[gentoo-commits] repo/gentoo:master commit in: dev-python/pytables/, dev-python/pytables/files/

[gentoo-commits] repo/gentoo:master commit in: dev-python/pytables/, dev-python/pytables/files/

[Benda XU]

commit:     6891e6348ac3444b82d655d97c244d05ef122a8e
Author:     Benda Xu <heroxbd <AT> gentoo <DOT> org>
AuthorDate: Mon Dec  4 03:23:15 2017 +0000
Commit:     Benda XU <heroxbd <AT> gentoo <DOT> org>
CommitDate: Mon Dec  4 03:23:15 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6891e634

dev-python/pytables: drop old version.

Reported-by: Orivej Desh <orivej <AT> gmx.fr>
Suggested-by: Nick Wallingford <nick <AT> wallingford.cc>
Bug: https://bugs.gentoo.org/590936
Package-Manager: Portage-2.3.16, Repoman-2.3.6

 dev-python/pytables/Manifest                       |  3 +-
 .../pytables/files/pytables-3.1.1-blosc.patch      | 16 -----
 .../files/pytables-3.1.1-cython-backport.patch     | 65 -------------------
 .../files/pytables-3.1.1-numpy19-backport.patch    | 51 ---------------
 dev-python/pytables/pytables-3.1.1-r2.ebuild       | 75 ----------------------
 5 files changed, 1 insertion(+), 209 deletions(-)

diff --git a/dev-python/pytables/Manifest b/dev-python/pytables/Manifest
index e18340aad94..0e5ff0132fe 100644
--- a/dev-python/pytables/Manifest
+++ b/dev-python/pytables/Manifest
@@ -1,3 +1,2 @@
-DIST tables-3.1.1.tar.gz 6715786 SHA256 39b9036376f1185599771c19276f13b5b9119d98f9108f58595745ded3fe2da3 SHA512 b5b2052dd81c4748c5e26c1f61f9f92891f48335b0a553f7602ab11c9029dd673d27b91e24cac0da21a81df0c26dbcd9a438214fa58af1ae831c5f04dfa212a6 WHIRLPOOL 86fd6dc9e12503fdbd23013b75f33a41eadbbac0e6dd5ac9a91476d073195077fc6b3d5ad24b1dd4b4c18ae7ed8abc8ea1708262e52240f4c2c3b1153f8c9e91
 DIST tables-3.3.0.tar.gz 7004337 SHA256 8383ccf02e041a5d55494a09fc5514140b4653055a2732c981b5fd0f7408822c SHA512 e19445f0f5f2530d49ce55f258931babb7b05df2366637ddbc306323a1f75b7f7dcf91d70a8cc1f41b182d4cdd9c83872873168592bdcce7bd5acae9f3274f36 WHIRLPOOL f270f741d6886775cc730fbcb79de215fbbe2d9b7b2b6efc6b5b3fa7d141046e7c69daad140ad7cc533b439bfae801ea0e1567939dc4258e5c3b6a88f27cd86c
-DIST tables-3.4.2.tar.gz 7593471 SHA256 fdbbea4edb6bad0ac0e53fc7bc6970e78e12eef4944aa4146bcdcb573201676c SHA512 8c3bb9113e5082f8b44866b04728a04dae37fbd576c3259309fc305fd4cc0c4f74925557e74f6bd1bd1fc5150d8091648139c4c702e5ed9f53e0ace11c2ac58b WHIRLPOOL 392e117a3ad372ee91a02ee66994f3c03e67b4ae7473f5761e13215ce33084fc3ac8e9e371ca9b59f374066523bcd3ebbced01c49faaa84d4af75a26811ee35f
+DIST tables-3.4.2.tar.gz 7593471 BLAKE2B 1a011a2a910a25d4e7cad68b5a1a267482f5ed958aa824dfba5a6c902200c56253c7d5609cd674dfcb288f6ebf2ecb76f4324e53b852f70d0cfc60d6b222510a SHA512 8c3bb9113e5082f8b44866b04728a04dae37fbd576c3259309fc305fd4cc0c4f74925557e74f6bd1bd1fc5150d8091648139c4c702e5ed9f53e0ace11c2ac58b

diff --git a/dev-python/pytables/files/pytables-3.1.1-blosc.patch b/dev-python/pytables/files/pytables-3.1.1-blosc.patch
deleted file mode 100644
index 3a4ba18e5e7..00000000000
--- a/dev-python/pytables/files/pytables-3.1.1-blosc.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- setup.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/setup.py b/setup.py
-index 2c0c126..1448eb1 100755
---- a/setup.py
-+++ b/setup.py
-@@ -768,7 +768,7 @@ if 'BLOSC' not in optional_libs:
-             print("Setting compiler flag '-msse2'")
-             CFLAGS.append("-msse2")
- else:
--    ADDLIBS += ['blosc']
-+    ADDLIBS += ['blosc', 'blosc_filter']
- 
- 
- utilsExtension_libs = LIBS + ADDLIBS

