py-diameter-synthesis, py-morph-tool, py-neurots, py-region-grower: U…

…pdate synthesis suite (#2102)

* py-diameter-synthesis, py-morph-tool, py-neurots, py-region-grower: Update synthesis suite

* Fix constraints

* Fix constraints

* py-neurots: fix dependencies

* Add Python constraint

* fx

* py-tmd: fix pypi url

* fx

* fx

* Make NeuroTS and diameter-synthesis available as modules

* Make only NeuroTS available as modules since diameter-synthesis is included

* fx

* Simpligy py-region-grower

* Use region-grower 1.1.1 and relax Pandas

* Remove NeuroTS from modules as it is included in region-grower

---------

Co-authored-by: Matthias Wolf <matthias.wolf@epfl.ch>
Co-authored-by: Eleftherios Zisis <eleftherios.zisis@epfl.ch>

bluebrain/repo-bluebrain/packages/py-diameter-synthesis/package.py

@@ -13,6 +13,7 @@ class PyDiameterSynthesis(PythonPackage):
     git = "https://github.com/BlueBrain/diameter-synthesis.git"
 
     version("develop", branch="main")
+    version("0.5.4", tag="0.5.4")
     version("0.5.3", tag="0.5.3")
     version("0.4.1", tag="0.4.1")  # Compatible with NeuroTS >= 3.1
     version("0.3.3", tag="0.3.3")
@@ -22,10 +23,15 @@ class PyDiameterSynthesis(PythonPackage):
     depends_on("py-setuptools-scm", type="build")
 
     depends_on("py-click@7.0:", type=("build", "run"))
-    depends_on("py-numpy@1.15.0:", type=("build", "run"))
-    depends_on("py-scipy@0.13.3:", type=("build", "run"))
-    depends_on("py-matplotlib@2.2:", type=("build", "run"))
-    depends_on("py-pandas@0.24:", type=("build", "run"))
+    depends_on("py-numpy@1.22.0:", type=("build", "run"), when="@0.5:")
+    depends_on("py-numpy@1.15.0:", type=("build", "run"), when="@:0.4")
+    depends_on("py-scipy@1.6:", type=("build", "run"), when="@0.5:")
+    depends_on("py-scipy@0.13.3:", type=("build", "run"), when="@:0.4")
+    depends_on("py-matplotlib@3.4:", type=("build", "run"), when="@0.5:")
+    depends_on("py-matplotlib@2.2:", type=("build", "run"), when="@:0.4")
+    depends_on("py-pandas@1.0.5:", type=("build", "run"), when="@0.5:")
+    depends_on("py-pandas@0.24:", type=("build", "run"), when="@:0.4")
     depends_on("py-neurom@3.0:3", type=("build", "run"))
-    depends_on("py-morphio@2.3.4:", type=("build", "run"))
+    depends_on("py-morphio@3.3.4:", type=("build", "run"), when="@0.5:")
+    depends_on("py-morphio@2.3.4:", type=("build", "run"), when="@:0.4")
     depends_on("py-jsonschema@3:", type=("build", "run"))

bluebrain/repo-bluebrain/packages/py-morph-tool/package.py

@@ -11,9 +11,10 @@ class PyMorphTool(PythonPackage):
 
     homepage = "https://github.com/BlueBrain/morph-tool"
     git = "https://github.com/BlueBrain/morph-tool.git"
-    pypi = "morph-tool/morph-tool-2.4.1.tar.gz"
+    pypi = "morph-tool/morph-tool-2.9.1.tar.gz"
 
     version("develop", branch="master")
+    version("2.9.1", sha256="305e9456c8047726588b23dfa070eb95ccbe5573e9fea3e0a83dc93eacdf61dc")
     version("2.9.0", sha256="c60d4010e17ddcc3f53c864c374fffee05713c8f8fd2ba4eed7706041ce1fa47")
 
     variant("neuron", default=False, description="Enable additional neuron support")
@@ -33,4 +34,5 @@ class PyMorphTool(PythonPackage):
     depends_on("py-bluepyopt@1.9.37:", type=("build", "run"), when="+neuron")
 
