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xyluo25 refactor from master: refactored utils.py and summary.py using Python 3.10, CI tests passed #145

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xyluo25 refactor from master: refactored utils.py and summary.py using Python 3.10, CI tests passed #145

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b55defa
update gitignore
xyluo25 Oct 1, 2023
812a6c8
refactored utils.py
xyluo25 Oct 1, 2023
ef0b16c
refactored search.py
xyluo25 Oct 1, 2023
de5553d
refactored kernels.py
xyluo25 Oct 1, 2023
0a4f104
refactored mgwr to python v3.10
xyluo25 Jan 25, 2024
1c4b732
Merge branch 'xyluo25_func_refactoring'
xyluo25 Jan 25, 2024
08213ea
Revert "Merge branch 'xyluo25_func_refactoring'"
xyluo25 Feb 11, 2024
1e0ac97
Merge branch 'master' of https://github.com/xyluo25/mgwr
xyluo25 Feb 11, 2024
aeda536
Revert "Merge branch 'master' of https://github.com/xyluo25/mgwr"
xyluo25 Feb 11, 2024
5d92533
Revert "Revert "Merge branch 'xyluo25_func_refactoring'""
xyluo25 Feb 11, 2024
d95fc94
Revert "Merge branch 'xyluo25_func_refactoring'"
xyluo25 Feb 11, 2024
4e5afde
Revert "Merge branch 'xyluo25_func_refactoring'"
xyluo25 Feb 11, 2024
7b24ac2
Revert "refactored mgwr to python v3.10"
xyluo25 Feb 11, 2024
73cfc08
back to pysal master
xyluo25 Feb 11, 2024
36915c6
update unittest assertalmostequals to assertalmostequal
xyluo25 Feb 11, 2024
65771ed
refactored utils.py: add type hint, reformatted docstring
xyluo25 Feb 11, 2024
bff0af8
refactor summary.py: add type hints, add docstring for functions
xyluo25 Feb 11, 2024
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68 changes: 36 additions & 32 deletions mgwr/summary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,27 +4,32 @@
from .diagnostics import get_AICc


def summaryModel(self):
summary = '=' * 75 + '\n'
summary += "%-54s %20s\n" % ('Model type', self.family.__class__.__name__)
summary += "%-60s %14d\n" % ('Number of observations:', self.n)
summary += "%-60s %14d\n\n" % ('Number of covariates:', self.k)
def summaryModel(self) -> str:
"""Summary of model

Returns:
str: print out the model summary information
"""
summary = f"{'=' * 75} \n"
summary += f"{'Model type':<54s} {self.family.__class__.__name__:20s}\n"
summary += f"{'Number of observations:':<60s} {self.n:14d}\n"
summary += f"{'Number of covariates:':<60s} {self.k:14d}\n\n"
return summary


def summaryGLM(self):
def summaryGLM(self) -> str:
"""Summary of GLM

if self.name_x is not None:
XNames = list(self.name_x)
if len(XNames) < self.k:
XNames = ["Intercept"] + XNames
else:
XNames = ["X" + str(i) for i in range(self.k)]
Returns:
str: print out the GLM summary information
"""

XNames = [f"X{i}" for i in range(self.k)]
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@martinfleis martinfleis Feb 12, 2024

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This is not equivalent of the original code. You are removing functionality here.

glm_rslt = GLM(self.model.y, self.model.X, constant=False,
family=self.family).fit()

summary = "%s\n" % ('Global Regression Results')
summary += '-' * 75 + '\n'
summary = "Global Regression Results\n"
summary += f"{'-' * 75} \n"

if isinstance(self.family, Gaussian):
summary += "%-62s %12.3f\n" % ('Residual sum of squares:',
Expand Down Expand Up @@ -52,20 +57,20 @@ def summaryGLM(self):
'-' * 10, '-' * 10)
for i in range(self.k):
summary += "%-31s %10.3f %10.3f %10.3f %10.3f\n" % (
XNames[i][:30], glm_rslt.params[i], glm_rslt.bse[i],
XNames[i], glm_rslt.params[i], glm_rslt.bse[i],
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@martinfleis martinfleis Feb 12, 2024

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Why are you removing [:30]? That is not a stylistic change and there is a reason it is in the original code.

glm_rslt.tvalues[i], glm_rslt.pvalues[i])
summary += "\n"
return summary


def summaryGWR(self):
if self.name_x is not None:
XNames = list(self.name_x)
if len(XNames) < self.k:
XNames = ["Intercept"] + XNames
def summaryGWR(self) -> str:
"""Summary of GWR

else:
XNames = ["X" + str(i) for i in range(self.k)]
Returns:
str: print out the GWR summary information
"""