diff --git a/dev-python/pytables/files/pytables-3.1.1-cython-backport.patch b/dev-python/pytables/files/pytables-3.1.1-cython-backport.patch
deleted file mode 100644
index 7db41d2e1a6..00000000000
--- a/dev-python/pytables/files/pytables-3.1.1-cython-backport.patch
+++ /dev/null
@@ -1,65 +0,0 @@
- setup.py               | 13 +++++++------
- tables/req_versions.py |  2 +-
- 2 files changed, 8 insertions(+), 7 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 0f2f3f7..52cda49 100755
---- a/setup.py
-+++ b/setup.py
-@@ -25,6 +25,7 @@ from distutils.core import Extension
- from distutils.dep_util import newer
- from distutils.util import convert_path
- from distutils.ccompiler import new_compiler
-+from distutils.version import LooseVersion
- 
- cmdclass = {}
- setuptools_kwargs = {}
-@@ -106,7 +107,7 @@ def check_import(pkgname, pkgver):
-             "You need %(pkgname)s %(pkgver)s or greater to run PyTables!"
-             % {'pkgname': pkgname, 'pkgver': pkgver})
-     else:
--        if mod.__version__ < pkgver:
-+        if mod.__version__ < LooseVersion(pkgver):
-             exit_with_error(
-                 "You need %(pkgname)s %(pkgver)s or greater to run PyTables!"
-                 % {'pkgname': pkgname, 'pkgver': pkgver})
-@@ -122,21 +123,21 @@ if not has_setuptools:
- 
- # Check if Cython is installed or not (requisite)
- try:
-+    from Cython import __version__ as cython_version
-     from Cython.Distutils import build_ext
--    from Cython.Compiler.Main import Version
-     cmdclass['build_ext'] = build_ext
- except ImportError:
-     exit_with_error(
-         "You need %(pkgname)s %(pkgver)s or greater to compile PyTables!"
-         % {'pkgname': 'Cython', 'pkgver': min_cython_version})
- 
--if Version.version < min_cython_version:
-+if LooseVersion(cython_version) < min_cython_version:
-     exit_with_error(
--        "At least Cython %s is needed so as to generate extensions!"
--        % (min_cython_version))
-+        "You need %(pkgname)s %(pkgver)s or greater to run PyTables!"
-+        % {'pkgname': 'Cython', 'pkgver': min_cython_version})
- else:
-     print("* Found %(pkgname)s %(pkgver)s package installed."
--          % {'pkgname': 'Cython', 'pkgver': Version.version})
-+          % {'pkgname': 'Cython', 'pkgver': cython_version})
- 
- VERSION = open('VERSION').read().strip()
- 
-diff --git a/tables/req_versions.py b/tables/req_versions.py
-index 2c9ca01..bd498c3 100644
---- a/tables/req_versions.py
-+++ b/tables/req_versions.py
-@@ -17,7 +17,7 @@
- # Minimum recommended versions for mandatory packages
- min_numpy_version = '1.4.1'
- min_numexpr_version = '2.0.0'
--min_cython_version = '0.13'
-+min_cython_version = '0.14'
- 
- # The THG team has decided to fix an API inconsistency in the definition
- # of the H5Z_class_t structure in version 1.8.3

diff --git a/dev-python/pytables/files/pytables-3.1.1-numpy19-backport.patch b/dev-python/pytables/files/pytables-3.1.1-numpy19-backport.patch
deleted file mode 100644
index c2f0c2280f0..00000000000
--- a/dev-python/pytables/files/pytables-3.1.1-numpy19-backport.patch
+++ /dev/null
@@ -1,51 +0,0 @@
-From 854d5798ca9fd78c00e18710de2e93202f675f3e Mon Sep 17 00:00:00 2001
-From: Antonio Valentino <antonio.valentino@tiscali.it>
-Date: Sun, 6 Jul 2014 21:21:39 +0200
-Subject: [PATCH] Fix a compatibility problem with numpy 1.9 (close: #362)
-
----
- RELEASE_NOTES.txt | 6 ++++++
- tables/table.py   | 6 +++++-
- 2 files changed, 11 insertions(+), 1 deletion(-)
-
-diff --git a/RELEASE_NOTES.txt b/RELEASE_NOTES.txt
-index f219eb3..1da20e2 100644
---- a/RELEASE_NOTES.txt
-+++ b/RELEASE_NOTES.txt
-@@ -19,6 +19,12 @@ Improvements
-   requiring strict access alignment.
- 
- 
-+Bugs fixed
-+----------
-+
-+- Fixed compatibitily problems with numpy 1.9 (closes :issue:`362`)
-+
-+
- Changes from 3.1.0 to 3.1.1
- ===========================
- 
-diff --git a/tables/table.py b/tables/table.py
-index 235f599..ffe8fd6 100644
---- a/tables/table.py
-+++ b/tables/table.py
-@@ -3406,6 +3406,10 @@ def _getindex(self):
-                      associated with this column (None if the column is not
-                      indexed).""")
- 
-+    @lazyattr
-+    def _itemtype(self):
-+        return self.descr._v_dtypes[self.name]
-+
-     def _getshape(self):
-         return (self.table.nrows,) + self.descr._v_dtypes[self.name].shape
- 
-@@ -3529,7 +3533,7 @@ def __iter__(self):
-         table = self.table
-         itemsize = self.dtype.itemsize
-         nrowsinbuf = table._v_file.params['IO_BUFFER_SIZE'] // itemsize
--        buf = numpy.empty((nrowsinbuf, ), self.dtype)
-+        buf = numpy.empty((nrowsinbuf, ), self._itemtype)
-         max_row = len(self)
-         for start_row in xrange(0, len(self), nrowsinbuf):
-             end_row = min(start_row + nrowsinbuf, max_row)

