Merge remote-tracking branch 'origin/master' into staging-next

Conflicts:
 pkgs/shells/ion/default.nix
 pkgs/tools/misc/cicero-tui/default.nix

3 files changed, 30 insertions, 1 deletions

diff --git a/pkgs/applications/science/math/sage/patches/sphinx-3.5-code-output.patch b/pkgs/applications/science/math/sage/patches/sphinx-3.5-code-output.patch
new file mode 100644
index 0000000000000..f17897d4c89f6
--- /dev/null
+++ b/pkgs/applications/science/math/sage/patches/sphinx-3.5-code-output.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py
+index 6bad826a88..f4d7b8651c 100644
+--- a/src/sage/misc/sagedoc.py
++++ b/src/sage/misc/sagedoc.py
+@@ -24,7 +24,7 @@ see :trac:`12849`::
+     ....:     for line in fobj:
+     ....:         if "#sage.symbolic.expression.Expression.numerical_approx" in line:
+     ....:             print(line)
+-    <code class="sig-name descname">numerical_approx</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">prec</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">digits</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">algorithm</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span>...
++    <code class="sig-name descname"><span class="pre">numerical_approx</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">prec</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">digits</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">algorithm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span>...
+ 
+ Check that sphinx is not imported at Sage start-up::
+ 
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index 36715764d09a1..57234c660a5a8 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -79,6 +79,22 @@ stdenv.mkDerivation rec {
     # ignore a deprecation warning for usage of `cmp` in the attrs library in the doctests
     ./patches/ignore-cmp-deprecation.patch
 
+    # sphinx 3.5 pretty-prints code slightly differently than sphinx
+    # 3.1--3.3. a similar patch is available at the sphinx 4 ticket
+    # (https://trac.sagemath.org/ticket/31696), but sphinx 3.5 uses
+    # <code> tags while sphinx 4 uses <span> tags so we cannot just
+    # import the patch from trac.
+    ./patches/sphinx-3.5-code-output.patch
+
+    # remove use of matplotlib function deprecated in 3.4
+    # https://trac.sagemath.org/ticket/31827
+    (fetchSageDiff {
+      base = "9.3";
+      name = "remove-matplotlib-deprecated-function.patch";
+      rev = "32b2bcaefddc4fa3d2aee6fa690ce1466cbb5948";
+      sha256 = "sha256-SXcUGBMOoE9HpuBzgKC3P6cUmM5MiktXbe/7dVdrfWo=";
+    })
+
     # https://trac.sagemath.org/ticket/30801. this patch has
     # positive_review but has not been merged upstream yet, so we
     # don't use fetchSageDiff because it returns a file that contains
diff --git a/pkgs/applications/science/math/sage/sagedoc.nix b/pkgs/applications/science/math/sage/sagedoc.nix
index 603c1a585c79b..f4a8bf19b69c1 100644
--- a/pkgs/applications/science/math/sage/sagedoc.nix
+++ b/pkgs/applications/science/math/sage/sagedoc.nix
@@ -76,7 +76,7 @@ stdenv.mkDerivation rec {
     mv html/en/_static{,.tmp}
     for _dir in `find -name _static` ; do
           rm -r $_dir
-          ln -s /share/doc/sage/html/en/_static $_dir
+          ln -s html/en/_static $_dir
     done
     mv html/en/_static{.tmp,}
   '';