From 03636cd6ac2859e800a23191b18de163de223a43 Mon Sep 17 00:00:00 2001 From: Rocco Meli Date: Mon, 13 Mar 2023 21:01:24 +0100 Subject: Update MDAnalysis and addition of MDAnalysisTests (#36052) * update mda dependencies * apply black * mdanalysis draft * update * small fixes * Update var/spack/repos/builtin/packages/py-mdanalysis/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-mdanalysis/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-mdanalysis/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-mdanalysis/package.py Co-authored-by: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-mdanalysis/package.py Co-authored-by: Adam J. Stewart --------- Co-authored-by: Adam J. Stewart --- .../builtin/packages/py-mdanalysis/package.py | 114 ++++++++++++++++----- .../builtin/packages/py-mdanalysistests/package.py | 27 +++++ 2 files changed, 117 insertions(+), 24 deletions(-) create mode 100644 var/spack/repos/builtin/packages/py-mdanalysistests/package.py diff --git a/var/spack/repos/builtin/packages/py-mdanalysis/package.py b/var/spack/repos/builtin/packages/py-mdanalysis/package.py index 9aff0e76cd..50f4713a12 100644 --- a/var/spack/repos/builtin/packages/py-mdanalysis/package.py +++ b/var/spack/repos/builtin/packages/py-mdanalysis/package.py @@ -14,38 +14,92 @@ class PyMdanalysis(PythonPackage): topology formats.)""" homepage = "https://www.mdanalysis.org" - pypi = "MDAnalysis/MDAnalysis-0.19.2.tar.gz" - - version("1.0.0", sha256="f45a024aca45e390ff1c45ca90beb2180b78881be377e2a1aa9cd6c109bcfa81") - version("0.20.1", sha256="d04b71b193b9716d2597ffb9938b93f43487fa535da1bb5c1f2baccf356d7df9") - version("0.19.2", sha256="c5395bbafa5efca2e1aee4715d26129844140c47cb8301da0293106cb969de7d") - version("0.19.1", sha256="ff1d694f8598c0833ec340de6a6adb3b5e62b92d0fa94ee6401718ba972db3cc") - version("0.19.0", sha256="248e3b37fc6150e31c609cc18a3927c32aee37b76d29cbfedf635e7e1aa982cf") - version("0.18.0", sha256="a08acea1755112411e7db55e3f282e164b47a59e15794b38744cce6c596f252a") - version("0.17.0", sha256="9bd61760334698cc7b8a57ad26456451e926e9c9e66722594ad8816561348cde") - version("0.16.2", sha256="407d9a9ff1ab8a5e47973714d06fabff220f8d08a28792dee93e88e70e995b0a") - version("0.16.1", sha256="3dc8f5d639ab3a0d152cbd7259ae9372ec8a9bac0f8cb7d3b80ce5adc1e3ee57") - version("0.16.0", sha256="c4824fa1fddd336daa39371436187ebb023366885fb250c2827ed7fce2546bd4") - version("0.15.0", sha256="9088786048b47339cba1f8a586977bbb3bb04ae1bcd0462b59e45bda37e25533") + pypi = "MDAnalysis/MDAnalysis-2.4.2.tar.gz" + + maintainers("RMeli") + + version("2.4.2", sha256="ae2ee5627391e73f74eaa3c547af3ec6ab8b040d27dedffe3a7ece8e0cd27636") + version( + "1.0.0", + sha256="f45a024aca45e390ff1c45ca90beb2180b78881be377e2a1aa9cd6c109bcfa81", + deprecated=True, + ) + version( + "0.20.1", + sha256="d04b71b193b9716d2597ffb9938b93f43487fa535da1bb5c1f2baccf356d7df9", + deprecated=True, + ) + version( + "0.19.2", + sha256="c5395bbafa5efca2e1aee4715d26129844140c47cb8301da0293106cb969de7d", + deprecated=True, + ) + version( + "0.19.1", + sha256="ff1d694f8598c0833ec340de6a6adb3b5e62b92d0fa94ee6401718ba972db3cc", + deprecated=True, + ) + version( + "0.19.0", + sha256="248e3b37fc6150e31c609cc18a3927c32aee37b76d29cbfedf635e7e1aa982cf", + deprecated=True, + ) + version( + "0.18.0", + sha256="a08acea1755112411e7db55e3f282e164b47a59e15794b38744cce6c596f252a", + deprecated=True, + ) + version( + "0.17.0", + sha256="9bd61760334698cc7b8a57ad26456451e926e9c9e66722594ad8816561348cde", + deprecated=True, + ) + version( + "0.16.2", + sha256="407d9a9ff1ab8a5e47973714d06fabff220f8d08a28792dee93e88e70e995b0a", + deprecated=True, + ) + version( + "0.16.1", + sha256="3dc8f5d639ab3a0d152cbd7259ae9372ec8a9bac0f8cb7d3b80ce5adc1e3ee57", + deprecated=True, + ) + version( + "0.16.0", + sha256="c4824fa1fddd336daa39371436187ebb023366885fb250c2827ed7fce2546bd4", + deprecated=True, + ) + version( + "0.15.0", + sha256="9088786048b47339cba1f8a586977bbb3bb04ae1bcd0462b59e45bda37e25533", + deprecated=True, + ) variant( "analysis", default=True, description="Enable analysis packages: matplotlib, scipy, seaborn", ) - variant("amber", default=False, description="Support AMBER netcdf format.") + variant("amber", default=False, when="@:1.0.0", description="Support AMBER netcdf format.") + variant("extra_formats", default=False, when="@2.4.0:", description="Support extra