diff --git a/dev-python/pytables/pytables-3.1.1-r2.ebuild b/dev-python/pytables/pytables-3.1.1-r2.ebuild
deleted file mode 100644
index f22a4f0c61e..00000000000
--- a/dev-python/pytables/pytables-3.1.1-r2.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
-PYTHON_REQ_USE="threads(+)"
-
-MY_PN=tables
-MY_P=${MY_PN}-${PV}
-
-inherit distutils-r1
-
-DESCRIPTION="Hierarchical datasets for Python"
-HOMEPAGE="http://www.pytables.org/"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-LICENSE="BSD"
-IUSE="doc examples"
-
-RDEPEND="
-	app-arch/bzip2:0=
-	dev-libs/c-blosc:0=[hdf5]
-	dev-libs/lzo:2=
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/numexpr[${PYTHON_USEDEP}]
-	sci-libs/hdf5:0="
-DEPEND="${RDEPEND}
-	>=dev-python/cython-0.14[${PYTHON_USEDEP}]"
-
-S="${WORKDIR}/${MY_P}"
-
-DOCS=( ANNOUNCE.txt RELEASE_NOTES.txt THANKS )
-
-PATCHES=(
-	"${FILESDIR}"/${P}-cython-backport.patch
-	"${FILESDIR}"/${P}-numpy19-backport.patch
-	"${FILESDIR}"/${P}-blosc.patch
-	)
-
-python_prepare_all() {
-	export HDF5_DIR="${EPREFIX}"/usr
-	sed \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e 's:"c-blosc/hdf5/blosc_filter.c"::g' \
-		-i setup.py || die
-	rm -r c-blosc/{blosc,hdf5,internal-complibs} || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-	distutils-r1_python_compile
-}
-
-python_test() {
-	cd "${BUILD_DIR}"/lib* || die
-	${EPYTHON} tables/tests/test_all.py || die
-}
-
-python_install_all() {
-	if use doc; then
-		HTML_DOCS=( doc/html/. )
-		DOCS+=( doc/scripts )
-	fi
-	distutils-r1_python_install_all
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-		doins -r contrib
-	fi
-}

[gentoo-commits] repo/gentoo:master commit in: dev-python/pytables/, dev-python/pytables/files/

[Michał Górny]

commit:     83308d078978f201c7848a90ee5a8435e6e0ab2a
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 20 17:37:10 2021 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Jun 20 17:38:41 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=83308d07

dev-python/pytables: Fix test failures with recent numpy

Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 .../files/pytables-3.6.1-numpy-float.patch         | 176 +++++++++++++++++++++
 dev-python/pytables/pytables-3.6.1.ebuild          |  28 ++--
 2 files changed, 193 insertions(+), 11 deletions(-)

