From 210b2e8caa346719b1a73727c8bf49405f098bfe Mon Sep 17 00:00:00 2001 From: Rocco Meli Date: Fri, 31 Mar 2023 20:47:56 +0200 Subject: [PATCH] MDAnalysis 2.4.3 (#36541) * mda 2.4.3 * black * mda update and reshuffle * add tidynamics --- .../builtin/packages/py-mdanalysis/package.py | 62 ++++++++++++------- .../packages/py-mdanalysistests/package.py | 2 + .../builtin/packages/py-tidynamics/package.py | 21 +++++++ 3 files changed, 62 insertions(+), 23 deletions(-) create mode 100644 var/spack/repos/builtin/packages/py-tidynamics/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 50f4713a12..98fa00f711 100644 --- a/var/spack/repos/builtin/packages/py-mdanalysis/package.py +++ b/var/spack/repos/builtin/packages/py-mdanalysis/package.py @@ -18,6 +18,7 @@ class PyMdanalysis(PythonPackage): maintainers("RMeli") + version("2.4.3", sha256="c4fbdc414e4fdda69052fff2a6e412180fe6fa90a42c24793beee04123648c92") version("2.4.2", sha256="ae2ee5627391e73f74eaa3c547af3ec6ab8b040d27dedffe3a7ece8e0cd27636") version( "1.0.0", @@ -87,24 +88,11 @@ class PyMdanalysis(PythonPackage): 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", 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"), 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="@0.17.0:1.0.0", 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="@0.18.0:1.0.0", 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")) - depends_on("py-joblib@0.12:", when="@1.0.0:", type=("build", "run")) - + # MDAnalysis required dependencies (install_requires) 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="@0.20.1:1.0.0", type=("build", "run")) @@ -114,29 +102,57 @@ class PyMdanalysis(PythonPackage): 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-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-griddataformats@0.3.2:", when="@:0.16.2", 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")) - depends_on("py-matplotlib@1.5.1:", when="@0.16.2:", type=("build", "run")) + depends_on("py-mmtf-python@1.0.0:", when="@0.16.0:", type=("build", "run")) + + depends_on("py-joblib", when="@0.16.0:0.20.1", type=("build", "run")) + depends_on("py-joblib@0.12:", when="@1.0.0:", type=("build", "run")) 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="@0.18.0:1.0.0", 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-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")) + depends_on("py-matplotlib@1.5.1:", when="@0.16.2:", type=("build", "run")) + depends_on("py-tqdm@4.43.0:", when="@1.0.0:", type=("build", "run")) + + depends_on("py-threadpoolctl", type=("build", "run"), when="@2.4.0:") # Requirement from + + depends_on("py-packaging", when="@2.4.2:", type=("build", "run")) + + depends_on("py-fasteners", when="@2.4.2:", 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")) + + # extra_format (extras_require) 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("hdf5", when="+amber", type=("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")) + # analysis (extras_require) + depends_on("py-seaborn", when="+analysis", type=("build", "run")) + + depends_on("py-scikit-learn", when="@0.16.0:+analysis", type=("build", "run")) + + depends_on("py-tidynamics@1:", when="@2.4.0:+analysis", type=("build", "run")) + + # Deprecated after @1 + depends_on("py-mock", when="@0.18.0:1.0.0", type=("build", "run")) + depends_on("py-six@1.4.0:", type=("build", "run"), when="@:1.0.0") diff --git a/var/spack/repos/builtin/packages/py-mdanalysistests/package.py b/var/spack/repos/builtin/packages/py-mdanalysistests/package.py index 870d9b4e20..9494d0c30f 100644 --- a/var/spack/repos/builtin/packages/py-mdanalysistests/package.py +++ b/var/spack/repos/builtin/packages/py-mdanalysistests/package.py @@ -14,9 +14,11 @@ class PyMdanalysistests(PythonPackage): maintainers("RMeli") + version("2.4.3", sha256="6fbdeccdbfb249f76520ee3605d007cd70292187e3754d0184c71e5afe133abb") version("2.4.2", sha256="6e8fb210a4268691c77717ea5157e82d85874a4f7ee0f8f177718451a44ee793") # Version need to match MDAnalysis' + depends_on("py-mdanalysis@2.4.3", when="@2.4.3", type=("build", "run")) depends_on("py-mdanalysis@2.4.2", when="@2.4.2", type=("build", "run")) depends_on("python@3.8:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-tidynamics/package.py b/var/spack/repos/builtin/packages/py-tidynamics/package.py new file mode 100644 index 0000000000..5afbf5d70e --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tidynamics/package.py @@ -0,0 +1,21 @@ +# 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 PyTidynamics(PythonPackage): + """A tiny package to compute the dynamics of stochastic and molecular simulations.""" + + homepage = "https://lab.pdebuyl.be/tidynamics/" + pypi = "tidynamics/tidynamics-1.0.0.tar.gz" + + maintainers("RMeli") + + version("1.0.0", sha256="b7bd669d380b0f469f3a8aedfbc0e5fa967fe8dc44e196f54baf0edb59846976") + + depends_on("py-setuptools", type="build") + + depends_on("py-numpy", type=("build", "run"))