module instead of an entire package/library:
 
 ```python
 def use_parse_file(x, y, z):
-    parse_file = have_optional_dependency("pybtex.database", "parse_file")
+    parse_file = import_optional_dependency("pybtex.database", "parse_file")
     ...
 ```
 
@@ -143,7 +143,7 @@ class TestUtil(TestCase):
             pybamm.function_using_pybtex(x, y, z)
 
         # Test that the function works when pybtex is available
-        sys.modules["pybtex"] = pybamm.util.have_optional_dependency("pybtex")
+        sys.modules["pybtex"] = pybamm.util.import_optional_dependency("pybtex")
         pybamm.function_using_pybtex(x, y, z)
 ```
 

pybamm/__init__.py

@@ -47,7 +47,7 @@
     get_parameters_filepath,
     have_jax,
     install_jax,
-    have_optional_dependency,
+    import_optional_dependency,
     is_jax_compatible,
     get_git_commit_info,
 )

pybamm/citations.py

@@ -7,7 +7,7 @@
 import os
 import warnings
 from sys import _getframe
-from pybamm.util import have_optional_dependency
+from pybamm.util import import_optional_dependency
 
 
 class Citations:
@@ -74,7 +74,7 @@ def read_citations(self):
         """Reads the citations in `pybamm.CITATIONS.bib`. Other works can be cited
         by passing a BibTeX citation to :meth:`register`.
         """
-        parse_file = have_optional_dependency("pybtex.database", "parse_file")
+        parse_file = import_optional_dependency("pybtex.database", "parse_file")
         citations_file = os.path.join(pybamm.root_dir(), "pybamm", "CITATIONS.bib")
         bib_data = parse_file(citations_file, bib_format="bibtex")
         for key, entry in bib_data.entries.items():
@@ -85,7 +85,7 @@ def _add_citation(self, key, entry):
         previous entry is overwritten
         """
 
-        Entry = have_optional_dependency("pybtex.database", "Entry")
+        Entry = import_optional_dependency("pybtex.database", "Entry")
         # Check input types are correct
         if not isinstance(key, str) or not isinstance(entry, Entry):
             raise TypeError()
@@ -151,8 +151,8 @@ def _parse_citation(self, key):
         key: str
             A BibTeX formatted citation
         """
-        PybtexError = have_optional_dependency("pybtex.scanner", "PybtexError")
-        parse_string = have_optional_dependency("pybtex.database", "parse_string")
+        PybtexError = import_optional_dependency("pybtex.scanner", "PybtexError")
+        parse_string = import_optional_dependency("pybtex.database", "parse_string")
         try:
             # Parse string as a bibtex citation, and check that a citation was found
             bib_data = parse_string(key, bib_format="bibtex")
@@ -219,7 +219,7 @@ def print(self, filename=None, output_format="text", verbose=False):
         """
         # Parse citations that were not known keys at registration, but do not
         # fail if they cannot be parsed
-        pybtex = have_optional_dependency("pybtex")
+        pybtex = import_optional_dependency("pybtex")
         try:
             for key in self._unknown_citations:
                 self._parse_citation(key)

pybamm/expression_tree/functions.py

@@ -10,7 +10,7 @@
 from typing_extensions import TypeVar
 
 import pybamm
-from pybamm.util import have_optional_dependency
+from pybamm.util import import_optional_dependency
 
 
 class Function(pybamm.Symbol):
@@ -98,7 +98,7 @@ def _function_diff(self, children: Sequence[pybamm.Symbol], idx: float):
         Derivative with respect to child number 'idx'.
         See :meth:`pybamm.Symbol._diff()`.
         """
-        autograd = have_optional_dependency("autograd")
+        autograd = import_optional_dependency("autograd")
         # Store differentiated function, needed in case we want to convert to CasADi
         if self.derivative == "autograd":
             return Function(

pybamm/expression_tree/symbol.py

@@ -11,7 +11,7 @@
 from typing import TYPE_CHECKING, Sequence, cast
 
 import pybamm
-from pybamm.util import have_optional_dependency
+from pybamm.util import import_optional_dependency
 from pybamm.expression_tree.printing.print_name import prettify_print_name
 
 if TYPE_CHECKING:  # pragma: no cover
@@ -479,7 +479,7 @@ def render(self):  # pragma: no cover
         """
         Print out a visual representation of the tree (this node and its children)
         """
-        anytree = have_optional_dependency("anytree")
+        anytree = import_optional_dependency("anytree")
         for pre, _, node in anytree.RenderTree(self):
             if isinstance(node, pybamm.Scalar) and node.name != str(node.value):
                 print(f"{pre}{node.name} = {node.value}")
@@ -498,7 +498,7 @@ def visualise(self, filename: str):
             filename to output, must end in ".png"
         """
 
-        DotExporter = have_optional_dependency("anytree.exporter", "DotExporter")
+        DotExporter = import_optional_dependency("anytree.exporter", "DotExporter")
