Merge pull request #221718 from wegank/sage-fix

sage: add libpng to sagelib, import package update patches

pkgs/applications/science/math/sage/patches/numpy-1.24-upgrade.patch

@@ -0,0 +1,58 @@
+diff --git a/src/sage/misc/persist.pyx b/src/sage/misc/persist.pyx
+index 3ac5f1cc2b..cb1f327c19 100644
+--- a/src/sage/misc/persist.pyx
++++ b/src/sage/misc/persist.pyx
+@@ -157,7 +157,7 @@ def load(*filename, compress=True, verbose=True, **kwargs):
+         ....:     _ = f.write(code)
+         sage: load(t)
+         sage: hello
+-        <fortran object>
++        <fortran ...>
+     """
+     import sage.repl.load
+     if len(filename) != 1:
+diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
+index 6f0aeab87a..b77c69b2f7 100644
+--- a/src/sage/plot/complex_plot.pyx
++++ b/src/sage/plot/complex_plot.pyx
+@@ -461,6 +461,8 @@ def complex_to_rgb(z_values, contoured=False, tiled=False,
+             rgb[i, j, 2] = b
+ 
+     sig_off()
++    nan_indices = np.isnan(rgb).any(-1)     # Mask for undefined points
++    rgb[nan_indices] = 1                    # Make nan_indices white
+     return rgb
+ 
+ 
+diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
+index 3bc2b76b58..388c2d1391 100644
+--- a/src/sage/plot/histogram.py
++++ b/src/sage/plot/histogram.py
+@@ -87,13 +87,8 @@ class Histogram(GraphicPrimitive):
+ 
+         TESTS::
+ 
+-            sage: h = histogram([10,3,5], normed=True)[0]
+-            doctest:warning...:
+-            DeprecationWarning: the 'normed' option is deprecated. Use 'density' instead.
+-            See https://trac.sagemath.org/25260 for details.
++            sage: h = histogram([10,3,5], density=True)[0]
+             sage: h.get_minmax_data()
+-            doctest:warning ...
+-            ...VisibleDeprecationWarning: Passing `normed=True` on non-uniform bins has always been broken, and computes neither the probability density function nor the probability mass function. The result is only correct if the bins are uniform, when density=True will produce the same result anyway. The argument will be removed in a future version of numpy.
+             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
+         """
+         import numpy
+diff --git a/src/sage/repl/ipython_extension.py b/src/sage/repl/ipython_extension.py
+index 798671aab4..cad6a47ca8 100644
+--- a/src/sage/repl/ipython_extension.py
++++ b/src/sage/repl/ipython_extension.py
+@@ -405,7 +405,7 @@ class SageMagics(Magics):
+             ....: C END FILE FIB1.F
+             ....: ''')
+             sage: fib
+-            <fortran object>
++            <fortran ...>
+             sage: from numpy import array
+             sage: a = array(range(10), dtype=float)
+             sage: fib(a, 10)

pkgs/applications/science/math/sage/sage-src.nix

@@ -127,6 +127,23 @@ stdenv.mkDerivation rec {
       sha256 = "sha256-9BhQLFB3wUhiXRQsK9L+I62lSjvTfrqMNi7QUIQvH4U=";
     })
 
+    # https://github.com/sagemath/sage/pull/35235
+    (fetchpatch {
+      name = "ipython-8.11-upgrade.patch";
+      url = "https://github.com/sagemath/sage/commit/23471e2d242c4de8789d7b1fc8b07a4b1d1e595a.diff";
+      sha256 = "sha256-wvH4BvDiaBv7jbOP8LvOE5Vs16Kcwz/C9jLpEMohzLQ=";
+    })
+
+    # positively reviewed
+    (fetchpatch {
+      name = "matplotlib-3.7.0-upgrade.patch";
+      url = "https://github.com/sagemath/sage/pull/35177.diff";
+      sha256 = "sha256-YdPnMsjXBm9ZRm6a8hH8rSynkrABjLoIzqwp3F/rKAw=";
+    })
+
+    # rebased from https://github.com/sagemath/sage/pull/34994, merged in sage 10.0.beta2
+    ./patches/numpy-1.24-upgrade.patch
+
     # temporarily paper over https://github.com/jupyter-widgets/ipywidgets/issues/3669
     ./patches/ipywidgets-on_submit-deprecationwarning.patch
 

pkgs/applications/science/math/sage/sagelib.nix

@@ -22,6 +22,7 @@
 , gsl
 , iml
 , jinja2
+, libpng
 , lcalc
 , lrcalc
 , gap
@@ -99,6 +100,7 @@ buildPythonPackage rec {
     gd
     readline
     iml
+    libpng
   ];
 
   propagatedBuildInputs = [