Date: Wed, 15 Jan 2014 09:55:27 -0500 (EST) From: "John W. O'Brien" <john@saltant.com> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/185803: [MAINTAINER] math/py-pandas: Update to 0.13.0 Message-ID: <20140115145527.17FADB05CE@drivel.saltant.net> Resent-Message-ID: <201401151500.s0FF009j084919@freefall.freebsd.org>
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>Number: 185803
>Category: ports
>Synopsis: [MAINTAINER] math/py-pandas: Update to 0.13.0
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Wed Jan 15 15:00:00 UTC 2014
>Closed-Date:
>Last-Modified:
>Originator: John W. O'Brien
>Release: FreeBSD 9.2-STABLE amd64
>Organization:
Saltant Solutions
>Environment:
System: FreeBSD XXXX.saltant.net 9.2-STABLE FreeBSD 9.2-STABLE #1 r260112: Mon Dec 30 18:26:07 EST 2013 root@XXXX.saltant.net:/usr/obj/usr/src/sys/NARB amd64
>Description:
Change log
==========
- Update to 0.13.0
- Abandon easy_install
- Update pkg-message and TEST_DEPENDS to reflect current recommendations and
port availability
- Add erroneously-omitted lang/cython to TEST_DEPENDS (for 'build_ext -i')
- Conform regression-test target to upstream test procedure
QA
==
portlint: looks fine.
nose: no errors, no failures.
>How-To-Repeat:
N/A
>Fix:
Apply attached patch.
--- patch-math_py-pandas-0.13.0.txt begins here ---
Index: /usr/ports/math/py-pandas/Makefile
===================================================================
--- /usr/ports/math/py-pandas/Makefile (revision 339733)
+++ /usr/ports/math/py-pandas/Makefile (working copy)
@@ -1,8 +1,7 @@
# $FreeBSD$
PORTNAME= pandas
-PORTVERSION= 0.12.0
-PORTREVISION= 2
+PORTVERSION= 0.13.0
CATEGORIES= math devel python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -18,6 +17,7 @@
${PYTHON_PKGNAMEPREFIX}pytz>0:${PORTSDIR}/devel/py-pytz \
${PYTHON_PKGNAMEPREFIX}sqlite3>0:${PORTSDIR}/databases/py-sqlite3
TEST_DEPENDS= nosetests:${PORTSDIR}/devel/py-nose \
+ cython:${PORTSDIR}/lang/cython \
${PYTHON_PKGNAMEPREFIX}numexpr>0:${PORTSDIR}/math/py-numexpr \
${PYTHON_PKGNAMEPREFIX}tables>0:${PORTSDIR}/devel/py-tables \
${PYTHON_PKGNAMEPREFIX}scipy>0:${PORTSDIR}/science/py-scipy \
@@ -25,6 +25,8 @@
${PYTHON_PKGNAMEPREFIX}xlrd>0:${PORTSDIR}/textproc/py-xlrd \
${PYTHON_PKGNAMEPREFIX}xlwt>0:${PORTSDIR}/textproc/py-xlwt \
${PYTHON_PKGNAMEPREFIX}openpyxl>0:${PORTSDIR}/textproc/py-openpyxl \
+ ${PYTHON_PKGNAMEPREFIX}statsmodels>0:${PORTSDIR}/math/py-statsmodels \
+ ${PYTHON_PKGNAMEPREFIX}bottleneck>0:${PORTSDIR}/math/py-bottleneck \
${PYTHON_PKGNAMEPREFIX}beautifulsoup>0:${PORTSDIR}/www/py-beautifulsoup \
${PYTHON_PKGNAMEPREFIX}html5lib>0:${PORTSDIR}/www/py-html5lib \
${PYTHON_PKGNAMEPREFIX}lxml>0:${PORTSDIR}/devel/py-lxml
@@ -32,9 +34,8 @@
SUB_FILES= pkg-message
USE_PYTHON= yes
-USE_PYDISTUTILS= easy_install
+USE_PYDISTUTILS= yes
PYDISTUTILS_AUTOPLIST= yes
-PYEASYINSTALL_ARCHDEP= yes
# Uncomment the following line to enable regression-test
# on a headless (X11-less) host (eg: RedPorts)
@@ -43,7 +44,9 @@
regression-test: build
@(cd ${WRKSRC} && \
${PYTHON_CMD} ${PYSETUP} build_ext --inplace && \
- ${PYTHON_CMD} ${PYSETUP} nosetests \
+ ${PYTHON_CMD} ci/print_versions.py \
+ ci/script.sh \