         # check that filename ends in .png.
         if filename[-4:] != ".png":
             raise ValueError("filename should end in .png")
@@ -518,7 +518,7 @@ def relabel_tree(self, symbol: Symbol, counter: int):
         Finds all children of a symbol and assigns them a new id so that they can be
         visualised properly using the graphviz output
         """
-        anytree = have_optional_dependency("anytree")
+        anytree = import_optional_dependency("anytree")
         name = symbol.name
         if name == "div":
             name = "∇⋅"
@@ -561,7 +561,7 @@ def pre_order(self):
         a
         b
         """
-        anytree = have_optional_dependency("anytree")
+        anytree = import_optional_dependency("anytree")
         return anytree.PreOrderIter(self)
 
     def __str__(self):

pybamm/expression_tree/unary_operators.py

@@ -7,7 +7,7 @@
 from scipy.sparse import csr_matrix, issparse
 import sympy
 import pybamm
-from pybamm.util import have_optional_dependency
+from pybamm.util import import_optional_dependency
 from pybamm.type_definitions import DomainsType
 
 
@@ -450,7 +450,9 @@ def _unary_new_copy(self, child):
 
     def _sympy_operator(self, child):
         """Override :meth:`pybamm.UnaryOperator._sympy_operator`"""
-        sympy_Gradient = have_optional_dependency("sympy.vector.operators", "Gradient")
+        sympy_Gradient = import_optional_dependency(
+            "sympy.vector.operators", "Gradient"
+        )
         return sympy_Gradient(child)
 
 
@@ -484,7 +486,7 @@ def _unary_new_copy(self, child):
 
     def _sympy_operator(self, child):
         """Override :meth:`pybamm.UnaryOperator._sympy_operator`"""
-        sympy_Divergence = have_optional_dependency(
+        sympy_Divergence = import_optional_dependency(
             "sympy.vector.operators", "Divergence"
         )
         return sympy_Divergence(child)

pybamm/meshes/scikit_fem_submeshes.py

@@ -5,7 +5,7 @@
 from .meshes import SubMesh
 import numpy as np
 
-from pybamm.util import have_optional_dependency
+from pybamm.util import import_optional_dependency
 
 
 class ScikitSubMesh2D(SubMesh):
@@ -27,7 +27,7 @@ class ScikitSubMesh2D(SubMesh):
     """
 
     def __init__(self, edges, coord_sys, tabs):
-        skfem = have_optional_dependency("skfem")
+        skfem = import_optional_dependency("skfem")
         self.edges = edges
         self.nodes = dict.fromkeys(["y", "z"])
         for var in self.nodes.keys():

pybamm/models/base_model.py

@@ -13,7 +13,6 @@
 
 import pybamm
 from pybamm.expression_tree.operations.serialise import Serialise
-import sympy
 
 
 class BaseModel:
@@ -1185,8 +1184,7 @@ def latexify(self, filename=None, newline=True, output_variables=None):
         This will return first five model equations
         >>> model.latexify(newline=False)[1:5]
         """
-        if sympy:
-            from pybamm.expression_tree.operations.latexify import Latexify
+        from pybamm.expression_tree.operations.latexify import Latexify
 
         return Latexify(self, filename, newline).latexify(
             output_variables=output_variables

pybamm/plotting/plot.py

@@ -3,7 +3,7 @@
 #
 import pybamm
 from .quick_plot import ax_min, ax_max
-from pybamm.util import have_optional_dependency
+from pybamm.util import import_optional_dependency
 
 
 def plot(x, y, ax=None, show_plot=True, **kwargs):
@@ -27,7 +27,7 @@ def plot(x, y, ax=None, show_plot=True, **kwargs):
         Keyword arguments, passed to plt.plot
 
     """
-    plt = have_optional_dependency("matplotlib.pyplot")
+    plt = import_optional_dependency("matplotlib.pyplot")
 
     if not isinstance(x, pybamm.Array):
         raise TypeError("x must be 'pybamm.Array'")

pybamm/plotting/plot2D.py

@@ -3,7 +3,7 @@
 #
 import pybamm
 from .quick_plot import ax_min, ax_max
-from pybamm.util import have_optional_dependency
+from pybamm.util import import_optional_dependency
 
 
 def plot2D(x, y, z, ax=None, show_plot=True, **kwargs):
@@ -27,7 +27,7 @@ def plot2D(x, y, z, ax=None, show_plot=True, **kwargs):
         only display the plot after plt.show() has been called.
