python313Packages.segyio: fix build (#451169)

From 64f06c0643f1f8691a8f2757496b60f1ab98c866 Mon Sep 17 00:00:00 2001

From: =?UTF-8?q?Sa=C3=AFd=20Benaissa?= <sbenaissa@shearwatergeo.com>

Date: Fri, 8 Dec 2023 21:51:32 +0100

Subject: [PATCH] Add include for cstdint, fix segyio build on fedora

---

 lib/experimental/segyio/segyio.hpp | 1 +

 python/segyio/segyio.cpp           | 1 +

 python/setup.py                    | 2 +-

 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/experimental/segyio/segyio.hpp b/lib/experimental/segyio/segyio.hpp

index 706f07ff5..7ba3ffb99 100644

--- a/lib/experimental/segyio/segyio.hpp

+++ b/lib/experimental/segyio/segyio.hpp

@@ -13,6 +13,7 @@

 #include <vector>

 #include <segyio/segy.h>

+#include <cstdint>

 /*

  * KNOWN ISSUES AND TODOs:

diff --git a/python/segyio/segyio.cpp b/python/segyio/segyio.cpp

index 76da965c3..bd8a8622e 100644

--- a/python/segyio/segyio.cpp

+++ b/python/segyio/segyio.cpp

@@ -16,6 +16,7 @@

 #include <cstring>

 #include <sstream>

 #include <stdexcept>

+#include <cstdint>

 #if PY_MAJOR_VERSION >= 3

 #define IS_PY3K

diff --git a/python/setup.py b/python/setup.py

index 6c6553bc7..654075be9 100644

--- a/python/setup.py

+++ b/python/setup.py

@@ -1,6 +1,6 @@

 import os

 import sys

-import skbuild

+import skbuild  # pip install scikit-build

 import setuptools

 long_description = """

  lib,

  buildPythonPackage,

  fetchFromGitHub,

  fetchpatch,

  cmake,

  ninja,

  scikit-build,

  pyproject = false; # Built with cmake

  patches = [

    # https://github.com/equinor/segyio/pull/570

    ./add_missing_cstdint.patch

    # https://github.com/equinor/segyio/pull/576/

    ./fix-setuptools.patch

    ./explicitly-cast.patch

    ./numpy-2.patch

    # Bump minimum CMake version to 3.11

    (fetchpatch {

      url = "https://github.com/equinor/segyio/commit/3e2cbe6ca6d4bc7d4f4d95666f5d2983836e8461.patch?full_index=1";

      hash = "sha256-sOBHi8meMSkxEZy0AXwebAnIVPatpwQHd+4Co5zIhLQ=";

    })

  ];

  postPatch = ''

From eafe8476566e1d8e8b9a486ca808685cb439a767 Mon Sep 17 00:00:00 2001

From: Sveinung Rundhovde <ssru@equinor.com>

Date: Mon, 29 Jul 2024 10:46:35 +0200

Subject: [PATCH] Explicitly cast from BinField to int

Parsing segyio.BinField type as int in PyArg_ParseTuple is no longer

possible.

---

 python/segyio/open.py | 6 +++---

 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/python/segyio/open.py b/python/segyio/open.py

index cd902c15..80bc3a5b 100644

--- a/python/segyio/open.py

+++ b/python/segyio/open.py

@@ -166,8 +166,8 @@ def open(filename, mode="r", iline = 189,

     f = segyio.SegyFile(fd,

             filename = str(filename),

             mode = mode,

-            iline = iline,

-            xline = xline,

+            iline = int(iline),

+            xline = int(xline),

             endian = endian,

     )

@@ -189,4 +189,4 @@ def open(filename, mode="r", iline = 189,

     if ignore_geometry:

         return f

-    return infer_geometry(f, metrics, iline, xline, strict)

+    return infer_geometry(f, metrics, int(iline), int(xline), strict)

From 6df089258c2ef4356427263f652cff0c053c6173 Mon Sep 17 00:00:00 2001

From: Sveinung Rundhovde <ssru@equinor.com>

Date: Fri, 26 Jul 2024 15:03:33 +0200

Subject: [PATCH] Fix attribute error in setup.py

This line was causing a  error due to an update to scikit-build.  The

issue was that the setuptools.command.test module is not put into the

symbol table by the setuptools import, but it was put there during the

skbuild import causing it to be available. Due to changes in

scikit-build this is no longer the case and the line gives an

AttributError.

The rationale for this line was that scikit-builds test command implied

develop (this was obnoxious), something that is no longer true. There is

thus no longer any reason to keep this line, so we can fix this issue by

simply removing it.

---

 python/setup.py | 1 -

 1 file changed, 1 deletion(-)

diff --git a/python/setup.py b/python/setup.py

index 6c6553bc..6bae62f0 100644

--- a/python/setup.py

+++ b/python/setup.py

@@ -95,7 +95,6 @@ def src(x):

         # supported OS X release 10.9

         '-DCMAKE_OSX_DEPLOYMENT_TARGET=10.9',

     ],

-    cmdclass = { 'test': setuptools.command.test.test },

     classifiers = [

         'Development Status :: 5 - Production/Stable',

         'Environment :: Other Environment',

From 75b2156a6414e2464eb15663004b8ab928374135 Mon Sep 17 00:00:00 2001

From: Sveinung Rundhovde <ssru@equinor.com>

Date: Tue, 30 Jul 2024 08:32:56 +0200

Subject: [PATCH] Fix test failing due to Numpy 2.0 promotion rules

From Numpy 2.0 adding a numpy.float32 and a Python numeric type returns

a numy.float32 when it previously returned a numpy.float64. This changes

the behavior when using the Python builtin sum function on a

numpy.float32 array as the internal computations now will be performed

as numpy.float32 additions when it used to be numpy.float64.

Passing a numpy.double(0) as a start value to the innermost sum forces

the old behavior and provides consistent results for Numpy 1 and 2.

---

 python/test/segyio_c.py | 4 ++--

 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/test/segyio_c.py b/python/test/segyio_c.py

index 45fe95d89..b1e144d9d 100644

--- a/python/test/segyio_c.py

+++ b/python/test/segyio_c.py

@@ -540,10 +540,10 @@ def read_line(f, metrics, iline_idx, xline_idx):

     buf = numpy.zeros((len(iline_idx), samples), dtype=numpy.single)

     f.getline(xline_trace0, len(iline_idx), xline_stride, offsets, buf)

-    assert sum(sum(buf)) == approx(800.061169624, abs=1e-6)

+    assert sum(sum(buf), numpy.double(0)) == approx(800.061169624, abs=1e-6)

     f.getline(iline_trace0, len(xline_idx), iline_stride, offsets, buf)

-    assert sum(sum(buf)) == approx(305.061146736, abs=1e-6)

+    assert sum(sum(buf), numpy.double(0)) == approx(305.061146736, abs=1e-6)

     f.close()