+ ${PYTHON_CMD} ci/print_skipped.py \
)
.include <bsd.port.mk>
Index: /usr/ports/math/py-pandas/distinfo
===================================================================
--- /usr/ports/math/py-pandas/distinfo (revision 339733)
+++ /usr/ports/math/py-pandas/distinfo (working copy)
@@ -1,2 +1,2 @@
-SHA256 (pandas-0.12.0.tar.gz) = be9b4c3611801b366873531bc87a87dd16b19e7d78fa84c21898cd007931c86d
-SIZE (pandas-0.12.0.tar.gz) = 3155059
+SHA256 (pandas-0.13.0.tar.gz) = f034cd298e0d68fee24a2b0a68a9b8da41978d6f39474f908f7f352904ef7f3c
+SIZE (pandas-0.13.0.tar.gz) = 3572047
Index: /usr/ports/math/py-pandas/files/patch-MANIFEST.in
===================================================================
--- /usr/ports/math/py-pandas/files/patch-MANIFEST.in (revision 339733)
+++ /usr/ports/math/py-pandas/files/patch-MANIFEST.in (working copy)
@@ -1,12 +0,0 @@
---- ./MANIFEST.in.orig 2013-07-27 06:55:55.000000000 -0400
-+++ ./MANIFEST.in 2013-07-27 06:56:02.000000000 -0400
-@@ -2,9 +2,7 @@
- include LICENSE
- include RELEASE.md
- include README.rst
--include TODO.rst
- include setup.py
--include setupegg.py
-
- graft doc
- prune doc/build
Index: /usr/ports/math/py-pandas/files/patch-pandas-issue4353-pullrequest4356
===================================================================
--- /usr/ports/math/py-pandas/files/patch-pandas-issue4353-pullrequest4356 (revision 339733)
+++ /usr/ports/math/py-pandas/files/patch-pandas-issue4353-pullrequest4356 (working copy)
@@ -1,162 +0,0 @@
-This patch is adapted from the following upstream commit.
-
-[PATCH] TST/BUG/CLN: make stata IO tests use temporary files for writing
-c98e09951f74bf3445f8144363afaa769be69940
-
---- pandas/io/tests/test_stata.py.orig
-+++ pandas/io/tests/test_stata.py
-@@ -10,9 +10,8 @@ import numpy as np
-
- from pandas.core.frame import DataFrame, Series
- from pandas.io.parsers import read_csv
--from pandas.io.stata import read_stata, StataReader, StataWriter
-+from pandas.io.stata import read_stata, StataReader
- import pandas.util.testing as tm
--from pandas.util.testing import ensure_clean
- from pandas.util.misc import is_little_endian
-
-
-@@ -27,15 +26,12 @@ class StataTests(unittest.TestCase):
- self.dta3 = os.path.join(self.dirpath, 'stata3.dta')
- self.csv3 = os.path.join(self.dirpath, 'stata3.csv')
- self.dta4 = os.path.join(self.dirpath, 'stata4.dta')
-- self.dta5 = os.path.join(self.dirpath, 'stata5.dta')
-- self.dta6 = os.path.join(self.dirpath, 'stata6.dta')
- self.dta7 = os.path.join(self.dirpath, 'cancer.dta')
- self.csv7 = os.path.join(self.dirpath, 'cancer.csv')
- self.dta8 = os.path.join(self.dirpath, 'tbl19-3.dta')
- self.csv8 = os.path.join(self.dirpath, 'tbl19-3.csv')
- self.dta9 = os.path.join(self.dirpath, 'lbw.dta')
- self.csv9 = os.path.join(self.dirpath, 'lbw.csv')
-- self.dta10 = os.path.join(self.dirpath, 'stata10.dta')
-
- def read_dta(self, file):
- return read_stata(file, convert_dates=True)
-@@ -46,9 +42,11 @@ class StataTests(unittest.TestCase):
- def test_read_dta1(self):
- reader = StataReader(self.dta1)
- parsed = reader.data()
-- # Pandas uses np.nan as missing value. Thus, all columns will be of type float, regardless of their name.