diff --git a/dev-python/pytables/files/pytables-3.6.1-numpy-float.patch b/dev-python/pytables/files/pytables-3.6.1-numpy-float.patch
new file mode 100644
index 00000000000..71fa3b85dac
--- /dev/null
+++ b/dev-python/pytables/files/pytables-3.6.1-numpy-float.patch
@@ -0,0 +1,176 @@
+From d2a480d14f29fb1d2baee292bc6a2cca4817dcbd Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Zbigniew=20J=C4=99drzejewski-Szmek?= <zbyszek@in.waw.pl>
+Date: Sun, 24 Jan 2021 16:36:21 +0100
+Subject: [PATCH] Use lowercase float/int as numpy dtype
+
+Float64 is gone with numpy 1.20, which causes doctests to fail
+(https://bugzilla.redhat.com/show_bug.cgi?id=1914335).
+
+Similarly all uses of Float32, Int32 should be replaced by float32 and int32.
+
+>>> numpy.__version__
+'1.19.4'
+>>> [k for k in numpy.sctypeDict.keys() if str(k).lower().startswith('float')]
+['float16', 'Float16', 'float32', 'Float32', 'float64', 'Float64', 'float128', 'Float128', 'float_', 'float']
+
+>>> numpy.__version__
+'1.20.0rc2'
+>>> [k for k in numpy.sctypeDict.keys() if str(k).lower().startswith('float')]
+['float16', 'float32', 'float64', 'float128', 'float_', 'float']
+---
+ bench/bsddb-table-bench.py     | 10 +++++-----
+ bench/postgres-search-bench.py |  4 ++--
+ bench/pytables-search-bench.py |  6 +++---
+ bench/recarray2-test.py        |  2 +-
+ bench/shelve-bench.py          | 10 +++++-----
+ bench/sqlite-search-bench.py   |  4 ++--
+ tables/atom.py                 |  2 +-
+ 7 files changed, 19 insertions(+), 19 deletions(-)
+
+diff --git a/bench/bsddb-table-bench.py b/bench/bsddb-table-bench.py
+index dd9f875b..a2e02361 100644
+--- a/bench/bsddb-table-bench.py
++++ b/bench/bsddb-table-bench.py
+@@ -83,11 +83,11 @@ def createFile(filename, totalrows, recsize, verbose):
+     # Get the record object associated with the new table
+     if recsize == "big":
+         isrec = Big()
+-        arr = np.array(np.arange(32), type=np.Float64)
+-        arr2 = np.array(np.arange(32), type=np.Float64)
++        arr = np.array(np.arange(32), type=np.float64)
++        arr2 = np.array(np.arange(32), type=np.float64)
+     elif recsize == "medium":
+         isrec = Medium()
+-        arr = np.array(np.arange(2), type=np.Float64)
++        arr = np.array(np.arange(2), type=np.float64)
+     else:
+         isrec = Small()
+     # print d
+@@ -107,8 +107,8 @@ def createFile(filename, totalrows, recsize, verbose):
+             #d['TDCcount'] = i % 256
+             d['ADCcount'] = (i * 256) % (1 << 16)
+             if recsize == "big":
+-                #d.float1 = np.array([i]*32, np.Float64)
+-                #d.float2 = np.array([i**2]*32, np.Float64)
++                #d.float1 = np.array([i]*32, np.float64)
++                #d.float2 = np.array([i**2]*32, np.float64)
+                 arr[0] = 1.1
+                 d['float1'] = arr
+                 arr2[0] = 2.2
+diff --git a/bench/postgres-search-bench.py b/bench/postgres-search-bench.py
+index d2c9f4f4..7fe83f6a 100644
+--- a/bench/postgres-search-bench.py
++++ b/bench/postgres-search-bench.py
+@@ -15,11 +15,11 @@ def flatten(l):
+ 
+ 
+ def fill_arrays(start, stop):
+-    col_i = numpy.arange(start, stop, type=numpy.Int32)
++    col_i = numpy.arange(start, stop, type=numpy.int32)
+     if userandom:
+         col_j = numpy.random.uniform(0, nrows, size=[stop - start])
+     else:
+-        col_j = numpy.array(col_i, type=numpy.Float64)
++        col_j = numpy.array(col_i, type=numpy.float64)
+     return col_i, col_j
+ 
+ # Generator for ensure pytables benchmark compatibility
+diff --git a/bench/pytables-search-bench.py b/bench/pytables-search-bench.py
+index 726d30b1..6417186b 100644
+--- a/bench/pytables-search-bench.py
++++ b/bench/pytables-search-bench.py
+@@ -37,11 +37,11 @@ def create_db(filename, nrows):
+         stop = (j + 1) * step
+         if stop > nrows:
+             stop = nrows
+-        arr_f8 = np.arange(i, stop, type=np.Float64)
+-        arr_i4 = np.arange(i, stop, type=np.Int32)
++        arr_f8 = np.arange(i, stop, type=np.float64)
++        arr_i4 = np.arange(i, stop, type=np.int32)
+         if userandom:
+             arr_f8 += np.random.normal(0, stop * scale, shape=[stop - i])
+-            arr_i4 = np.array(arr_f8, type=np.Int32)
++            arr_i4 = np.array(arr_f8, type=np.int32)
+         recarr = np.rec.fromarrays([arr_i4, arr_i4, arr_f8, arr_f8])
+         table.append(recarr)
+         j += 1
+diff --git a/bench/recarray2-test.py b/bench/recarray2-test.py
+index a8602d80..bf55389d 100644
+--- a/bench/recarray2-test.py
++++ b/bench/recarray2-test.py
+@@ -22,7 +22,7 @@ delta = 0.000001
+ # Creation of recarrays objects for test
+ x1 = np.array(np.arange(reclen))
+ x2 = chararray.array(None, itemsize=7, shape=reclen)
+-x3 = np.array(np.arange(reclen, reclen * 3, 2), np.Float64)
++x3 = np.array(np.arange(reclen, reclen * 3, 2), np.float64)
+ r1 = recarray.fromarrays([x1, x2, x3], names='a,b,c')
+ r2 = recarray2.fromarrays([x1, x2, x3], names='a,b,c')
+ 
+diff --git a/bench/shelve-bench.py b/bench/shelve-bench.py
+index d30739d8..a591ed1e 100644
+--- a/bench/shelve-bench.py
++++ b/bench/shelve-bench.py
+@@ -65,8 +65,8 @@ def createFile(filename, totalrows, recsize):
+     # Get the record object associated with the new table
+     if recsize == "big":
+         d = Big()
+-        arr = NA.array(NA.arange(32), type=NA.Float64)
+-        arr2 = NA.array(NA.arange(32), type=NA.Float64)
++        arr = NA.array(NA.arange(32), type=NA.float64)
++        arr2 = NA.array(NA.arange(32), type=NA.float64)
+     elif recsize == "medium":
+         d = Medium()
+     else:
+@@ -87,15 +87,15 @@ def createFile(filename, totalrows, recsize):
+                 #d.TDCcount = i % 256
+                 d.ADCcount = (i * 256) % (1 << 16)
+                 if recsize == "big":
+-                    #d.float1 = NA.array([i]*32, NA.Float64)
+-                    #d.float2 = NA.array([i**2]*32, NA.Float64)
++                    #d.float1 = NA.array([i]*32, NA.float64)
++                    #d.float2 = NA.array([i**2]*32, NA.float64)
+                     arr[0] = 1.1
+                     d.float1 = arr
+                     arr2[0] = 2.2
+                     d.float2 = arr2
+                     pass
+                 else:
+-                    d.float1 = NA.array([i ** 2] * 2, NA.Float64)
++                    d.float1 = NA.array([i ** 2] * 2, NA.float64)
+                     #d.float1 = float(i)
+                     #d.float2 = float(i)
+                 d.grid_i = i
+diff --git a/bench/sqlite-search-bench.py b/bench/sqlite-search-bench.py
+index 76dc7c57..dc611695 100644
+--- a/bench/sqlite-search-bench.py
++++ b/bench/sqlite-search-bench.py
+@@ -136,10 +136,10 @@ CREATE INDEX ivar3 ON small(var3);
+             if randomvalues:
+                 var3 = np.random.uniform(minimum, maximum, shape=[j - i])
+             else:
+-                var3 = np.arange(i, j, type=np.Float64)
++                var3 = np.arange(i, j, type=np.float64)
+                 if noise:
+                     var3 += np.random.uniform(-3, 3, shape=[j - i])
+-            var2 = np.array(var3, type=np.Int32)
++            var2 = np.array(var3, type=np.int32)
+             var1 = np.array(None, shape=[j - i], dtype='s4')
+             if not heavy:
+                 for n in range(j - i):
+diff --git a/tables/atom.py b/tables/atom.py
+index f92e16ad..f93d915b 100644
+--- a/tables/atom.py
++++ b/tables/atom.py
+@@ -338,7 +338,7 @@ class Atom(metaclass=MetaAtom):
+             Traceback (most recent call last):
+             ...
+             ValueError: unknown NumPy scalar type: 'S5'
+-            >>> Atom.from_sctype('Float64')
++            >>> Atom.from_sctype('float64')
+             Float64Atom(shape=(), dflt=0.0)
+ 
+         """
+-- 
+2.32.0
+

