Update MDAnalysis (#39787)

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

* update mdanalysis

* 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>

var/spack/repos/builtin/packages/py-mdanalysis/package.py

@@ -18,6 +18,8 @@ class PyMdanalysis(PythonPackage):
 
     maintainers("RMeli")
 
+    version("2.6.1", sha256="9cc69b94bddd026f26ffcaf5bdbed6d568c1c10e19a341d84f8d37a2a70222f2")
+    version("2.6.0", sha256="210b198a115165004c36fbbbe5eb83a13323f52b10ccaef30dd40bfe25ba3e61")
     version("2.5.0", sha256="06ce4efab6ca1dbd2ee2959fc668049e1d574a8fe94ab948a4608244da1d016b")
     version("2.4.3", sha256="c4fbdc414e4fdda69052fff2a6e412180fe6fa90a42c24793beee04123648c92")
     version("2.4.2", sha256="ae2ee5627391e73f74eaa3c547af3ec6ab8b040d27dedffe3a7ece8e0cd27636")
@@ -37,6 +39,7 @@ class PyMdanalysis(PythonPackage):
     depends_on("py-cython@0.28:", type="build")
 
     # MDAnalysis required dependencies (install_requires)
+    depends_on("py-numpy@1.22.3:1", when="@2.6.0:", type=("build", "run"))
     depends_on("py-numpy@1.21.0:", when="@2.5.0:", type=("build", "run"))
     depends_on("py-numpy@1.20.0:", type=("build", "run"))
 
@@ -53,14 +56,23 @@ class PyMdanalysis(PythonPackage):
     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:", type=("build", "run"))
+    depends_on("py-gsd@1.9.3:", when="@:2.5.0", 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-pyedr@0.7.0:", when="+extra_formats", type=("build", "run"))
-    depends_on("py-pytng@0.2.3:", 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(
+        "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-seaborn", when="+analysis", type=("build", "run"))

var/spack/repos/builtin/packages/py-mdanalysistests/package.py

@@ -14,16 +14,20 @@ class PyMdanalysistests(PythonPackage):
 
     maintainers("RMeli")
 
+    version("2.6.1", sha256="043f7451f4d9c42ea9e6609a81a6002948e2c74fd268282e0831416789b22e5e")
+    version("2.6.0", sha256="16fdd10e5240b606e8f9210b7cbd9e4be110e6b8d79bb6e72ce6250c4731a817")
     version("2.5.0", sha256="a15b53b7f8bed67900a2bf542bbb3cab81dc71674fa6cddb3248dd11880e4c9d")
     version("2.4.3", sha256="6fbdeccdbfb249f76520ee3605d007cd70292187e3754d0184c71e5afe133abb")
     version("2.4.2", sha256="6e8fb210a4268691c77717ea5157e82d85874a4f7ee0f8f177718451a44ee793")
 
     # Version need to match MDAnalysis'
+    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"))
     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@3.9:", when="@2.5.0", type=("build", "run"))
+    depends_on("python@3.9:", when="@2.5.0:", type=("build", "run"))
     depends_on("python@3.8:", type=("build", "run"))
 
     depends_on("py-pytest@3.3.0:", type=("build", "run"))