science/{,py-}segyio: update 1.9.12 → 1.9.13

Reported by:	portscout

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