Move ruff, coverage, and pytest configs to pyproject.toml

.git-blame-ignore-revs

@@ -4,3 +4,5 @@
 a63e49ece0f9336d1f5c2562f7459e555c6e6693
 # activated standard pre-commits - https://github.com/pybamm-team/PyBaMM/pull/3192
 5273214b585c5a4286609aed40e0b092d0e05f42
+# migrate config to pyproject.toml - https://github.com/pybamm-team/PyBaMM/pull/3557
+12c5d77203bd93542785d237bac00bad5ed5469a

benchmarks/work_precision_sets/time_vs_abstols.py

@@ -96,7 +96,7 @@
 plt.savefig(f"benchmarks/benchmark_images/time_vs_abstols_{pybamm.__version__}.png")
 
 
-content = f"# PyBaMM {pybamm.__version__}\n## Solve Time vs Abstols\n<img src='./benchmark_images/time_vs_abstols_{pybamm.__version__}.png'>\n"  # noqa
+content = f"# PyBaMM {pybamm.__version__}\n## Solve Time vs Abstols\n<img src='./benchmark_images/time_vs_abstols_{pybamm.__version__}.png'>\n"
 
 with open("./benchmarks/release_work_precision_sets.md", "r") as original:
     data = original.read()

benchmarks/work_precision_sets/time_vs_dt_max.py

@@ -98,7 +98,7 @@
 plt.savefig(f"benchmarks/benchmark_images/time_vs_dt_max_{pybamm.__version__}.png")
 
 
-content = f"## Solve Time vs dt_max\n<img src='./benchmark_images/time_vs_dt_max_{pybamm.__version__}.png'>\n"  # noqa
+content = f"## Solve Time vs dt_max\n<img src='./benchmark_images/time_vs_dt_max_{pybamm.__version__}.png'>\n"
 
 with open("./benchmarks/release_work_precision_sets.md", "r") as original:
     data = original.read()

benchmarks/work_precision_sets/time_vs_mesh_size.py

@@ -78,7 +78,7 @@
 plt.savefig(f"benchmarks/benchmark_images/time_vs_mesh_size_{pybamm.__version__}.png")
 
 
-content = f"## Solve Time vs Mesh size\n<img src='./benchmark_images/time_vs_mesh_size_{pybamm.__version__}.png'>\n"  # noqa
+content = f"## Solve Time vs Mesh size\n<img src='./benchmark_images/time_vs_mesh_size_{pybamm.__version__}.png'>\n"
 
 with open("./benchmarks/release_work_precision_sets.md", "r") as original:
     data = original.read()

benchmarks/work_precision_sets/time_vs_no_of_states.py

@@ -82,7 +82,7 @@
 )
 
 
-content = f"## Solve Time vs Number of states\n<img src='./benchmark_images/time_vs_no_of_states_{pybamm.__version__}.png'>\n"  # noqa
+content = f"## Solve Time vs Number of states\n<img src='./benchmark_images/time_vs_no_of_states_{pybamm.__version__}.png'>\n"
 
 with open("./benchmarks/release_work_precision_sets.md", "r") as original:
     data = original.read()

benchmarks/work_precision_sets/time_vs_reltols.py

@@ -102,7 +102,7 @@
 plt.savefig(f"benchmarks/benchmark_images/time_vs_reltols_{pybamm.__version__}.png")
 
 
-content = f"## Solve Time vs Reltols\n<img src='./benchmark_images/time_vs_reltols_{pybamm.__version__}.png'>\n"  # noqa
+content = f"## Solve Time vs Reltols\n<img src='./benchmark_images/time_vs_reltols_{pybamm.__version__}.png'>\n"
 
 with open("./benchmarks/release_work_precision_sets.md", "r") as original:
     data = original.read()

docs/source/examples/notebooks/models/jelly-roll-model.ipynb

@@ -84,7 +84,7 @@
     "delta = pybamm.Parameter(\"Current collector thickness\")\n",
     "delta_p = delta  # assume same thickness\n",
     "delta_n = delta  # assume same thickness\n",
-    "l = 1/2 - delta_p - delta_n  # active material thickness  # noqa: E741\n",
+    "l = 1/2 - delta_p - delta_n  # active material thickness\n",
     "sigma_p = pybamm.Parameter(\"Positive current collector conductivity\")\n",
     "sigma_n = pybamm.Parameter(\"Negative current collector conductivity\")\n",
     "sigma_a = pybamm.Parameter(\"Active material conductivity\")"

