gnu: python-statsmodels: Update to 0.8.0.

* gnu/packages/statistics.scm (python-statsmodels, python2-statsmodels):
Update to 0.8.0.
[source]: Use 'pypi-uri'.
[arguments]: Add more files to matplotlib backend substitution.
* gnu/packages/patches/python-statsmodels-fix-tests.patch: Drop test that
fails with numpy 1.12. Remove previous contents.

2 files changed, 34 insertions, 201 deletions

diff --git a/gnu/packages/patches/python-statsmodels-fix-tests.patch b/gnu/packages/patches/python-statsmodels-fix-tests.patch
index 3315ddbd5f..f910b4b5a5 100644
--- a/gnu/packages/patches/python-statsmodels-fix-tests.patch
+++ b/gnu/packages/patches/python-statsmodels-fix-tests.patch
@@ -1,196 +1,28 @@
-This patch fixes a couple of test failures introduced by changes to the pandas
-package.  It was extracted from this pull request:
-
-https://github.com/statsmodels/statsmodels/pull/2675
-
-
-From c9ef60a7bc4407766ab9e9f12c8a6b89013046ee Mon Sep 17 00:00:00 2001
-From: Ralf Gommers <ralf.gommers@gmail.com>
-Date: Tue, 20 Oct 2015 07:34:11 +0200
-Subject: [PATCH 1/4] MAINT: fix use of old_behavior kw for numpy.correlate. 
- Was removed in 1.10.0
-
-Numpy PR that removed it: https://github.com/numpy/numpy/pull/5991
-
-Closes gh-2667.
----
- statsmodels/tsa/ar_model.py | 6 ++----
- 1 file changed, 2 insertions(+), 4 deletions(-)
-
-diff --git a/statsmodels/tsa/ar_model.py b/statsmodels/tsa/ar_model.py
-index 087a9e0..02984bd 100644
---- a/statsmodels/tsa/ar_model.py
-+++ b/statsmodels/tsa/ar_model.py
-@@ -261,10 +261,8 @@ def _presample_varcov(self, params):
- 
-         Vpinv = np.zeros((p, p), dtype=params.dtype)
-         for i in range(1, p1):
--            Vpinv[i-1, i-1:] = np.correlate(params0, params0[:i],
--                                            old_behavior=False)[:-1]
--            Vpinv[i-1, i-1:] -= np.correlate(params0[-i:], params0,
--                                             old_behavior=False)[:-1]
-+            Vpinv[i-1, i-1:] = np.correlate(params0, params0[:i],)[:-1]
-+            Vpinv[i-1, i-1:] -= np.correlate(params0[-i:], params0,)[:-1]
- 
-         Vpinv = Vpinv + Vpinv.T - np.diag(Vpinv.diagonal())
-         return Vpinv
-
-From f1dc8979b09bc1736149993f895943b3158ee2db Mon Sep 17 00:00:00 2001
-From: Ralf Gommers <ralf.gommers@gmail.com>
-Date: Wed, 21 Oct 2015 22:05:52 +0200
-Subject: [PATCH 2/4] MAINT: fix graphics module for changes in recent pandas
- versions.
-
----
- statsmodels/graphics/tests/test_mosaicplot.py | 2 +-
- statsmodels/graphics/tests/test_tsaplots.py   | 6 +++---
- statsmodels/graphics/tsaplots.py              | 2 +-
- 3 files changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/statsmodels/graphics/tests/test_mosaicplot.py b/statsmodels/graphics/tests/test_mosaicplot.py
-index cb9bbbe..e41020e 100644
---- a/statsmodels/graphics/tests/test_mosaicplot.py
-+++ b/statsmodels/graphics/tests/test_mosaicplot.py
-@@ -113,7 +113,7 @@ def test_mosaic():
-     # sort by the marriage quality and give meaningful name
-     # [rate_marriage, age, yrs_married, children,
-     # religious, educ, occupation, occupation_husb]
--    datas = datas.sort(['rate_marriage', 'religious'])
-+    datas = datas.sort_values(by=['rate_marriage', 'religious'])
-     num_to_desc = {1: 'awful', 2: 'bad', 3: 'intermediate',
-                       4: 'good', 5: 'wonderful'}
-     datas['rate_marriage'] = datas['rate_marriage'].map(num_to_desc)
-diff --git a/statsmodels/graphics/tests/test_tsaplots.py b/statsmodels/graphics/tests/test_tsaplots.py
-index 511f18f..365be82 100644
---- a/statsmodels/graphics/tests/test_tsaplots.py
-+++ b/statsmodels/graphics/tests/test_tsaplots.py
-@@ -1,4 +1,4 @@
--from statsmodels.compat.python import lmap, lzip, map
-+from statsmodels.compat.python import lmap, map
- import numpy as np
- import pandas as pd
- from numpy.testing import dec
-@@ -51,8 +51,8 @@ def test_plot_month():
-     dta = sm.datasets.elnino.load_pandas().data
-     dta['YEAR'] = dta.YEAR.astype(int).apply(str)
-     dta = dta.set_index('YEAR').T.unstack()
--    dates = lmap(lambda x : pd.datetools.parse('1 '+' '.join(x)),
--                                            dta.index.values)
-+    dates = lmap(lambda x : pd.datetools.parse_time_string('1 '+' '.join(x))[0],
-+                                                           dta.index.values)
- 
-     # test dates argument
-     fig = month_plot(dta.values, dates=dates, ylabel='el nino')
-diff --git a/statsmodels/graphics/tsaplots.py b/statsmodels/graphics/tsaplots.py
-index 3d04692..94626c9 100644
---- a/statsmodels/graphics/tsaplots.py
-+++ b/statsmodels/graphics/tsaplots.py
-@@ -200,7 +200,7 @@ def seasonal_plot(grouped_x, xticklabels, ylabel=None, ax=None):
