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MDAnalysis: add v2.7.0 (#41907)

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* ensure umpire~cuda~rocm when ~cuda~rocm

* MDAnalysis: add v2.7.0

* Apply suggestions from code review

* license

* review changes

* add gsd and py-cmake versions

* Update package.py

* py-cmake

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* fix and reorder

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This commit is contained in:
Rocco Meli 2024-01-29 15:31:34 +01:00 committed by GitHub
parent 2170386ad9
commit 7ec93a496d
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GPG key ID: B5690EEEBB952194
4 changed files with 33 additions and 16 deletions
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21
var/spack/repos/builtin/packages/py-cmake/package.py
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@ -5,6 +5,13 @@
from spack.package import *
pycmake_versions = {
"3.27.9": "d8a40eef1268c91e5b520b28fd5fe0591d750e48e44276dbfd493a14ee595c41",
"3.22.2": "b5bd5eeb488b13cf64ec963800f3d979eaeb90b4382861b86909df503379e219",
"3.21.4": "30fa5ed8a5ad66dcd263adb87f3ce3dc2d0ec0ac3958f5becff577e4b62cd065",
"3.18.0": "52b98c5ee70b5fa30a8623e96482227e065292f78794eb085fdf0fecb204b79b",
}
class PyCmake(PythonPackage):
"""CMake is an open-source, cross-platform family of tools designed to
@ -17,24 +24,24 @@ class PyCmake(PythonPackage):
license("Apache-2.0")
version("3.22.2", sha256="b5bd5eeb488b13cf64ec963800f3d979eaeb90b4382861b86909df503379e219")
version("3.21.4", sha256="30fa5ed8a5ad66dcd263adb87f3ce3dc2d0ec0ac3958f5becff577e4b62cd065")
version("3.18.0", sha256="52b98c5ee70b5fa30a8623e96482227e065292f78794eb085fdf0fecb204b79b")
for v, sha in pycmake_versions.items():
version(v, sha256=sha)
depends_on("ninja", type="build")
depends_on("py-scikit-build@0.12:", type="build")
depends_on("py-setuptools@42:", type="build")
depends_on("py-setuptools-scm+toml", when="@3.27.9:", type="build")
# in newer pip versions --install-option does not exist
depends_on("py-pip@:23.0", type="build")
depends_on("git", type="build")
depends_on("cmake@3.22.2", type=("build", "link", "run"), when="@3.22.2")
depends_on("cmake@3.21.4", type=("build", "link", "run"), when="@3.21.4")
depends_on("cmake@3.18.0", type=("build", "link", "run"), when="@3.18.0")
for v in pycmake_versions.keys():
depends_on(f"cmake@{v}", type=("build", "link", "run"), when=f"@{v}")
# see:
# https://github.com/scikit-build/cmake-python-distributions/issues/227
# https://github.com/spack/spack/pull/28760#issuecomment-1029362288
for v in ["3.22.2", "3.21.4", "3.18.0"]:
for v in pycmake_versions.keys():
resource(
name="cmake-src",
git="https://gitlab.kitware.com/cmake/cmake.git",

5
var/spack/repos/builtin/packages/py-gsd/package.py
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@ -22,11 +22,16 @@ class PyGsd(PythonPackage):
license("BSD-2-Clause")
version("3.2.0", sha256="cf3c8419ec66085b2b9853577058861d9e738bfe397b0170ead821b866ab49b9")
version("3.1.1", sha256="6802b79d7f078536faf5a96ac300518613dd285cf3bc21ed81e1f2d0f7155bf5")
version("3.1.0", sha256="35a70419c6a519825afd9d5e47a570d98cec7273c39f43e2ab0aa3e7166ad198")
version("3.0.1", sha256="7b3ce7428d9f9f708618b3a2ef19ab122cc36b658ea53b70d0de40189d19647c")
version("2.8.0", sha256="f2b031a26a7a5bee5f3940dc2f36c5a5b6670307b297c526adf2e26c1f5b46ae")
version("1.9.3", sha256="c6b37344e69020f69fda2b8d97f894cb41fd720840abeda682edd680d1cff838")
depends_on("py-setuptools", type="build")
depends_on("py-setuptools@42:", type="build", when="@2.8.0:")
depends_on("py-setuptools@64:", type="build", when="@3.0.1:")
depends_on("py-cython", type="build")
depends_on("py-numpy@1.9.3:", type=("build", "run"))
depends_on("py-numpy@1.9.3:1", when="@:1", type=("build", "run"))

