Divide examples into folders (#559)

* Divide examples into folders * Update file paths * Update CHANGELOG.md --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
pybop-team · Nov 22, 2024 · 4116c5c · 4116c5c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ## Features
 
+- [#282](https://github.com/pybop-team/PyBOP/issues/282) - Restructures the examples directory.
 - [#396](https://github.com/pybop-team/PyBOP/issues/396) - Adds `ecm_with_tau.py` example script.
 - [#452](https://github.com/pybop-team/PyBOP/issues/452) - Extends `cell_mass` and `approximate_capacity` for half-cell models.
 - [#544](https://github.com/pybop-team/PyBOP/issues/544) - Allows iterative plotting using `StandardPlot`.

diff --git a/examples/scripts/Chen_example.csv → examples/data/Chen_example.csv b/examples/scripts/Chen_example.csv → examples/data/Chen_example.csv
diff --git a/examples/notebooks/ecm_trust-constr.ipynb → ...y_parameterisation/ecm_trust-constr.ipynb b/examples/notebooks/ecm_trust-constr.ipynb → ...y_parameterisation/ecm_trust-constr.ipynb
diff --git a/examples/notebooks/electrode_balancing.ipynb → ...arameterisation/electrode_balancing.ipynb b/examples/notebooks/electrode_balancing.ipynb → ...arameterisation/electrode_balancing.ipynb
diff --git a/...s/equivalent_circuit_identification.ipynb → ...n/equivalent_circuit_identification.ipynb b/...s/equivalent_circuit_identification.ipynb → ...n/equivalent_circuit_identification.ipynb
@@ -104,7 +104,7 @@
    "source": [
     "## Importing Parameters\n",
     "\n",
-    "This can be completed by importing a JSON representation, such as the one in the PyBOP [examples](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/parameters/initial_ecm_parameters.json). To import via JSON, either download the example file, or create your own and update the path below to reference the corresponding file."
+    "This can be completed by importing a JSON representation, such as the one in the PyBOP [examples](https://github.com/pybop-team/PyBOP/blob/develop/examples/parameters/initial_ecm_parameters.json). To import via JSON, either download the example file, or create your own and update the path below to reference the corresponding file."
    ]
   },
   {
@@ -115,7 +115,7 @@
    "outputs": [],
    "source": [
     "# parameter_set = pybop.ParameterSet(\n",
-    "# json_path=\"examples/scripts/parameters/initial_ecm_parameters.json\"\n",
+    "# json_path=\"examples/parameters/initial_ecm_parameters.json\"\n",
     "# )\n",
     "# parameter_set.import_parameters()"
    ]

diff --git a/...ivalent_circuit_identification_hppc.ipynb → ...ivalent_circuit_identification_hppc.ipynb b/...ivalent_circuit_identification_hppc.ipynb → ...ivalent_circuit_identification_hppc.ipynb
@@ -141,7 +141,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "file_loc = r\"../data/Samsung_INR21700/sample_hppc_pulse.xlsx\"\n",
+    "file_loc = r\"../../data/Samsung_INR21700/sample_hppc_pulse.xlsx\"\n",
     "df = pd.read_excel(file_loc, index_col=None, na_values=[\"NA\"])\n",
     "df = df.drop_duplicates(subset=[\"Time\"], keep=\"first\")\n",
     "\n",
@@ -459,7 +459,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "file_loc = r\"../data/Samsung_INR21700/sample_drive_cycle.xlsx\"\n",
+    "file_loc = r\"../../data/Samsung_INR21700/sample_drive_cycle.xlsx\"\n",
     "df = pd.read_excel(file_loc, sheet_name=\"Sheet3\", index_col=None, na_values=[\"NA\"])\n",
     "\n",
     "# Remove duplicate rows, keeping the first occurrence\n",

diff --git a/...t_circuit_identification_multipulse.ipynb → ...t_circuit_identification_multipulse.ipynb b/...t_circuit_identification_multipulse.ipynb → ...t_circuit_identification_multipulse.ipynb
@@ -144,7 +144,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "file_loc = r\"../data/Samsung_INR21700/multipulse_hppc.xlsx\"\n",
+    "file_loc = r\"../../data/Samsung_INR21700/multipulse_hppc.xlsx\"\n",
     "df = pd.read_excel(file_loc, index_col=None, na_values=[\"NA\"])\n",
     "df = df.drop_duplicates(subset=[\"Time\"], keep=\"first\")\n",
     "\n",