diff --git a/dev-python/pytables/pytables-3.6.1.ebuild b/dev-python/pytables/pytables-3.6.1.ebuild
index 0c4f1afc0ab..b504eaf8f32 100644
--- a/dev-python/pytables/pytables-3.6.1.ebuild
+++ b/dev-python/pytables/pytables-3.6.1.ebuild
@@ -1,10 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-DISTUTILS_USE_SETUPTOOLS=rdepend
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..9} )
 PYTHON_REQ_USE="threads(+)"
 
 MY_PN=tables
@@ -15,6 +14,7 @@ inherit distutils-r1 flag-o-matic
 DESCRIPTION="Hierarchical datasets for Python"
 HOMEPAGE="https://www.pytables.org/"
 SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
 
 SLOT="0"
 KEYWORDS="amd64 ~arm ~arm64 x86 ~amd64-linux ~x86-linux"
@@ -22,26 +22,32 @@ LICENSE="BSD"
 IUSE="doc examples test"
 RESTRICT="!test? ( test )"
 
-RDEPEND="
+DEPEND="
 	app-arch/bzip2:0=
 	app-arch/lz4:0=
 	>=app-arch/zstd-1.0.0:=
 	>=dev-libs/c-blosc-1.11.1:0=
 	dev-libs/lzo:2=
 	>=dev-python/numpy-1.8.1[${PYTHON_USEDEP}]
-	>=dev-python/numexpr-2.5.2[${PYTHON_USEDEP}]
-	dev-python/six[${PYTHON_USEDEP}]
 	>=sci-libs/hdf5-1.8.15:0=
 "
-DEPEND="${RDEPEND}
+RDEPEND="${DEPEND}
+	>=dev-python/numexpr-2.5.2[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]"
+BDEPEND="
 	>=dev-python/cython-0.21[${PYTHON_USEDEP}]
-	test? ( dev-python/mock[${PYTHON_USEDEP}] )
+	test? (
+		dev-python/mock[${PYTHON_USEDEP}]
+		${RDEPEND}
+	)
 "
 
-S="${WORKDIR}/${MY_P}"
-
 DOCS=( RELEASE_NOTES.txt THANKS )
 
+PATCHES=(
+	"${FILESDIR}"/${P}-numpy-float.patch
+)
+
 python_prepare_all() {
 	export HDF5_DIR="${EPREFIX}"/usr
 	rm tables/*.c || die

[gentoo-commits] repo/gentoo:master commit in: dev-python/pytables/, dev-python/pytables/files/

[Sam James]

commit:     a9a3566f532b65a95141b1e5a9f013cb5c3df009
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 20 06:42:53 2021 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Nov 20 06:42:53 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a9a3566f

dev-python/pytables: skip some known-failing tests on big endian

Use Debian's patch for this.

