Migrate to PyBaMM 22.10

.gitignore

@@ -5,4 +5,6 @@ plot.png
 tempCodeRunnerFile.py
 plot.gif
 .coverage
-.ipynb_checkpoints
+.ipynb_checkpoints
+plot*.png
+.DS_Store

CONTRIBUTING.md

@@ -24,9 +24,9 @@ This will install all the dependencies in your local system including the latest
 
 4. To check if the installation worked, execute (this will take some time) - 
 ```bash
-python -m unittest
+python -m unittest -v
 # or if you haven't completed the pre-installation process, this -
-python -m unittest discover ./test/without_keys/
+python -m unittest discover ./test/without_keys/ -v
 ```
 **Note: The tests written in `with_keys` subdirectory will fail if you haven't completed the pre-installation process, again, you don't necessarily need the `Twitter Developer Account` to contribute to this repository.**
 

bot/plotting/comparison_generator.py

@@ -20,8 +20,8 @@ class ComparisonGenerator:
             }
             Provide only 1 model for "parameter comparison" and 2 or more models for
             "model comparison".
-        chemistry : dict
-            Chemistry for the models.
+        chemistry : str
+            A PyBaMM chemistry.
         is_experiment : bool
             If the comparison includes an experiment.
         params : pybamm.ParameterValues
@@ -163,7 +163,7 @@ def model_comparison(self, testing=False):
         )
 
         if self.is_experiment:
-            if self.chemistry == pybamm.parameter_sets.Ai2020:
+            if self.chemistry == "Ai2020":
                 batch_study.solve(calc_esoh=False)
             else:
                 batch_study.solve()
@@ -254,7 +254,7 @@ def parameter_comparison(self, testing=False):
         )
 
         if self.is_experiment:
-            if self.chemistry == pybamm.parameter_sets.Ai2020:
+            if self.chemistry == "Ai2020":
                 batch_study.solve(calc_esoh=False)
             else:
                 batch_study.solve()

bot/plotting/config_generator.py

@@ -6,10 +6,10 @@
 
 # possible chemistries for the bot
 chemistries = [
-    pybamm.parameter_sets.Ai2020,
-    pybamm.parameter_sets.Chen2020,
-    pybamm.parameter_sets.Marquis2019,
-    pybamm.parameter_sets.OKane2022
+    "Ai2020",
+    "Chen2020",
+    "Marquis2019",
+    "OKane2022"
 ]
 
 # possible "particle mechanics" for the bot, to be used with Ai2020 parameters
@@ -101,7 +101,7 @@ def config_generator(
         chemistry = test_config["chemistry"]
     # use only Mohtat2020 and SPM till others are fixed
     elif choice == "degradation comparison":
-        chemistry = pybamm.parameter_sets.Mohtat2020
+        chemistry = "Mohtat2020"
     else:
         chemistry = random.choice(chemistries)
     parameter_values = pybamm.ParameterValues(chemistry)
@@ -110,15 +110,15 @@ def config_generator(
     if choice == "degradation comparison":
 
         # add degradation / update model options
-        if chemistry == pybamm.parameter_sets.Ai2020:
+        if chemistry == "Ai2020":
             degradation_value = particle_mechanics_list[0]
             degradation_mode = "particle mechanics"
             model_options.update(
                 {
                     degradation_mode: degradation_value,
                 }
             )
-        elif chemistry == pybamm.parameter_sets.Mohtat2020:
+        elif chemistry == "Mohtat2020":
             if test_config["degradation_mode"] is None:
                 degradation_mode = random.choice(["SEI", "particle mechanics"])
             else:

