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Clean up API documentation #559

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Jul 27, 2021
Merged

Clean up API documentation #559

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31bc57e
docs: fix broken link in README.md
wd15 Mar 29, 2021
fd2dc8b
docs: update readme with correct link for examples
wd15 Jul 17, 2021
07504c7
Merge branch 'master' into issue547-api
wd15 Jul 17, 2021
186cb23
doc: clean up api
wd15 Jul 19, 2021
76bce9f
docs: clean up api
wd15 Jul 20, 2021
05029ef
doc: improve test documentation
wd15 Jul 20, 2021
2c1b585
docs(notebooks): prevent fig object showing up
wd15 Jul 20, 2021
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13 changes: 7 additions & 6 deletions README.md
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Expand Up @@ -42,15 +42,16 @@ and localization linkages, and tools for discretizing the microstructure. In add
PyMKS has modules for generating synthetic data sets using conventional numerical
simulations.

To learn about PyMKS start with the [PyMKS examples](./index.ipynb),
especially the [introductory example](notebooks/intro.ipynb).
To learn more about the methods consult the
[technical overview](http://pymks.org/en/stable/rst/notebooks/tech_overview.html)
To learn about PyMKS start with the [PyMKS
examples](http://pymks.org/en/stable/EXAMPLES.rst), especially the
[introductory example](notebooks/intro.ipynb). To learn more about the
methods consult the [technical overview](notebooks/tech_overview.html)
for an introduction.


The two principle objects that PyMKS provides are the
`TwoPointCorrelation` transformer and the `LocalizationRegressor`
[`TwoPointCorrelation`](http://pymks.org/en/stable/API.html#pymks.TwoPointCorrelation)
transformer and the
[`LocalizationRegressor`](http://pymks.org/en/stable/API.html#pymks.LocalizationRegressor)
which provide the homogenization and localization functionality. The
objects provided by PyMKS all work as either transformers or
regressors in a Scikit-Learn pipeline and use both Numpy and Dask
Expand Down
1 change: 1 addition & 0 deletions doc/EXAMPLES.rst
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Expand Up @@ -23,6 +23,7 @@ Homogenization

rst/notebooks/stress.ipynb
rst/notebooks/fiber.ipynb
rst/notebooks/graph-descriptors.ipynb

