[netcdf4-python] 03/04: Add patch to use NamedTemporaryFile instead of deprecated mktemp.
Sebastiaan Couwenberg
sebastic at moszumanska.debian.org
Sun Mar 27 20:46:45 UTC 2016
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sebastic pushed a commit to branch master
in repository netcdf4-python.
commit f3a8d66ede6ae78fffa13089af66b2c7d56ffe7d
Author: Bas Couwenberg <sebastic at xs4all.nl>
Date: Sun Mar 27 18:16:23 2016 +0200
Add patch to use NamedTemporaryFile instead of deprecated mktemp.
---
debian/changelog | 1 +
debian/patches/series | 1 +
debian/patches/tempfile-mktemp.patch | 391 +++++++++++++++++++++++++++++++++++
3 files changed, 393 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index e03bd35..75293b3 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ netcdf4-python (1.2.3.1-2) UNRELEASED; urgency=medium
* Enable all hardening buildflags.
* Add build dependency on netcdf-bin for ncdump (required for tests).
+ * Add patch to use NamedTemporaryFile instead of deprecated mktemp.
-- Bas Couwenberg <sebastic at debian.org> Sun, 27 Mar 2016 16:43:31 +0200
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..9618aed
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+tempfile-mktemp.patch
diff --git a/debian/patches/tempfile-mktemp.patch b/debian/patches/tempfile-mktemp.patch
new file mode 100644
index 0000000..23102c7
--- /dev/null
+++ b/debian/patches/tempfile-mktemp.patch
@@ -0,0 +1,391 @@
+Description: Use NamedTemporaryFile instead of deprecated mktemp.
+ See: https://docs.python.org/2/library/tempfile.html#tempfile.mktemp
+Author: Bas Couwenberg <sebastic at debian.org>
+Forwarded: https://github.com/Unidata/netcdf4-python/pull/543
+
+--- a/test/tst_atts.py
++++ b/test/tst_atts.py
+@@ -14,7 +14,7 @@ except ImportError: # or else use drop-i
+ from ordereddict import OrderedDict
+
+ # test attribute creation.
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ VAR_NAME="dummy_var"
+ GROUP_NAME = "dummy_group"
+ DIM1_NAME="x"
+--- a/test/tst_cdf5.py
++++ b/test/tst_cdf5.py
+@@ -3,7 +3,7 @@ import numpy as np
+ import sys, os, unittest, tempfile
+ from numpy.testing import assert_array_equal
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ dimsize = np.iinfo(np.int64).max # max unsigned 64 bit integer
+ ndim = 100
+ arrdata = np.random.randint(np.iinfo(np.uint8).min,np.iinfo(np.uint8).max,size=ndim)
+--- a/test/tst_compound_alignment.py
++++ b/test/tst_compound_alignment.py
+@@ -75,7 +75,7 @@ cells = numpy.array([ (387, 289, 65.
+ (396, 290, 65.71821594238281, -167.9770050048828, 3545, -10149, 8941, -16614, 9, 34164, 1, 0, 200, 526, 511, 301, 170, 65528, 35, 1480, 2350, 3029, 2645, 2928, 5907, 11842, 6208, 16528, 7384, 7988, 870, 527, 661, 3054, 2504, 3291, 3235, 2490, 3424, 354, 354, 10039, 10988, 7958, 7395, 7902, 8811, 14853, 16836, 17231, 20852, 13, 7, 6, 15, 15, 15, 15, 0, 10, 5, 8, 8, 4, 5, 4, 7, 0, 0, 12, 13, 15, 5, 12, 2, 2, 6, 3, 15, 15, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 28, 28, 6, 6, 6, 0, 6, 0, 0, [...]
+ dtype=[('mxd03_granule_row', '<i2'), ('mxd03_granule_column', '<i2'), ('mxd03_latitude', '<f4'), ('mxd03_longitude', '<f4'), ('mxd03_sensor_zenith', '<i2'), ('mxd03_sensor_azimuth', '<i2'), ('mxd03_solar_zenith', '<i2'), ('mxd03_solar_azimuth', '<i2'), ('mxd03_height', '<i2'), ('mxd03_range', '<u2'), ('mxd03_land_sea_mask', '|u1'), ('mxd03_gflags', '|u1'), ('mxd02_band_1A', '<u2'), ('mxd02_band_2A', '<u2'), ('mxd02_band_3A', '<u2'), ('mxd02_band_4A', '<u2'), ('mxd02_band_5A', '<u2 [...]
