From dac4719e0b05e7bfc95eb17a8cb8500b288ad019 Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Fri, 2 Aug 2019 18:00:41 +0200
Subject: [PATCH 1/3] sage: add patch to debug transient issue

---
 .../configurationpy-error-verbose.patch       | 19 +++++++++++++++++++
 .../science/math/sage/sage-src.nix            |  6 +++++-
 2 files changed, 24 insertions(+), 1 deletion(-)
 create mode 100644 pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch

diff --git a/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch b/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch
new file mode 100644
index 000000000000..e687281ad1a7
--- /dev/null
+++ b/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch
@@ -0,0 +1,19 @@
+diff --git a/src/sage/repl/configuration.py b/src/sage/repl/configuration.py
+index 67d7d2accf..18279581e2 100644
+--- a/src/sage/repl/configuration.py
++++ b/src/sage/repl/configuration.py
+@@ -9,10 +9,11 @@ the IPython simple prompt is being used::
+     sage: cmd = 'print([sys.stdin.isatty(), sys.stdout.isatty()])'
+     sage: import pexpect
+     sage: output = pexpect.run(
+-    ....:     'bash -c \'echo "{0}" | sage\''.format(cmd),
++    ....:     'bash -c \'export SAGE_BANNER=no; echo "{0}" | sage\''.format(cmd),
+     ....: ).decode('utf-8', 'surrogateescape')
+-    sage: 'sage: [False, True]' in output
+-    True
++    sage: print(output)
++    sage...[False, True]
++    sage...Exiting Sage ...
+ """
+ 
+ #*****************************************************************************
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index 51460154c5de..84c2ef3ec785 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -61,7 +61,11 @@ stdenv.mkDerivation rec {
   # Since sage unfortunately does not release bugfix releases, packagers must
   # fix those bugs themselves. This is for critical bugfixes, where "critical"
   # == "causes (transient) doctest failures / somebody complained".
-  bugfixPatches = [ ];
+  bugfixPatches = [
+    # To help debug the transient error in
+    # https://trac.sagemath.org/ticket/23087 when it next occurs.
+    ./patches/configurationpy-error-verbose.patch
+  ];
 
   # Patches needed because of package updates. We could just pin the versions of
   # dependencies, but that would lead to rebuilds, confusion and the burdons of

From 69d9700c61ff1648f5094f997ca2d754299441ae Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Fri, 2 Aug 2019 18:01:26 +0200
Subject: [PATCH 2/3] sage: add list of past test failures

---
 .../science/math/sage/dist-tests.nix            | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 pkgs/applications/science/math/sage/dist-tests.nix

diff --git a/pkgs/applications/science/math/sage/dist-tests.nix b/pkgs/applications/science/math/sage/dist-tests.nix
new file mode 100644
index 000000000000..24a86a8f37a4
--- /dev/null
+++ b/pkgs/applications/science/math/sage/dist-tests.nix
@@ -0,0 +1,17 @@
+# Lists past failures and files associated with it. The intention is to build
+# up a subset of a testsuite that catches 95% of failures that are relevant for
+# distributions while only taking ~5m to run. This in turn makes it more
+# reasonable to re-test sage on dependency changes and makes it easier for
+# users to override the sage derivation.
+# This is an experiment for now. If it turns out that there really is a small
+# subset of files responsible for the vast majority of packaging tests, we can
+# think about moving this upstream.
+[
+	"src/sage/env.py" # [1]
+	"src/sage/misc/persist.pyx" # [1]
+	"src/sage/misc/inline_fortran.py" # [1]
+	"src/sage/repl/ipython_extension.py" # [1]
+]
+
+# Numbered list of past failures to annotate files with
+# [1] PYTHONPATH related issue https://github.com/NixOS/nixpkgs/commit/ec7f569211091282410050e89e68832d4fe60528

From 41bb3194622637aa26fe5a28880165d9ecb2f2df Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Fri, 16 Aug 2019 23:50:55 +0200
Subject: [PATCH 3/3] sage: avoid running out of memory during tests

---
 pkgs/applications/science/math/sage/sage-tests.nix | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/pkgs/applications/science/math/sage/sage-tests.nix b/pkgs/applications/science/math/sage/sage-tests.nix
index 591fa192d563..0cd5b5d976a1 100644
--- a/pkgs/applications/science/math/sage/sage-tests.nix
+++ b/pkgs/applications/science/math/sage/sage-tests.nix
@@ -51,6 +51,10 @@ stdenv.mkDerivation rec {
     export HOME="$TMPDIR/sage-home"
     mkdir -p "$HOME"
 
+    # avoid running out of memory with many threads in subprocesses, see
+    # https://github.com/NixOS/nixpkgs/pull/65802
+    export GLIBC_TUNABLES=glibc.malloc.arena_max=4
+
     echo "Running sage tests with arguments ${timeSpecifier} ${patienceSpecifier} ${testArgs}"
     "sage" -t --nthreads "$NIX_BUILD_CORES" --optional=sage ${timeSpecifier} ${patienceSpecifier} ${testArgs}
   '';