new package: py-alphafold (#27849)

* new package: alphafold

and related dependencies, depends on #27138

* [@spackbot] updating style on behalf of aweits

* fix

Co-authored-by: aweits <aweits@users.noreply.github.com>

var/spack/repos/builtin/packages/hh-suite/package.py

@@ -0,0 +1,33 @@
+# Copyright 2013-2021 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)
+
+
+from spack.package import *
+
+
+class HhSuite(CMakePackage):
+    """HH-suite is a widely used open source software suite for
+    sensitive sequence similarity searches and protein fold
+    recognition. It is based on pairwise alignment of profile Hidden
+    Markov models (HMMs), which represent multiple sequence alignments
+    of homologous proteins."""
+
+    homepage = "https://github.com/soedinglab/hh-suite"
+    url = "https://github.com/soedinglab/hh-suite/archive/refs/tags/v3.3.0.tar.gz"
+
+    version("3.3.0", sha256="dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964")
+
+    variant("mpi", default=True, description="Enable MPI support")
+
+    depends_on("cmake@2.8.12:", type="build")
+    depends_on("mpi", when="+mpi")
+
+    def build_args(self, spec, prefix):
+        args = []
+        if "+mpi" in self.spec:
+            args.append("-DCHECK_MPI=1")
+        else:
+            args.append("-DCHECK_MPI=0")
+        return args

var/spack/repos/builtin/packages/kalign/package.py

@@ -0,0 +1,20 @@
+# Copyright 2013-2021 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)
+
+
+from spack.package import *
+
+
+class Kalign(AutotoolsPackage):
+    """A fast multiple sequence alignment program for biological sequences."""
+
+    homepage = "https://github.com/TimoLassmann/kalign"
+    url = "https://github.com/TimoLassmann/kalign/archive/refs/tags/v3.3.1.tar.gz"
+
+    version("3.3.1", sha256="7f10acf9a3fa15deabbc0304e7c14efa25cea39108318c9f02b47257de2d7390")
+
+    depends_on("autoconf", type="build")
+    depends_on("automake", type="build")
+    depends_on("libtool", type="build")

var/spack/repos/builtin/packages/openmm/package.py

@@ -19,6 +19,8 @@ class Openmm(CMakePackage, CudaPackage):
     homepage = "https://openmm.org/"
     url = "https://github.com/openmm/openmm/archive/7.4.1.tar.gz"
 
+    version("7.6.0", sha256="5a99c491ded9ba83ecc3fb1d8d22fca550f45da92e14f64f25378fda0048a89d")
+    version("7.5.1", sha256="c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7")
     version("7.5.0", sha256="516748b4f1ae936c4d70cc6401174fc9384244c65cd3aef27bc2c53eac6d6de5")
     version("7.4.1", sha256="e8102b68133e6dcf7fcf29bc76a11ea54f30af71d8a7705aec0aee957ebe3a6d")
 

var/spack/repos/builtin/packages/py-alphafold/package.py

@@ -0,0 +1,85 @@
+# Copyright 2013-2021 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"]
+
+    version("2.1.1", sha256="1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7")
+
+    conflicts("platform=darwin", msg="alphafold is only supported on Linux")
+
+    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"))
+    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"))
+    depends_on("py-dm-tree@0.1.6:", type=("build", "run"))
+    depends_on("py-immutabledict@2.0.0:", type=("build", "run"))
+    depends_on("py-jax@0.2.14:", type=("build", "run"))
+    for arch in CudaPackage.cuda_arch_values:
+        depends_on(
+            "py-jax@0.2.14:+cuda cuda_arch={0}".format(arch),
+            type=("build", "run"),
+            when="cuda_arch={0}".format(arch),
+        )
+    depends_on("py-ml-collections@0.1.0:", type=("build", "run"))
+    depends_on("py-numpy@1.19.5:", type=("build", "run"))
+    depends_on("py-pandas@1.3.4:", type=("build", "run"))
+    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"))
+    depends_on(
+        "openmm@7.5.1+cuda",
+        type="run",
+        patches=[
+            patch(
+                "https://raw.githubusercontent.com/deepmind/alphafold/main/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 = "#!{0}\n".format(self.spec["python"].command)
+        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)

var/spack/repos/builtin/packages/py-biopython/package.py

@@ -16,6 +16,7 @@ class PyBiopython(PythonPackage):
     homepage = "https://biopython.org/wiki/Main_Page"
     url = "https://biopython.org/DIST/biopython-1.65.tar.gz"
 
