Rename cathode and anode

CHANGELOG.md

@@ -32,6 +32,7 @@
 
 ## Breaking changes
 
+-   All example notebooks in PyBaMM's GitHub repository must now include the command `pybamm.print_citations()`, otherwise the tests will fail. This is to encourage people to use this command to cite the relevant papers ([#1340](https://github.com/pybamm-team/PyBaMM/pull/1340))
 -   Notation has been homogenised to use positive and negative electrode (instead of cathode and anode). This applies to the parameter folders (now called `'positive_electrodes'` and `'negative_electrodes'`) and the options of `active_material` and `particle_cracking` submodels (now called `'positive'` and `'negative'`) ([#1337](https://github.com/pybamm-team/PyBaMM/pull/1337))
 -   `Interpolant` now takes `x` and `y` instead of a single `data` entry ([#1312](https://github.com/pybamm-team/PyBaMM/pull/1312))
 -   Boolean model options ('sei porosity change', 'convection') must now be given in string format ('true' or 'false' instead of True or False) ([#1280](https://github.com/pybamm-team/PyBaMM/pull/1280))

examples/notebooks/parameter-management.ipynb

@@ -146,11 +146,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "anodes\n",
+      "cathodes\n",
       "cells\n",
       "electrolytes\n",
       "experiments\n",
-      "negative_electrodes\n",
-      "positive_electrodes\n",
       "seis\n",
       "separators\n"
      ]
@@ -382,12 +382,33 @@
     "rm -rf lithium-ion"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## References\n",
+    "\n",
+    "The relevant papers for this notebook are:"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 14,
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[1] Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, Julian Taylor, Sebastian Berg, Nathaniel J. Smith, and others. Array programming with NumPy. Nature, 585(7825):357–362, 2020. doi:10.1038/s41586-020-2649-2.\n",
+      "[2] Valentin Sulzer, Scott G. Marquis, Robert Timms, Martin Robinson, and S. Jon Chapman. Python Battery Mathematical Modelling (PyBaMM). ECSarXiv. February, 2020. doi:10.1149/osf.io/67ckj.\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "pybamm.print_citations()"
+   ]
   }
  ],
  "metadata": {

examples/notebooks/parameter-values.ipynb

@@ -122,7 +122,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Marquis2019 chemistry set is {'chemistry': 'lithium-ion', 'cell': 'kokam_Marquis2019', 'negative electrode': 'graphite_mcmb2528_Marquis2019', 'separator': 'separator_Marquis2019', 'positive electrode': 'lico2_Marquis2019', 'electrolyte': 'lipf6_Marquis2019', 'experiment': '1C_discharge_from_full_Marquis2019', 'sei': 'example', 'citation': 'marquis2019asymptotic'}\n",
+      "Marquis2019 chemistry set is {'chemistry': 'lithium-ion', 'cell': 'kokam_Marquis2019', 'negative electrode': 'graphite_mcmb2528_Marquis2019', 'separator': 'separator_Marquis2019', 'positive electrode': 'lico2_Marquis2019', 'electrolyte': 'lipf6_Marquis2019', 'experiment': '1C_discharge_from_full_Marquis2019', 'sei': 'example', 'citation': 'Marquis2019'}\n",
       "Negative current collector thickness is 2.5e-05 m\n"
      ]
     }
@@ -154,7 +154,7 @@
       "parameter values are {'a': 4,\n",
       " 'b': 5,\n",
       " 'c': 6,\n",
-      " 'cube function': <function cubed at 0x7f10f48c6830>}\n"
+      " 'cube function': <function cubed at 0x7f256a6a2c20>}\n"
      ]
     }
    ],
@@ -184,8 +184,8 @@
       "parameter values are {'a': 4,\n",
       " 'b': 5,\n",
       " 'c': 6,\n",
-      " 'cube function': <function cubed at 0x7f10f48c6830>,\n",
-      " 'square function': <function squared at 0x7f10f48c6ef0>}\n"
+      " 'cube function': <function cubed at 0x7f256a6a2c20>,\n",
+      " 'square function': <function squared at 0x7f256a6a6a70>}\n"
      ]
     }
    ],
@@ -422,7 +422,7 @@
     {
      "data": {
       "text/plain": [
-       "{Variable(-0x32b84c9e07545152, u, children=[], domain=[], auxiliary_domains={}): Multiplication(-0x13c9e646b0e82c50, *, children=['-a', 'y[0:1]'], domain=[], auxiliary_domains={})}"
+       "{Variable(-0x2e6cebb54b15a377, u, children=[], domain=[], auxiliary_domains={}): Multiplication(0x666a98b3f8fc11c2, *, children=['-a', 'y[0:1]'], domain=[], auxiliary_domains={})}"
       ]
      },
      "execution_count": 12,

pybamm/parameters/parameter_values.py

@@ -5,6 +5,7 @@
 import pandas as pd
 import os
 import numbers
+import warnings
 from pprint import pformat
 from collections import defaultdict
 
@@ -152,6 +153,28 @@ def update_from_chemistry(self, chemistry):
         if "sei" in chemistry:
             component_groups += ["sei"]
 
+        if "anode" in chemistry.keys():
+            chemistry["negative electrode"] = chemistry["anode"]
+            warnings.warn(
+                "the 'anode' component notation will be deprecated in the next "
+                "release, as it has now been renamed to 'negative electrode'. "
+                "Simulation will continue passing the 'anode' component as 'negative "
+                "electrode' (it might overwrite any existing definition of the "
+                "component).",
+                DeprecationWarning,
+            )
+
+        if "cathode" in chemistry.keys():
+            chemistry["positive electrode"] = chemistry["cathode"]
+            warnings.warn(
+                "the 'cathode' component notation will be deprecated in the next "
+                "release, as it has now been renamed to 'positive electrode'. "
+                "Simulation will continue passing the 'cathode' component as 'positive "
+                "electrode' (it might overwrite any existing definition of the "
+                "component).",
+                DeprecationWarning,
+            )
+
         for component_group in component_groups:
             # Make sure component is provided
             try:

tests/unit/test_parameters/test_parameter_values.py

@@ -649,6 +649,17 @@ def some_function(self):
         self.assertEqual(df[1]["b"], "[function]some_function")
         self.assertEqual(df[1]["c"], "[data]some_data")
 
+    def test_deprecate_anode_cathode(self):
+        chemistry = pybamm.parameter_sets.Ecker2015
+        chemistry["anode"] = chemistry["negative electrode"]
+        with self.assertWarnsRegex(DeprecationWarning, "anode"):
+            pybamm.ParameterValues(chemistry=chemistry)
+
+        chemistry = pybamm.parameter_sets.Ecker2015
+        chemistry["cathode"] = chemistry["positive electrode"]
+        with self.assertWarnsRegex(DeprecationWarning, "cathode"):
+            pybamm.ParameterValues(chemistry=chemistry)
+
 
 if __name__ == "__main__":
     print("Add -v for more debug output")