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Replace pybop.MAP with pybop.LogPosterior #483

Merged
merged 17 commits into from
Sep 9, 2024
Merged

Replace pybop.MAP with pybop.LogPosterior #483

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0e3a1c0
refactor: removes pybop.MAP with replacement pybop.LogPosterior, adds…
BradyPlanden Sep 4, 2024
936e5e9
Update notebook, add type hints + docstring update
BradyPlanden Sep 5, 2024
03e096c
fix: updates for pybamm v24.9, adds IDAKLU t_interp functionality
BradyPlanden Sep 5, 2024
843d471
examples: restore scripts
BradyPlanden Sep 5, 2024
a3b2a54
tests: adds observer integration tests, small tidy to observer unit test
BradyPlanden Sep 6, 2024
47365f0
fix: convergence improvement for tau constrained thevenin example
BradyPlanden Sep 6, 2024
3760fac
examples: reduces runtime across examples
BradyPlanden Sep 6, 2024
831bc90
examples: adds example for cost/likelihood class evaluation and compute
BradyPlanden Aug 22, 2024
f9a1c23
examples: updates formatting and grammar
BradyPlanden Aug 28, 2024
3b0d43d
examples: update MAP notebook
BradyPlanden Sep 6, 2024
856305e
Merge branch 'refs/heads/develop' into 459-replace-MAP-class
BradyPlanden Sep 8, 2024
0c69dad
examples: additions to MAP notebook
BradyPlanden Sep 9, 2024
f3a7b2c
tests: adds non logpdfS1 prior test for LogPosterior class
BradyPlanden Sep 9, 2024
79ad4f6
tests: adds parameters.__repr__ tests
BradyPlanden Sep 9, 2024
ef18243
examples: adds "notebook_connect" renderer
BradyPlanden Sep 9, 2024
04d1d19
examples: small fixes to maximum_a_posteriori.ipynb
BradyPlanden Sep 9, 2024
9018f75
apply suggestions from review
BradyPlanden Sep 9, 2024
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39 changes: 5 additions & 34 deletions examples/notebooks/comparing_cost_functions.ipynb
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Expand Up @@ -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",
Expand Down Expand Up @@ -206,7 +177,7 @@
{
"data": {
"text/plain": [
"2.0269652551213878e-10"
"1.1753460077019054e-09"
]
},
"execution_count": null,
Expand Down Expand Up @@ -240,7 +211,7 @@
{
"data": {
"text/plain": [
"2.0269652551213878e-10"
"1.1753460077019054e-09"
]
},
"execution_count": null,
Expand Down Expand Up @@ -269,13 +240,13 @@
"name": "stdout",
"output_type": "stream",
"text": [
"[8.19241247e-05 5.09035035e-06]\n"
"[7.60957550e-05 5.48691392e-06]\n"
]
},
{
"data": {
"text/plain": [
"0.030472774516224807"
"0.014466627355628724"
]
},
"execution_count": null,
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21 changes: 0 additions & 21 deletions examples/notebooks/cost-compute-methods.ipynb
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Expand Up @@ -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",
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878 changes: 878 additions & 0 deletions examples/notebooks/maximum_a_posteriori.ipynb
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31 changes: 1 addition & 30 deletions examples/notebooks/multi_model_identification.ipynb
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Expand Up @@ -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"
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4 changes: 2 additions & 2 deletions examples/scripts/spm_MAP.py
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Expand Up @@ -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,
Expand Down
1 change: 0 additions & 1 deletion pybop/__init__.py
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Expand Up @@ -111,7 +111,6 @@
GaussianLogLikelihood,
GaussianLogLikelihoodKnownSigma,
LogPosterior,
MAP,
)
from .costs._weighted_cost import WeightedCost

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