git: f012e5a09144 - main - science/{,py-}segyio: update 1.9.12 → 1.9.13
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Date: Thu, 06 Feb 2025 15:06:11 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=f012e5a091442e8c96bcba41946d35d2db40c3e6
commit f012e5a091442e8c96bcba41946d35d2db40c3e6
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2025-02-06 15:04:05 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2025-02-06 15:05:46 +0000
science/{,py-}segyio: update 1.9.12 → 1.9.13
Reported by: portscout
---
science/py-segyio/Makefile | 4 +-
science/py-segyio/distinfo | 6 +-
science/py-segyio/files/patch-2to3 | 302 ---------------------------------
science/py-segyio/files/patch-setup.py | 13 --
science/segyio/Makefile | 2 +-
science/segyio/distinfo | 6 +-
6 files changed, 10 insertions(+), 323 deletions(-)
diff --git a/science/py-segyio/Makefile b/science/py-segyio/Makefile
index a06580fb8d16..2f8fbf844b46 100644
--- a/science/py-segyio/Makefile
+++ b/science/py-segyio/Makefile
@@ -1,6 +1,6 @@
PORTNAME= segyio
DISTVERSIONPREFIX= v
-DISTVERSION= 1.9.12
+DISTVERSION= 1.9.13
CATEGORIES= science python
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -39,4 +39,6 @@ post-install:
pre-test:
@cd ${WRKSRC} && ${PYTHON_CMD} ${PYSETUP} build_ext --inplace
+# tests as of 1.9.13: 208 passed, 8 warnings in 3.65s
+
.include <bsd.port.mk>
diff --git a/science/py-segyio/distinfo b/science/py-segyio/distinfo
index dd07edce3aec..7cf4ed3a0cba 100644
--- a/science/py-segyio/distinfo
+++ b/science/py-segyio/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1712537010
-SHA256 (equinor-segyio-v1.9.12_GH0.tar.gz) = 79f1baa969deb613870c812655544af0c61370ffba3731f7f59836949495dd81
-SIZE (equinor-segyio-v1.9.12_GH0.tar.gz) = 3911812
+TIMESTAMP = 1738831045
+SHA256 (equinor-segyio-v1.9.13_GH0.tar.gz) = c68cd225e346c79ad1f70f86281d82dcc1520e137a6d74298d5732f94d71f04d
+SIZE (equinor-segyio-v1.9.13_GH0.tar.gz) = 3912066
diff --git a/science/py-segyio/files/patch-2to3 b/science/py-segyio/files/patch-2to3
deleted file mode 100644
index 5e35d56f2dc5..000000000000
--- a/science/py-segyio/files/patch-2to3
+++ /dev/null
@@ -1,302 +0,0 @@
---- segyio/__init__.py.orig 2022-02-18 06:49:44 UTC
-+++ segyio/__init__.py
-@@ -51,7 +51,7 @@ class Enum(object):
- return int(self._value)
-
- def __str__(self):
-- for k, v in self.__class__.__dict__.items():
-+ for k, v in list(self.__class__.__dict__.items()):
- if isinstance(v, int) and self._value == v:
- return k
- return "Unknown Enum"
-@@ -76,7 +76,7 @@ class Enum(object):
- @classmethod
- def enums(cls):
- result = []
-- for v in cls.__dict__.values():
-+ for v in list(cls.__dict__.values()):
- if isinstance(v, int):
- result.append(cls(v))
-
---- segyio/create.py.orig 2022-02-18 06:49:44 UTC
-+++ segyio/create.py
-@@ -200,7 +200,7 @@ def create(filename, spec):
-
- if endian not in endians:
- problem = 'unknown endianness {}, expected one of: '
-- opts = ' '.join(endians.keys())
-+ opts = ' '.join(list(endians.keys()))
- raise ValueError(problem.format(endian) + opts)
-
- fd = _segyio.segyiofd(str(filename), 'w+', endians[endian])
---- segyio/depth.py.orig 2022-02-18 06:49:44 UTC
-+++ segyio/depth.py
-@@ -172,7 +172,7 @@ class Depth(Sequence):
- >>> depth[::2] = other
- """
- if isinstance(depth, slice):
-- for i, x in zip(range(*depth.indices(len(self))), val):
-+ for i, x in zip(list(range(*depth.indices(len(self)))), val):
- self[i] = x
- return
-
---- segyio/field.py.orig 2022-02-18 06:49:44 UTC
-+++ segyio/field.py
-@@ -456,7 +456,7 @@ class Field(MutableMapping):
- return False
-
- def intkeys(d):
-- return { int(k): v for k, v in d.items() }
-+ return { int(k): v for k, v in list(d.items()) }
-
- return intkeys(self) == intkeys(other)
-
-@@ -513,13 +513,13 @@ class Field(MutableMapping):