bot/plotting/degradation_comparison_generator.py

@@ -12,8 +12,8 @@ class DegradationComparisonGenerator:
     ----------
         model : :class:`pybamm.BaseBatteryModel`
             Model to be used in the comparison.
-        chemistry : dict
-            Chemistry to be used in the comparison.
+        chemistry : str
+            A PyBaMM chemistry.
         param_values : list
             Parameter values with one degradation parameter varied. Should be of the
             form -
@@ -75,9 +75,9 @@ def create_simulation(self, experiment):
                 experiment=experiment,
                 parameter_values=self.param_values[i],
             )
-            if self.chemistry == pybamm.parameter_sets.Ai2020:  # pragma: no cover
+            if self.chemistry == "Ai2020":  # pragma: no cover
                 sim.solve(calc_esoh=False)
-            elif self.chemistry == pybamm.parameter_sets.Mohtat2020:
+            elif self.chemistry == "Mohtat2020":
                 sim.solve(initial_soc=1)
             else:  # pragma: no cover
                 sim.solve()
@@ -99,7 +99,7 @@ def solve(self):
         """
         Solves an experiment with the given configuration.
         """
-        if self.chemistry == pybamm.parameter_sets.Ai2020:  # pragma: no cover
+        if self.chemistry == "Ai2020":  # pragma: no cover
             experiment = pybamm.Experiment(self.cycle * self.number)
         else:
             experiment = pybamm.Experiment(
@@ -121,7 +121,7 @@ def generate_summary_variables(self):
         """
         Creates and saves a picture of summary variable comparison plot.
         """
-        if self.chemistry == pybamm.parameter_sets.Ai2020:  # pragma: no cover
+        if self.chemistry == "Ai2020":  # pragma: no cover
             vars_to_plot = [
                 "Measured capacity [A.h]",
                 "Loss of lithium inventory [%]",

bot/run-simulation.ipynb

@@ -151,7 +151,7 @@
     "if config[\"is_experiment\"] and not config[\"is_comparison\"]:\n",
     "\n",
     "    # don't terminate early if Ai2020 parameter sets were used\n",
-    "    if config[\"chemistry\"] == pybamm.parameter_sets.Ai2020:\n",
+    "    if config[\"chemistry\"] == \"Ai2020\":\n",
     "        experiment = pybamm.Experiment(\n",
     "            config[\"cycle\"] * config[\"number\"]\n",
     "        )\n",
@@ -163,7 +163,7 @@
     "    parameter_values = pybamm.ParameterValues(config[\"chemistry\"])\n",
     "\n",
     "    # update parameter sets for Mohtat2020 chemistry\n",
-    "    if config[\"chemistry\"] == pybamm.parameter_sets.Mohtat2020:\n",
+    "    if config[\"chemistry\"] == \"Mohtat2020\":\n",
     "        def lico2_volume_change_Ai2020(sto):\n",
     "            omega = pybamm.Parameter(\"Positive electrode partial molar volume [m3.mol-1]\")\n",
     "            c_p_max = pybamm.Parameter(\"Maximum concentration in positive electrode [mol.m-3]\")\n",
@@ -251,17 +251,17 @@
     "            parameter_values=param_list[i],\n",
     "        )\n",
     "\n",
-    "        if config[\"chemistry\"] == pybamm.parameter_sets.Ai2020:\n",
+    "        if config[\"chemistry\"] == \"Ai2020\":\n",
     "            sim.solve(calc_esoh=False)\n",
-    "        elif config[\"chemistry\"] == pybamm.parameter_sets.Mohtat2020:\n",
+    "        elif config[\"chemistry\"] == \"Mohtat2020\":\n",
     "            sim.solve(initial_soc=1)\n",
     "        else:\n",
     "            sim.solve()\n",
     "        solution = sim.solution\n",
     "        solutions.append(solution)\n",
     "\n",
     "    # defining the summary variables\n",
-    "    if config[\"chemistry\"] == pybamm.parameter_sets.Ai2020:\n",
+    "    if config[\"chemistry\"] == \"Ai2020\":\n",
     "        vars_to_plot = [\n",
     "            \"Measured capacity [A.h]\",\n",
     "            \"Loss of lithium inventory [%]\",\n",
@@ -406,7 +406,7 @@
     "        t_end = 3700\n",
     "\n",
     "    # solving\n",
-    "    if config[\"chemistry\"] == pybamm.parameter_sets.Ai2020:\n",
+    "    if config[\"chemistry\"] == \"Ai2020\":\n",
     "        s.solve([0, t_end], calc_esoh=False)\n",
     "    else:\n",
     "        s.solve([0, t_end])\n",
@@ -489,7 +489,7 @@
     "    )\n",
     "\n",
     "    # solving\n",
-    "    if config[\"chemistry\"] == pybamm.parameter_sets.Ai2020:\n",
+    "    if config[\"chemistry\"] == \"Ai2020\":\n",
     "        s.solve(calc_esoh=False)\n",
     "    else:\n",
     "        s.solve()\n",
@@ -526,7 +526,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -540,9 +540,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.0"
+   "version": "3.9.6"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}