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+
+ class CompoundAlignTestCase(unittest.TestCase):
+
+--- a/test/tst_compoundatt.py
++++ b/test/tst_compoundatt.py
+@@ -9,7 +9,7 @@ from numpy.testing import assert_array_e
+
+ # test compound attributes.
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ DIM_NAME = 'time'
+ VAR_NAME = 'wind'
+ VAR_NAME2 = 'forecast_wind'
+--- a/test/tst_compoundvar.py
++++ b/test/tst_compoundvar.py
+@@ -9,7 +9,7 @@ from numpy.testing import assert_array_e
+
+ # test compound data types.
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ #FILE_NAME = 'test.nc'
+ DIM_NAME = 'phony_dim'
+ GROUP_NAME = 'phony_group'
+--- a/test/tst_compression.py
++++ b/test/tst_compression.py
+@@ -8,7 +8,7 @@ ndim = 100000
+ ndim2 = 100
+ chunk1 = 10; chunk2 = ndim2
+ nfiles = 7
+-files = [tempfile.mktemp(".nc") for nfile in range(nfiles)]
++files = [tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name for nfile in range(nfiles)]
+ array = uniform(size=(ndim,))
+ array2 = uniform(size=(ndim,ndim2))
+ lsd = 3
+--- a/test/tst_dims.py
++++ b/test/tst_dims.py
+@@ -6,7 +6,7 @@ import numpy as NP
+ from numpy.random.mtrand import uniform
+ import netCDF4
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ LAT_NAME="lat"
+ LAT_LEN = 25
+ LAT_LENG = 50
+--- a/test/tst_diskless.py
++++ b/test/tst_diskless.py
+@@ -12,8 +12,8 @@ n2dim = 73
+ n3dim = 144
+ ranarr = 100.*uniform(size=(n1dim,n2dim,n3dim))
+ ranarr2 = 100.*uniform(size=(n1dim,n2dim,n3dim))
+-FILE_NAME = tempfile.mktemp(".nc")
+-FILE_NAME2 = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=True).name
++FILE_NAME2 = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+
+ class DisklessTestCase(unittest.TestCase):
+
+--- a/test/tst_endian.py
++++ b/test/tst_endian.py
+@@ -4,8 +4,8 @@ import unittest, os, tempfile
+ from numpy.testing import assert_array_equal, assert_array_almost_equal
+
+ data = np.arange(12,dtype='f4').reshape(3,4)
+-FILE_NAME = tempfile.mktemp(".nc")
+-FILE_NAME2 = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
++FILE_NAME2 = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+
+ def create_file(file,format,data):
+ import warnings
+--- a/test/tst_enum.py
++++ b/test/tst_enum.py
+@@ -6,7 +6,7 @@ from netCDF4 import Dataset
+ import numpy as np
+ from numpy.testing import assert_array_equal
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ ENUM_NAME = 'cloud_t'
+ ENUM_BASETYPE = np.int8
+ VAR_NAME = 'primary_cloud'
+--- a/test/tst_fancyslicing.py
++++ b/test/tst_fancyslicing.py
+@@ -19,7 +19,7 @@ to be checked.)
+ See test2unlim below for an example.
+ """
+
+-file_name = tempfile.mktemp(".nc")
++file_name = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ xdim=9; ydim=10; zdim=11
+ i = np.array([2,5,7],'i4')
+ i2 = np.array([0,8],'i4')
+--- a/test/tst_grps.py
++++ b/test/tst_grps.py
+@@ -7,8 +7,8 @@ import netCDF4
+
+ # test group creation.
+
+-FILE_NAME1 = tempfile.mktemp(".nc")
+-FILE_NAME2 = tempfile.mktemp(".nc")
++FILE_NAME1 = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
++FILE_NAME2 = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ DYNASTY=u"Tudor"
+ HENRY_VII=u"Henry_VII"
+ MARGARET=u"Margaret"
+--- a/test/tst_grps2.py
++++ b/test/tst_grps2.py
+@@ -9,7 +9,7 @@ import netCDF4
+ # in createVariable and createGroups (added in 1.1.8).
+ # also test Dataset.__getitem__, also added in 1.1.8.
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+
+ class Groups2TestCase(unittest.TestCase):
+
+--- a/test/tst_masked.py
++++ b/test/tst_masked.py
+@@ -12,7 +12,7 @@ import netCDF4
+ # packing/unpacking of short ints.
+
+ # create an n1dim by n2dim random ranarr.