Localization
------------
Expand Down
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10 changes: 5 additions & 5 deletions notebooks/cahn_hilliard.ipynb
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Expand Up @@ -348,7 +348,7 @@
}
],
"source": [
"plot_microstructures(x_data[0], y_data[0], titles=(\"Input Concentration\", \"Output Concentration\"))"
"plot_microstructures(x_data[0], y_data[0], titles=(\"Input Concentration\", \"Output Concentration\"));"
]
},
{
Expand Down Expand Up @@ -579,7 +579,7 @@
" coeff.real[..., 2],\n",
" coeff.real[..., 3],\n",
" titles=['Influence Coeff {0}'.format(i) for i in range(4)]\n",
")"
");"
]
},
{
Expand Down Expand Up @@ -654,7 +654,7 @@
}
],
"source": [
"plot_microstructures(y_test[0], y_predict.reshape((1, 41, 41))[0], titles=('Simulation', 'MKS Prediction'))"
"plot_microstructures(y_test[0], y_predict.reshape((1, 41, 41))[0], titles=('Simulation', 'MKS Prediction'));"
]
},
{
Expand Down Expand Up @@ -752,7 +752,7 @@
}
],
"source": [
"plot_microstructures(y_large[0], y_large_predict.reshape(shape)[0], titles=('Simulation', 'MKS Prediction'))"
"plot_microstructures(y_large[0], y_large_predict.reshape(shape)[0], titles=('Simulation', 'MKS Prediction'));"
]
},
{
Expand Down Expand Up @@ -780,7 +780,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.6"
"version": "3.8.5"
}
},
"nbformat": 4,
Expand Down
14 changes: 7 additions & 7 deletions notebooks/cahn_hilliard_legendre.ipynb
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Expand Up @@ -144,7 +144,7 @@
}
],
"source": [
"plot_microstructures(x_data[0], y_data[0], titles=(\"Input Concentration\", \"Output Concentration\"))"
"plot_microstructures(x_data[0], y_data[0], titles=(\"Input Concentration\", \"Output Concentration\"));"
]
},
{
Expand Down Expand Up @@ -335,7 +335,7 @@
}
],
"source": [
"plot_microstructures(*(primitive_coeff[:, :, i] for i in range(4)))"
"plot_microstructures(*(primitive_coeff[:, :, i] for i in range(4)));"
]
},
{
Expand Down Expand Up @@ -364,7 +364,7 @@
}
],
"source": [
"plot_microstructures(*(legendre_coeff[:, :, i] for i in range(4)))"
"plot_microstructures(*(legendre_coeff[:, :, i] for i in range(4)));"
]
},
{
Expand Down Expand Up @@ -436,7 +436,7 @@
" y_primitive[0],\n",
" y_test1[0],\n",
" titles=('Legendre', 'Primitive', 'Simulation')\n",
")"
");"
]
},
{
Expand Down Expand Up @@ -553,7 +553,7 @@
}
],
"source": [
"plot_microstructures(x_large[0], y_large[0], titles=['Initial Concentration', 'Final Concentration'])"
"plot_microstructures(x_large[0], y_large[0], titles=['Initial Concentration', 'Final Concentration']);"
]
},
{
Expand Down Expand Up @@ -597,7 +597,7 @@
" y_primitive_large[0],\n",
" y_legendre_large[0],\n",
" titles=('Simulation', 'Primitive', 'Legendre')\n",
")"
");"
]
},
{
Expand Down Expand Up @@ -671,7 +671,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6"
"version": "3.8.5"
}
},
"nbformat": 4,
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8 changes: 4 additions & 4 deletions notebooks/checkerboard.ipynb
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Expand Up @@ -175,7 +175,7 @@
}
],
"source": [
"plot_microstructures(x_stats[0, :, :, 0], x_stats[0, :, :, 1], titles=['0 -> 0', '1 -> 1'], cmap='bwr')"
"plot_microstructures(x_stats[0, :, :, 0], x_stats[0, :, :, 1], titles=['0 -> 0', '1 -> 1'], cmap='bwr');"
]
},
{
Expand Down Expand Up @@ -204,7 +204,7 @@
}
],
"source": [
"plot_microstructures(x_stats[0, :, :, 2], titles=['0 -> 1'], cmap='bwr')"
"plot_microstructures(x_stats[0, :, :, 2], titles=['0 -> 1'], cmap='bwr');"
]
},
{
Expand Down Expand Up @@ -297,7 +297,7 @@
}
],
"source": [
"plot_microstructures(x_stats[0, :, :, 0], x_stats[0, :, :, 1], titles=['0 -> 0', '1 -> 1'], cmap='bwr')"
"plot_microstructures(x_stats[0, :, :, 0], x_stats[0, :, :, 1], titles=['0 -> 0', '1 -> 1'], cmap='bwr');"
]
},
{
Expand All @@ -319,7 +319,7 @@
}
],
"source": [
"plot_microstructures(x_stats[0, :, :, 2], titles=['0 -> 1'], cmap='bwr')"
"plot_microstructures(x_stats[0, :, :, 2], titles=['0 -> 1'], cmap='bwr');"
]
},
{
Expand Down
2 changes: 1 addition & 1 deletion notebooks/derivation.ipynb
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Expand Up @@ -217,7 +217,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6"
"version": "3.8.5"
}
},
"nbformat": 4,
Expand Down
22 changes: 11 additions & 11 deletions notebooks/elasticity.ipynb
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Expand Up @@ -141,7 +141,7 @@
],
"source": [
"x_delta = generate_delta(n_phases=2, shape=(21, 21)).persist()\n",
"plot_microstructures(x_delta[0], x_delta[1], titles=(\"X[0]\", \"X[1]\"), cmap='gray')"
"plot_microstructures(x_delta[0], x_delta[1], titles=(\"X[0]\", \"X[1]\"), cmap='gray');"
]
},
{
Expand Down Expand Up @@ -208,7 +208,7 @@
" y_delta[0],\n",