diff --git a/...ooks/monte_carlo_ecm_identification.ipynb → ...tion/monte_carlo_ecm_identification.ipynb b/...ooks/monte_carlo_ecm_identification.ipynb → ...tion/monte_carlo_ecm_identification.ipynb
@@ -63,7 +63,7 @@
    "outputs": [],
    "source": [
     "ocv_df = pd.read_csv(\n",
-    "    \"../data/Tesla_4680/T-cell_pOCV_data.txt\",\n",
+    "    \"../../data/Tesla_4680/T-cell_pOCV_data.txt\",\n",
     "    sep=\"\\t\",\n",
     "    decimal=\",\",\n",
     ")"
@@ -217,7 +217,7 @@
    ],
    "source": [
     "cycling_df = pd.read_csv(\n",
-    "    \"../data/Tesla_4680/601-828_Capacity_03_MB_CB1_subset.txt\",\n",
+    "    \"../../data/Tesla_4680/601-828_Capacity_03_MB_CB1_subset.txt\",\n",
     "    sep=\"\\t\",\n",
     ")\n",
     "filter_cycling = cycling_df.loc[54811:61000].copy()  # Full cycle is [54811:127689]\n",

diff --git a/...otebooks/multi_model_identification.ipynb → ...risation/multi_model_identification.ipynb b/...otebooks/multi_model_identification.ipynb → ...risation/multi_model_identification.ipynb
diff --git a/...notebooks/pouch_cell_identification.ipynb → ...erisation/pouch_cell_identification.ipynb b/...notebooks/pouch_cell_identification.ipynb → ...erisation/pouch_cell_identification.ipynb
diff --git a/...otebooks/single_pulse_circuit_model.ipynb → ...risation/single_pulse_circuit_model.ipynb b/...otebooks/single_pulse_circuit_model.ipynb → ...risation/single_pulse_circuit_model.ipynb
@@ -135,13 +135,15 @@
    "outputs": [],
    "source": [
     "ocp = loadmat(\n",
-    "    \"../data/LG_M50_ECM/data/LGM50_5Ah_OCV.mat\", simplify_cells=True, mat_dtype=False\n",
+    "    \"../../data/LG_M50_ECM/data/LGM50_5Ah_OCV.mat\", simplify_cells=True, mat_dtype=False\n",
     ")\n",
     "pulse_data = loadmat(\n",
-    "    \"../data/LG_M50_ECM/data/LGM50_5Ah_Pulse.mat\", simplify_cells=True, mat_dtype=False\n",
+    "    \"../../data/LG_M50_ECM/data/LGM50_5Ah_Pulse.mat\",\n",
+    "    simplify_cells=True,\n",
+    "    mat_dtype=False,\n",
     ")\n",
     "rate_data = loadmat(\n",
-    "    \"../data/LG_M50_ECM/data/LGM50_5Ah_RateTest.mat\",\n",
+    "    \"../../data/LG_M50_ECM/data/LGM50_5Ah_RateTest.mat\",\n",
     "    simplify_cells=True,\n",
     "    mat_dtype=False,\n",
     ")"

