Merge branch 'pybamm-team:develop' into jax_cli

.github/workflows/test_on_push.yml

@@ -87,16 +87,16 @@ jobs:
       if: matrix.os == 'ubuntu-latest'
       run: tox -e pybamm-requires
 
-    - name: Run unit tests for GNU/Linux with Python 3.8 and 3.9
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version != 3.7
+    - name: Run unit tests for GNU/Linux with Python 3.7 and 3.8
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version != 3.9
       run: python -m tox -e unit
 
-    - name: Run unit tests for GNU/Linux with Python 3.7 and generate coverage report
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7
+    - name: Run unit tests for GNU/Linux with Python 3.9 and generate coverage report
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
       run: tox -e coverage
 
     - name: Upload coverage report
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
       uses: codecov/codecov-action@v2.1.0
 
     - name: Run integration tests for GNU/Linux

CHANGELOG.md

@@ -6,7 +6,9 @@
 
 ## Bug fixes
 
+-   Parameters can now be imported from any given path in `Windows` ([#1900](https://github.com/pybamm-team/PyBaMM/pull/1900))
 -   Fixed initial conditions for the EC SEI model ([#1895](https://github.com/pybamm-team/PyBaMM/pull/1895))
+-   Fixed issue in extraction of sensitivites ([#1894](https://github.com/pybamm-team/PyBaMM/pull/1894))
 
 # [v21.12](https://github.com/pybamm-team/PyBaMM/tree/v21.11) - 2021-12-29
 
@@ -17,7 +19,6 @@
 -   Added cylindrical geometry and finite volume method ([#1824](https://github.com/pybamm-team/PyBaMM/pull/1824))
 
 ## Bug fixes
-
 -   `PyBaMM` is now importable in `Linux` systems where `jax` is already installed ([#1874](https://github.com/pybamm-team/PyBaMM/pull/1874))
 -   Simulations with drive cycles now support `initial_soc` ([#1842](https://github.com/pybamm-team/PyBaMM/pull/1842))
 -   Fixed bug in expression tree simplification ([#1831](https://github.com/pybamm-team/PyBaMM/pull/1831))

pybamm/parameters/parameter_values.py

@@ -942,8 +942,13 @@ def find_parameter(path):
         """Look for parameter file in the different locations
         in PARAMETER_PATH
         """
+        # Check for absolute path
+        if os.path.isfile(path) and os.path.isabs(path):
+            pybamm.logger.verbose(f"Using absolute path: '{path}'")
+            return path
         for location in pybamm.PARAMETER_PATH:
             trial_path = os.path.join(location, path)
             if os.path.isfile(trial_path):
+                pybamm.logger.verbose(f"Using path: '{location}' + '{path}'")
                 return trial_path
         raise FileNotFoundError("Could not find parameter {}".format(path))

pybamm/solvers/base_solver.py

@@ -1459,7 +1459,12 @@ def _set_up_ext_and_inputs(
                 inputs[name] = casadi.MX.sym(name, input_param._expected_size)
 
         external_variables = external_variables or {}
-        ext_and_inputs = {**external_variables, **inputs}
+
+        ordered_inputs_names = list(inputs.keys())
+        ordered_inputs_names.sort()
+        ordered_inputs = {name: inputs[name] for name in ordered_inputs_names}
+
+        ext_and_inputs = {**external_variables, **ordered_inputs}
         return ext_and_inputs
 
 

pybamm/solvers/processed_variable.py

@@ -351,10 +351,14 @@ def initialise_2D(self):
             self.second_dimension = "x"
             self.R_sol = first_dim_pts
             self.x_sol = second_dim_pts
-        elif self.domain[0] in [
-            "negative particle size",
-            "positive particle size",
-        ] and self.auxiliary_domains["secondary"] == ["current collector"]:
+        elif (
+            self.domain[0]
+            in [
+                "negative particle size",
+                "positive particle size",
+            ]
+            and self.auxiliary_domains["secondary"] == ["current collector"]
+        ):
             self.first_dimension = "R"
             self.second_dimension = "z"
             self.R_sol = first_dim_pts
@@ -563,6 +567,7 @@ def initialise_sensitivity_explicit_forward(self):
             name: casadi.MX.sym(name, value.shape[0])
             for name, value in self.all_inputs[0].items()
         }
+
         p_casadi_stacked = casadi.vertcat(*[p for p in p_casadi.values()])
 