bot/twitter_api/tweet_plot.py

@@ -28,7 +28,7 @@ def __init__(self, testing=False, choice=None):
         """
         Defines video tweet properties
         """
-        super().__init__()
+        # super().__init__()
         # create a random GIF
         while True:
             manager = multiprocessing.Manager()

bot/twitter_api/tweet_reply.py

@@ -127,11 +127,11 @@ def generate_reply(self, tweet_text, testing=False):
         models_for_comp = dict(list(enumerate(models)))
 
         if "chen2020" in text_list:
-            chemistry = pybamm.parameter_sets.Chen2020
+            chemistry = "Chen2020"
         elif "marquis2019" in text_list:
-            chemistry = pybamm.parameter_sets.Marquis2019
+            chemistry = "Marquis2019"
         elif "ai2020" in text_list:
-            chemistry = pybamm.parameter_sets.Ai2020
+            chemistry = "Ai2020"
         else:
             # if no chemistry is provided
             raise Exception(

bot/utils/degradation_parameter_generator.py

@@ -62,7 +62,7 @@ def degradation_parameter_generator(
 
     params = pybamm.ParameterValues(chemistry)
 
-    if chemistry == pybamm.parameter_sets.Mohtat2020:
+    if chemistry == "Mohtat2020":
         params.update(
             {
                 # mechanical properties
@@ -93,7 +93,7 @@ def degradation_parameter_generator(
             check_already_exists=False,
         )
     if degradation_mode == "particle mechanics":
-        if chemistry == pybamm.parameter_sets.Ai2020:
+        if chemistry == "Ai2020":
             degradation_parameters = {
                 "Negative electrode Paris' law constant b": {
                     "print_name": None,
@@ -136,7 +136,7 @@ def degradation_parameter_generator(
                     "bounds": (None, None),
                 },
             }
-        elif chemistry == pybamm.parameter_sets.Mohtat2020:
+        elif chemistry == "Mohtat2020":
             degradation_parameters = {
                 "Positive electrode LAM constant proportional term [s-1]": {
                     "print_name": None,

bot/utils/tweet_text_generator.py

@@ -1,3 +1,6 @@
+import pybamm
+
+
 def tweet_text_generator(
     chemistry,
     model,
@@ -15,7 +18,7 @@ def tweet_text_generator(
 
     Parameters
     ----------
-        chemistry : dict
+        chemistry : str
         model : :class:`pybamm.BaseBatteryModel` or dict
         is_experiment : bool
         cycle : list or None
@@ -34,6 +37,8 @@ def tweet_text_generator(
             Not none if the tweet text exceeds twitter limit.
     """
 