diff --git a/.../notebooks/comparing_cost_functions.ipynb → ...n_examples/comparing_cost_functions.ipynb b/.../notebooks/comparing_cost_functions.ipynb → ...n_examples/comparing_cost_functions.ipynb
diff --git a/...ooks/multi_optimiser_identification.ipynb → ...ples/multi_optimiser_identification.ipynb b/...ooks/multi_optimiser_identification.ipynb → ...ples/multi_optimiser_identification.ipynb
diff --git a/...les/notebooks/optimiser_calibration.ipynb → ...ison_examples/optimiser_calibration.ipynb b/...les/notebooks/optimiser_calibration.ipynb → ...ison_examples/optimiser_calibration.ipynb
diff --git a/examples/notebooks/solver_selection.ipynb → ...omparison_examples/solver_selection.ipynb b/examples/notebooks/solver_selection.ipynb → ...omparison_examples/solver_selection.ipynb
diff --git a/...books/energy_based_electrode_design.ipynb → ...ation/energy_based_electrode_design.ipynb b/...books/energy_based_electrode_design.ipynb → ...ation/energy_based_electrode_design.ipynb
diff --git a/...ples/notebooks/adamw_identification.ipynb → ...etting_started/adamw_identification.ipynb b/...ples/notebooks/adamw_identification.ipynb → ...etting_started/adamw_identification.ipynb
diff --git a/...ples/notebooks/cost_compute_methods.ipynb → ...etting_started/cost_compute_methods.ipynb b/...ples/notebooks/cost_compute_methods.ipynb → ...etting_started/cost_compute_methods.ipynb
diff --git a/examples/notebooks/creating_a_model.ipynb → ...ks/getting_started/creating_a_model.ipynb b/examples/notebooks/creating_a_model.ipynb → ...ks/getting_started/creating_a_model.ipynb
diff --git a/...ples/notebooks/maximum_a_posteriori.ipynb → ...etting_started/maximum_a_posteriori.ipynb b/...ples/notebooks/maximum_a_posteriori.ipynb → ...etting_started/maximum_a_posteriori.ipynb
diff --git a/examples/notebooks/optimiser_interface.ipynb → ...getting_started/optimiser_interface.ipynb b/examples/notebooks/optimiser_interface.ipynb → ...getting_started/optimiser_interface.ipynb
@@ -104,7 +104,7 @@
    "source": [
     "# Load the parameters\n",
     "parameter_set = pybop.ParameterSet(\n",
-    "    json_path=\"../scripts/parameters/initial_ecm_parameters.json\"\n",
+    "    json_path=\"../../parameters/initial_ecm_parameters.json\"\n",
     ")\n",
     "parameter_set.import_parameters()\n",
     "# Define the model\n",