- for key in other:
- self.putfield(buf, int(key), other[key])
- elif hasattr(other, "keys"):
-- for key in other.keys():
-+ for key in list(other.keys()):
- self.putfield(buf, int(key), other[key])
- else:
- for key, value in other:
- self.putfield(buf, int(key), value)
-
-- for key, value in kwargs.items():
-+ for key, value in list(kwargs.items()):
- self.putfield(buf, int(self._kwargs[key]), value)
-
- self.buf = buf
-@@ -543,4 +543,4 @@ class Field(MutableMapping):
- ).reload()
-
- def __repr__(self):
-- return repr(self[self.keys()])
-+ return repr(self[list(self.keys())])
---- segyio/gather.py.orig 2022-02-18 06:49:44 UTC
-+++ segyio/gather.py
-@@ -119,7 +119,7 @@ class Gather(object):
- offs = slice(off, off + 1, 1)
-
- xs = list(filter(self.offsets.__contains__,
-- range(*offs.indices(self.offsets[-1]+1))))
-+ list(range(*offs.indices(self.offsets[-1]+1)))))
-
- empty = np.empty(0, dtype = self.trace.dtype)
- # gather[int,int,:]
-@@ -138,8 +138,8 @@ class Gather(object):
- # buffered, and traces can be read from the iline. This is the
- # least efficient when there are very few traces read per inline,
- # but huge savings with larger subcubes
-- last_il = self.iline.keys()[-1] + 1
-- last_xl = self.xline.keys()[-1] + 1
-+ last_il = list(self.iline.keys())[-1] + 1
-+ last_xl = list(self.xline.keys())[-1] + 1
-
- il_slice = il if isslice(il) else slice(il, il+1)
- xl_slice = xl if isslice(xl) else slice(xl, xl+1)
-@@ -149,15 +149,15 @@ class Gather(object):
- # but it's unnecessary to chck all keys up until the first xline
- # because that will never be a hit anyway
- if il_slice.start is None:
-- start = self.iline.keys()[0]
-+ start = list(self.iline.keys())[0]
- il_slice = slice(start, il_slice.stop, il_slice.step)
-
- if xl_slice.start is None:
-- start = self.xline.keys()[0]
-+ start = list(self.xline.keys())[0]
- xl_slice = slice(start, xl_slice.stop, xl_slice.step)
-
-- il_range = range(*il_slice.indices(last_il))
-- xl_range = range(*xl_slice.indices(last_xl))
-+ il_range = list(range(*il_slice.indices(last_il)))
-+ xl_range = list(range(*xl_slice.indices(last_xl)))
-
- # the try-except-else is essentially a filter on in/xl keys, but
- # delegates the work (and decision) to the iline and xline modes
-@@ -372,7 +372,7 @@ class Groups(Mapping):
- pass
-
- try:
-- items = key.items()
-+ items = list(key.items())
- except AttributeError:
- items = iter(key)
-
-@@ -420,15 +420,15 @@ class Groups(Mapping):
- return Group(key, self, self.bins[key])
-
- def values(self):
-- for key, index in self.bins.items():
-+ for key, index in list(self.bins.items()):
- yield Group(key, self, index)
-
- def items(self):
-- for key, index in self.bins.items():
-+ for key, index in list(self.bins.items()):
- yield key, Group(key, self, index)
-
- def __iter__(self):
-- return self.bins.keys()
-+ return list(self.bins.keys())
-
- def sort(self, fields):
- """
-@@ -436,7 +436,7 @@ class Groups(Mapping):
- """
- bins = collections.OrderedDict()
-
-- for key, index in self.bins.items():
-+ for key, index in list(self.bins.items()):
- g = Group(key, self, index)
- g.sort(fields)
- bins[key] = g.index
---- segyio/line.py.orig 2022-02-18 06:49:44 UTC
-+++ segyio/line.py
-@@ -91,12 +91,12 @@ class Line(Mapping):
- if not isinstance(offset, slice):
- offset = slice(offset, offset + 1)
-
-- index = sanitize_slice(index, self.heads.keys())
-- offset = sanitize_slice(offset, self.offsets.keys())
-- irange = range(*index.indices(max(self.heads.keys()) + 1))
-- orange = range(*offset.indices(max(self.offsets.keys()) + 1))
-- irange = filter(self.heads.__contains__, irange)
-- orange = filter(self.offsets.__contains__, orange)
-+ index = sanitize_slice(index, list(self.heads.keys()))
-+ offset = sanitize_slice(offset, list(self.offsets.keys()))