-     ticks = []
-     for season, df in grouped_x:
-         df = df.copy() # or sort balks for series. may be better way
--        df.sort()
-+        df.sort_values(inplace=True)
-         nobs = len(df)
-         x_plot = np.arange(start, start + nobs)
-         ticks.append(x_plot.mean())
-
-From 4cfbef6af137629c6953f1f025d9cfc781874256 Mon Sep 17 00:00:00 2001
-From: Ralf Gommers <ralf.gommers@gmail.com>
-Date: Wed, 21 Oct 2015 22:15:25 +0200
-Subject: [PATCH 3/4] MAINT: work around pandas breaking backwards compat for
- pandas.version
-
----
- setup.py                     | 5 ++++-
- statsmodels/tools/testing.py | 6 ++----
- 2 files changed, 6 insertions(+), 5 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 0002840..74aefb8 100644
---- a/setup.py
-+++ b/setup.py
-@@ -134,7 +134,10 @@ def check_dependency_versions(min_versions):
-                               (spversion, min_versions['scipy']))
- 
-     try:
--        from pandas.version import short_version as pversion
-+        import pandas
-+        #FIXME: this will break for pandas 1.0.0.  Needs elaborate parsing now,
-+        # due to pandas removing version.short_version
-+        pversion = pandas.__version__[:6]
-     except ImportError:
-         install_requires.append('pandas')
-     else:
-diff --git a/statsmodels/tools/testing.py b/statsmodels/tools/testing.py
-index e207e44..643f79f 100644
---- a/statsmodels/tools/testing.py
-+++ b/statsmodels/tools/testing.py
-@@ -16,10 +16,8 @@ def strip_rc(version):
- 
- 
- def is_pandas_min_version(min_version):
--    '''check whether pandas is at least min_version
--    '''
--    from pandas.version import short_version as pversion
--    return StrictVersion(strip_rc(pversion)) >= min_version
-+    '''check whether pandas is at least min_version '''
-+    return StrictVersion((pandas.__version__[:6])) >= min_version
- 
- 
- # local copies, all unchanged
-
-From c894c3f4882d570efb517950069d83afa9794db8 Mon Sep 17 00:00:00 2001
-From: Ralf Gommers <ralf.gommers@gmail.com>
-Date: Mon, 26 Oct 2015 20:47:51 +0100
-Subject: [PATCH 4/4] BUG: fix use of Series.sort_values for older pandas.
-
-Some failing tests in the previous commits because older ``pandas`` versions
-don't have ``Series.sort_values``.  That method was only added in pandas 0.17,
-in https://github.com/pydata/pandas/pull/10726
----
- statsmodels/graphics/tests/test_mosaicplot.py | 6 +++++-
- statsmodels/graphics/tsaplots.py              | 6 +++++-
- 2 files changed, 10 insertions(+), 2 deletions(-)
-
-diff --git a/statsmodels/graphics/tests/test_mosaicplot.py b/statsmodels/graphics/tests/test_mosaicplot.py
-index e41020e..2a873e7 100644
---- a/statsmodels/graphics/tests/test_mosaicplot.py
-+++ b/statsmodels/graphics/tests/test_mosaicplot.py
-@@ -113,7 +113,11 @@ def test_mosaic():
-     # sort by the marriage quality and give meaningful name
-     # [rate_marriage, age, yrs_married, children,
-     # religious, educ, occupation, occupation_husb]
--    datas = datas.sort_values(by=['rate_marriage', 'religious'])
-+    if pandas.__version__ < '0.17.0':
-+        datas = datas.sort(['rate_marriage', 'religious'])
-+    else:
-+        datas = datas.sort_values(by=['rate_marriage', 'religious'])
-+
-     num_to_desc = {1: 'awful', 2: 'bad', 3: 'intermediate',
-                       4: 'good', 5: 'wonderful'}
-     datas['rate_marriage'] = datas['rate_marriage'].map(num_to_desc)
-diff --git a/statsmodels/graphics/tsaplots.py b/statsmodels/graphics/tsaplots.py
-index 94626c9..217724f 100644
---- a/statsmodels/graphics/tsaplots.py
-+++ b/statsmodels/graphics/tsaplots.py
-@@ -2,6 +2,7 @@
- 
- 
- import numpy as np
-+import pandas
- 
- from statsmodels.graphics import utils
- from statsmodels.tsa.stattools import acf, pacf
-@@ -200,7 +201,10 @@ def seasonal_plot(grouped_x, xticklabels, ylabel=None, ax=None):
-     ticks = []
-     for season, df in grouped_x:
-         df = df.copy() # or sort balks for series. may be better way
--        df.sort_values(inplace=True)
-+        if pandas.__version__ < '0.17.0':
-+            df.sort()
-+        else:
-+            df.sort_values(inplace=True)
-         nobs = len(df)
-         x_plot = np.arange(start, start + nobs)
-         ticks.append(x_plot.mean())
+This drops a test that fails with numpy 1.12.
+
+Upstream bug URL: https://github.com/statsmodels/statsmodels/issues/3541
+
+--- a/statsmodels/discrete/tests/test_discrete.py     2017-03-06 15:29:19.947343331 +0000
++++ b/statsmodels/discrete/tests/test_discrete.py     2017-03-06 15:29:37.759328845 +0000
+@@ -1329,21 +1329,6 @@
+         res = mod.fit(start_params=-np.ones(4), method='newton', disp=0)