-+ # Pandas uses np.nan as missing value.
-+ # Thus, all columns will be of type float, regardless of their name.
- expected = DataFrame([(np.nan, np.nan, np.nan, np.nan, np.nan)],
-- columns=['float_miss', 'double_miss', 'byte_miss', 'int_miss', 'long_miss'])
-+ columns=['float_miss', 'double_miss', 'byte_miss',
-+ 'int_miss', 'long_miss'])
-
- for i, col in enumerate(parsed.columns):
- np.testing.assert_almost_equal(
-@@ -90,7 +88,9 @@ class StataTests(unittest.TestCase):
- np.datetime64('NaT')
- )
- ],
-- columns=['datetime_c', 'datetime_big_c', 'date', 'weekly_date', 'monthly_date', 'quarterly_date', 'half_yearly_date', 'yearly_date']
-+ columns=['datetime_c', 'datetime_big_c', 'date', 'weekly_date',
-+ 'monthly_date', 'quarterly_date', 'half_yearly_date',
-+ 'yearly_date']
- )
-
- with warnings.catch_warnings(record=True) as w:
-@@ -125,34 +125,40 @@ class StataTests(unittest.TestCase):
- ["nine", "two", 9, np.nan, "nine"],
- ["ten", "one", "ten", np.nan, "ten"]
- ],
-- columns=['fully_labeled', 'fully_labeled2', 'incompletely_labeled', 'labeled_with_missings', 'float_labelled'])
-+ columns=['fully_labeled', 'fully_labeled2', 'incompletely_labeled',
-+ 'labeled_with_missings', 'float_labelled'])
-
- tm.assert_frame_equal(parsed, expected)
-
-- def test_write_dta5(self):
-+ def test_read_write_dta5(self):
- if not is_little_endian():
-- raise nose.SkipTest("known failure of test_write_dta5 on non-little endian")
-+ raise nose.SkipTest("known failure of test_write_dta5 on "
-+ "non-little endian")
-
- original = DataFrame([(np.nan, np.nan, np.nan, np.nan, np.nan)],
-- columns=['float_miss', 'double_miss', 'byte_miss', 'int_miss', 'long_miss'])
-+ columns=['float_miss', 'double_miss', 'byte_miss',
-+ 'int_miss', 'long_miss'])
- original.index.name = 'index'
-
-- with ensure_clean(self.dta5) as path:
-+ with tm.ensure_clean() as path:
- original.to_stata(path, None, False)
- written_and_read_again = self.read_dta(path)
-- tm.assert_frame_equal(written_and_read_again.set_index('index'), original)
-+ tm.assert_frame_equal(written_and_read_again.set_index('index'),
-+ original)
-
- def test_write_dta6(self):
- if not is_little_endian():
-- raise nose.SkipTest("known failure of test_write_dta6 on non-little endian")
-+ raise nose.SkipTest("known failure of test_write_dta6 on "
-+ "non-little endian")
-
- original = self.read_csv(self.csv3)
- original.index.name = 'index'
-
-- with ensure_clean(self.dta6) as path:
-+ with tm.ensure_clean() as path:
- original.to_stata(path, None, False)
- written_and_read_again = self.read_dta(path)
-- tm.assert_frame_equal(written_and_read_again.set_index('index'), original)
-+ tm.assert_frame_equal(written_and_read_again.set_index('index'),
-+ original)
-
- @nose.tools.nottest
- def test_read_dta7(self):
-@@ -190,29 +196,30 @@ class StataTests(unittest.TestCase):
- decimal=3
- )
-
-- def test_read_dta10(self):
-+ def test_read_write_dta10(self):
- if not is_little_endian():
-- raise nose.SkipTest("known failure of test_write_dta10 on non-little endian")
-+ raise nose.SkipTest("known failure of test_write_dta10 on "
-+ "non-little endian")
-
-- original = DataFrame(
-- data=
-- [
-- ["string", "object", 1, 1.1, np.datetime64('2003-12-25')]
-- ],