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ ndim = 10
+ ranarr = 100.*uniform(size=(ndim))
+ ranarr2 = 100.*uniform(size=(ndim))
+--- a/test/tst_masked2.py
++++ b/test/tst_masked2.py
+@@ -12,9 +12,9 @@ seterr(over='ignore') # don't print warn
+ # test automatic conversion of masked arrays, and
+ # packing/unpacking of short ints.
+
+-FILE_NAME1 = tempfile.mktemp(".nc")
+-FILE_NAME2 = tempfile.mktemp(".nc")
+-FILE_NAME3 = tempfile.mktemp(".nc")
++FILE_NAME1 = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
++FILE_NAME2 = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
++FILE_NAME3 = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ datacheck1 =\
+ ma.array([0,5000.0,4000.0,0],dtype=np.float,mask=[True,False,False,True])
+ datacheck2 =\
+--- a/test/tst_masked3.py
++++ b/test/tst_masked3.py
+@@ -15,7 +15,7 @@ class SetAutoMaskTestBase(unittest.TestC
+
+ def setUp(self):
+
+- self.testfile = tempfile.mktemp(".nc")
++ self.testfile = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+
+ self.fillval = default_fillvals["i2"]
+ self.v = np.array([self.fillval, 5, 4, -9999], dtype = "i2")
+@@ -137,7 +137,7 @@ class GlobalSetAutoMaskTest(unittest.Tes
+
+ def setUp(self):
+
+- self.testfile = tempfile.mktemp(".nc")
++ self.testfile = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+
+ f = Dataset(self.testfile, 'w')
+
+--- a/test/tst_multifile.py
++++ b/test/tst_multifile.py
+@@ -8,7 +8,7 @@ import tempfile, unittest, os, datetime
+ nx=100; ydim=5; zdim=1
+ nfiles = 10
+ ninc = nx/nfiles
+-files = [tempfile.mktemp(".nc") for nfile in range(nfiles)]
++files = [tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name for nfile in range(nfiles)]
+ data = randint(0,10,size=(nx,ydim,zdim))
+ missval = 99
+ data[::10] = missval
+@@ -66,7 +66,7 @@ class NonuniformTimeTestCase(unittest.Te
+ ninc = 365
+ def setUp(self):
+
+- self.files = [tempfile.mktemp(".nc") for nfile in range(2)]
++ self.files = [tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name for nfile in range(2)]
+ for nfile,file in enumerate(self.files):
+ f = Dataset(file,'w',format='NETCDF4_CLASSIC')
+ f.createDimension('time',None)
+--- a/test/tst_multifile2.py
++++ b/test/tst_multifile2.py
+@@ -8,7 +8,7 @@ import tempfile, unittest, os, datetime
+ nx=100; ydim=5; zdim=1
+ nfiles = 10
+ ninc = nx/nfiles
+-files = [tempfile.mktemp(".nc") for nfile in range(nfiles)]
++files = [tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name for nfile in range(nfiles)]
+ data = randint(0,10,size=(nx,ydim,zdim))
+ missval = 99
+ data[::10] = missval
+@@ -68,7 +68,7 @@ class NonuniformTimeTestCase(unittest.Te
+ ninc = 365
+ def setUp(self):
+
+- self.files = [tempfile.mktemp(".nc") for nfile in range(2)]
++ self.files = [tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name for nfile in range(2)]
+ for nfile,file in enumerate(self.files):
+ f = Dataset(file,'w',format='NETCDF4_CLASSIC')
+ f.createDimension('time',None)
+--- a/test/tst_netcdftime.py
++++ b/test/tst_netcdftime.py
+@@ -506,7 +506,7 @@ class TestDate2index(unittest.TestCase):
+ self.standardtime = self.TestTime(datetime(1950, 1, 1), 366, 24,
+ 'hours since 1900-01-01', 'standard')
+
+- self.file = tempfile.mktemp(".nc")
++ self.file = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ f = Dataset(self.file, 'w')
+ f.createDimension('time', None)
+ time = f.createVariable('time', float, ('time',))
+--- a/test/tst_refcount.py
++++ b/test/tst_refcount.py
+@@ -1,6 +1,6 @@
+ import unittest, netCDF4, tempfile, os
+
+-file_name = tempfile.mktemp(".nc")
++file_name = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+
+ class RefCountTestCase(unittest.TestCase):
+
+--- a/test/tst_rename.py
++++ b/test/tst_rename.py
+@@ -9,7 +9,7 @@ from netCDF4 import __has_rename_grp__
+ # test changing dimension, variable names
+ # and deleting attributes.