 
     """
-    plt = have_optional_dependency("matplotlib.pyplot")
+    plt = import_optional_dependency("matplotlib.pyplot")
 
     if not isinstance(x, pybamm.Array):
         raise TypeError("x must be 'pybamm.Array'")

pybamm/plotting/plot_summary_variables.py

@@ -3,7 +3,7 @@
 #
 import numpy as np
 import pybamm
-from pybamm.util import have_optional_dependency
+from pybamm.util import import_optional_dependency
 
 
 def plot_summary_variables(
@@ -27,7 +27,7 @@ def plot_summary_variables(
         Keyword arguments, passed to plt.subplots.
 
     """
-    plt = have_optional_dependency("matplotlib.pyplot")
+    plt = import_optional_dependency("matplotlib.pyplot")
 
     if isinstance(solutions, pybamm.Solution):
         solutions = [solutions]

pybamm/plotting/plot_voltage_components.py

@@ -3,7 +3,7 @@
 #
 import numpy as np
 
-from pybamm.util import have_optional_dependency
+from pybamm.util import import_optional_dependency
 from pybamm.simulation import Simulation
 from pybamm.solvers.solution import Solution
 
@@ -42,7 +42,7 @@ def plot_voltage_components(
         solution = input_data.solution
     elif isinstance(input_data, Solution):
         solution = input_data
-    plt = have_optional_dependency("matplotlib.pyplot")
+    plt = import_optional_dependency("matplotlib.pyplot")
 
     # Set a default value for alpha, the opacity
     kwargs_fill = {"alpha": 0.6, **kwargs_fill}

pybamm/plotting/quick_plot.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pybamm
 from collections import defaultdict
-from pybamm.util import have_optional_dependency
+from pybamm.util import import_optional_dependency
 
 
 class LoopList(list):
@@ -46,7 +46,7 @@ def split_long_string(title, max_words=None):
 
 def close_plots():
     """Close all open figures"""
-    plt = have_optional_dependency("matplotlib.pyplot")
+    plt = import_optional_dependency("matplotlib.pyplot")
 
     plt.close("all")
 
@@ -473,10 +473,10 @@ def plot(self, t, dynamic=False):
             Dimensional time (in 'time_units') at which to plot.
         """
 
-        plt = have_optional_dependency("matplotlib.pyplot")
-        gridspec = have_optional_dependency("matplotlib.gridspec")
-        cm = have_optional_dependency("matplotlib", "cm")
-        colors = have_optional_dependency("matplotlib", "colors")
+        plt = import_optional_dependency("matplotlib.pyplot")
+        gridspec = import_optional_dependency("matplotlib.gridspec")
+        cm = import_optional_dependency("matplotlib", "cm")
+        colors = import_optional_dependency("matplotlib", "colors")
 
         t_in_seconds = t * self.time_scaling_factor
         self.fig = plt.figure(figsize=self.figsize)
@@ -674,8 +674,8 @@ def dynamic_plot(self, show_plot=True, step=None):
                 continuous_update=False,
             )
         else:
-            plt = have_optional_dependency("matplotlib.pyplot")
-            Slider = have_optional_dependency("matplotlib.widgets", "Slider")
+            plt = import_optional_dependency("matplotlib.pyplot")
+            Slider = import_optional_dependency("matplotlib.widgets", "Slider")
 
             # create an initial plot at time self.min_t
             self.plot(self.min_t, dynamic=True)
@@ -779,8 +779,8 @@ def create_gif(self, number_of_images=80, duration=0.1, output_filename="plot.gi
             Name of the generated GIF file.
 
         """
-        imageio = have_optional_dependency("imageio.v2")
-        plt = have_optional_dependency("matplotlib.pyplot")
+        imageio = import_optional_dependency("imageio.v2")
+        plt = import_optional_dependency("matplotlib.pyplot")
 
         # time stamps at which the images/plots will be created
         time_array = np.linspace(self.min_t, self.max_t, num=number_of_images)

pybamm/simulation.py

@@ -11,7 +11,7 @@
 import sys
 from functools import lru_cache
 from datetime import timedelta
-from pybamm.util import have_optional_dependency
+from pybamm.util import import_optional_dependency
 
 from pybamm.expression_tree.operations.serialise import Serialise
 
@@ -699,7 +699,7 @@ def solve(
 
             # check if a user has tqdm installed
             if showprogress:
-                tqdm = have_optional_dependency("tqdm")
+                tqdm = import_optional_dependency("tqdm")
                 cycle_lengths = tqdm.tqdm(
                     self.experiment.cycle_lengths,
                     desc="Cycling",