     depends_on("py-neurom@3.0:3.999,develop", type=("build", "run"))
-    depends_on("py-morphio@3.0:3.999,develop", type=("build", "run"))
+    depends_on("py-morphio@3.3.6:3,develop", type=("build", "run"), when="@2.9.1:")
+    depends_on("py-morphio@3.0:3,develop", type=("build", "run"), when="@2.9.0")

bluebrain/repo-bluebrain/packages/py-neurots/package.py

@@ -13,6 +13,7 @@ class PyNeurots(PythonPackage):
     git = "https://github.com/BlueBrain/NeuroTS.git"
 
     version("develop", branch="main")
+    version("3.4.0", tag="3.4.0")
     version("3.3.1", tag="3.3.1")
     version("3.1.0", tag="3.1.0")  # Breaking change to use diameter-synthesis >= 0.4
     version("3.0.0", tag="3.0.0")  # First version of NeuroTS
@@ -21,13 +22,14 @@ class PyNeurots(PythonPackage):
     depends_on("py-setuptools", type="build")
     depends_on("py-setuptools-scm", type="build")
 
-    depends_on("py-diameter-synthesis@0.5.3:", type=("build", "run"), when="@3.3.1:")
+    depends_on("py-diameter-synthesis@0.5.4:", type=("build", "run"), when="@3.4:")
+    depends_on("py-diameter-synthesis@0.5.2:", type=("build", "run"), when="@3.3")
     depends_on("py-matplotlib@1.3.1:", type=("build", "run"))
     depends_on("py-tmd@2.2.0:", type=("build", "run"))
-    depends_on("py-morphio@3.0:3.999", type=("build", "run"))
-    depends_on("py-neurom@3:3.999", type=("build", "run"))
-    depends_on("py-scipy@1.6:", type=("build", "run"), when="@3.0.0:")
-    depends_on("py-scipy@0.13.3:", type=("build", "run"), when="@:2.999")
-    depends_on("py-numpy@1.15:1.21", type=("build", "run"), when="@:2.5.0")
-    depends_on("py-numpy@1.22:", type=("build", "run"), when="@3.0.0:")
+    depends_on("py-morphio@3", type=("build", "run"))
+    depends_on("py-neurom@3", type=("build", "run"))
+    depends_on("py-scipy@0.13.3:", type=("build", "run"), when="@:2")
+    depends_on("py-scipy@1.6:", type=("build", "run"), when="@3:")
+    depends_on("py-numpy@1.15:1.21", type=("build", "run"), when="@2.5.0")
+    depends_on("py-numpy@1.22:", type=("build", "run"), when="@3:")
     depends_on("py-jsonschema@3.0.1:", type=("build", "run"))

bluebrain/repo-bluebrain/packages/py-region-grower/package.py

@@ -13,30 +13,23 @@ class PyRegionGrower(PythonPackage):
     git = "ssh://git@bbpgitlab.epfl.ch/neuromath/region-grower.git"
 
     version("develop", branch="main")
-    version("0.4.3", tag="region-grower-v0.4.3")
-    version("0.3.1", tag="region-grower-v0.3.1")
+    version("1.1.1", tag="region-grower-v1.1.1")
 
     depends_on("py-setuptools", type="build")
 