-+ irange = list(range(*index.indices(max(self.heads.keys()) + 1)))
-+ orange = list(range(*offset.indices(max(self.offsets.keys()) + 1)))
-+ irange = list(filter(self.heads.__contains__, irange))
-+ orange = list(filter(self.offsets.__contains__, orange))
- # offset-range is used in inner loops, so make it a list for
- # reusability. offsets are usually few, so no real punishment by using
- # non-generators here
-@@ -344,7 +344,7 @@ class Line(Mapping):
-
- def items(self):
- """D.values() -> generator of D's (key,values), as 2-tuples"""
-- return zip(self.keys(), self[:])
-+ return zip(list(self.keys()), self[:])
-
- class HeaderLine(Line):
- """
---- segyio/open.py.orig 2022-02-18 06:49:44 UTC
-+++ segyio/open.py
-@@ -155,7 +155,7 @@ def open(filename, mode="r", iline = 189,
-
- if endian not in endians:
- problem = 'unknown endianness {}, expected one of: '
-- opts = ' '.join(endians.keys())
-+ opts = ' '.join(list(endians.keys()))
- raise ValueError(problem.format(endian) + opts)
-
- from . import _segyio
---- segyio/segy.py.orig 2022-02-18 06:49:44 UTC
-+++ segyio/segy.py
-@@ -910,7 +910,7 @@ class SegyFile(object):
-
- if sorting not in valid_sortings:
- error = "Invalid sorting"
-- solution = "valid sorting options are: {}".format(valid_sortings.keys())
-+ solution = "valid sorting options are: {}".format(list(valid_sortings.keys()))
- raise ValueError('{}, {}'.format(error, solution))
-
- if offsets is None:
---- segyio/su/file.py.orig 2022-02-18 06:49:44 UTC
-+++ segyio/su/file.py
-@@ -89,7 +89,7 @@ def open(filename, mode = 'r', iline = 189,
-
- if endian not in endians:
- problem = 'unknown endianness, must be one of: '
-- candidates = ' '.join(endians.keys())
-+ candidates = ' '.join(list(endians.keys()))
- raise ValueError(problem + candidates)
-
- from .. import _segyio
---- segyio/tools.py.orig 2022-02-18 06:49:44 UTC
-+++ segyio/tools.py
-@@ -289,7 +289,7 @@ def rotation(f, line = 'fast'):
-
- if line not in lines:
- error = "Unknown line {}".format(line)
-- solution = "Must be any of: {}".format(' '.join(lines.keys()))
-+ solution = "Must be any of: {}".format(' '.join(list(lines.keys())))
- raise ValueError('{} {}'.format(error, solution))
-
- l = lines[line]
-@@ -299,7 +299,7 @@ def rotation(f, line = 'fast'):
- rot = f.xfd.rotation( len(l),
- l.stride,
- len(f.offsets),
-- np.fromiter(l.keys(), dtype = np.intc) )
-+ np.fromiter(list(l.keys()), dtype = np.intc) )
- return rot, cdpx, cdpy
-
- def metadata(f):
-@@ -466,7 +466,7 @@ def from_array(filename, data, iline=189,
- data = np.asarray(data)
- dimensions = len(data.shape)
-
-- if dimensions not in range(2, 5):
-+ if dimensions not in list(range(2, 5)):
- problem = "Expected 2, 3, or 4 dimensions, {} was given".format(dimensions)
- raise ValueError(problem)
-
---- segyio/trace.py.orig 2022-02-18 06:49:44 UTC
-+++ segyio/trace.py
-@@ -198,7 +198,7 @@ class Trace(Sequence):
- step = 1
- single = True
-
-- n_elements = len(range(start, stop, step))
-+ n_elements = len(list(range(start, stop, step)))
-
- try:
- i = self.wrapindex(i)
-@@ -278,7 +278,7 @@ class Trace(Sequence):
-
- """
- if isinstance(i, slice):
-- for j, x in zip(range(*i.indices(len(self))), val):
-+ for j, x in zip(list(range(*i.indices(len(self)))), val):
- self[j] = x
-
- return
-@@ -388,7 +388,7 @@ class RawTrace(Trace):
- msg = 'trace indices must be integers or slices, not {}'
- raise TypeError(msg.format(type(i).__name__))
- start, _, step = indices
-- length = len(range(*indices))
-+ length = len(list(range(*indices)))
- buf = np.empty((length, self.shape), dtype = self.dtype)
- return self.filehandle.gettr(buf, start, step, length, 0, self.shape, 1, self.shape)
-
-@@ -435,7 +435,7 @@ class RefTrace(Trace):
- be useful in certain contexts to provide stronger guarantees.
