Merge pull request #483 from pybop-team/459-replace-MAP-class

Replace `pybop.MAP` with `pybop.LogPosterior`
pybop-team · Sep 9, 2024 · 1822ddb · 1822ddb
2 parents eb5a632 + 9018f75
commit 1822ddb
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Showing 18 changed files with 1,040 additions and 303 deletions.
diff --git a/examples/notebooks/comparing_cost_functions.ipynb b/examples/notebooks/comparing_cost_functions.ipynb
@@ -15,36 +15,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Note: you may need to restart the kernel to use updated packages.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Note: you may need to restart the kernel to use updated packages.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%pip install --upgrade pip ipywidgets -q\n",
     "%pip install pybop -q\n",
@@ -206,7 +177,7 @@
     {
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+       "1.1753460077019054e-09"
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@@ -240,7 +211,7 @@
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@@ -269,13 +240,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[8.19241247e-05 5.09035035e-06]\n"
+      "[7.60957550e-05 5.48691392e-06]\n"
      ]
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+       "0.014466627355628724"
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      "execution_count": null,

diff --git a/examples/notebooks/cost-compute-methods.ipynb b/examples/notebooks/cost-compute-methods.ipynb
@@ -19,27 +19,6 @@
    "id": "1",
    "metadata": {},
    "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Note: you may need to restart the kernel to use updated packages.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",

diff --git a/examples/notebooks/maximum_a_posteriori.ipynb b/examples/notebooks/maximum_a_posteriori.ipynb
diff --git a/examples/notebooks/multi_model_identification.ipynb b/examples/notebooks/multi_model_identification.ipynb
@@ -25,36 +25,7 @@
     "id": "X87NUGPW04py",
     "outputId": "0d785b07-7cff-4aeb-e60a-4ff5a669afbf"
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Note: you may need to restart the kernel to use updated packages.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "/Users/engs2510/Documents/Git/PyBOP/.nox/notebooks-overwrite/bin/python3: No module named pip\r\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Note: you may need to restart the kernel to use updated packages.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%pip install --upgrade pip ipywidgets pybamm -q\n",
     "%pip install pybop -q"

diff --git a/examples/scripts/spm_MAP.py b/examples/scripts/spm_MAP.py
@@ -60,8 +60,8 @@
 
 # Generate problem, cost function, and optimisation class
 problem = pybop.FittingProblem(model, parameters, dataset)
-cost = pybop.MAP(problem, pybop.GaussianLogLikelihoodKnownSigma, sigma0=sigma)
-optim = pybop.AdamW(
+cost = pybop.LogPosterior(pybop.GaussianLogLikelihoodKnownSigma(problem, sigma0=sigma))
+optim = pybop.IRPropMin(
     cost,
     sigma0=0.05,
     max_unchanged_iterations=20,

diff --git a/pybop/__init__.py b/pybop/__init__.py
@@ -111,7 +111,6 @@
     GaussianLogLikelihood,
     GaussianLogLikelihoodKnownSigma,
     LogPosterior,
-    MAP,
 )
 from .costs._weighted_cost import WeightedCost