python313Packages.segyio: fix build

pkgs/development/python-modules/segyio/default.nix

@@ -17,6 +17,10 @@ buildPythonPackage rec {
   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
   ];
 
   postPatch = ''
@@ -49,10 +53,10 @@ buildPythonPackage rec {
     numpy
   ];
 
-  meta = with lib; {
+  meta = {
     description = "Fast Python library for SEGY files";
     homepage = "https://github.com/equinor/segyio";
-    license = licenses.lgpl3Only;
-    maintainers = with maintainers; [ atila ];
+    license = lib.licenses.lgpl3Only;
+    maintainers = with lib.maintainers; [ atila ];
   };
 }

pkgs/development/python-modules/segyio/explicitly-cast.patch

@@ -0,0 +1,32 @@
+From eafe8476566e1d8e8b9a486ca808685cb439a767 Mon Sep 17 00:00:00 2001
+From: Sveinung Rundhovde <[email protected]>
+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)

pkgs/development/python-modules/segyio/fix-setuptools.patch

@@ -0,0 +1,32 @@
+From 6df089258c2ef4356427263f652cff0c053c6173 Mon Sep 17 00:00:00 2001
+From: Sveinung Rundhovde <[email protected]>
+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',

pkgs/development/python-modules/segyio/numpy-2.patch

@@ -0,0 +1,34 @@
+From 75b2156a6414e2464eb15663004b8ab928374135 Mon Sep 17 00:00:00 2001
+From: Sveinung Rundhovde <[email protected]>
+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()
+