-- columns=['string', 'object', 'integer', 'float', 'datetime'])
-+ original = DataFrame(data=[["string", "object", 1, 1.1,
-+ np.datetime64('2003-12-25')]],
-+ columns=['string', 'object', 'integer', 'float',
-+ 'datetime'])
- original["object"] = Series(original["object"], dtype=object)
- original.index.name = 'index'
-
-- with ensure_clean(self.dta10) as path:
-+ with tm.ensure_clean() as path:
- original.to_stata(path, {'datetime': 'tc'}, False)
- written_and_read_again = self.read_dta(path)
-- tm.assert_frame_equal(written_and_read_again.set_index('index'), original)
-+ tm.assert_frame_equal(written_and_read_again.set_index('index'),
-+ original)
-
- def test_stata_doc_examples(self):
-- with ensure_clean(self.dta5) as path:
-+ with tm.ensure_clean() as path:
- df = DataFrame(np.random.randn(10, 2), columns=list('AB'))
- df.to_stata(path)
-
-+
- if __name__ == '__main__':
- nose.runmodule(argv=[__file__, '-vvs', '-x', '--pdb', '--pdb-failure'],
- exit=False)
---- pandas/util/testing.py.orig
-+++ pandas/util/testing.py
-@@ -86,7 +86,7 @@ def set_trace():
- #------------------------------------------------------------------------------
- # contextmanager to ensure the file cleanup
- @contextmanager
--def ensure_clean(filename = None):
-+def ensure_clean(filename=None):
- # if we are not passed a filename, generate a temporary
- if filename is None:
- filename = tempfile.mkstemp()[1]
Index: /usr/ports/math/py-pandas/files/pkg-message.in
===================================================================
--- /usr/ports/math/py-pandas/files/pkg-message.in (revision 339733)
+++ /usr/ports/math/py-pandas/files/pkg-message.in (working copy)
@@ -2,16 +2,21 @@
Note that the following ports are not strict dependencies but are highly
recommended to get the most out of pandas. Install them as needed.
-numexpr math/py-numexpr
-scipy science/py-scipy
-pytables devel/py-tables
-matplotlib math/py-matplotlib
-xlrd textproc/py-xlrd
-xlwt textproc/py-xlwt
-openpyxl textproc/py-openpyxl
+Library Port origin Purpose
+------- ----------- -------
+boto devel/py-boto access Amazon S3
+pytables devel/py-tables necessary for HDF5-based storage
+bottleneck math/py-bottleneck accelerate certain NaN evals
+matplotlib math/py-matplotlib plotting
+numexpr math/py-numexpr accelerate certain numerical ops
+statsmodels math/py-statsmodels enables parts of pandas.stats
+scipy science/py-scipy misc. statistical functions
+openpyxl textproc/py-openpyxl Excel 2007+ I/O
+xlrd textproc/py-xlrd Excel input
+xlwt textproc/py-xlwt Excel output
-To use the HTML table parsing capabilities that are new to 0.12.0, you
-will need to install
+To use the HTML table parsing capabilities that were introduced in
+pandas 0.12.0, you will need to install
beautifulsoup www/py-beautifulsoup
@@ -23,9 +28,4 @@
Please read the pandas documentation before deciding:
http://pandas.pydata.org/pandas-docs/stable/gotchas.html#html-gotchas
-
-Also recommended, but not yet available in ports are:
-
-bottleneck http://berkeleyanalytics.com/bottleneck/
-scikits.statsmodels http://statsmodels.sourceforge.net/
===
--- patch-math_py-pandas-0.13.0.txt ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted:
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