125206d44d
This commit adds a layer of indirection to improve build isolation with
and without external Python, as well as usability of environment views.
It adds `python-venv` as a dependency to all packages that `extends("python")`,
which has the following advantages:
1. Build isolation: only `PYTHONPATH` is considered in builds, not
user / system packages
2. Stable install layout: fixes the problem on Debian, RHEL and Fedora where
external / system python produces `bin/local` subdirs in Spack install prefixes.
3. Environment views are Python virtual environments (and if you add
`py-pip` things like `pip list` work)
Views work whether they're symlink, hardlink or copy type.
This commit additionally makes `spec["python"].command` return
`spec["python-venv"].command`. The rationale is that packages in repos we do
not own do not pass the underlying python to the build system, which could still
result in incorrectly computed install layouts.
Other attributes like `libs`, `headers` should be on `python` anyways and need no change.
92 lines
4.0 KiB
Python
92 lines
4.0 KiB
Python
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
|
|
# Spack Project Developers. See the top-level COPYRIGHT file for details.
|
|
#
|
|
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
|
|
|
|
import glob
|
|
|
|
from spack.package import *
|
|
|
|
|
|
class PyAlphafold(PythonPackage, CudaPackage):
|
|
"""AlphaFold is an AI system developed by DeepMind that predicts a
|
|
protein's 3D structure from its amino acid sequence. It regularly
|
|
achieves accuracy competitive with experiment."""
|
|
|
|
homepage = "https://github.com/deepmind/alphafold"
|
|
url = "https://github.com/deepmind/alphafold/archive/refs/tags/v2.1.1.tar.gz"
|
|
maintainers("aweits")
|
|
|
|
license("Apache-2.0")
|
|
|
|
version("2.2.4", sha256="8d756e16f6dc7897331d834aade8493820d0ff6a03bf60ce511bac4756c1b1e8")
|
|
version("2.1.1", sha256="1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7")
|
|
|
|
conflicts("platform=darwin", msg="alphafold is only supported on Linux")
|
|
|
|
# lots of hints on versions and patching taken from docker/Dockerfile
|
|
# and requirements.txt
|
|
depends_on("python@3.7:", type=("build", "run"))
|
|
depends_on("py-setuptools", type="build")
|
|
depends_on("py-absl-py@0.13.0:", type=("build", "run"), when="@2.1.1")
|
|
depends_on("py-absl-py@1.0.0:", type=("build", "run"), when="@2.2.4")
|
|
depends_on("py-biopython@1.79:", type=("build", "run"))
|
|
depends_on("py-chex@0.0.7:", type=("build", "run"))
|
|
depends_on("py-dm-haiku@0.0.4:", type=("build", "run"), when="@2.1.1")
|
|
depends_on("py-dm-haiku@0.0.7:", type=("build", "run"), when="@2.2.4")
|
|
depends_on("py-dm-tree@0.1.6:", type=("build", "run"))
|
|
depends_on("py-docker", type=("build", "run"))
|
|
depends_on("py-immutabledict@2.0.0:", type=("build", "run"))
|
|
depends_on("py-jax@0.2.14:", type=("build", "run"), when="@2.1.1")
|
|
depends_on("py-jax@0.3.17:", type=("build", "run"), when="@2.2.4")
|
|
depends_on("py-ml-collections@0.1.0:", type=("build", "run"))
|
|
depends_on("py-numpy@1.19.5:", type=("build", "run"), when="@2.1.1")
|
|
depends_on("py-numpy@1.21.6:", type=("build", "run"), when="@2.2.4")
|
|
depends_on("py-pandas@1.3.4:", type=("build", "run"))
|
|
depends_on("py-protobuf@3.19:", type=("build", "run"), when="@2.2.4")
|
|
depends_on("py-scipy@1.7.0:", type=("build", "run"))
|
|
depends_on("py-pdbfixer@1.7", type=("build", "run"))
|
|
depends_on("py-tensorflow@2.5:", type=("build", "run"), when="@2.1.1")
|
|
depends_on("py-tensorflow@2.9:", type=("build", "run"), when="@2.2.4")
|
|
depends_on(
|
|
"openmm@7.5.1+cuda",
|
|
type="run",
|
|
patches=[
|
|
patch(
|
|
"https://raw.githubusercontent.com/google-deepmind/alphafold/2819de4ddd075340b81d36bcf7932a0ff0fbe404/docker/openmm.patch",
|
|
sha256="a5a0ced820f3ecc56ae634c3111f80614863559b0587954a2658c8d4b2a07ae3",
|
|
working_dir="wrappers/python",
|
|
level=0,
|
|
)
|
|
],
|
|
)
|
|
depends_on("hmmer", type="run")
|
|
depends_on("kalign", type="run")
|
|
depends_on("hh-suite", type="run")
|
|
depends_on("aria2", type="run")
|
|
|
|
resource(
|
|
name="chemprops",
|
|
url="https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt",
|
|
destination="",
|
|
sha256="24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451",
|
|
expand=False,
|
|
placement="chemprops",
|
|
)
|
|
|
|
@run_after("install")
|
|
def install_scripts(self):
|
|
mkdirp(self.prefix.bin)
|
|
shebang = f"#!{python.path}\n"
|
|
for fname in glob.glob("run_alphafold*.py"):
|
|
destfile = join_path(self.prefix.bin, fname)
|
|
with open(fname, "r") as src:
|
|
srcdata = src.read()
|
|
with open(destfile, "w") as dest:
|
|
dest.write(shebang + srcdata)
|
|
set_executable(destfile)
|
|
|
|
python_dir = join_path(self.prefix, python_platlib, "alphafold", "common")
|
|
install("chemprops/stereo_chemical_props.txt", python_dir)
|
|
install_tree("scripts", self.prefix.scripts)
|