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authorRocco Meli <r.meli@bluemail.ch>2023-03-13 21:01:24 +0100
committerGitHub <noreply@github.com>2023-03-13 15:01:24 -0500
commit03636cd6ac2859e800a23191b18de163de223a43 (patch)
treef15fa136980ff0bce69e8225545a1c4564f81935 /var
parentee1ea1f43046a54d9c1b06901f9de4aa1b6c3ee8 (diff)
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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 <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-mdanalysis/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-mdanalysis/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-mdanalysis/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-mdanalysis/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/py-mdanalysis/package.py114
-rw-r--r--var/spack/repos/builtin/packages/py-mdanalysistests/package.py27
2 files changed, 117 insertions, 24 deletions
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")