+    depends_on("python@3.9:", type=("build", "run"))
+
     depends_on("py-attrs@19.3.0:", type=("build", "run"))
-    depends_on("py-click@7.0:", type=("build", "run"))
-    depends_on(
-        "py-dask+dataframe+distributed@2.15.0:2021.8.0,2021.9.0:",
-        type=("build", "run"),
-        when="@0.3.1",
-    )
-    depends_on("py-dask+dataframe+distributed@2021.9:", type=("build", "run"), when="@0.4.3:")
-    depends_on("py-diameter-synthesis@0.4.1:0.999", type=("build", "run"), when="@0.3.1")
-    depends_on("py-diameter-synthesis@0.5.3:", type=("build", "run"), when="@0.4.3:")
-    depends_on("py-morphio@3.0:3", type=("build", "run"), when="@0.3.1")
-    depends_on("py-morphio@3.3.3:3", type=("build", "run"), when="@0.4.3:")
+    depends_on("py-click@8.0:", type=("build", "run"))
+    depends_on("py-dask+dataframe+distributed@2023.3.2:", type=("build", "run"))
+    depends_on("py-diameter-synthesis@0.5.4:", type=("build", "run"))
+    depends_on("py-morphio@3.3.4:3", type=("build", "run"))
     depends_on("py-morph-tool@2.9.0:2 +neuron", type=("build", "run"))
     depends_on("py-neuroc@0.2.8:", type=("build", "run"))
     depends_on("py-neurom@3.0:3", type=("build", "run"))
-    depends_on("py-neurots@3.1:3", type=("build", "run"), when="@0.3.1")
-    depends_on("py-neurots@3.3.1:3", type=("build", "run"), when="@0.4.3:")
+    depends_on("py-neurots@3.4.0:3", type=("build", "run"))
+    depends_on("py-pandas@1.5.3:", type=("build", "run"))
     depends_on("py-tqdm@4.28.1:", type=("build", "run"))
-    depends_on("py-voxcell@2.7:3", type=("build", "run"), when="@0.3.1")
-    depends_on("py-voxcell@3.1.1:3", type=("build", "run"), when="@0.4.3:")
-    depends_on("py-dask-mpi@2.0.0:", type=("build", "run"))
-    depends_on("py-mpi4py@3.0.3:", type=("build", "run"))
+    depends_on("py-voxcell@3.1.1:3", type=("build", "run"))
+    depends_on("py-dask-mpi@2022.4:", type=("build", "run"))
+    depends_on("py-mpi4py@3.1.1:", type=("build", "run"))

bluebrain/repo-bluebrain/packages/py-tmd/package.py

@@ -10,8 +10,9 @@ class PyTmd(PythonPackage):
     """Python library for the topological analysis of neurons"""
 
     homepage = "https://github.com/BlueBrain/TMD"
-    pypi = "tmd/tmd-2.0.9.tar.gz"
+    pypi = "TMD/TMD-2.3.1.tar.gz"
 
+    version("2.3.1", sha256="b8c4d5398ae269ba489e659b5ba33971b26f1df2e295429360d040b541cd58a8")
     version("2.2.0", sha256="a5e7753fbd7f2b0ef8a5271030cf172bdefba9d215f5147cf90318641d803bdb")
     version("2.0.11", sha256="ba19167d19eb2132af766b760a6f09f423abbdcf871c23c2bfdf8c9064ba888e")
     version("2.0.9", sha256="9bfb4b014e2c735c9db5f3ee61e4ccdbac29248f608ba49a43d862e4835b88a5")

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

@@ -48,7 +48,7 @@ class PyDistributed(PythonPackage):
     depends_on("py-click@8.0:", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-cloudpickle@1.5.0:", type=("build", "run"))
     depends_on("py-jinja2", type=("build", "run"), when="@2022.2.1:")
-    depends_on("py-jinja2@2.10.3", type=("build", "run"), when="@2023.4.1:")
+    depends_on("py-jinja2@2.10.3:", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-locket@1:", type=("build", "run"), when="@2022.2.1:")
     depends_on("py-msgpack@0.6.0:", type=("build", "run"))
     depends_on("py-msgpack@1.0.0:", type=("build", "run"), when="@2023.4.1:")

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

@@ -17,6 +17,7 @@ class PyPandas(PythonPackage):
 
     maintainers = ["adamjstewart"]
 
+    version("1.5.3", sha256="74a3fd7e5a7ec052f183273dc7b0acd3a863edf7520f5d3a1765c04ffdb3b0b1")
     version("1.5.1", sha256="249cec5f2a5b22096440bd85c33106b6102e0672204abd2d5c014106459804ee")
     version("1.5.0", sha256="3ee61b881d2f64dd90c356eb4a4a4de75376586cd3c9341c6c0fcaae18d52977")
     version("1.4.4", sha256="ab6c0d738617b675183e5f28db32b5148b694ad9bba0a40c3ea26d96b431db67")