[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
01/01: gnu: python-statsmodels: Fix tests.
|
From: |
Ricardo Wurmus |
|
Subject: |
01/01: gnu: python-statsmodels: Fix tests. |
|
Date: |
Thu, 4 Aug 2016 11:41:21 +0000 (UTC) |
rekado pushed a commit to branch master
in repository guix.
commit 8b52167e7706bb982bf809036bdc247c709779bb
Author: Ricardo Wurmus <address@hidden>
Date: Thu Aug 4 12:48:25 2016 +0200
gnu: python-statsmodels: Fix tests.
* gnu/packages/statistics.scm (python-statsmodels): Add patch to fix tests.
(python2-statsmodels)[propagated-inputs]: Add python2-pytz.
* gnu/packages/patches/python-statsmodels-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
gnu/local.mk | 1 +
.../patches/python-statsmodels-fix-tests.patch | 196 ++++++++++++++++++++
gnu/packages/statistics.scm | 6 +-
3 files changed, 201 insertions(+), 2 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 4dcc547..3444c20 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -739,6 +739,7 @@ dist_patch_DATA =
\
%D%/packages/patches/python-ipython-inputhook-ctype.patch \
%D%/packages/patches/python-rarfile-fix-tests.patch \
%D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch \
+ %D%/packages/patches/python-statsmodels-fix-tests.patch \
%D%/packages/patches/python-configobj-setuptools.patch \
%D%/packages/patches/python-paste-remove-website-test.patch \
%D%/packages/patches/python-paste-remove-timing-test.patch \
diff --git a/gnu/packages/patches/python-statsmodels-fix-tests.patch
b/gnu/packages/patches/python-statsmodels-fix-tests.patch
new file mode 100644
index 0000000..3315ddb
--- /dev/null
+++ b/gnu/packages/patches/python-statsmodels-fix-tests.patch
@@ -0,0 +1,196 @@
+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 <address@hidden>
+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 <address@hidden>
+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 <address@hidden>
+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 <address@hidden>
+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())
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 2365149..990f2fc 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1331,7 +1331,8 @@ building design matrices.")
"s/statsmodels/statsmodels-" version ".tar.gz"))
(sha256
(base32
- "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy"))))
+ "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy"))
+ (patches (search-patches "python-statsmodels-fix-tests.patch"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -1375,7 +1376,8 @@ inference for statistical models.")
(let ((stats (package-with-python2 python-statsmodels)))
(package (inherit stats)
(propagated-inputs
- `(("python2-numpy" ,python2-numpy)
+ `(("python2-pytz" ,python2-pytz)
+ ("python2-numpy" ,python2-numpy)
("python2-scipy" ,python2-scipy)
("python2-pandas" ,python2-pandas)
("python2-patsy" ,python2-patsy)