XNames = ["X" + str(i) for i in range(self.k)]
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@martinfleis martinfleis Feb 12, 2024

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Again, this is not equivalent!


summary = "%s\n" % ('Geographically Weighted Regression (GWR) Results')
summary += '-' * 75 + '\n'
Expand Down Expand Up @@ -122,7 +127,7 @@ def summaryGWR(self):
'-' * 20, '-' * 10, '-' * 10, '-' * 10, '-' * 10, '-' * 10)
for i in range(self.k):
summary += "%-20s %10.3f %10.3f %10.3f %10.3f %10.3f\n" % (
XNames[i][:20], np.mean(self.params[:, i]), np.std(self.params[:, i]),
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@martinfleis martinfleis Feb 12, 2024

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Same as above.

XNames[i], np.mean(self.params[:, i]), np.std(self.params[:, i]),
np.min(self.params[:, i]), np.median(self.params[:, i]),
np.max(self.params[:, i]))

Expand All @@ -131,15 +136,14 @@ def summaryGWR(self):
return summary


def summaryMGWR(self):
def summaryMGWR(self) -> str:
"""Summary of MGWR

if self.name_x is not None:
XNames = list(self.name_x)
if len(XNames) < self.k:
XNames = ["Intercept"] + XNames
Returns:
str: print out the MGWR summary information
"""

else:
XNames = ["X" + str(i) for i in range(self.k)]
XNames = ["X" + str(i) for i in range(self.k)]
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@martinfleis martinfleis Feb 12, 2024

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Same as above


summary = ''
summary += "%s\n" % (
Expand Down Expand Up @@ -199,9 +203,9 @@ def summaryMGWR(self):
'-' * 20, '-' * 10, '-' * 10, '-' * 10, '-' * 10, '-' * 10)
for i in range(self.k):
summary += "%-20s %10.3f %10.3f %10.3f %10.3f %10.3f\n" % (
XNames[i][:20], np.mean(self.params[:, i]), np.std(self.params[:, i]),
XNames[i], np.mean(self.params[:, i]), np.std(self.params[:, i]),
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@martinfleis martinfleis Feb 12, 2024

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Same as above

np.min(self.params[:, i]), np.median(self.params[:, i]),
np.max(self.params[:, i]))

summary += '=' * 75 + '\n'
return summary
return summary
106 changes: 53 additions & 53 deletions mgwr/tests/test_gwr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,10 +66,10 @@ def test_BS_F(self):
BIC = get_BIC(rslt)
CV = get_CV(rslt)

self.assertAlmostEquals(np.floor(AICc), 894.0)
self.assertAlmostEquals(np.floor(AIC), 890.0)
self.assertAlmostEquals(np.floor(BIC), 944.0)
self.assertAlmostEquals(np.round(CV, 2), 18.25)
self.assertAlmostEqual(np.floor(AICc), 894.0)
self.assertAlmostEqual(np.floor(AIC), 890.0)
self.assertAlmostEqual(np.floor(BIC), 944.0)
self.assertAlmostEqual(np.round(CV, 2), 18.25)
np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-04)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-04)
np.testing.assert_allclose(t_Int, rslt.tvalues[:, 0], rtol=1e-04)
Expand Down Expand Up @@ -135,12 +135,12 @@ def test_BS_NN(self):
np.testing.assert_allclose(
adj_alpha, np.array([0.02034978, 0.01017489, 0.0002035]),
rtol=1e-04)
self.assertAlmostEquals(critical_t, 2.6011011542649394)
self.assertAlmostEquals(np.around(R2, 4), 0.5924)
self.assertAlmostEquals(np.floor(AICc), 896.0)
self.assertAlmostEquals(np.floor(AIC), 892.0)
self.assertAlmostEquals(np.floor(BIC), 941.0)
self.assertAlmostEquals(np.around(CV, 2), 19.19)
self.assertAlmostEqual(critical_t, 2.6011011542649394)
self.assertAlmostEqual(np.around(R2, 4), 0.5924)
self.assertAlmostEqual(np.floor(AICc), 896.0)
self.assertAlmostEqual(np.floor(AIC), 892.0)
self.assertAlmostEqual(np.floor(BIC), 941.0)
self.assertAlmostEqual(np.around(CV, 2), 19.19)
np.testing.assert_allclose(corr1, corr2, rtol=1e-04)
np.testing.assert_allclose(vif1, vif2, rtol=1e-04)
np.testing.assert_allclose(cn1, cn2, rtol=1e-04)
Expand Down Expand Up @@ -202,10 +202,10 @@ def test_GS_F(self):
BIC = get_BIC(rslt)
CV = get_CV(rslt)