- """
- garbage = []
-- for i, (x, signature) in self.refs.items():
-+ for i, (x, signature) in list(self.refs.items()):
- if sys.getrefcount(x) == 3:
- garbage.append(i)
-
-@@ -841,7 +841,7 @@ class Attributes(Sequence):
- field = self.field
-
- start, stop, step = i.indices(traces)
-- indices = range(start, stop, step)
-+ indices = list(range(start, stop, step))
- attrs = np.empty(len(indices), dtype = self.dtype)
- return filehandle.field_forall(attrs, start, stop, step, field)
-
-@@ -955,7 +955,7 @@ class Text(Sequence):
- msg = 'trace indices must be integers or slices, not {}'
- raise TypeError(msg.format(type(i).__name__))
-
-- for i, text in zip(range(*indices), val):
-+ for i, text in zip(list(range(*indices)), val):
- if isinstance(text, Text):
- text = text[0]
- self.filehandle.puttext(i, text)
diff --git a/science/py-segyio/files/patch-setup.py b/science/py-segyio/files/patch-setup.py
deleted file mode 100644
index 9e084d954ae7..000000000000
--- a/science/py-segyio/files/patch-setup.py
+++ /dev/null
@@ -1,13 +0,0 @@
-- workaround for https://github.com/equinor/segyio/issues/586
-
---- setup.py.orig 2024-12-11 05:38:29 UTC
-+++ setup.py
-@@ -95,7 +95,7 @@ skbuild.setup(
- # supported OS X release 10.9
- '-DCMAKE_OSX_DEPLOYMENT_TARGET=10.9',
- ],
-- cmdclass = { 'test': setuptools.command.test.test },
-+ #cmdclass = { 'test': setuptools.command.test.test },
- classifiers = [
- 'Development Status :: 5 - Production/Stable',
- 'Environment :: Other Environment',
diff --git a/science/segyio/Makefile b/science/segyio/Makefile
index d1c873a01a1d..bd8049d3d89d 100644
--- a/science/segyio/Makefile
+++ b/science/segyio/Makefile
@@ -1,6 +1,6 @@
PORTNAME= segyio
DISTVERSIONPREFIX= v
-DISTVERSION= 1.9.12
+DISTVERSION= 1.9.13
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
diff --git a/science/segyio/distinfo b/science/segyio/distinfo
index 71f3f2d26f81..605e8383b008 100644
--- a/science/segyio/distinfo
+++ b/science/segyio/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1712536794
-SHA256 (equinor-segyio-v1.9.12_GH0.tar.gz) = 79f1baa969deb613870c812655544af0c61370ffba3731f7f59836949495dd81
-SIZE (equinor-segyio-v1.9.12_GH0.tar.gz) = 3911812
+TIMESTAMP = 1738825199
+SHA256 (equinor-segyio-v1.9.13_GH0.tar.gz) = c68cd225e346c79ad1f70f86281d82dcc1520e137a6d74298d5732f94d71f04d
+SIZE (equinor-segyio-v1.9.13_GH0.tar.gz) = 3912066