+    version("1.79", sha256="edb07eac99d3b8abd7ba56ff4bedec9263f76dfc3c3f450e7d2e2bcdecf8559b")
     version("1.78", sha256="1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564")
     version("1.73", sha256="70c5cc27dc61c23d18bb33b6d38d70edc4b926033aea3b7434737c731c94a5e0")
     version("1.70", sha256="4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b")

var/spack/repos/builtin/packages/py-chex/package.py

@@ -0,0 +1,25 @@
+# Copyright 2013-2021 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)
+
+
+from spack.package import *
+
+
+class PyChex(PythonPackage):
+    """Chex is a library of utilities for helping to write reliable JAX code."""
+
+    homepage = "https://github.com/deepmind/chex"
+    pypi = "chex/chex-0.1.0.tar.gz"
+
+    version("0.1.0", sha256="9e032058f5fed2fc1d5e9bf8e12ece5910cf6a478c12d402b6d30984695f2161")
+
+    depends_on("python@3.7:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-absl-py@0.9.0:", type=("build", "run"))
+    depends_on("py-dm-tree@0.1.5:", type=("build", "run"))
+    depends_on("py-jax@0.1.55:", type=("build", "run"))
+    depends_on("py-jaxlib@0.1.37:", type=("build", "run"))
+    depends_on("py-numpy@1.18.0:", type=("build", "run"))
+    depends_on("py-toolz@0.9.0:", type=("build", "run"))

var/spack/repos/builtin/packages/py-dm-haiku/package.py

@@ -0,0 +1,24 @@
+# Copyright 2013-2021 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)
+
+
+from spack.package import *
+
+
+class PyDmHaiku(PythonPackage):
+    """JAX-based neural network library"""
+
+    homepage = "https://github.com/deepmind/dm-haiku"
+    pypi = "dm-haiku/dm-haiku-0.0.5.tar.gz"
+
+    version("0.0.5", sha256="e986237e1f840aa3bd26217ecad84b611bf1456e2139f0f79ea71f9c6222d231")
+    depends_on("python@3.7:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-absl-py@0.7.1:", type=("build", "run"))
+    depends_on("py-jmp@0.0.2:", type=("build", "run"))
+    depends_on("py-numpy@1.18.0:", type=("build", "run"))
+    depends_on("py-tabulate@0.8.9:", type=("build", "run"))
+    depends_on("py-typing-extensions", when="^python@:3.7", type=("build", "run"))
+    depends_on("py-jax", type=("build", "run"))

var/spack/repos/builtin/packages/py-dm-tree/package.py

@@ -19,6 +19,7 @@ class PyDmTree(PythonPackage):
 
     maintainers = ["aweits"]
 
+    version("0.1.6", sha256="6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a")
     version("0.1.5", sha256="a951d2239111dfcc468071bc8ff792c7b1e3192cab5a3c94d33a8b2bda3127fa")
 
     depends_on("py-setuptools", type="build")

var/spack/repos/builtin/packages/py-immutabledict/package.py

@@ -0,0 +1,28 @@
+# Copyright 2013-2021 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)
+
+
+from spack.package import *
+
+
+class PyImmutabledict(PythonPackage):
+    """A fork of frozendict, an immutable wrapper around
+    dictionaries. It implements the complete mapping interface and can be used as a
+    drop-in replacement for dictionaries where immutability is
+    desired. The immutabledict constructor mimics dict, and all of the
+    expected interfaces (iter, len, repr, hash, getitem) are
+    provided. Note that an immutabledict does not guarantee the
+    immutability of its values, so the utility of hash method is
+    restricted by usage. The only difference is that the copy() method
+    of immutable takes variable keyword arguments, which will be
+    present as key/value pairs in the new, immutable copy."""
+
+    homepage = "https://github.com/corenting/immutabledict"
+    pypi = "immutabledict/immutabledict-2.2.1.tar.gz"
+
+    version("2.2.1", sha256="1ddb0edf1bb6c70d0197eb90ce1fe2b2d58502334f5fdfde72d7c633d723ec3a")
+
+    depends_on("python@3.6:3", type=("build", "run"))
+    depends_on("py-poetry-core@1:", type="build")

