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{ stdenv
, fetchFromGitHub
, fetchpatch
, runtimeShell
}:
# This file is responsible for fetching the sage source and adding necessary patches.
# It does not actually build anything, it just copies the patched sources to $out.
# This is done because multiple derivations rely on these sources and they should
# all get the same sources with the same patches applied.
let
# Fetch a diff between `base` and `rev` on sage's git server.
# Used to fetch trac tickets by setting the `base` to the last release and the
# `rev` to the last commit of the ticket.
fetchSageDiff = { base, name, rev, sha256, ...}@args: (
fetchpatch ({
inherit name sha256;
url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}";
# We don't care about sage's own build system (which builds all its dependencies).
# Exclude build system changes to avoid conflicts.
excludes = [ "build/*" ];
} // builtins.removeAttrs args [ "rev" "base" "sha256" ])
);
in
stdenv.mkDerivation rec {
version = "9.2";
pname = "sage-src";
src = fetchFromGitHub {
owner = "sagemath";
repo = "sage";
rev = version;
sha256 = "103j8d5x6szl9fxaz0dvdi4y47q1af9h9y5hmjh2xayi62qmp5ql";
};
# Patches needed because of particularities of nix or the way this is packaged.
# The goal is to upstream all of them and get rid of this list.
nixPatches = [
# Make sure py2/py3 tests are only run when their expected context (all "sage"
# tests) are also run. That is necessary to test dochtml individually. See
# https://trac.sagemath.org/ticket/26110 for an upstream discussion.
# TODO: Determine if it is still necessary.
./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch
# Fixes a potential race condition which can lead to transient doctest failures.
./patches/fix-ecl-race.patch
# Not necessary since library location is set explicitly
# https://trac.sagemath.org/ticket/27660#ticket
./patches/do-not-test-find-library.patch
# Parallelize docubuild using subprocesses, fixing an isolation issue. See
# https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
./patches/sphinx-docbuild-subprocesses.patch
# Register sorted dict pprinter earlier (https://trac.sagemath.org/ticket/31053)
(fetchSageDiff {
base = "9.3.beta4";
name = "register-pretty-printer-earlier.patch";
rev = "d658230ce06ca19f4a3b3a4576297ee82f2d2151";
sha256 = "sha256-9mPUV7K5PoLDH2vVaYaOfvDLDpmxU0Aj7m/eaXYotDs=";
})
];
# 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 = [
# To help debug the transient error in
# https://trac.sagemath.org/ticket/23087 when it next occurs.
./patches/configurationpy-error-verbose.patch
# fix intermittent errors in Sage 9.2's psage.py (this patch is
# already included in Sage 9.3): https://trac.sagemath.org/ticket/30730
(fetchSageDiff {
base = "9.2.rc2";
name = "fix-psage-is-locked.patch";
rev = "75df605f216ddc7b6ca719be942d666b241520e9";
sha256 = "0g9pl1wbb3sgs26d3bvv70cpa77sfskylv4kd255y1794f1fgk4q";
})
# fix intermittent errors in sagespawn.pyx: https://trac.sagemath.org/ticket/31052
(fetchSageDiff {
base = "9.2";
name = "sagespawn-implicit-casting.patch";
rev = "2959ac792ebd6107fe87c9af1541083de5ba02d6";
sha256 = "sha256-bWIpEGir9Kawak5CJegBMNcHm/CqhWmdru+emeSsvO0=";
})
# fix intermittent errors in doctest/test.py: https://trac.sagemath.org/ticket/26912
(fetchSageDiff {
base = "9.3.beta8";
name = "set-cysignals-crash-ndebug.patch";
rev = "ca5257a5d0f32efc9f8f07e126020856270b1a18";
sha256 = "sha256-KViw63xE3O0eUiOYzoxNrr4NL+csql9GPJLDJCf/EZs=";
})
];
