[pkgsrc/trunk]: pkgsrc/math/py-statsmodels math/py-statsmodels: Update to 0.10.2

[minskim <minskim%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/b7461b51061b
branches:  trunk
changeset: 420779:b7461b51061b
user:      minskim <minskim%pkgsrc.org@localhost>
date:      Wed Jan 08 01:23:22 2020 +0000

description:
math/py-statsmodels: Update to 0.10.2

This is a major release from 0.9.0 and includes a number new
statistical models and many bug fixes.

Highlights include:

* Generalized Additive Models. This major feature is experimental and
  may change.
* Conditional Models such as ConditionalLogit, which are known as
  fixed effect models in Econometrics.
* Dimension Reduction Methods include Sliced Inverse Regression,
  Principal Hessian Directions and Sliced Avg. Variance Estimation
* Regression using Quadratic Inference Functions (QIF)
* Gaussian Process Regression

diffstat:

 math/py-statsmodels/DESCR    |    9 +-
 math/py-statsmodels/Makefile |   35 +---
 math/py-statsmodels/PLIST    |  339 ++++++++++++++++++++++++++++++++----------
 math/py-statsmodels/distinfo |   10 +-
 4 files changed, 279 insertions(+), 114 deletions(-)

diffs (truncated from 860 to 300 lines):

diff -r 5396e8bc25f7 -r b7461b51061b math/py-statsmodels/DESCR
--- a/math/py-statsmodels/DESCR Wed Jan 08 01:20:36 2020 +0000
+++ b/math/py-statsmodels/DESCR Wed Jan 08 01:23:22 2020 +0000
@@ -1,3 +1,6 @@
-Statsmodels is a Python package that provides a complement to scipy
-for statistical computations including descriptive statistics and
-estimation and inference for statistical models
+statsmodels is a Python module that provides classes and functions for
+the estimation of many different statistical models, as well as for
+conducting statistical tests, and statistical data exploration. An
+extensive list of result statistics are available for each
+estimator. The results are tested against existing statistical
+packages to ensure that they are correct.
diff -r 5396e8bc25f7 -r b7461b51061b math/py-statsmodels/Makefile
--- a/math/py-statsmodels/Makefile      Wed Jan 08 01:20:36 2020 +0000
+++ b/math/py-statsmodels/Makefile      Wed Jan 08 01:23:22 2020 +0000
@@ -1,41 +1,24 @@
-# $NetBSD: Makefile,v 1.5 2019/09/27 09:00:38 wiz Exp $
+# $NetBSD: Makefile,v 1.6 2020/01/08 01:23:22 minskim Exp $
 
-DISTNAME=      statsmodels-0.9.0
-PKGREVISION=   2
+DISTNAME=      statsmodels-0.10.2
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=s/statsmodels/}
 
 MAINTAINER=    jihbed.research%gmail.com@localhost
-HOMEPAGE=      http://www.statsmodels.org/stable/index.html
-COMMENT=       Statistical computations and models for use with SciPy
+HOMEPAGE=      https://www.statsmodels.org/
+COMMENT=       Statistical computations and models for Python
 LICENSE=       modified-bsd
 
-DEPENDS+=      ${PYPKGPREFIX}-cython>=0.14.1:../../devel/py-cython
-DEPENDS+=      ${PYPKGPREFIX}-pandas>=0.14.1:../../math/py-pandas
-DEPENDS+=      ${PYPKGPREFIX}-patsy>=0.3.0:../../math/py-patsy
-DEPENDS+=      ${PYPKGPREFIX}-scipy>=0.12.0:../../math/py-scipy
+BUILD_DEPENDS+=        ${PYPKGPREFIX}-cython>=0.24:../../devel/py-cython
+DEPENDS+=      ${PYPKGPREFIX}-pandas>=0.19:../../math/py-pandas
+DEPENDS+=      ${PYPKGPREFIX}-patsy>=0.4.0:../../math/py-patsy
+DEPENDS+=      ${PYPKGPREFIX}-scipy>=0.18:../../math/py-scipy
 