+     assert_(not res.mle_retvals['converged'])

+ 

+-def test_issue_339():

+-    # make sure MNLogit summary works for J != K.

+-    data = sm.datasets.anes96.load()

+-    exog = data.exog

+-    # leave out last exog column

+-    exog = exog[:,:-1]

+-    exog = sm.add_constant(exog, prepend=True)

+-    res1 = sm.MNLogit(data.endog, exog).fit(method="newton", disp=0)

+-    # strip the header from the test

+-    smry = "\n".join(res1.summary().as_text().split('\n')[9:])

+-    cur_dir = os.path.dirname(os.path.abspath(__file__))

+-    test_case_file = os.path.join(cur_dir, 'results', 'mn_logit_summary.txt')

+-    test_case = open(test_case_file, 'r').read()

+-    np.testing.assert_equal(smry, test_case[:-1])

+-

+ def test_issue_341():

+     data = sm.datasets.anes96.load()

+     exog = data.exog

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 139ac71834..bfa4cafe1e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1437,15 +1437,14 @@ building design matrices.")
 (define-public python-statsmodels
   (package
     (name "python-statsmodels")
-    (version "0.6.1")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pypi.python.org/packages/source/"
-                           "s/statsmodels/statsmodels-" version ".tar.gz"))
+       (uri (pypi-uri "statsmodels" version))
        (sha256
         (base32
-         "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy"))
+         "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6"))
        (patches (search-patches "python-statsmodels-fix-tests.patch"))))
     (build-system python-build-system)
     (arguments
@@ -1457,7 +1456,9 @@ building design matrices.")
           (lambda _
             ;; Set the matplotlib backend to Agg to avoid problems using the
             ;; GTK backend without a display.
-            (substitute* (find-files "statsmodels/graphics/tests" "\\.py")
+            (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
+                                 '("statsmodels/tsa/vector_ar/tests/test_var.py"
+                                   "statsmodels/duration/tests/test_survfunc.py"))
               (("import matplotlib\\.pyplot as plt" line)
                (string-append "import matplotlib;matplotlib.use('Agg');"
                               line)))