self.assertAlmostEquals(np.floor(AICc), 895.0)
self.assertAlmostEquals(np.floor(AIC), 890.0)
self.assertAlmostEquals(np.floor(BIC), 943.0)
self.assertAlmostEquals(np.around(CV, 2), 18.21)
self.assertAlmostEqual(np.floor(AICc), 895.0)
self.assertAlmostEqual(np.floor(AIC), 890.0)
self.assertAlmostEqual(np.floor(BIC), 943.0)
self.assertAlmostEqual(np.around(CV, 2), 18.21)
np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-04)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-04)
np.testing.assert_allclose(t_Int, rslt.tvalues[:, 0], rtol=1e-04)
Expand Down Expand Up @@ -254,10 +254,10 @@ def test_GS_NN(self):
BIC = get_BIC(rslt)
CV = get_CV(rslt)

self.assertAlmostEquals(np.floor(AICc), 896.0)
self.assertAlmostEquals(np.floor(AIC), 894.0)
self.assertAlmostEquals(np.floor(BIC), 922.0)
self.assertAlmostEquals(np.around(CV, 2), 17.91)
self.assertAlmostEqual(np.floor(AICc), 896.0)
self.assertAlmostEqual(np.floor(AIC), 894.0)
self.assertAlmostEqual(np.floor(BIC), 922.0)
self.assertAlmostEqual(np.around(CV, 2), 17.91)
np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-04)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-04)
np.testing.assert_allclose(t_Int, rslt.tvalues[:, 0], rtol=1e-04)
Expand Down Expand Up @@ -473,11 +473,11 @@ def test_BS_NN_longlat(self):
CV = get_CV(rslt)
R2 = rslt.R2

self.assertAlmostEquals(np.around(R2, 4), 0.5921)
self.assertAlmostEquals(np.floor(AICc), 896.0)
self.assertAlmostEquals(np.floor(AIC), 892.0)
self.assertAlmostEquals(np.floor(BIC), 941.0)
self.assertAlmostEquals(np.around(CV, 2), 19.11)
self.assertAlmostEqual(np.around(R2, 4), 0.5921)
self.assertAlmostEqual(np.floor(AICc), 896.0)
self.assertAlmostEqual(np.floor(AIC), 892.0)
self.assertAlmostEqual(np.floor(BIC), 941.0)
self.assertAlmostEqual(np.around(CV, 2), 19.11)
np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-04)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-04)
np.testing.assert_allclose(t_Int, rslt.tvalues[:, 0], rtol=1e-04)
Expand Down Expand Up @@ -557,9 +557,9 @@ def test_BS_F(self):
AIC = get_AIC(rslt)
BIC = get_BIC(rslt)

self.assertAlmostEquals(np.floor(AICc), 13294.0)
self.assertAlmostEquals(np.floor(AIC), 13247.0)
self.assertAlmostEquals(np.floor(BIC), 13485.0)
self.assertAlmostEqual(np.floor(AICc), 13294.0)
self.assertAlmostEqual(np.floor(AIC), 13247.0)
self.assertAlmostEqual(np.floor(BIC), 13485.0)

np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-05)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-03)
Expand Down Expand Up @@ -607,10 +607,10 @@ def test_BS_NN(self):
BIC = get_BIC(rslt)
D2 = rslt.D2

self.assertAlmostEquals(np.floor(AICc), 13285)
self.assertAlmostEquals(np.floor(AIC), 13259.0)
self.assertAlmostEquals(np.floor(BIC), 13442.0)
self.assertAlmostEquals(np.round(D2, 3), 0.747)
self.assertAlmostEqual(np.floor(AICc), 13285)
self.assertAlmostEqual(np.floor(AIC), 13259.0)
self.assertAlmostEqual(np.floor(BIC), 13442.0)
self.assertAlmostEqual(np.round(D2, 3), 0.747)

np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-04)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-02)
Expand Down Expand Up @@ -659,10 +659,10 @@ def test_BS_NN_Offset(self):
BIC = get_BIC(rslt)
D2 = rslt.D2

self.assertAlmostEquals(np.floor(AICc), 367.0)
self.assertAlmostEquals(np.floor(AIC), 361.0)
self.assertAlmostEquals(np.floor(BIC), 451.0)
self.assertAlmostEquals(np.round(D2, 3), 0.676)
self.assertAlmostEqual(np.floor(AICc), 367.0)
self.assertAlmostEqual(np.floor(AIC), 361.0)
self.assertAlmostEqual(np.floor(BIC), 451.0)
self.assertAlmostEqual(np.round(D2, 3), 0.676)