docs/source/examples/notebooks/models/latexify.ipynb

@@ -1252,7 +1252,7 @@
    "source": [
     "spme_latex = model_spme.latexify(newline=False)\n",
     "for line in spme_latex:\n",
-    "    display(line)       # noqa: F821"
+    "    display(line)"
    ]
   },
   {

docs/source/user_guide/installation/index.rst

@@ -154,6 +154,7 @@ Dependency
 `pre-commit <https://pre-commit.com/index.html>`__                               \-                 dev                For managing and maintaining multi-language pre-commit hooks.
 `ruff <https://beta.ruff.rs/docs/>`__                                            \-                 dev                For code formatting.
 `nox <https://nox.thea.codes/en/stable/>`__                                      \-                 dev                For running testing sessions in multiple environments.
+`coverage <https://coverage.readthedocs.io/en/>`__                               \-                 dev                For calculating coverage of tests.
 `pytest <https://docs.pytest.org/en/stable/>`__                                  6.0.0              dev                For running Jupyter notebooks tests.
 `pytest-xdist <https://pytest-xdist.readthedocs.io/en/latest/>`__                \-                 dev                For running tests in parallel across distributed workers.
 `nbmake <https://github.com/treebeardtech/nbmake/>`__                            \-                 dev                A ``pytest`` plugin for executing Jupyter notebooks.

examples/scripts/print_model_parameter_combinations.py

@@ -19,13 +19,13 @@
             try:
                 model = pybamm.lithium_ion.SPM(options.copy())
             except pybamm.OptionError as e:
-                print(f"Cannot create model with {options}. (OptionError: {str(e)})")
+                print(f"Cannot create model with {options}. (OptionError: {e!s})")
             except pybamm.ModelError as e:
                 # todo: properly resolve the cases that raise these errors
-                print(f"Cannot create model with {options}. (ModelError: {str(e)})")
+                print(f"Cannot create model with {options}. (ModelError: {e!s})")
             except AttributeError as e:
                 # todo: properly resolve the cases that raise these errors
-                print(f"Cannot create model with {options}. (AttributeError: {str(e)})")
+                print(f"Cannot create model with {options}. (AttributeError: {e!s})")
             else:
                 output = f"{options} with {parameter_set} parameters: "
                 try:

noxfile.py

@@ -38,7 +38,7 @@ def set_environment_variables(env_dict, session):
 
 @nox.session(name="pybamm-requires")
 def run_pybamm_requires(session):
-    """Download, compile, and install the build-time requirements for Linux and macOS: the SuiteSparse and SUNDIALS libraries."""  # noqa: E501
+    """Download, compile, and install the build-time requirements for Linux and macOS: the SuiteSparse and SUNDIALS libraries."""
     set_environment_variables(PYBAMM_ENV, session=session)
     if sys.platform != "win32":
         session.install("wget", "cmake", silent=False)
@@ -64,7 +64,7 @@ def run_coverage(session):
         session.install("-e", ".[all,odes,jax]", silent=False)
     else:
         session.install("-e", ".[all]", silent=False)
-    session.run("coverage", "run", "--rcfile=.coveragerc", "run-tests.py", "--nosub")
+    session.run("coverage", "run", "run-tests.py", "--nosub")
     session.run("coverage", "combine")
     session.run("coverage", "xml")
 

pybamm/citations.py

@@ -267,7 +267,7 @@ def print_citations(filename=None, output_format="text", verbose=False):
         if verbose:  # pragma: no cover
             if filename is not None:  # pragma: no cover
                 raise Exception(
-                    "Verbose output is available only for the terminal and not for printing to files",  # noqa: E501
+                    "Verbose output is available only for the terminal and not for printing to files",
                 )
             else:
                 citations.print(filename, output_format, verbose=True)

pybamm/discretisations/discretisation.py

@@ -461,7 +461,7 @@ def process_boundary_conditions(self, model):
                 if (
                     self.mesh[subdomain].coord_sys
                     in ["spherical polar", "cylindrical polar"]
-                    and list(self.mesh.geometry[subdomain].values())[0]["min"] == 0
+                    and next(iter(self.mesh.geometry[subdomain].values()))["min"] == 0
                 ):
                     if bcs["left"][0].value != 0 or bcs["left"][1] != "Neumann":
                         raise pybamm.ModelError(
@@ -753,7 +753,7 @@ def _process_symbol(self, symbol):
             spatial_method = self.spatial_methods[symbol.domain[0]]
             # If boundary conditions are provided, need to check for BCs on tabs
             if self.bcs:
-                key_id = list(self.bcs.keys())[0]
+                key_id = next(iter(self.bcs.keys()))
                 if any("tab" in side for side in list(self.bcs[key_id].keys())):
                     self.bcs[key_id] = self.check_tab_conditions(
                         symbol, self.bcs[key_id]