 PYTHON_VERSIONS_INCOMPATIBLE=  27      # py-matplotlib, py-scipy
 USE_LANGUAGES=                 c
 
-SUBST_CLASSES+=                scipy
-SUBST_STAGE.scipy=     pre-configure
-SUBST_MESSAGE.scipy=   Fix for newer SciPy
-SUBST_FILES.scipy=     statsmodels/distributions/edgeworth.py
-SUBST_FILES.scipy+=    statsmodels/distributions/tests/test_edgeworth.py
-SUBST_FILES.scipy+=    statsmodels/graphics/functional.py
-SUBST_FILES.scipy+=    statsmodels/miscmodels/count.py
-SUBST_FILES.scipy+=    statsmodels/sandbox/distributions/genpareto.py
-SUBST_FILES.scipy+=    statsmodels/sandbox/infotheo.py
-SUBST_FILES.scipy+=    statsmodels/sandbox/nonparametric/densityorthopoly.py
-SUBST_FILES.scipy+=    statsmodels/sandbox/nonparametric/kernels.py
-SUBST_FILES.scipy+=    statsmodels/sandbox/stats/runs.py
-SUBST_FILES.scipy+=    statsmodels/stats/moment_helpers.py
-SUBST_FILES.scipy+=    statsmodels/tsa/regime_switching/markov_switching.py
-SUBST_SED.scipy=       -e 's,\(from scipy\).misc,\1.special,'
-
 .include "../../lang/python/egg.mk"
-BUILDLINK_API_DEPENDS.py-numpy+=       ${PYPKGPREFIX}-numpy>=0.12.0
+BUILDLINK_API_DEPENDS.py-numpy+=       ${PYPKGPREFIX}-numpy>=1.11
 .include "../../math/py-numpy/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff -r 5396e8bc25f7 -r b7461b51061b math/py-statsmodels/PLIST
--- a/math/py-statsmodels/PLIST Wed Jan 08 01:20:36 2020 +0000
+++ b/math/py-statsmodels/PLIST Wed Jan 08 01:23:22 2020 +0000
@@ -1,13 +1,17 @@
-@comment $NetBSD: PLIST,v 1.4 2019/09/27 09:00:38 wiz Exp $
+@comment $NetBSD: PLIST,v 1.5 2020/01/08 01:23:22 minskim Exp $
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
 ${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
 ${PYSITELIB}/${EGG_INFODIR}/requires.txt
 ${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/statsmodels/LICENSE.txt
 ${PYSITELIB}/statsmodels/__init__.py
 ${PYSITELIB}/statsmodels/__init__.pyc
 ${PYSITELIB}/statsmodels/__init__.pyo
+${PYSITELIB}/statsmodels/_version.py
+${PYSITELIB}/statsmodels/_version.pyc
+${PYSITELIB}/statsmodels/_version.pyo
 ${PYSITELIB}/statsmodels/api.py
 ${PYSITELIB}/statsmodels/api.pyc
 ${PYSITELIB}/statsmodels/api.pyo
@@ -17,9 +21,18 @@
 ${PYSITELIB}/statsmodels/base/_constraints.py
 ${PYSITELIB}/statsmodels/base/_constraints.pyc
 ${PYSITELIB}/statsmodels/base/_constraints.pyo
+${PYSITELIB}/statsmodels/base/_parameter_inference.py
+${PYSITELIB}/statsmodels/base/_parameter_inference.pyc
+${PYSITELIB}/statsmodels/base/_parameter_inference.pyo
+${PYSITELIB}/statsmodels/base/_penalized.py
+${PYSITELIB}/statsmodels/base/_penalized.pyc
+${PYSITELIB}/statsmodels/base/_penalized.pyo
 ${PYSITELIB}/statsmodels/base/_penalties.py
 ${PYSITELIB}/statsmodels/base/_penalties.pyc