formats") - depends_on("python@2.7:", type=("build", "run")) + depends_on("python@2.7:", type=("build", "run"), when="@:1.0.0") + depends_on("python@3.8:", type=("build", "run"), when="@2.4.0:") depends_on("py-setuptools", type="build") - depends_on("py-cython@0.16:", type="build") + depends_on("py-cython@0.16:", type="build", when="@:1.0.0") + depends_on("py-cython@0.28:", type="build", when="@2.4.0:") + + depends_on("py-threadpoolctl", when="@2.4.0:") - depends_on("py-six@1.4.0:", type=("build", "run")) - depends_on("py-networkx@1.0:", type=("build", "run")) + depends_on("py-six@1.4.0:", type=("build", "run"), when="@:1.0.0") + depends_on("py-networkx@1.0:", type=("build", "run"), when="@:1.0.0") + depends_on("py-networkx@2.0:", type=("build", "run"), when="@2.4.0:") - depends_on("py-gsd@1.4.0:", when="@0.17.0:", type=("build", "run")) + depends_on("py-gsd@1.4.0:", when="@0.17.0:1.0.0", type=("build", "run")) + depends_on("py-gsd@1.9.3:", when="@2.4.0:", type=("build", "run")) depends_on("py-mmtf-python@1.0.0:", when="@0.16.0:", type=("build", "run")) - depends_on("py-mock", when="@0.18.0:", type=("build", "run")) + depends_on("py-mock", when="@0.18.0:1.0.0", type=("build", "run")) depends_on("py-tqdm@4.43.0:", when="@1.0.0:", type=("build", "run")) depends_on("py-joblib", when="@0.16.0:0.20.1", type=("build", "run")) @@ -53,13 +107,15 @@ class PyMdanalysis(PythonPackage): depends_on("py-numpy@1.5.0:", when="@:0.15.0", type=("build", "run")) depends_on("py-numpy@1.10.4:", when="@0.16.0:0.19.2", type=("build", "run")) - depends_on("py-numpy@1.13.3:", when="@0.20.1:", type=("build", "run")) + depends_on("py-numpy@1.13.3:", when="@0.20.1:1.0.0", type=("build", "run")) + depends_on("py-numpy@1.20.0:", when="@2.4.0:", type=("build", "run")) depends_on("py-biopython@1.59:", when="@:0.17.0", type=("build", "run")) - depends_on("py-biopython@1.71:", when="@0.18.0:", type=("build", "run")) + depends_on("py-biopython@1.71:", when="@0.18.0:1.0.0", type=("build", "run")) + depends_on("py-biopython@1.80:", when="@2.4.0:", type=("build", "run")) depends_on("py-griddataformats@0.3.2:", when="@:0.16.2", type=("build", "run")) - depends_on("py-griddataformats@0.4:", when="@0.17.0:", type=("build", "run")) + depends_on("py-griddataformats@0.4.0:", when="@0.17.0:", type=("build", "run")) depends_on("py-matplotlib", when="@:0.15.0+analysis", type=("build", "run")) depends_on("py-matplotlib@1.5.1:", when="@0.16.0:0.16.1+analysis", type=("build", "run")) @@ -67,10 +123,20 @@ class PyMdanalysis(PythonPackage): depends_on("py-scipy", when="@:0.16.1+analysis", type=("build", "run")) depends_on("py-scipy", when="@0.16.2:0.17.0", type=("build", "run")) - depends_on("py-scipy@1.0.0:", when="@0.18.0:", type=("build", "run")) + depends_on("py-scipy@1.0.0:", when="@0.18.0:1.0.0", type=("build", "run")) + depends_on("py-scipy@1.5.0:", when="@2.4.0:", type=("build", "run")) depends_on("py-scikit-learn", when="@0.16.0:+analysis", type=("build", "run")) depends_on("py-seaborn", when="+analysis", type=("build", "run")) depends_on("py-netcdf4@1.0:", when="+amber", type=("build", "run")) depends_on("hdf5", when="+amber", type=("run")) + 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="@2.4.0:+extra_formats", type=("build", "run")) + depends_on("py-chemfiles@0.10:", when="@2.4.0:+extra_formats", type=("build", "run")) + depends_on("py-pyedr@0.7.0:", when="@2.4.0:+extra_formats", type=("build", "run")) + + depends_on("py-fasteners", when="@2.4.2:", type=("build", "run")) + depends_on("py-packaging", when="@2.4.2:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-mdanalysistests/package.py b/var/spack/repos/builtin/packages/py-mdanalysistests/package.py new file mode 100644 index 0000000000..870d9b4e20 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-mdanalysistests/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2023 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 PyMdanalysistests(PythonPackage): + """Test suite for MDAnalysis""" + + homepage = "https://www.mdanalysis.org" + pypi = "MDAnalysisTests/MDAnalysisTests-2.4.2.tar.gz" + + maintainers("RMeli") + + version("2.4.2", sha256="6e8fb210a4268691c77717ea5157e82d85874a4f7ee0f8f177718451a44ee793") + + # Version need to match MDAnalysis' + depends_on("py-mdanalysis@2.4.2", when="@2.4.2", type=("build", "run")) + + depends_on("python@3.8:", type=("build", "run")) + + depends_on("py-pytest@3.3.0:", type=("build", "run")) + depends_on("py-hypothesis", type=("build", "run")) + + depends_on("py-setuptools", type="build") -- cgit v1.2.3-60-g2f50