diff --git a/...tebooks/transformation_introduction.ipynb → ...started/transformation_introduction.ipynb b/...tebooks/transformation_introduction.ipynb → ...started/transformation_introduction.ipynb
diff --git a/examples/scripts/parameters/example_BPX.json → examples/parameters/example_BPX.json b/examples/scripts/parameters/example_BPX.json → examples/parameters/example_BPX.json
diff --git a/...ts/parameters/initial_ecm_parameters.json → ...es/parameters/initial_ecm_parameters.json b/...ts/parameters/initial_ecm_parameters.json → ...es/parameters/initial_ecm_parameters.json
diff --git a/examples/scripts/ecm_CMAES.py → ...pts/battery_parameterisation/ecm_CMAES.py b/examples/scripts/ecm_CMAES.py → ...pts/battery_parameterisation/ecm_CMAES.py
diff --git a/examples/scripts/ecm_tau_constraints.py → ...y_parameterisation/ecm_tau_constraints.py b/examples/scripts/ecm_tau_constraints.py → ...y_parameterisation/ecm_tau_constraints.py
diff --git a/examples/scripts/ecm_with_tau.py → .../battery_parameterisation/ecm_with_tau.py b/examples/scripts/ecm_with_tau.py → .../battery_parameterisation/ecm_with_tau.py
diff --git a/examples/scripts/eis_fitting.py → ...s/battery_parameterisation/eis_fitting.py b/examples/scripts/eis_fitting.py → ...s/battery_parameterisation/eis_fitting.py
diff --git a/examples/scripts/gitt.py → .../scripts/battery_parameterisation/gitt.py b/examples/scripts/gitt.py → .../scripts/battery_parameterisation/gitt.py
diff --git a/examples/scripts/ocp_balancing.py → ...battery_parameterisation/ocp_balancing.py b/examples/scripts/ocp_balancing.py → ...battery_parameterisation/ocp_balancing.py
diff --git a/examples/scripts/cuckoo.py → ...les/scripts/comparison_examples/cuckoo.py b/examples/scripts/cuckoo.py → ...les/scripts/comparison_examples/cuckoo.py
diff --git a/examples/scripts/exp_UKF.py → ...es/scripts/comparison_examples/exp_UKF.py b/examples/scripts/exp_UKF.py → ...es/scripts/comparison_examples/exp_UKF.py
diff --git a/examples/scripts/maximum_a_posteriori.py → ...mparison_examples/maximum_a_posteriori.py b/examples/scripts/maximum_a_posteriori.py → ...mparison_examples/maximum_a_posteriori.py
diff --git a/examples/scripts/maximum_likelihood.py → ...comparison_examples/maximum_likelihood.py b/examples/scripts/maximum_likelihood.py → ...comparison_examples/maximum_likelihood.py
diff --git a/examples/scripts/selecting_a_solver.py → ...comparison_examples/selecting_a_solver.py b/examples/scripts/selecting_a_solver.py → ...comparison_examples/selecting_a_solver.py
diff --git a/examples/scripts/spm_AdamW.py → .../scripts/comparison_examples/spm_AdamW.py b/examples/scripts/spm_AdamW.py → .../scripts/comparison_examples/spm_AdamW.py
diff --git a/examples/scripts/spm_CMAES.py → .../scripts/comparison_examples/spm_CMAES.py b/examples/scripts/spm_CMAES.py → .../scripts/comparison_examples/spm_CMAES.py
diff --git a/examples/scripts/spm_IRPropMin.py → ...ipts/comparison_examples/spm_IRPropMin.py b/examples/scripts/spm_IRPropMin.py → ...ipts/comparison_examples/spm_IRPropMin.py
diff --git a/examples/scripts/spm_NelderMead.py → ...pts/comparison_examples/spm_NelderMead.py b/examples/scripts/spm_NelderMead.py → ...pts/comparison_examples/spm_NelderMead.py
diff --git a/examples/scripts/spm_SNES.py → ...s/scripts/comparison_examples/spm_SNES.py b/examples/scripts/spm_SNES.py → ...s/scripts/comparison_examples/spm_SNES.py
diff --git a/examples/scripts/spm_UKF.py → ...es/scripts/comparison_examples/spm_UKF.py b/examples/scripts/spm_UKF.py → ...es/scripts/comparison_examples/spm_UKF.py
diff --git a/examples/scripts/spm_XNES.py → ...s/scripts/comparison_examples/spm_XNES.py b/examples/scripts/spm_XNES.py → ...s/scripts/comparison_examples/spm_XNES.py
diff --git a/examples/scripts/spm_descent.py → ...cripts/comparison_examples/spm_descent.py b/examples/scripts/spm_descent.py → ...cripts/comparison_examples/spm_descent.py
diff --git a/examples/scripts/spm_pso.py → ...es/scripts/comparison_examples/spm_pso.py b/examples/scripts/spm_pso.py → ...es/scripts/comparison_examples/spm_pso.py
diff --git a/examples/scripts/spm_scipymin.py → ...ripts/comparison_examples/spm_scipymin.py b/examples/scripts/spm_scipymin.py → ...ripts/comparison_examples/spm_scipymin.py
@@ -3,7 +3,7 @@
 import pybop
 
 # Form dataset
-Measurements = pd.read_csv("examples/scripts/Chen_example.csv", comment="#").to_numpy()
+Measurements = pd.read_csv("examples/data/Chen_example.csv", comment="#").to_numpy()
 dataset = pybop.Dataset(
     {
         "Time [s]": Measurements[:, 0],