pybamm/expression_tree/array.py

@@ -97,7 +97,7 @@ def entries_string(self, value):
     def set_id(self):
         """See :meth:`pybamm.Symbol.set_id()`."""
         self._id = hash(
-            (self.__class__, self.name) + self.entries_string + tuple(self.domain)
+            (self.__class__, self.name, *self.entries_string, *tuple(self.domain))
         )
 
     def _jac(self, variable):

pybamm/expression_tree/interpolant.py

@@ -222,9 +222,7 @@ def entries_string(self, value):
     def set_id(self):
         """See :meth:`pybamm.Symbol.set_id()`."""
         self._id = hash(
-            (self.__class__, self.name, self.entries_string)
-            + tuple([child.id for child in self.children])
-            + tuple(self.domain)
+            (self.__class__, self.name, self.entries_string, *tuple([child.id for child in self.children]), *tuple(self.domain))
         )
 
     def _function_new_copy(self, children):

pybamm/expression_tree/operations/evaluate_python.py

@@ -42,7 +42,7 @@ class JaxCooMatrix:
     def __init__(self, row, col, data, shape):
         if not pybamm.have_jax():  # pragma: no cover
             raise ModuleNotFoundError(
-                "Jax or jaxlib is not installed, please see https://docs.pybamm.org/en/latest/source/user_guide/installation/GNU-linux.html#optional-jaxsolver"  # noqa: E501
+                "Jax or jaxlib is not installed, please see https://docs.pybamm.org/en/latest/source/user_guide/installation/GNU-linux.html#optional-jaxsolver"
             )
 
         self.row = jax.numpy.array(row)
@@ -537,7 +537,7 @@ class EvaluatorJax:
     def __init__(self, symbol):
         if not pybamm.have_jax():  # pragma: no cover
             raise ModuleNotFoundError(
-                "Jax or jaxlib is not installed, please see https://docs.pybamm.org/en/latest/source/user_guide/installation/GNU-linux.html#optional-jaxsolver"  # noqa: E501
+                "Jax or jaxlib is not installed, please see https://docs.pybamm.org/en/latest/source/user_guide/installation/GNU-linux.html#optional-jaxsolver"
             )
 
         constants, python_str = pybamm.to_python(symbol, debug=False, output_jax=True)

pybamm/expression_tree/operations/latexify.py

@@ -93,9 +93,9 @@ def _get_bcs_displays(self, var):
 
         if bcs:
             # Take range minimum from the first domain
-            var_name = list(self.model.default_geometry[var.domain[0]].keys())[0]
-            rng_left = list(self.model.default_geometry[var.domain[0]].values())[0]
-            rng_right = list(self.model.default_geometry[var.domain[-1]].values())[0]
+            var_name = next(iter(self.model.default_geometry[var.domain[0]].keys()))
+            rng_left = next(iter(self.model.default_geometry[var.domain[0]].values()))
+            rng_right = next(iter(self.model.default_geometry[var.domain[-1]].values()))
 
             # Trim name (r_n --> r)
             var_name = re.findall(r"(.)_*.*", str(var_name))[0]

pybamm/expression_tree/parameter.py

@@ -152,9 +152,7 @@ def input_names(self, inp=None):
     def set_id(self):
         """See :meth:`pybamm.Symbol.set_id`"""
         self._id = hash(
-            (self.__class__, self.name, self.diff_variable)
-            + tuple([child.id for child in self.children])
-            + tuple(self.domain)
+            (self.__class__, self.name, self.diff_variable, *tuple([child.id for child in self.children]), *tuple(self.domain))
         )
 
     def diff(self, variable):

pybamm/expression_tree/state_vector.py

@@ -107,8 +107,7 @@ def set_evaluation_array(self, y_slices, evaluation_array):
     def set_id(self):
         """See :meth:`pybamm.Symbol.set_id()`"""
         self._id = hash(
-            (self.__class__, self.name, tuple(self.evaluation_array))
-            + tuple(self.domain)
+            (self.__class__, self.name, tuple(self.evaluation_array), *tuple(self.domain))
         )
 
     def _jac_diff_vector(self, variable):

pybamm/expression_tree/symbol.py

@@ -403,9 +403,7 @@ def set_id(self):
         need to hash once.
         """
         self._id = hash(
-            (self.__class__, self.name)
-            + tuple([child.id for child in self.children])
-            + tuple([(k, tuple(v)) for k, v in self.domains.items() if v != []])
+            (self.__class__, self.name, *tuple([child.id for child in self.children]), *tuple([(k, tuple(v)) for k, v in self.domains.items() if v != []]))
         )
 