21
var/spack/repos/builtin/packages/py-mdanalysis/package.py
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@ -20,6 +20,7 @@ class PyMdanalysis(PythonPackage):
license("CC-BY-ND-3.0")
version("2.7.0", sha256="572e82945e5d058e3749ec5f18e6b3831ef7f2119cb54672567ae9a977201e93")
version("2.6.1", sha256="9cc69b94bddd026f26ffcaf5bdbed6d568c1c10e19a341d84f8d37a2a70222f2")
version("2.6.0", sha256="210b198a115165004c36fbbbe5eb83a13323f52b10ccaef30dd40bfe25ba3e61")
version("2.5.0", sha256="06ce4efab6ca1dbd2ee2959fc668049e1d574a8fe94ab948a4608244da1d016b")
@ -45,38 +46,40 @@ class PyMdanalysis(PythonPackage):
depends_on("py-numpy@1.21.0:", when="@2.5.0:", type=("build", "run"))
depends_on("py-numpy@1.20.0:", type=("build", "run"))
depends_on("py-biopython@1.80:", type=("build", "run"))
depends_on("py-networkx@2.0:", type=("build", "run"))
depends_on("py-griddataformats@0.4.0:", type=("build", "run"))
depends_on("py-mmtf-python@1.0.0:", type=("build", "run"))
depends_on("py-joblib@0.12:", type=("build", "run"))
depends_on("py-scipy@1.5.0:", type=("build", "run"))
depends_on("py-matplotlib@1.5.1:", type=("build", "run"))
depends_on("py-tqdm@4.43.0:", type=("build", "run"))
depends_on("py-threadpoolctl", type=("build", "run"))
depends_on("py-packaging", type=("build", "run"))
depends_on("py-fasteners", type=("build", "run"))
depends_on("py-gsd@1.9.3:", when="@:2.5.0", type=("build", "run"))
depends_on("py-mda-xdrlib", when="@2.7.0:", type=("build", "run"))
# extra_format (extras_require)
depends_on("py-netcdf4@1.0:", when="+extra_formats", type=("build", "run"))
depends_on("py-h5py@2.10:", when="+extra_formats", type=("build", "run"))
depends_on("py-pytng@0.2.3:", when="+extra_formats", type=("build", "run"))
depends_on("py-chemfiles@0.10:", when="+extra_formats", type=("build", "run"))
depends_on("py-parmed", when="+extra_formats @2.6.0:", type=("build", "run"))
depends_on("py-pyedr@0.7.0:", when="+extra_formats", type=("build", "run"))
# py-gsd is now an optional dependency and requires >3.0.0
# gsd>=2.9.0 requires setuptools>=64 and can't be concretised with py-numpy
# depends_on("py-gsd@3.0.1:", when="+extra_formats @2.6.0:", type=("build", "run"))
depends_on("py-pytng@0.2.3:", when="+extra_formats", type=("build", "run"))
depends_on("py-gsd@3.0.1:", when="+extra_formats @2.6.0:", type=("build", "run"))
depends_on(
"rdkit@2020.03.1: +python ~coordgen ~maeparser ~yaehmop ~descriptors3d",
when="+extra_formats @2.6.0:",
type=("build", "run"),
)
depends_on("py-parmed", when="+extra_formats @2.6.0:", type=("build", "run"))
# analysis (extras_require)
depends_on("py-biopython@1.80:", when="@2.7.0: +analysis", type=("build", "run"))
depends_on("py-seaborn", when="+analysis", type=("build", "run"))
depends_on("py-scikit-learn", when="+analysis", type=("build", "run"))
depends_on("py-tidynamics@1:", when="+analysis", type=("build", "run"))
depends_on("py-networkx@2.0:", when="@2.7.0 +analysis", type=("build", "run"))
# historical dependencies
depends_on("py-gsd@1.9.3:", when="@:2.5.0", type=("build", "run"))
depends_on("py-biopython@1.80:", when="@:2.6.1", type=("build", "run"))
depends_on("py-networkx@2.0:", when="@:2.6.1", type=("build", "run"))

2
var/spack/repos/builtin/packages/py-mdanalysistests/package.py
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@ -16,6 +16,7 @@ class PyMdanalysistests(PythonPackage):
license("GPL-3.0-or-later")
version("2.7.0", sha256="326d65d7f14da8d1b047aab87ca312a68459a5fd18ddf6d8cb9ac9c3ca51d9e5")
version("2.6.1", sha256="043f7451f4d9c42ea9e6609a81a6002948e2c74fd268282e0831416789b22e5e")
version("2.6.0", sha256="16fdd10e5240b606e8f9210b7cbd9e4be110e6b8d79bb6e72ce6250c4731a817")
version("2.5.0", sha256="a15b53b7f8bed67900a2bf542bbb3cab81dc71674fa6cddb3248dd11880e4c9d")
@ -23,6 +24,7 @@ class PyMdanalysistests(PythonPackage):
version("2.4.2", sha256="6e8fb210a4268691c77717ea5157e82d85874a4f7ee0f8f177718451a44ee793")
# Version need to match MDAnalysis'
depends_on("py-mdanalysis@2.7.0", when="@2.7.0", type=("build", "run"))
depends_on("py-mdanalysis@2.6.1", when="@2.6.1", type=("build", "run"))
depends_on("py-mdanalysis@2.6.0", when="@2.6.0", type=("build", "run"))
depends_on("py-mdanalysis@2.5.0", when="@2.5.0", type=("build", "run"))