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ LAT_NAME="lat"
+ LON_NAME="lon"
+ LON_NAME2 = "longitude"
+--- a/test/tst_scalarvar.py
++++ b/test/tst_scalarvar.py
+@@ -10,7 +10,7 @@ import math
+ VAR_NAME='temp'
+ VAR_TYPE='f4'
+ VAR_VAL=math.pi
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ GROUP_NAME = 'subgroup'
+
+ # test scalar variable creation and retrieval.
+--- a/test/tst_scaled.py
++++ b/test/tst_scaled.py
+@@ -16,7 +16,7 @@ class SetAutoScaleTestBase(unittest.Test
+
+ def setUp(self):
+
+- self.testfile = tempfile.mktemp(".nc")
++ self.testfile = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+
+ self.fillval = default_fillvals["i2"]
+ self.missing_value = -9999
+@@ -184,7 +184,7 @@ class GlobalSetAutoScaleTest(unittest.Te
+
+ def setUp(self):
+
+- self.testfile = tempfile.mktemp(".nc")
++ self.testfile = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+
+ f = Dataset(self.testfile, 'w')
+
+--- a/test/tst_shape.py
++++ b/test/tst_shape.py
+@@ -2,7 +2,7 @@ from netCDF4 import Dataset
+ import tempfile, unittest, os
+ import numpy as np
+
+-file_name = tempfile.mktemp(".nc")
++file_name = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ xdim=None; ydim=121; zdim=169
+ datashape = (ydim,zdim)
+ data = np.ones(datashape,dtype=np.float)
+--- a/test/tst_slicing.py
++++ b/test/tst_slicing.py
+@@ -5,7 +5,7 @@ assert_array_almost_equal
+ import tempfile, unittest, os, random
+ import numpy as np
+
+-file_name = tempfile.mktemp(".nc")
++file_name = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ xdim=9; ydim=10; zdim=11
+ #seed(9) # fix seed
+ data = randint(0,10,size=(xdim,ydim,zdim)).astype('u1')
+--- a/test/tst_types.py
++++ b/test/tst_types.py
+@@ -10,7 +10,7 @@ import netCDF4
+ # test primitive data types.
+
+ # create an n1dim by n2dim random ranarr.
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ n1dim = 5
+ n2dim = 10
+ ranarr = 100.*uniform(size=(n1dim,n2dim))
+--- a/test/tst_unicode.py
++++ b/test/tst_unicode.py
+@@ -4,7 +4,7 @@ import sys, unittest, os, tempfile
+
+ netCDF4.default_encoding = 'utf-8'
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ ATT1 = u'\u03a0\u03a3\u03a9'
+ ATT2 = u'x\xb0'
+ ATT3 = [u'\u03a0',u'\u03a3',u'\u03a9']
+--- a/test/tst_unicode3.py
++++ b/test/tst_unicode3.py
+@@ -4,7 +4,7 @@ import sys, unittest, os, tempfile
+
+ netCDF4.default_encoding = 'utf-8'
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ ATT1 = '\u03a0\u03a3\u03a9'
+ ATT2 = 'x\xb0'
+ ATT3 = ['\u03a0','\u03a3','\u03a9']
+--- a/test/tst_unlimdim.py
++++ b/test/tst_unlimdim.py
+@@ -15,7 +15,7 @@ n1dim = 4
+ n2dim = 10
+ n3dim = 8
+ ranarr = 100.*uniform(size=(n1dim,n2dim,n3dim))
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+
+ class UnlimdimTestCase(unittest.TestCase):
+
+--- a/test/tst_vars.py
++++ b/test/tst_vars.py
+@@ -9,7 +9,7 @@ import netCDF4
+
+ # test variable creation.
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ VAR_DOUBLE_NAME="dummy_var"
+ VAR_SHORT_NAME='dummy_var_short'
+ VARNAMES = sorted([VAR_DOUBLE_NAME,VAR_SHORT_NAME])
+--- a/test/tst_vlen.py
++++ b/test/tst_vlen.py
+@@ -6,7 +6,7 @@ from netCDF4 import Dataset
+ import numpy as np
+ from numpy.testing import assert_array_equal
+
+-FILE_NAME = tempfile.mktemp(".nc")
++FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+ VL_NAME = 'vlen_type'
+ VL_BASETYPE = np.int16
+ DIM1_NAME = 'lon'
--
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