     @property

pybamm/expression_tree/unary_operators.py

@@ -287,14 +287,7 @@ def _unary_jac(self, child_jac):
     def set_id(self):
         """See :meth:`pybamm.Symbol.set_id()`"""
         self._id = hash(
-            (
-                self.__class__,
-                self.name,
-                self.slice.start,
-                self.slice.stop,
-                self.children[0].id,
-            )
-            + tuple(self.domain)
+            (self.__class__, self.name, self.slice.start, self.slice.stop, self.children[0].id, *tuple(self.domain))
         )
 
     def _unary_evaluate(self, child):
@@ -554,15 +547,7 @@ def integration_variable(self):
     def set_id(self):
         """See :meth:`pybamm.Symbol.set_id()`"""
         self._id = hash(
-            (self.__class__, self.name)
-            + tuple(
-                [
-                    integration_variable.id
-                    for integration_variable in self.integration_variable
-                ]
-            )
-            + (self.children[0].id,)
-            + tuple(self.domain)
+            (self.__class__, self.name, *tuple([integration_variable.id for integration_variable in self.integration_variable]), self.children[0].id, *tuple(self.domain))
         )
 
     def _unary_new_copy(self, child):
@@ -702,9 +687,7 @@ def __init__(self, child, vector_type="row"):
     def set_id(self):
         """See :meth:`pybamm.Symbol.set_id()`"""
         self._id = hash(
-            (self.__class__, self.name, self.vector_type)
-            + (self.children[0].id,)
-            + tuple(self.domain)
+            (self.__class__, self.name, self.vector_type, self.children[0].id, *tuple(self.domain))
         )
 
     def _unary_new_copy(self, child):
@@ -757,7 +740,7 @@ def __init__(self, child, region="entire"):
     def set_id(self):
         """See :meth:`pybamm.Symbol.set_id()`"""
         self._id = hash(
-            (self.__class__, self.name) + (self.children[0].id,) + tuple(self.domain)
+            (self.__class__, self.name, self.children[0].id, *tuple(self.domain))
         )
 
     def _unary_new_copy(self, child):
@@ -798,8 +781,7 @@ def __init__(self, child, side, domain):
     def set_id(self):
         """See :meth:`pybamm.Symbol.set_id()`"""
         self._id = hash(
-            (self.__class__, self.name, self.side, self.children[0].id)
-            + tuple([(k, tuple(v)) for k, v in self.domains.items()])
+            (self.__class__, self.name, self.side, self.children[0].id, *tuple([(k, tuple(v)) for k, v in self.domains.items()]))
         )
 
     def _evaluates_on_edges(self, dimension):
@@ -857,8 +839,7 @@ def __init__(self, name, child, side):
     def set_id(self):
         """See :meth:`pybamm.Symbol.set_id()`"""
         self._id = hash(
-            (self.__class__, self.name, self.side, self.children[0].id)
-            + tuple([(k, tuple(v)) for k, v in self.domains.items()])
+            (self.__class__, self.name, self.side, self.children[0].id, *tuple([(k, tuple(v)) for k, v in self.domains.items()]))
         )
 
     def _unary_new_copy(self, child):

pybamm/expression_tree/variable.py

@@ -103,8 +103,7 @@ def bounds(self, values):
 
     def set_id(self):
         self._id = hash(
-            (self.__class__, self.name, self.scale, self.reference)
-            + tuple([(k, tuple(v)) for k, v in self.domains.items() if v != []])
+            (self.__class__, self.name, self.scale, self.reference, *tuple([(k, tuple(v)) for k, v in self.domains.items() if v != []]))
         )
 
     def create_copy(self):

pybamm/install_odes.py

@@ -66,7 +66,7 @@ def install_sundials(download_dir, install_dir):
 
     print("-" * 10, "Running CMake prepare", "-" * 40)
     subprocess.run(
-        ["cmake", "../sundials-{}".format(sundials_version)] + cmake_args,
+        ["cmake", "../sundials-{}".format(sundials_version), *cmake_args],
         cwd=build_directory,
         check=True,
     )

pybamm/meshes/zero_dimensional_submesh.py

@@ -31,7 +31,7 @@ def __init__(self, position, npts=None):
             raise pybamm.GeometryError("position should only contain a single variable")
 