 ${PYSITELIB}/statsmodels/base/_penalties.pyo
+${PYSITELIB}/statsmodels/base/_screening.py
+${PYSITELIB}/statsmodels/base/_screening.pyc
+${PYSITELIB}/statsmodels/base/_screening.pyo
 ${PYSITELIB}/statsmodels/base/covtype.py
 ${PYSITELIB}/statsmodels/base/covtype.pyc
 ${PYSITELIB}/statsmodels/base/covtype.pyo
@@ -62,9 +75,18 @@
 ${PYSITELIB}/statsmodels/base/tests/test_optimize.py
 ${PYSITELIB}/statsmodels/base/tests/test_optimize.pyc
 ${PYSITELIB}/statsmodels/base/tests/test_optimize.pyo
+${PYSITELIB}/statsmodels/base/tests/test_penalized.py
+${PYSITELIB}/statsmodels/base/tests/test_penalized.pyc
+${PYSITELIB}/statsmodels/base/tests/test_penalized.pyo
+${PYSITELIB}/statsmodels/base/tests/test_penalties.py
+${PYSITELIB}/statsmodels/base/tests/test_penalties.pyc
+${PYSITELIB}/statsmodels/base/tests/test_penalties.pyo
 ${PYSITELIB}/statsmodels/base/tests/test_predict.py
 ${PYSITELIB}/statsmodels/base/tests/test_predict.pyc
 ${PYSITELIB}/statsmodels/base/tests/test_predict.pyo
+${PYSITELIB}/statsmodels/base/tests/test_screening.py
+${PYSITELIB}/statsmodels/base/tests/test_screening.pyc
+${PYSITELIB}/statsmodels/base/tests/test_screening.pyo
 ${PYSITELIB}/statsmodels/base/tests/test_shrink_pickle.py
 ${PYSITELIB}/statsmodels/base/tests/test_shrink_pickle.pyc
 ${PYSITELIB}/statsmodels/base/tests/test_shrink_pickle.pyo
@@ -80,42 +102,34 @@
 ${PYSITELIB}/statsmodels/compat/__init__.py
 ${PYSITELIB}/statsmodels/compat/__init__.pyc
 ${PYSITELIB}/statsmodels/compat/__init__.pyo
-${PYSITELIB}/statsmodels/compat/collections.py
-${PYSITELIB}/statsmodels/compat/collections.pyc
-${PYSITELIB}/statsmodels/compat/collections.pyo
-${PYSITELIB}/statsmodels/compat/counter.py
-${PYSITELIB}/statsmodels/compat/counter.pyc
-${PYSITELIB}/statsmodels/compat/counter.pyo
 ${PYSITELIB}/statsmodels/compat/numpy.py
 ${PYSITELIB}/statsmodels/compat/numpy.pyc
 ${PYSITELIB}/statsmodels/compat/numpy.pyo
-${PYSITELIB}/statsmodels/compat/ordereddict.py
-${PYSITELIB}/statsmodels/compat/ordereddict.pyc
-${PYSITELIB}/statsmodels/compat/ordereddict.pyo
 ${PYSITELIB}/statsmodels/compat/pandas.py
 ${PYSITELIB}/statsmodels/compat/pandas.pyc
 ${PYSITELIB}/statsmodels/compat/pandas.pyo
+${PYSITELIB}/statsmodels/compat/platform.py
+${PYSITELIB}/statsmodels/compat/platform.pyc
+${PYSITELIB}/statsmodels/compat/platform.pyo
 ${PYSITELIB}/statsmodels/compat/python.py
 ${PYSITELIB}/statsmodels/compat/python.pyc
 ${PYSITELIB}/statsmodels/compat/python.pyo
 ${PYSITELIB}/statsmodels/compat/scipy.py
 ${PYSITELIB}/statsmodels/compat/scipy.pyc
 ${PYSITELIB}/statsmodels/compat/scipy.pyo
-${PYSITELIB}/statsmodels/compat/testing.py
-${PYSITELIB}/statsmodels/compat/testing.pyc
-${PYSITELIB}/statsmodels/compat/testing.pyo
 ${PYSITELIB}/statsmodels/compat/tests/__init__.py