Bug: https://bugs.gentoo.org/805995
Signed-off-by: Sam James <sam <AT> gentoo.org>

 ...tables-3.6.1-big-endian-tests-skip-subset.patch | 36 ++++++++++++++++++++++
 dev-python/pytables/pytables-3.6.1-r1.ebuild       |  1 +
 2 files changed, 37 insertions(+)

diff --git a/dev-python/pytables/files/pytables-3.6.1-big-endian-tests-skip-subset.patch b/dev-python/pytables/files/pytables-3.6.1-big-endian-tests-skip-subset.patch
new file mode 100644
index 000000000000..6a492a1a581f
--- /dev/null
+++ b/dev-python/pytables/files/pytables-3.6.1-big-endian-tests-skip-subset.patch
@@ -0,0 +1,36 @@
+https://bugs.gentoo.org/805995
+https://github.com/PyTables/PyTables/issues/735
+https://sources.debian.org/src/pytables/3.6.1-5/debian/patches/0005-Skip-index-backcompat-tests-on-bingendian.patch/
+
+From: Antonio Valentino <antonio.valentino@tiscali.it>
+Date: Sat, 3 Aug 2019 16:22:13 +0000
+Subject: Skip index backcompat tests on bingendian
+
+Forwarded: not-needed
+--- a/tables/tests/test_index_backcompat.py
++++ b/tables/tests/test_index_backcompat.py
+@@ -6,8 +6,10 @@ from tables.tests.common import verbose
+ from tables.tests.common import unittest, test_filename
+ from tables.tests.common import PyTablesTestCase as TestCase
+ 
++import sys
+ 
+ # Check indexes from PyTables version 2.0
++@unittest.skipIf(sys.byteorder != 'little', 'broken on big-endian')
+ class IndexesTestCase(common.TestFileMixin, TestCase):
+ 
+     def setUp(self):
+@@ -145,11 +147,13 @@ class IndexesTestCase(common.TestFileMixin, TestCase):
+ 
+ 
+ # Check indexes from PyTables version 2.0
++@unittest.skipIf(sys.byteorder != 'little', 'broken on big-endian')
+ class Indexes2_0TestCase(IndexesTestCase):
+     h5fname = test_filename("indexes_2_0.h5")
+ 
+ 
+ # Check indexes from PyTables version 2.1
++@unittest.skipIf(sys.byteorder != 'little', 'broken on big-endian')
+ class Indexes2_1TestCase(IndexesTestCase):
+     h5fname = test_filename("indexes_2_1.h5")
+ 

diff --git a/dev-python/pytables/pytables-3.6.1-r1.ebuild b/dev-python/pytables/pytables-3.6.1-r1.ebuild
index b9fcf11be120..bcad8167a71a 100644
--- a/dev-python/pytables/pytables-3.6.1-r1.ebuild
+++ b/dev-python/pytables/pytables-3.6.1-r1.ebuild
@@ -49,6 +49,7 @@ DOCS=( RELEASE_NOTES.txt THANKS )
 PATCHES=(
 	"${FILESDIR}"/${P}-numpy-float.patch
 	"${FILESDIR}"/${P}-py310.patch
+	"${FILESDIR}"/${PN}-3.6.1-big-endian-tests-skip-subset.patch
 )
 
 python_prepare_all() {

[gentoo-commits] repo/gentoo:master commit in: dev-python/pytables/, dev-python/pytables/files/

[Michał Górny]

commit:     6ed4d325a2563a195b41caef2c2c58ca18581e40
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Wed Dec 28 15:06:59 2022 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Wed Dec 28 15:31:55 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6ed4d325

dev-python/pytables: Bump to 3.8.0

Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 dev-python/pytables/Manifest                       |  1 +
 .../pytables/files/pytables-3.8.0-blosc2.patch     | 30 ++++++++
 dev-python/pytables/pytables-3.8.0.ebuild          | 83 ++++++++++++++++++++++
 3 files changed, 114 insertions(+)

diff --git a/dev-python/pytables/Manifest b/dev-python/pytables/Manifest
index c456f554b2d0..ea9d491502ea 100644
--- a/dev-python/pytables/Manifest
+++ b/dev-python/pytables/Manifest
@@ -1 +1,2 @@
 DIST tables-3.7.0.tar.gz 8227955 BLAKE2B 0d5b7b765375c4787f1210138e5fd02e3c0ce429ef209a3a8d4fd3bc094f68486ab6f4d0a960ce86efea6991ed691ef2a3e9e8f37a49fe91cb8d6372cadea80e SHA512 eaa368d063b5fad87e6d0f9ab6f02da0b2a3542740a52fe8c2bb58e41121495d07b6d2710ad402a28891294aa61a11238c6a7e2cf2933a1bb11391b79cf4fd13
+DIST tables-3.8.0.tar.gz 8014052 BLAKE2B 28d120ad609ebc9ae8cd97286bb3fb9c484bd8a179edcf0de1b96e4400b7a21b4db835d94fae3aaee84924bd46b84b84da12c538b39517362d805651e7aa3aef SHA512 1616c00787a2e88ff3dc2aebe3a1b2ad428b5a8ea48fc94058b49c509f1c040b540b3f62551b16b3246d2fed58e0b33443cbdaaf1dfcba5a6eead5f3e8028029

