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Bug fix for py-cython with python 3.10+ (installs in subdir local) #186

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merged 8 commits into from
Nov 1, 2022
Merged

Bug fix for py-cython with python 3.10+ (installs in subdir local) #186

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645871b
py-shapely: add v1.8.3 (#32218)
adamjstewart Aug 22, 2022
3ea62b8
py-shapely: add v1.8.5 (#33259)
adamjstewart Oct 13, 2022
1ad96b2
Bug fix for py-cython when using [email protected]
climbfuji Oct 21, 2022
fb75bc6
Black-format var/spack/repos/builtin/packages/py-cython/package.py
climbfuji Oct 21, 2022
f390fb4
Improve solution for finding bin and lib directory in py-cython
climbfuji Oct 24, 2022
994773a
Add lib64 option, yet another workaround
climbfuji Oct 25, 2022
18d71ec
Black-format var/spack/repos/builtin/packages/py-cython/package.py
climbfuji Oct 25, 2022
c97b38d
Merge branch 'jcsda_emc_spack_stack' into feature/updates_bugfixes_py…
climbfuji Oct 31, 2022
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23 changes: 23 additions & 0 deletions var/spack/repos/builtin/packages/py-cython/package.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

import os

from spack.package import *


Expand Down Expand Up @@ -46,6 +48,23 @@ class PyCython(PythonPackage):
depends_on("py-setuptools", type=("build", "run"))
depends_on("[email protected]:", type="test")

@property
def prefix(self):
prefix = super(PyCython, self).prefix
if os.path.isdir(os.path.join(prefix, "local", "bin")) and not os.path.isdir(
os.path.join(prefix, "bin")
):
prefix.bin = os.path.join(prefix, "local", "bin")
if os.path.isdir(os.path.join(prefix, "local", "lib")) and not os.path.isdir(
os.path.join(prefix, "lib")
):
prefix.lib = os.path.join(prefix, "local", "lib")
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This won't help if you're on an OS that uses lib64 instead of lib.

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You are right, added an additional elif clause to cover this. Don't like any of these solutions, but the solutions you mentioned above aren't available in the authoritative spack repo yet.

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@adamjstewart adamjstewart Oct 25, 2022 •
edited
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Note that you'll also need to do what you're doing here for every Python package in Spack...

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I know ... my strategy is to have this fixed temporarily (because it's the only package in our fairly comprehensive software stack that has this problem) and then get the clean solution from spack once that is available.

elif os.path.isdir(os.path.join(prefix, "local", "lib64")) and not os.path.isdir(
os.path.join(prefix, "lib64")
):
prefix.lib = os.path.join(prefix, "local", "lib64")
return prefix

@property
def command(self):
"""Returns the Cython command"""
Expand All @@ -56,3 +75,7 @@ def command(self):
def build_test(self):
# Warning: full suite of unit tests takes a very long time
python("runtests.py", "-j", str(make_jobs))

def setup_dependent_build_environment(self, env, dependent_spec):
env.prepend_path("PATH", self.prefix.bin)
env.prepend_path("LD_LIBRARY_PATH", self.prefix.lib)
3 changes: 2 additions & 1 deletion var/spack/repos/builtin/packages/py-shapely/package.py
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Expand Up @@ -52,7 +52,8 @@ class PyShapely(PythonPackage):
# the hacky logic in [email protected] looks for libgeos_c.so in the miniconda
# install tree ... need to comment that out so that spack's libgeos_c.so is found.
# Also need to add logic to find libgeos_c.so from spack geos modules, if loaded.
patch("shapely-1.8.0-geos.py.patch", when="@1.8.0:1.8.3")
# This patch only works for 1.8.0/1.8.1, but may also be needed for 1.8.2-1.8.5
patch("shapely-1.8.0-geos.py.patch", when="@1.8.0:1.8.1")

@when("^[email protected]:")
def patch(self):
Expand Down