# 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
# maintaining multiple versions of dependencies. Instead we try to make sage
# compatible with never dependency versions when possible. All these changes
# should come from or be proposed to upstream. This list will probably never
# be empty since dependencies update all the time.
packageUpgradePatches = [
# After updating smypow to (https://trac.sagemath.org/ticket/3360) we can
# now set the cache dir to be withing the .sage directory. This is not
# strictly necessary, but keeps us from littering in the user's HOME.
./patches/sympow-cache.patch
# ignore a deprecation warning for usage of `cmp` in the attrs library in the doctests
./patches/ignore-cmp-deprecation.patch
# adapt sage's Image class to pillow 8.0.1 (https://trac.sagemath.org/ticket/30971)
(fetchSageDiff {
base = "9.3.beta2";
name = "pillow-8.0.1-update.patch";
rev = "f05f2d0aac9c4b5abe68105cee2cc7f2c8461847";
sha256 = "sha256-uY2UlgSd5hhOUUukB4Xc3Gjy0/e7p/qyq9jdvz10IOs=";
})
# don't use deprecated numpy type aliases (https://trac.sagemath.org/ticket/31364)
(fetchSageDiff {
base = "9.3.beta7";
name = "dont-use-deprecated-numpy-type-aliases.patch";
rev = "dfdef60515d4a4269e82d91280f76a7fdf10bf97";
sha256 = "sha256-77/3LkT5J7DQN8IPlGJKB6ZcJPaF7xwje06JNns+0AE=";
})
# fix test output with sympy 1.7 (https://trac.sagemath.org/ticket/30985)
./patches/sympy-1.7-update.patch
# workaround until we use sage's fork of threejs, which contains a "version" file
./patches/dont-grep-threejs-version-from-minified-js.patch
# updated eclib output has punctuation changes and tidier whitespace
./patches/eclib-20210223-test-formatting.patch
# upgrade arb to 2.18.1 (https://trac.sagemath.org/ticket/28623)
(fetchSageDiff {
base = "9.3.beta3";
name = "arb-2.18.1-update.patch";
rev = "0c9c4ed35c2eaf34ae0d19387c07b7f460e4abce";
sha256 = "sha256-CjOJIsyyVCziAfvE6pWSihPO35IZMcY2/taXAsqhPLY=";
})
# giac 1.6.0-47 update (https://trac.sagemath.org/ticket/30537)
(fetchSageDiff {
base = "9.3.beta7";
name = "giac-1.6.0-47-update.patch";
rev = "f05720bf63dfaf33a4e3b6d3ed2c2c0ec46b5d31";
sha256 = "sha256-gDUq+84eXd5GxLBWUSI61GMJpBF2KX4LBVOt3mS1NF8=";
})
# Make gcd/lcm interact better with pari and gmpy2 (https://trac.sagemath.org/ticket/30849)
# needed for pari 2.13.1 update, which we will do in the future
(fetchSageDiff {
base = "9.3.beta0";
name = "make-gcd-lcm-interact-better-with-pari-and-gmpy2.patch";
rev = "75c1516f0abb9e6f8c335e38e4031f6ef674ed30";
sha256 = "sha256-RukkieIZcXNrju904H2oyGKdtpdE+9vNzvyjN2IBNg0=";
})
# cypari 2.1.2 update (https://trac.sagemath.org/ticket/31029)
(fetchSageDiff {
base = "9.3.beta3";
name = "cypari-2.1.2-update.patch";
rev = "b9aadfd08e81d74ca7c229bb80eb853b592887d0";
sha256 = "sha256-eKaMy7kpu+YKdL8bPStgocxBCTfc2Z/10RrGy2LENFw=";
})
];
patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;
postPatch = ''
# make sure shebangs etc are fixed, but sage-python23 still works
find . -type f -exec sed \
-e 's/sage-python23/python3/g' \
-i {} \;
echo '#!${runtimeShell}
python3 "$@"' > build/bin/sage-python23
# Make sure sage can at least be imported without setting any environment
# variables. It won't be close to feature complete though.
sed -i \
"s|var('SAGE_ROOT'.*|var('SAGE_ROOT', '$out')|" \
src/sage/env.py
# Do not use sage-env-config (generated by ./configure).
# Instead variables are set manually.
echo '# do nothing' > src/bin/sage-env-config
'';
# Test src/doc/en/reference/spkg/conf.py will fail if
# src/doc/en/reference/spkg/index.rst is not generated. It is
# generated by src/doc/bootstrap, so I've copied the relevant part
# here. An alternative would be to create an empty
# src/doc/en/reference/spkg/index.rst file.
configurePhase = ''
OUTPUT_DIR="src/doc/en/reference/spkg"
mkdir -p "$OUTPUT_DIR"
OUTPUT_INDEX="$OUTPUT_DIR"/index.rst
cat > "$OUTPUT_INDEX" <<EOF
External Packages
=================
.. toctree::
:maxdepth: 1
EOF
for PKG_SCRIPTS in build/pkgs/*; do
if [ -d "$PKG_SCRIPTS" ]; then
PKG_BASE=$(basename "$PKG_SCRIPTS")
if [ -f "$PKG_SCRIPTS"/SPKG.rst ]; then
# Instead of just copying, we may want to call
# a version of sage-spkg-info to format extra information.
cp "$PKG_SCRIPTS"/SPKG.rst "$OUTPUT_DIR"/$PKG_BASE.rst
echo >> "$OUTPUT_INDEX" " $PKG_BASE"
fi
fi
done
cat >> "$OUTPUT_INDEX" <<EOF
.. include:: ../footer.txt
EOF
'';
buildPhase = "# do nothing";
installPhase = ''
cp -r . "$out"
'';
}
|