MDAnalysis 2.4.3 (#36541)

* mda 2.4.3

* black

* mda update and reshuffle

* add tidynamics

3 files changed, 62 insertions, 23 deletions

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"))