 ${PYSITELIB}/statsmodels/compat/tests/__init__.pyc
 ${PYSITELIB}/statsmodels/compat/tests/__init__.pyo
-${PYSITELIB}/statsmodels/compat/tests/test_collections.py
-${PYSITELIB}/statsmodels/compat/tests/test_collections.pyc
-${PYSITELIB}/statsmodels/compat/tests/test_collections.pyo
 ${PYSITELIB}/statsmodels/compat/tests/test_itercompat.py
 ${PYSITELIB}/statsmodels/compat/tests/test_itercompat.pyc
 ${PYSITELIB}/statsmodels/compat/tests/test_itercompat.pyo
 ${PYSITELIB}/statsmodels/compat/tests/test_scipy_compat.py
 ${PYSITELIB}/statsmodels/compat/tests/test_scipy_compat.pyc
 ${PYSITELIB}/statsmodels/compat/tests/test_scipy_compat.pyo
+${PYSITELIB}/statsmodels/conftest.py
+${PYSITELIB}/statsmodels/conftest.pyc
+${PYSITELIB}/statsmodels/conftest.pyo
+${PYSITELIB}/statsmodels/datasets/README.txt
 ${PYSITELIB}/statsmodels/datasets/__init__.py
 ${PYSITELIB}/statsmodels/datasets/__init__.pyc
 ${PYSITELIB}/statsmodels/datasets/__init__.pyo
@@ -317,9 +331,6 @@
 ${PYSITELIB}/statsmodels/datasets/tests/__init__.py
 ${PYSITELIB}/statsmodels/datasets/tests/__init__.pyc
 ${PYSITELIB}/statsmodels/datasets/tests/__init__.pyo
-${PYSITELIB}/statsmodels/datasets/tests/raw.github.com,vincentarelbundock,Rdatasets,master,csv,car,Duncan.csv.zip
-${PYSITELIB}/statsmodels/datasets/tests/raw.github.com,vincentarelbundock,Rdatasets,master,datasets.csv.zip
-${PYSITELIB}/statsmodels/datasets/tests/raw.github.com,vincentarelbundock,Rdatasets,master,doc,car,rst,Duncan.rst.zip
 ${PYSITELIB}/statsmodels/datasets/tests/test_data.py
 ${PYSITELIB}/statsmodels/datasets/tests/test_data.pyc
 ${PYSITELIB}/statsmodels/datasets/tests/test_data.pyo
@@ -335,6 +346,9 @@
 ${PYSITELIB}/statsmodels/discrete/_diagnostics_count.py
 ${PYSITELIB}/statsmodels/discrete/_diagnostics_count.pyc
 ${PYSITELIB}/statsmodels/discrete/_diagnostics_count.pyo
+${PYSITELIB}/statsmodels/discrete/conditional_models.py
+${PYSITELIB}/statsmodels/discrete/conditional_models.pyc
+${PYSITELIB}/statsmodels/discrete/conditional_models.pyo
 ${PYSITELIB}/statsmodels/discrete/count_model.py
 ${PYSITELIB}/statsmodels/discrete/count_model.pyc
 ${PYSITELIB}/statsmodels/discrete/count_model.pyo
@@ -375,6 +389,9 @@
 ${PYSITELIB}/statsmodels/discrete/tests/results/sm3533.csv
 ${PYSITELIB}/statsmodels/discrete/tests/results/yhat_mnlogit.csv
 ${PYSITELIB}/statsmodels/discrete/tests/results/yhat_poisson.csv
+${PYSITELIB}/statsmodels/discrete/tests/test_conditional.py
+${PYSITELIB}/statsmodels/discrete/tests/test_conditional.pyc
+${PYSITELIB}/statsmodels/discrete/tests/test_conditional.pyo
 ${PYSITELIB}/statsmodels/discrete/tests/test_constrained.py
 ${PYSITELIB}/statsmodels/discrete/tests/test_constrained.pyc
 ${PYSITELIB}/statsmodels/discrete/tests/test_constrained.pyo