var/spack/repos/builtin/packages/py-jax/package.py

@@ -0,0 +1,42 @@
+# Copyright 2013-2021 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)
+
+
+from spack.package import *
+
+
+class PyJax(PythonPackage, CudaPackage):
+    """JAX is Autograd and XLA, brought together for high-performance
+    machine learning research. With its updated version of Autograd,
+    JAX can automatically differentiate native Python and NumPy
+    functions. It can differentiate through loops, branches,
+    recursion, and closures, and it can take derivatives of
+    derivatives of derivatives. It supports reverse-mode
+    differentiation (a.k.a. backpropagation) via grad as well as
+    forward-mode differentiation, and the two can be composed
+    arbitrarily to any order."""
+
+    homepage = "https://github.com/google/jax"
+    pypi = "jax/jax-0.2.25.tar.gz"
+
+    version("0.2.25", sha256="822e8d1e06257eaa0fdc4c0a0686c4556e9f33647fa2a766755f984786ae7446")
+
+    variant("cuda", default=True, description="CUDA support")
+
+    depends_on("python@3.7:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy@1.18:", type=("build", "run"))
+    depends_on("py-absl-py", type=("build", "run"))
+    depends_on("py-opt-einsum", type=("build", "run"))
+    depends_on("py-scipy@1.2.1:", type=("build", "run"))
+    depends_on("py-typing-extensions", type=("build", "run"))
+    depends_on("py-jaxlib@0.1.69:", type=("build", "run"), when="~cuda")
+    depends_on("py-jaxlib@0.1.69:+cuda", type=("build", "run"), when="+cuda")
+    for arch in CudaPackage.cuda_arch_values:
+        depends_on(
+            "py-jaxlib@0.1.69:+cuda cuda_arch={0}".format(arch),
+            type=("build", "run"),
+            when="cuda_arch={0}".format(arch),
+        )

var/spack/repos/builtin/packages/py-jaxlib/package.py

@@ -0,0 +1,69 @@
+# Copyright 2013-2021 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 tempfile
+
+import llnl.util.tty as tty
+
+from spack.package import *
+
+
+class PyJaxlib(PythonPackage, CudaPackage):
+    """XLA library for Jax"""
+
+    homepage = "https://github.com/google/jax"
+    url = "https://github.com/google/jax/archive/refs/tags/jaxlib-v0.1.74.tar.gz"
+
+    tmp_path = ""
+
+    version("0.1.74", sha256="bbc78c7a4927012dcb1b7cd135c7521f782d7dad516a2401b56d3190f81afe35")
+
+    depends_on("python@3.7:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy@1.18:", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-absl-py", type=("build", "run"))
+    depends_on("py-flatbuffers@1.12:2", type=("build", "run"))
+    depends_on("bazel@4.1.0:", type=("build"))
+    depends_on("cudnn@8.0.5:", when="+cuda")
+    depends_on("cuda@11.1:", when="+cuda")
+
+    def install(self, spec, prefix):
+        args = []
+        args.append("build/build.py")
+        if "+cuda" in spec:
+            args.append("--enable_cuda")
+            args.append("--cuda_path={0}".format(self.spec["cuda"].prefix))
+            args.append("--cudnn_path={0}".format(self.spec["cudnn"].prefix))
+            capabilities = ",".join(
+                "{0:.1f}".format(float(i) / 10.0) for i in spec.variants["cuda_arch"].value
+            )
+            args.append("--cuda_compute_capabilities={0}".format(capabilities))
+        args.append("--bazel_startup_options=" "--output_user_root={0}".format(self.buildtmp))
+        python(*args)
+        with working_dir(self.tmp_path):
+            tty.warn("in dir " + self.tmp_path)
+            args = std_pip_args + ["--prefix=" + self.prefix, "."]
+            pip(*args)
+        remove_linked_tree(self.tmp_path)
+        remove_linked_tree(self.buildtmp)
+
+    def patch(self):
+        self.tmp_path = tempfile.mkdtemp(prefix="spack")
+        self.buildtmp = tempfile.mkdtemp(prefix="spack")
+        filter_file(
+            """f"--output_path={output_path}",""",
+            """f"--output_path={output_path}","""
+            """f"--sources_path=%s","""
+            """f"--nohome_rc'","""
+            """f"--nosystem_rc'",""" % self.tmp_path,
+            "build/build.py",
+        )
+        filter_file(
+            "args = parser.parse_args()",
+            "args,junk = parser.parse_known_args()",
+            "build/build_wheel.py",
+            string=True,
+        )

