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>

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")