@@ -441,25 +458,25 @@
 ${PYSITELIB}/statsmodels/duration/tests/__init__.py
 ${PYSITELIB}/statsmodels/duration/tests/__init__.pyc
 ${PYSITELIB}/statsmodels/duration/tests/__init__.pyo
-${PYSITELIB}/statsmodels/duration/tests/phreg_gentests.py
-${PYSITELIB}/statsmodels/duration/tests/phreg_gentests.pyc
-${PYSITELIB}/statsmodels/duration/tests/phreg_gentests.pyo
 ${PYSITELIB}/statsmodels/duration/tests/results/__init__.py
 ${PYSITELIB}/statsmodels/duration/tests/results/__init__.pyc
 ${PYSITELIB}/statsmodels/duration/tests/results/__init__.pyo
 ${PYSITELIB}/statsmodels/duration/tests/results/bmt.csv
 ${PYSITELIB}/statsmodels/duration/tests/results/bmt_results.csv
+${PYSITELIB}/statsmodels/duration/tests/results/phreg_gentests.py
+${PYSITELIB}/statsmodels/duration/tests/results/phreg_gentests.pyc
+${PYSITELIB}/statsmodels/duration/tests/results/phreg_gentests.pyo
 ${PYSITELIB}/statsmodels/duration/tests/results/survival_data_1000_10.csv
 ${PYSITELIB}/statsmodels/duration/tests/results/survival_data_100_5.csv
 ${PYSITELIB}/statsmodels/duration/tests/results/survival_data_20_1.csv
 ${PYSITELIB}/statsmodels/duration/tests/results/survival_data_50_1.csv
 ${PYSITELIB}/statsmodels/duration/tests/results/survival_data_50_2.csv
-${PYSITELIB}/statsmodels/duration/tests/survival_enet_r_results.py
-${PYSITELIB}/statsmodels/duration/tests/survival_enet_r_results.pyc
-${PYSITELIB}/statsmodels/duration/tests/survival_enet_r_results.pyo
-${PYSITELIB}/statsmodels/duration/tests/survival_r_results.py
-${PYSITELIB}/statsmodels/duration/tests/survival_r_results.pyc
-${PYSITELIB}/statsmodels/duration/tests/survival_r_results.pyo
+${PYSITELIB}/statsmodels/duration/tests/results/survival_enet_r_results.py
+${PYSITELIB}/statsmodels/duration/tests/results/survival_enet_r_results.pyc
+${PYSITELIB}/statsmodels/duration/tests/results/survival_enet_r_results.pyo
+${PYSITELIB}/statsmodels/duration/tests/results/survival_r_results.py
+${PYSITELIB}/statsmodels/duration/tests/results/survival_r_results.pyc
+${PYSITELIB}/statsmodels/duration/tests/results/survival_r_results.pyo
 ${PYSITELIB}/statsmodels/duration/tests/test_phreg.py
 ${PYSITELIB}/statsmodels/duration/tests/test_phreg.pyc
 ${PYSITELIB}/statsmodels/duration/tests/test_phreg.pyo
@@ -484,9 +501,6 @@
 ${PYSITELIB}/statsmodels/emplike/elregress.py
 ${PYSITELIB}/statsmodels/emplike/elregress.pyc
 ${PYSITELIB}/statsmodels/emplike/elregress.pyo
-${PYSITELIB}/statsmodels/emplike/koul_and_mc.py
-${PYSITELIB}/statsmodels/emplike/koul_and_mc.pyc
-${PYSITELIB}/statsmodels/emplike/koul_and_mc.pyo
 ${PYSITELIB}/statsmodels/emplike/originregress.py
 ${PYSITELIB}/statsmodels/emplike/originregress.pyc
 ${PYSITELIB}/statsmodels/emplike/originregress.pyo
@@ -529,6 +543,62 @@