" y_delta[1],\n",
" titles=(r'$\\mathbf{\\varepsilon_{xx}}$ [0]', r'$\\mathbf{\\varepsilon_{xx}}$ [1]')\n",
")"
");"
]
},
{
Expand Down Expand Up @@ -277,7 +277,7 @@
"to_real = lambda x: coeff_to_real(x.steps[1][1].coeff).real\n",
"\n",
"coeff = to_real(model)\n",
"plot_microstructures(coeff[...,0], coeff[...,1], titles=['Influence coeff [0]', 'Influence coeff [1]'])"
"plot_microstructures(coeff[...,0], coeff[...,1], titles=['Influence coeff [0]', 'Influence coeff [1]']);"
]
},
{
Expand Down Expand Up @@ -327,7 +327,7 @@
}
],
"source": [
"plot_microstructures(y_data[0], titles=[r'$\\mathbf{\\varepsilon_{xx}}$'])"
"plot_microstructures(y_data[0], titles=[r'$\\mathbf{\\varepsilon_{xx}}$']);"
]
},
{
Expand Down Expand Up @@ -374,7 +374,7 @@
}
],
"source": [
"plot_microstructures(y_data[0], y_predict[0], titles=['Actual', 'Predicted'])"
"plot_microstructures(y_data[0], y_predict[0], titles=['Actual', 'Predicted']);"
]
},
{
Expand Down Expand Up @@ -403,7 +403,7 @@
}
],
"source": [
"plot_microstructures(y_data[0] - y_predict[0], titles=['Finite Element - MKS'])"
"plot_microstructures(y_data[0] - y_predict[0], titles=['Finite Element - MKS']);"
]
},
{
Expand Down Expand Up @@ -452,7 +452,7 @@
}
],
"source": [
"plot_microstructures(y_large[0], titles=[r'$\\mathbf{\\varepsilon_{xx}}$'])"
"plot_microstructures(y_large[0], titles=[r'$\\mathbf{\\varepsilon_{xx}}$']);"
]
},
{
Expand Down Expand Up @@ -498,7 +498,7 @@
],
"source": [
"coeff = to_real(model)\n",
"plot_microstructures(coeff[...,0], coeff[...,1], titles=['Influence coeff [0]', 'Influence coeff [1]'])"
"plot_microstructures(coeff[...,0], coeff[...,1], titles=['Influence coeff [0]', 'Influence coeff [1]']);"
]
},
{
Expand Down Expand Up @@ -536,7 +536,7 @@
}
],
"source": [
"plot_microstructures(y_large[0], y_predict_large[0], titles=['Actual', 'Predicted'])"
"plot_microstructures(y_large[0], y_predict_large[0], titles=['Actual', 'Predicted']);"
]
},
{
Expand Down Expand Up @@ -565,7 +565,7 @@
}
],
"source": [
"plot_microstructures(y_large[0] - y_predict_large[0], titles=['Finite Element - MKS'])"
"plot_microstructures(y_large[0] - y_predict_large[0], titles=['Finite Element - MKS']);"
]
},
{
Expand Down Expand Up @@ -620,7 +620,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6"
"version": "3.8.5"
}
},
"nbformat": 4,
Expand Down
18 changes: 9 additions & 9 deletions notebooks/elasticity3d.ipynb
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Expand Up @@ -104,7 +104,7 @@
" x_delta[1, x_delta.shape[1] // 2],\n",
" titles=['[0]', '[1]'],\n",
" cmap='gray'\n",
")"
");"
]
},
{
Expand Down Expand Up @@ -168,7 +168,7 @@
"plot_microstructures(\n",
" y_delta[0, x_delta.shape[1] // 2, :, :],\n",
" titles=[r'$\\mathbf{\\varepsilon_{xx}}$']\n",
")"
");"
]
},
{
Expand Down Expand Up @@ -234,7 +234,7 @@
" coeff[x_delta.shape[1] // 2, :, :, 0],\n",
" coeff[x_delta.shape[1] // 2, :, :, 1],\n",
" titles=['Influence coeff [0]', 'Influence coeff [1]']\n",
")"
");"
]
},
{
Expand Down Expand Up @@ -297,7 +297,7 @@
"plot_microstructures(\n",
" x_data[0, x_delta.shape[1] // 2, :, :],\n",
" titles=['Microstructure']\n",
")"
");"
]
},
{
Expand All @@ -322,7 +322,7 @@
"plot_microstructures(\n",
" y_data[0, x_delta.shape[1] // 2, :, :],\n",
" titles=[r'$\\mathbf{\\varepsilon_{xx}}$']\n",
")"
");"
]
},
{
Expand Down Expand Up @@ -387,7 +387,7 @@
" r'$\\mathbf{\\varepsilon_{xx}}$ - FE',\n",
" r'$\\mathbf{\\varepsilon_{xx}}$ - MKS'\n",
" ]\n",
")"
");"
]
},
{
Expand Down Expand Up @@ -421,7 +421,7 @@
"plot_microstructures(\n",
" (y_data - y_predict)[0, x_delta.shape[1] // 2, :, :],\n",
" titles=['FE - MKS']\n",
")"
");"
]
},
{
Expand Down Expand Up @@ -512,7 +512,7 @@
}
],
"source": [
"plot_microstructures(y_large[0, x_delta.shape[1] // 2], titles=[r'$\\mathbf{\\varepsilon_{xx}}$'])"
"plot_microstructures(y_large[0, x_delta.shape[1] // 2], titles=[r'$\\mathbf{\\varepsilon_{xx}}$']);"
]
},
{
Expand Down Expand Up @@ -557,7 +557,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6"
"version": "3.8.5"
}
},
"nbformat": 4,
Expand Down
4 changes: 2 additions & 2 deletions notebooks/fiber.ipynb
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Expand Up @@ -309,7 +309,7 @@
}
],
"source": [
"plot_microstructures(*x_data[::100], cmap='gray', colorbar=False)"
"plot_microstructures(*x_data[::100], cmap='gray', colorbar=False);"
]
},
{
Expand Down Expand Up @@ -351,7 +351,7 @@
}
],
"source": [
"plot_microstructures(*y_stress[::100])"
"plot_microstructures(*y_stress[::100]);"
]
},
{
Expand Down
2 changes: 1 addition & 1 deletion notebooks/filter.ipynb
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Expand Up @@ -254,7 +254,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6"
"version": "3.8.5"
}
},
"nbformat": 4,
Expand Down
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