diff --git a/dev-python/pytables/files/pytables-3.8.0-blosc2.patch b/dev-python/pytables/files/pytables-3.8.0-blosc2.patch
new file mode 100644
index 000000000000..59403cdec12d
--- /dev/null
+++ b/dev-python/pytables/files/pytables-3.8.0-blosc2.patch
@@ -0,0 +1,30 @@
+From 99a7f336635aaeb666ea8dc791743177a030dc18 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <mgorny@gentoo.org>
+Date: Wed, 28 Dec 2022 15:53:08 +0100
+Subject: [PATCH] Workaround blosc2 detection via blosc2 package
+
+---
+ setup.py | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index 966be028..2708deb9 100755
+--- a/setup.py
++++ b/setup.py
+@@ -262,11 +262,11 @@ if __name__ == "__main__":
+ 
+     debug = "--debug" in sys.argv
+ 
+-    blosc2_inc, blosc2_lib = get_blosc2_directories()
++    blosc2_inc, blosc2_lib = "", ""
+ 
+     # Global variables
+     lib_dirs = [blosc2_lib]
+-    inc_dirs = [Path("hdf5-blosc/src"), Path("hdf5-blosc2/src"), blosc2_inc]
++    inc_dirs = [Path("hdf5-blosc/src"), Path("hdf5-blosc2/src")]
+     optional_libs = []
+     copy_libs = []
+ 
+-- 
+2.39.0
+

diff --git a/dev-python/pytables/pytables-3.8.0.ebuild b/dev-python/pytables/pytables-3.8.0.ebuild
new file mode 100644
index 000000000000..889a681566ed
--- /dev/null
+++ b/dev-python/pytables/pytables-3.8.0.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..11} )
+PYTHON_REQ_USE="threads(+)"
+
+inherit distutils-r1
+
+MY_PN=tables
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="Hierarchical datasets for Python"
+HOMEPAGE="
+	https://www.pytables.org/
+	https://github.com/PyTables/PyTables/
+	https://pypi.org/project/tables/
+"
+SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
+S=${WORKDIR}/${MY_P}
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="examples test"
+RESTRICT="!test? ( test )"
+
+DEPEND="
+	app-arch/bzip2:0=
+	app-arch/lz4:0=
+	>=app-arch/zstd-1.0.0:=
+	>=dev-libs/c-blosc-1.11.1:0=
+	dev-libs/c-blosc2:=
+	dev-libs/lzo:2=
+	>=dev-python/numpy-1.19[${PYTHON_USEDEP}]
+	>=sci-libs/hdf5-1.8.4:=
+"
+RDEPEND="
+	${DEPEND}
+	>=dev-python/numexpr-2.6.2[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/py-cpuinfo[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	>=dev-python/cython-0.21[${PYTHON_USEDEP}]
+	dev-python/py-cpuinfo[${PYTHON_USEDEP}]
+	virtual/pkgconfig
+	test? (
+		${RDEPEND}
+	)
+"
+
+python_prepare_all() {
+	local PATCHES=(
+		"${FILESDIR}"/${P}-blosc2.patch
+	)
+
+	export PYTABLES_NO_EMBEDDED_LIBS=1
+	export USE_PKGCONFIG=TRUE
+
+	rm -r c-blosc/{blosc,internal-complibs} || die
+	rm tables/libblosc2.so || die
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	distutils-r1_python_compile -j1
+}
+
+python_test() {
+	cd "${BUILD_DIR}"/lib* || die
+	"${EPYTHON}" tables/tests/test_all.py -v || die
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+
+	if use examples; then
+		dodoc -r contrib examples
+		docompress -x /usr/share/doc/${PF}/{contrib,examples}
+	fi
+}

[gentoo-commits] repo/gentoo:master commit in: dev-python/pytables/, dev-python/pytables/files/

[Sam James]

commit:     637784cae39a93920b9738e8094d46d24331769d
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Mon Apr  3 01:50:20 2023 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Mon Apr  3 01:50:20 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=637784ca

dev-python/pytables: tweak cpuinfo patch

Signed-off-by: Sam James <sam <AT> gentoo.org>

 dev-python/pytables/files/pytables-3.8.0-optional-cpuinfo.patch  | 9 ++++++---
 .../{pytables-3.8.0-r2.ebuild => pytables-3.8.0-r3.ebuild}       | 0
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/dev-python/pytables/files/pytables-3.8.0-optional-cpuinfo.patch b/dev-python/pytables/files/pytables-3.8.0-optional-cpuinfo.patch
index f56854b05289..2843914f4a87 100644
--- a/dev-python/pytables/files/pytables-3.8.0-optional-cpuinfo.patch
+++ b/dev-python/pytables/files/pytables-3.8.0-optional-cpuinfo.patch
@@ -1,6 +1,6 @@
 https://github.com/PyTables/PyTables/pull/1013
 