         # Convert variable to casadi format for differentiating

pybamm/util.py

@@ -284,19 +284,38 @@ def load_function(filename):
     # Assign path to _ and filename to tail
     _, tail = os.path.split(filename)
 
+    # Store the current working directory
+    orig_dir = os.getcwd()
+
     # Strip absolute path to pybamm/input/example.py
     if "pybamm" in filename:
         root_path = filename[filename.rfind("pybamm") :]
+    # If the function is in the current working directory
     elif os.getcwd() in filename:
+        root_path = filename.replace(os.getcwd(), "")
+        # getcwd() returns "C:\\" when in the root drive and "C:\\a\\b\\c" otherwise
+        if root_path[0] == "\\" or root_path[0] == "/":
+            root_path = root_path[1:]
+    # If the function is not in the current working directory and the path provided is
+    # absolute
+    elif os.path.isabs(filename) and not os.getcwd() in filename:   # pragma: no cover
+        # Change directory to import the function
+        dir_path = os.path.split(filename)[0]
+        os.chdir(dir_path)
         root_path = filename.replace(os.getcwd(), "")
         root_path = root_path[1:]
     else:
         root_path = filename
 
     path = root_path.replace("/", ".")
     path = path.replace("\\", ".")
+    pybamm.logger.debug(
+        f"Importing function '{tail}' from file '{filename}' via path '{path}'"
+    )
     module_object = importlib.import_module(path)
 
+    # Revert back current working directory if it was changed
+    os.chdir(orig_dir)
     return getattr(module_object, tail)
 
 

tests/unit/test_expression_tree/test_operations/test_convert_to_casadi.py

@@ -119,7 +119,6 @@ def test_special_functions(self):
         for np_fun in [
             np.sqrt,
             np.tanh,
-            np.cosh,
             np.sinh,
             np.exp,
             np.log,
@@ -133,6 +132,21 @@ def test_special_functions(self):
                 pybamm.Function(np_fun, c).to_casadi(), casadi.MX(np_fun(3)), evalf=True
             )
 
+        # A workaround to fix the tests running on GitHub Actions -
+        # casadi.evalf(
+        #       pybamm.Function(np_fun, c).to_casadi()
+        # ) - casadi.evalf(casadi.MX(np_fun(3)))
+        # is not zero, but a small number of the order 10^-15 when np_func is np.cosh
+        for np_fun in [
+            np.cosh
+        ]:
+            self.assert_casadi_almost_equal(
+                pybamm.Function(np_fun, c).to_casadi(),
+                casadi.MX(np_fun(3)),
+                decimal=14,
+                evalf=True,
+            )
+
         # test functions with assert_casadi_almost_equal
         for np_fun in [special.erf]:
             self.assert_casadi_almost_equal(

tests/unit/test_parameters/test_parameter_values.py

@@ -60,6 +60,18 @@ def test_init(self):
         )
         self.assertEqual(param["Positive electrode porosity"], 0.3)
 
+        # from file, absolute path
+        param = pybamm.ParameterValues(
+            os.path.join(
+                pybamm.root_dir(),
+                "pybamm",
+                "input",
+                "parameters",
+                "lithium_ion/positive_electrodes/lico2_Marquis2019/parameters.csv",
+            )
+        )
+        self.assertEqual(param["Positive electrode porosity"], 0.3)
+
         # values vs chemistry
         with self.assertRaisesRegex(
             ValueError, "values and chemistry cannot both be None"

tests/unit/test_solvers/test_casadi_solver.py

@@ -589,9 +589,10 @@ def test_solve_sensitivity_scalar_var_scalar_input(self):
         solution = solver.solve(
             model,
             t_eval,
-            inputs={"p": 0.1, "q": 2, "r": -1, "s": 0.5},
+            inputs={"r": -1, "s": 0.5, "q": 2, "p": 0.1},
             calculate_sensitivities=True,
         )
+
         np.testing.assert_allclose(solution.y[0], -1 + 0.2 * solution.t)
         np.testing.assert_allclose(
             solution.sensitivities["p"],