+    param_values = pybamm.ParameterValues(chemistry)
+
     if is_comparison:
         # calculate C-rate and Temperature to add in tweet text
         c_rate = round(
@@ -46,7 +51,7 @@ def tweet_text_generator(
     # summary variable
     if is_experiment and not is_comparison:
         tweet_text = (
-            f"Plotting {model.name} with {chemistry['citation']} "
+            f"Plotting {model.name} with {param_values['citations'][0]} "
             f"parameters and {degradation_value} {degradation_mode} "
             f"for the following experiment: {cycle} * {number}"
         )
@@ -58,21 +63,21 @@ def tweet_text_generator(
             if len(model) == 2:
                 tweet_text = (
                     f"Comparing {model[0].name} and {model[1].name} "
-                    f"with {chemistry['citation']} parameters at {temp}°C for the "
-                    f"following experiment: {cycle} * {number}"
+                    f"with {param_values['citations'][0]} parameters at {temp}°C for "
+                    f"the following experiment: {cycle} * {number}"
                 )
             else:
                 tweet_text = (
                     f"Comparing {model[0].name}, {model[1].name}, and "
-                    f"{model[2].name} with {chemistry['citation']} "
+                    f"{model[2].name} with {param_values['citations'][0]} "
                     f"parameters at {temp}°C for the following experiment: "
                     f"{cycle} * {number}"
                 )
         # comparing a single model and a single experiment while varying
         # a parameter
         elif param_to_vary is not None and is_comparison:
             tweet_text = (
-                f"{model[0].name} with {chemistry['citation']} parameters "
+                f"{model[0].name} with {param_values['citations'][0]} parameters "
                 f"varying '{param_to_vary}' at {temp}°C for the following experiment: "
                 f"{cycle} * {number}"
             )
@@ -85,20 +90,20 @@ def tweet_text_generator(
             if len(model) == 2:
                 tweet_text = (
                     f"Comparing {model[0].name} and {model[1].name} with "
-                    f"{chemistry['citation']} parameters for a {c_rate} C "
+                    f"{param_values['citations'][0]} parameters for a {c_rate} C "
                     f"discharge at {temp}°C"
                 )
             else:
                 tweet_text = (
                     f"Comparing {model[0].name}, {model[1].name}, and "
-                    f"{model[2].name} with {chemistry['citation']} "
+                    f"{model[2].name} with {param_values['citations'][0]} "
                     f"parameters for a {c_rate} C discharge at {temp}°C"
                 )
 
         # comparing a single model by varying a parameter value
         elif param_to_vary is not None and is_comparison:
             tweet_text = (
-                f"{model[0].name} with {chemistry['citation']} parameters "
+                f"{model[0].name} with {param_values['citations'][0]} parameters "
                 f"varying '{param_to_vary}' for a {c_rate} C discharge at "
                 f"{temp}°C"
             )

test/with_keys/test_tweet_plot.py

@@ -15,7 +15,7 @@ def test_tweet(self):
         assert os.path.exists(tweet.plot)
         self.assertIsNone(tweet.processing_info)
         self.assertIsInstance(tweet.model, pybamm.BaseModel)
-        self.assertIsInstance(tweet.chemistry, dict)
+        self.assertIsInstance(tweet.chemistry, str)
         self.assertIsInstance(tweet.is_experiment, bool)
         self.assertTrue(tweet.is_experiment)
         self.assertIsInstance(tweet.cycle, list)
@@ -48,7 +48,7 @@ def test_tweet(self):
         assert os.path.exists(tweet.plot)
         self.assertIsNone(tweet.processing_info)
         self.assertIsInstance(tweet.model, dict)
-        self.assertIsInstance(tweet.chemistry, dict)
+        self.assertIsInstance(tweet.chemistry, str)
         self.assertIsInstance(tweet.is_experiment, bool)
         self.assertIsInstance(tweet.is_comparison, bool)
         self.assertTrue(tweet.is_comparison)
@@ -79,7 +79,7 @@ def test_tweet(self):
         assert os.path.exists(tweet.plot)
         self.assertIsNone(tweet.processing_info)
         self.assertIsInstance(tweet.model, dict)
-        self.assertIsInstance(tweet.chemistry, dict)
+        self.assertIsInstance(tweet.chemistry, str)
         self.assertIsInstance(tweet.is_experiment, bool)
         self.assertIsInstance(tweet.is_comparison, bool)
         self.assertTrue(tweet.is_comparison)
@@ -113,7 +113,7 @@ def test_tweet(self):
             isinstance(tweet.model, dict)
             or isinstance(tweet.model, pybamm.BaseModel)
         )
-        self.assertIsInstance(tweet.chemistry, dict)
+        self.assertIsInstance(tweet.chemistry, str)
         self.assertIsInstance(tweet.is_experiment, bool)
         self.assertIsInstance(tweet.is_comparison, bool)
         self.assertIsInstance(tweet.testing, bool)