-From 557f8c22b772506bfbb9e7eb4d60c0cf2125998b Mon Sep 17 00:00:00 2001
+From 9d2487eb53af940de3b5c79200c9f4c2b90f51f2 Mon Sep 17 00:00:00 2001
 From: Sam James <sam@gentoo.org>
 Date: Mon, 3 Apr 2023 02:07:47 +0100
 Subject: [PATCH] Handle py-cpuinfo not being installed
@@ -15,19 +15,20 @@ in places where py-cpuinfo isn't yet ported.
 Signed-off-by: Sam James <sam@gentoo.org>
 --- a/tables/leaf.py
 +++ b/tables/leaf.py
-@@ -4,7 +4,10 @@
+@@ -4,7 +4,11 @@ import warnings
  import math
  
  import numpy as np
 -import cpuinfo
 +try:
 +    import cpuinfo
++    missing_cpuinfo = False
 +except ImportError:
 +    missing_cpuinfo = True
  
  from .flavor import (check_flavor, internal_flavor, toarray,
                       alias_map as flavor_alias_map)
-@@ -336,20 +339,21 @@ def _calc_chunkshape(self, expectedrows, rowsize, itemsize):
+@@ -336,20 +340,21 @@ class Leaf(Node):
              # Use a decent default value for chunksize
              chunksize *= 16
              # Now, go explore the L3 size and try to find a smarter chunksize
@@ -63,4 +64,6 @@ Signed-off-by: Sam James <sam@gentoo.org>
              # In Blosc2, the chunksize cannot be larger than 2 GB - BLOSC2_MAX_BUFFERSIZE
              if chunksize > 2**31 - 32:
                  chunksize = 2**31 - 32
+-- 
+2.40.0
 

diff --git a/dev-python/pytables/pytables-3.8.0-r2.ebuild b/dev-python/pytables/pytables-3.8.0-r3.ebuild
similarity index 100%
rename from dev-python/pytables/pytables-3.8.0-r2.ebuild
rename to dev-python/pytables/pytables-3.8.0-r3.ebuild

[gentoo-commits] repo/gentoo:master commit in: dev-python/pytables/, dev-python/pytables/files/

[Michał Górny]

commit:     fe9b3c589dc0033b806bf3632e4fa9a445a696cd
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Thu May 11 06:20:47 2023 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Thu May 11 06:22:22 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fe9b3c58

dev-python/pytables: Backport cython-3 fix

Closes: https://bugs.gentoo.org/898710
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 .../pytables/files/pytables-3.8.0-cython3.patch    | 40 ++++++++++++++++++++++
 dev-python/pytables/pytables-3.8.0-r3.ebuild       |  1 +
 2 files changed, 41 insertions(+)

diff --git a/dev-python/pytables/files/pytables-3.8.0-cython3.patch b/dev-python/pytables/files/pytables-3.8.0-cython3.patch
new file mode 100644
index 000000000000..9ad0b72d224a
--- /dev/null
+++ b/dev-python/pytables/files/pytables-3.8.0-cython3.patch
@@ -0,0 +1,40 @@
+From a70e36f0b0d4fb15b0b50e7ca513c4e4452767cc Mon Sep 17 00:00:00 2001
+From: Matus Valo <matusvalo@gmail.com>
+Date: Wed, 15 Mar 2023 22:49:07 +0100
+Subject: [PATCH] Fix build errors when compiled using cython 3.0.0b1.
+
+---
+ pyproject.toml            | 2 +-
+ tables/tableextension.pyx | 2 +-
+ tables/utilsextension.pyx | 2 +-
+ 3 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/tables/tableextension.pyx b/tables/tableextension.pyx
+index 8f3bb01b..4a50c6ab 100644
+--- a/tables/tableextension.pyx
++++ b/tables/tableextension.pyx
+@@ -37,7 +37,7 @@ from .utils import SizeType
+ from .utilsextension cimport get_native_type, cstr_to_pystr
+ 
+ # numpy functions & objects
+-from hdf5extension cimport Leaf
++from .hdf5extension cimport Leaf
+ from cpython cimport PyErr_Clear
+ from libc.stdio cimport snprintf
+ from libc.stdlib cimport malloc, free
+diff --git a/tables/utilsextension.pyx b/tables/utilsextension.pyx
+index 5b16dcd3..664e1ea5 100644
+--- a/tables/utilsextension.pyx
++++ b/tables/utilsextension.pyx
+@@ -344,7 +344,7 @@ except ImportError:
+ #---------------------------------------------------------------------
+ 
+ # Error handling helpers
+-cdef herr_t e_walk_cb(unsigned n, const H5E_error_t *err, void *data) with gil:
++cdef herr_t e_walk_cb(unsigned n, const H5E_error_t *err, void *data) noexcept with gil:
+     cdef object bt = <object>data   # list
+     #cdef char major_msg[256]
+     #cdef char minor_msg[256]
+-- 
+2.40.1
+

diff --git a/dev-python/pytables/pytables-3.8.0-r3.ebuild b/dev-python/pytables/pytables-3.8.0-r3.ebuild
index c2dfebf6f12b..4eb70e76b350 100644
--- a/dev-python/pytables/pytables-3.8.0-r3.ebuild
+++ b/dev-python/pytables/pytables-3.8.0-r3.ebuild
@@ -52,6 +52,7 @@ python_prepare_all() {
 	local PATCHES=(
 		"${FILESDIR}"/${P}-blosc2.patch
 		"${FILESDIR}"/${P}-optional-cpuinfo.patch
+		"${FILESDIR}"/${P}-cython3.patch
 	)
 
 	export PYTABLES_NO_EMBEDDED_LIBS=1