np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-02,
atol=1e-02)
Expand Down Expand Up @@ -724,9 +724,9 @@ def test_GS_F(self):
AIC = get_AIC(rslt)
BIC = get_BIC(rslt)

self.assertAlmostEquals(np.floor(AICc), 11283.0)
self.assertAlmostEquals(np.floor(AIC), 11211.0)
self.assertAlmostEquals(np.floor(BIC), 11497.0)
self.assertAlmostEqual(np.floor(AICc), 11283.0)
self.assertAlmostEqual(np.floor(AIC), 11211.0)
self.assertAlmostEqual(np.floor(BIC), 11497.0)
np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-03)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-02)
np.testing.assert_allclose(t_Int, rslt.tvalues[:, 0], rtol=1e-02)
Expand Down Expand Up @@ -772,9 +772,9 @@ def test_GS_NN(self):
AIC = get_AIC(rslt)
BIC = get_BIC(rslt)

self.assertAlmostEquals(np.floor(AICc), 21070.0)
self.assertAlmostEquals(np.floor(AIC), 21069.0)
self.assertAlmostEquals(np.floor(BIC), 21111.0)
self.assertAlmostEqual(np.floor(AICc), 21070.0)
self.assertAlmostEqual(np.floor(AIC), 21069.0)
self.assertAlmostEqual(np.floor(BIC), 21111.0)
np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-04)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-02)
np.testing.assert_allclose(t_Int, rslt.tvalues[:, 0], rtol=1e-02)
Expand Down Expand Up @@ -859,9 +859,9 @@ def test_BS_F(self):
AIC = get_AIC(rslt)
BIC = get_BIC(rslt)

self.assertAlmostEquals(np.floor(AICc), 275.0)
self.assertAlmostEquals(np.floor(AIC), 271.0)
self.assertAlmostEquals(np.floor(BIC), 349.0)
self.assertAlmostEqual(np.floor(AICc), 275.0)
self.assertAlmostEqual(np.floor(AIC), 271.0)
self.assertAlmostEqual(np.floor(BIC), 349.0)
np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-00)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-00)
np.testing.assert_allclose(t_Int, rslt.tvalues[:, 0], rtol=1e-00)
Expand Down Expand Up @@ -923,10 +923,10 @@ def test_BS_NN(self):
BIC = get_BIC(rslt)
D2 = rslt.D2

self.assertAlmostEquals(np.floor(AICc), 277.0)
self.assertAlmostEquals(np.floor(AIC), 271.0)
self.assertAlmostEquals(np.floor(BIC), 358.0)
self.assertAlmostEquals(np.round(D2, 3), 0.319)
self.assertAlmostEqual(np.floor(AICc), 277.0)
self.assertAlmostEqual(np.floor(AIC), 271.0)
self.assertAlmostEqual(np.floor(BIC), 358.0)
self.assertAlmostEqual(np.round(D2, 3), 0.319)

np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-00)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-00)
Expand Down Expand Up @@ -989,9 +989,9 @@ def test_GS_F(self):
AIC = get_AIC(rslt)
BIC = get_BIC(rslt)

self.assertAlmostEquals(np.floor(AICc), 276.0)
self.assertAlmostEquals(np.floor(AIC), 272.0)
self.assertAlmostEquals(np.floor(BIC), 341.0)
self.assertAlmostEqual(np.floor(AICc), 276.0)
self.assertAlmostEqual(np.floor(AIC), 272.0)
self.assertAlmostEqual(np.floor(BIC), 341.0)
np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-00)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-00)
np.testing.assert_allclose(t_Int, rslt.tvalues[:, 0], rtol=1e-00)
Expand Down Expand Up @@ -1052,9 +1052,9 @@ def test_GS_NN(self):
AIC = get_AIC(rslt)
BIC = get_BIC(rslt)

self.assertAlmostEquals(np.floor(AICc), 276.0)
self.assertAlmostEquals(np.floor(AIC), 273.0)
self.assertAlmostEquals(np.floor(BIC), 331.0)
self.assertAlmostEqual(np.floor(AICc), 276.0)
self.assertAlmostEqual(np.floor(AIC), 273.0)
self.assertAlmostEqual(np.floor(BIC), 331.0)
np.testing.assert_allclose(est_Int, rslt.params[:, 0], rtol=1e-00)
np.testing.assert_allclose(se_Int, rslt.bse[:, 0], rtol=1e-00)
np.testing.assert_allclose(t_Int, rslt.tvalues[:, 0], rtol=1e-00)
Expand Down
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