 ${PYSITELIB}/statsmodels/formula/tests/test_formula.py
 ${PYSITELIB}/statsmodels/formula/tests/test_formula.pyc
 ${PYSITELIB}/statsmodels/formula/tests/test_formula.pyo
+${PYSITELIB}/statsmodels/gam/__init__.py
+${PYSITELIB}/statsmodels/gam/__init__.pyc
+${PYSITELIB}/statsmodels/gam/__init__.pyo
+${PYSITELIB}/statsmodels/gam/api.py
+${PYSITELIB}/statsmodels/gam/api.pyc
+${PYSITELIB}/statsmodels/gam/api.pyo
+${PYSITELIB}/statsmodels/gam/gam_cross_validation/__init__.py
+${PYSITELIB}/statsmodels/gam/gam_cross_validation/__init__.pyc
+${PYSITELIB}/statsmodels/gam/gam_cross_validation/__init__.pyo
+${PYSITELIB}/statsmodels/gam/gam_cross_validation/cross_validators.py
+${PYSITELIB}/statsmodels/gam/gam_cross_validation/cross_validators.pyc
+${PYSITELIB}/statsmodels/gam/gam_cross_validation/cross_validators.pyo
+${PYSITELIB}/statsmodels/gam/gam_cross_validation/gam_cross_validation.py
+${PYSITELIB}/statsmodels/gam/gam_cross_validation/gam_cross_validation.pyc
+${PYSITELIB}/statsmodels/gam/gam_cross_validation/gam_cross_validation.pyo
+${PYSITELIB}/statsmodels/gam/gam_penalties.py
+${PYSITELIB}/statsmodels/gam/gam_penalties.pyc
+${PYSITELIB}/statsmodels/gam/gam_penalties.pyo
+${PYSITELIB}/statsmodels/gam/generalized_additive_model.py
+${PYSITELIB}/statsmodels/gam/generalized_additive_model.pyc
+${PYSITELIB}/statsmodels/gam/generalized_additive_model.pyo
+${PYSITELIB}/statsmodels/gam/smooth_basis.py
+${PYSITELIB}/statsmodels/gam/smooth_basis.pyc
+${PYSITELIB}/statsmodels/gam/smooth_basis.pyo
+${PYSITELIB}/statsmodels/gam/tests/__init__.py
+${PYSITELIB}/statsmodels/gam/tests/__init__.pyc
+${PYSITELIB}/statsmodels/gam/tests/__init__.pyo
+${PYSITELIB}/statsmodels/gam/tests/results/__init__.py
+${PYSITELIB}/statsmodels/gam/tests/results/__init__.pyc
+${PYSITELIB}/statsmodels/gam/tests/results/__init__.pyo
+${PYSITELIB}/statsmodels/gam/tests/results/autos.csv
+${PYSITELIB}/statsmodels/gam/tests/results/autos_exog.csv
+${PYSITELIB}/statsmodels/gam/tests/results/autos_predict.csv
+${PYSITELIB}/statsmodels/gam/tests/results/cubic_cyclic_splines_from_mgcv.csv
+${PYSITELIB}/statsmodels/gam/tests/results/gam_PIRLS_results.csv
+${PYSITELIB}/statsmodels/gam/tests/results/logit_gam_mgcv.csv
+${PYSITELIB}/statsmodels/gam/tests/results/motorcycle.csv
+${PYSITELIB}/statsmodels/gam/tests/results/prediction_from_mgcv.csv
+${PYSITELIB}/statsmodels/gam/tests/results/results_mpg_bs.py
+${PYSITELIB}/statsmodels/gam/tests/results/results_mpg_bs.pyc
+${PYSITELIB}/statsmodels/gam/tests/results/results_mpg_bs.pyo
+${PYSITELIB}/statsmodels/gam/tests/results/results_mpg_bs_poisson.py
+${PYSITELIB}/statsmodels/gam/tests/results/results_mpg_bs_poisson.pyc
+${PYSITELIB}/statsmodels/gam/tests/results/results_mpg_bs_poisson.pyo