         # extract the position
-        position = list(position.values())[0]
+        position = next(iter(position.values()))
         spatial_position = position["position"]
         self.nodes = np.array([spatial_position])
         self.edges = np.array([spatial_position])

pybamm/models/base_model.py

@@ -1205,7 +1205,7 @@ def check_and_convert_equations(self, equations):
             for var, eqn in equations.items():
                 if eqn.has_symbol_of_classes(pybamm.Variable):
                     unpacker = pybamm.SymbolUnpacker(pybamm.Variable)
-                    variable_in_equation = list(unpacker.unpack_symbol(eqn))[0]
+                    variable_in_equation = next(iter(unpacker.unpack_symbol(eqn)))
                     raise TypeError(
                         "Initial conditions cannot contain 'Variable' objects, "
                         "but '{!r}' found in initial conditions for '{}'".format(

pybamm/models/submodels/electrolyte_conductivity/surface_potential_form/full_surface_form_conductivity.py

@@ -224,7 +224,7 @@ class FullAlgebraic(BaseModel):
         The parameters to use for this submodel
     options : dict, optional
         A dictionary of options to be passed to the model.
-    """  # noqa: E501
+    """
 
     def __init__(self, param, domain, options=None):
         super().__init__(param, domain, options)
@@ -258,7 +258,7 @@ class FullDifferential(BaseModel):
         The parameters to use for this submodel
     options : dict, optional
         A dictionary of options to be passed to the model.
-    """  # noqa: E501
+    """
 
     def __init__(self, param, domain, options=None):
         super().__init__(param, domain, options)

pybamm/parameters_cli.py

@@ -2,7 +2,7 @@ def raise_error():
     raise NotImplementedError(
         "parameters cli has been deprecated. "
         "Parameters should now be defined via python files (see "
-        "https://github.com/pybamm-team/PyBaMM/tree/develop/pybamm/input/parameters/lithium_ion/Ai2020.py"  # noqa: E501
+        "https://github.com/pybamm-team/PyBaMM/tree/develop/pybamm/input/parameters/lithium_ion/Ai2020.py"
         " for example)"
     )
 

pybamm/plotting/quick_plot.py

@@ -534,7 +534,7 @@ def plot(self, t, dynamic=False):
                 # 1D plot: plot as a function of x at time t
                 # Read dictionary of spatial variables
                 spatial_vars = self.spatial_variable_dict[key]
-                spatial_var_name = list(spatial_vars.keys())[0]
+                spatial_var_name = next(iter(spatial_vars.keys()))
                 ax.set_xlabel(
                     "{} [{}]".format(spatial_var_name, self.spatial_unit),
                 )
@@ -568,12 +568,12 @@ def plot(self, t, dynamic=False):
                 # different order based on whether the domains are x-r, x-z or y-z, etc
                 if self.x_first_and_y_second[key] is False:
                     x_name = list(spatial_vars.keys())[1][0]
-                    y_name = list(spatial_vars.keys())[0][0]
+                    y_name = next(iter(spatial_vars.keys()))[0]
                     x = self.second_spatial_variable[key]
                     y = self.first_spatial_variable[key]
                     var = variable(t_in_seconds, **spatial_vars, warn=False)
                 else:
-                    x_name = list(spatial_vars.keys())[0][0]
+                    x_name = next(iter(spatial_vars.keys()))[0]
                     y_name = list(spatial_vars.keys())[1][0]
                     x = self.first_spatial_variable[key]
                     y = self.second_spatial_variable[key]

pybamm/simulation.py

@@ -375,7 +375,7 @@ def set_initial_soc(self, initial_soc):
         param = self._model.param
         if options["open-circuit potential"] == "MSMR":
             self._parameter_values = (
-                self._unprocessed_parameter_values.set_initial_ocps(  # noqa: E501
+                self._unprocessed_parameter_values.set_initial_ocps(
                     initial_soc, param=param, inplace=False, options=options
                 )
             )