diff --git a/examples/scripts/maximising_energy.py → .../design_optimisation/maximising_energy.py b/examples/scripts/maximising_energy.py → .../design_optimisation/maximising_energy.py
diff --git a/examples/scripts/maximising_power.py → ...s/design_optimisation/maximising_power.py b/examples/scripts/maximising_power.py → ...s/design_optimisation/maximising_power.py
diff --git a/examples/scripts/BPX_spm.py → examples/scripts/getting_started/BPX_spm.py b/examples/scripts/BPX_spm.py → examples/scripts/getting_started/BPX_spm.py
diff --git a/examples/scripts/functional_parameters.py → .../getting_started/functional_parameters.py b/examples/scripts/functional_parameters.py → .../getting_started/functional_parameters.py
diff --git a/examples/scripts/linked_parameters.py → ...ipts/getting_started/linked_parameters.py b/examples/scripts/linked_parameters.py → ...ipts/getting_started/linked_parameters.py
diff --git a/examples/scripts/mcmc_example.py → ...s/scripts/getting_started/mcmc_example.py b/examples/scripts/mcmc_example.py → ...s/scripts/getting_started/mcmc_example.py
diff --git a/examples/scripts/multi_fitting.py → .../scripts/getting_started/multi_fitting.py b/examples/scripts/multi_fitting.py → .../scripts/getting_started/multi_fitting.py
diff --git a/examples/scripts/spm_weighted_cost.py → ...ipts/getting_started/spm_weighted_cost.py b/examples/scripts/spm_weighted_cost.py → ...ipts/getting_started/spm_weighted_cost.py
diff --git a/tests/integration/test_monte_carlo_thevenin.py b/tests/integration/test_monte_carlo_thevenin.py
@@ -40,7 +40,7 @@ def setup(self):
     @pytest.fixture
     def model(self):
         parameter_set = pybop.ParameterSet(
-            json_path="examples/scripts/parameters/initial_ecm_parameters.json"
+            json_path="examples/parameters/initial_ecm_parameters.json"
         )
         parameter_set.import_parameters()
         parameter_set.params.update(

diff --git a/tests/integration/test_thevenin_parameterisation.py b/tests/integration/test_thevenin_parameterisation.py
@@ -20,7 +20,7 @@ def setup(self):
     @pytest.fixture
     def model(self):
         parameter_set = pybop.ParameterSet(
-            json_path="examples/scripts/parameters/initial_ecm_parameters.json"
+            json_path="examples/parameters/initial_ecm_parameters.json"
         )
         parameter_set.import_parameters()
         parameter_set.params.update(

diff --git a/tests/integration/test_transformation.py b/tests/integration/test_transformation.py
@@ -21,7 +21,7 @@ def setup(self):
     @pytest.fixture
     def model(self):
         parameter_set = pybop.ParameterSet(
-            json_path="examples/scripts/parameters/initial_ecm_parameters.json"
+            json_path="examples/parameters/initial_ecm_parameters.json"
         )
         parameter_set.import_parameters()
         parameter_set.params.update(

diff --git a/tests/unit/test_models.py b/tests/unit/test_models.py
@@ -355,7 +355,7 @@ def test_basemodel(self):
     @pytest.mark.unit
     def test_thevenin_model(self):
         parameter_set = pybop.ParameterSet(
-            json_path="examples/scripts/parameters/initial_ecm_parameters.json"
+            json_path="examples/parameters/initial_ecm_parameters.json"
         )
         parameter_set.import_parameters()
         assert parameter_set["Open-circuit voltage [V]"] == "default"

diff --git a/tests/unit/test_parameter_sets.py b/tests/unit/test_parameter_sets.py
@@ -38,7 +38,7 @@ def test_ecm_parameter_sets(self):
             json_params.import_parameters()
 
         json_params = pybop.ParameterSet(
-            json_path="examples/scripts/parameters/initial_ecm_parameters.json"
+            json_path="examples/parameters/initial_ecm_parameters.json"
         )
         json_params.import_parameters()
 
@@ -94,14 +94,14 @@ def test_ecm_parameter_sets(self):
             ),
         )
         params.export_parameters(
-            "examples/scripts/parameters/fit_ecm_parameters.json", fit_params=parameters
+            "examples/parameters/fit_ecm_parameters.json", fit_params=parameters
         )
 
         # Test error when there no parameters to export
         empty_params = pybop.ParameterSet()
         with pytest.raises(ValueError):
             empty_params.export_parameters(
-                "examples/scripts/parameters/fit_ecm_parameters.json"
+                "examples/parameters/fit_ecm_parameters.json"
             )
 
     @pytest.mark.unit
@@ -115,7 +115,7 @@ def test_bpx_parameter_sets(self):
             bpx_parameters.import_from_bpx()
 
         bpx_parameters = pybop.ParameterSet(
-            json_path="examples/scripts/parameters/example_BPX.json"
+            json_path="examples/parameters/example_BPX.json"
         )
         bpx_parameters.import_from_bpx()