diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/patches/python-statsmodels-fix-tests.patch | 196 | ||||
| -rw-r--r-- | gnu/packages/statistics.scm | 6 |
3 files changed, 201 insertions, 2 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 4dcc547e55..3444c2031f 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 0000000000..3315ddbd5f --- /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 <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()) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2365149fad..990f2fc132 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) |