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base repository: NixOS/nixpkgs
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  • 4 commits
  • 4 files changed
  • 1 contributor

Commits on Mar 3, 2019

  1. sage: patch for pip 19 

    pip 19 introduced a deprecation warning for python 2.7. Since sage
internally uses pip to query for installed packages, this deprecation
warning will show up at unexpected times. That is ugly and messes with
the testsuite.

Upstream: https://trac.sagemath.org/ticket/27405
    @timokau
    timokau committed Mar 3, 2019

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    rasendubi Oleksii Shmalko
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    2de81ee View commit details

  2. python.pkgs.rpy2: fix strictDeps fallout 

    See #54182 and
#55757.
    @timokau
    timokau committed Mar 3, 2019

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  3. sage: fix strictDeps fallout 

    See #54182 and
#55757.
    @timokau
    timokau committed Mar 3, 2019
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  4. Merge pull request #56781 from timokau/sage-python-upgrade-fixes 

    Sage python upgrade fixes
    @timokau
    timokau authored Mar 3, 2019
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22 changes: 22 additions & 0 deletions pkgs/applications/science/math/sage/patches/ignore-pip-deprecation.patch
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
diff --git a/src/sage/misc/package.py b/src/sage/misc/package.py
index 689e5a23b9..4e16fe3a8d 100644
--- a/src/sage/misc/package.py
+++ b/src/sage/misc/package.py
@@ -142,9 +142,14 @@ def pip_installed_packages():
sage: d['beautifulsoup'] # optional - beautifulsoup
u'...'
"""
- proc = subprocess.Popen(["pip", "list", "--no-index", "--format", "json"], stdout=subprocess.PIPE)
- stdout = proc.communicate()[0].decode()
- return {package['name'].lower():package['version'] for package in json.loads(stdout)}
+ with open(os.devnull, 'w') as devnull:
+ proc = subprocess.Popen(
+ ["pip", "list", "--no-index", "--format", "json"],
+ stdout=subprocess.PIPE,
+ stderr=devnull,
+ )
+ stdout = proc.communicate()[0].decode()
+ return {package['name'].lower():package['version'] for package in json.loads(stdout)}

def list_packages(*pkg_types, **opts):
r"""
3 changes: 3 additions & 0 deletions pkgs/applications/science/math/sage/sage-src.nix
View file
Original file line number Diff line number Diff line change
@@ -112,6 +112,9 @@ stdenv.mkDerivation rec {
url = "https://git.sagemath.org/sage.git/patch?id=a05b6b038e1571ab15464e98f76d1927c0c3fd12";
sha256 = "05yq97pq84xi60wb1p9skrad5h5x770gq98ll4frr7hvvmlwsf58";
})

# https://trac.sagemath.org/ticket/27405
./patches/ignore-pip-deprecation.patch
];

patches = nixPatches ++ packageUpgradePatches;
2 changes: 2 additions & 0 deletions pkgs/applications/science/math/sage/sagelib.nix
View file
Original file line number Diff line number Diff line change
@@ -65,11 +65,13 @@ buildPythonPackage rec {
perl
jupyter_core
pkg-config
pip # needed to query installed packages
];

buildInputs = [
gd
readline
iml
];

propagatedBuildInputs = [
4 changes: 4 additions & 0 deletions pkgs/development/python-modules/rpy2/default.nix
View file
Original file line number Diff line number Diff line change
@@ -58,6 +58,10 @@ buildPythonPackage rec {
tidyr
]) ++ extraRPackages ++ rWrapper.recommendedPackages;

nativeBuildInputs = [
R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
];

patches = [
# R_LIBS_SITE is used by the nix r package to point to the installed R libraries.
# This patch sets R_LIBS_SITE when rpy2 is imported.