var/spack/repos/builtin/packages/py-jmp/package.py

@@ -0,0 +1,23 @@
+# Copyright 2013-2021 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)
+
+
+from spack.package import *
+
+
+class PyJmp(PythonPackage):
+    """JMP is a Mixed Precision library for JAX."""
+
+    homepage = "https://github.com/deepmind/jmp"
+    # pypi tarball has requirements.txt missing
+    url = "https://github.com/deepmind/jmp/archive/refs/tags/v0.0.2.tar.gz"
+
+    version("0.0.2", sha256="4d242fb14502b15a7c072e112bdcd7cb5d8b373d9733162eea23e0b9b7dbb6d0")
+
+    depends_on("python@3.6:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy@1.19.5:", type=("build", "run"))
+    depends_on("py-dataclasses@0.7:", type=("build", "run"), when="^python@:3.6")
+    depends_on("py-jax@0.1.71:", type=("build", "run"))

var/spack/repos/builtin/packages/py-ml-collections/package.py

@@ -11,8 +11,10 @@ class PyMlCollections(PythonPackage):
 
     homepage = "https://https://github.com/google/ml_collections"
     pypi = "ml_collections/ml_collections-0.1.0.tar.gz"
+    git = "https://github.com/google/ml_collections"
 
     version("0.1.1", sha256="3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc")
+    version("0.1.0", commit="63a7c22d1bf3521c3bb3f9da6ebf07972c25fec4")
 
     depends_on("python@2.6:", type=("build", "run"))
     depends_on("py-setuptools", type=("build", "run"))
@@ -20,5 +22,5 @@ class PyMlCollections(PythonPackage):
     depends_on("py-absl-py", type=("build", "run"))
     depends_on("py-six", type=("build", "run"))
     depends_on("py-contextlib2", type=("build", "run"))
-    depends_on("py-dataclasses", type=("build", "run"), when="python@:3.6")
+    depends_on("py-dataclasses", type=("build", "run"), when="^python@:3.6")
-    depends_on("py-typing", type=("build", "run"), when="python@:3.5")
+    depends_on("py-typing", type=("build", "run"), when="^python@:3.4")

var/spack/repos/builtin/packages/py-pdbfixer/package.py

@@ -0,0 +1,23 @@
+# Copyright 2013-2021 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)
+
+
+from spack.package import *
+
+
+class PyPdbfixer(PythonPackage):
+    """PDBFixer is an easy to use application for fixing problems in
+    Protein Data Bank files in preparation for simulating them."""
+
+    homepage = "https://github.com/openmm/pdbfixer"
+    url = "https://github.com/openmm/pdbfixer/archive/refs/tags/v1.8.1.tar.gz"
+
+    version("1.8.1", sha256="d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595")
+    version("1.7", sha256="a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("openmm@7.1:7.5", type=("build", "run"), when="1.7")
+    depends_on("openmm@7.6:", type=("build", "run"), when="@1.8:")
+    depends_on("py-numpy", type=("build", "run"))