feat: update bluebrain packages

packages/py-bluepyefe/package.py

@@ -12,9 +12,10 @@ class PyBluepyefe(PythonPackage):
     """Blue Brain Python E-feature extraction"""
 
     homepage = "https://github.com/BlueBrain/BluePyEfe"
-    pypi = "bluepyefe/bluepyefe-0.3.13.tar.gz"
+    pypi = "bluepyefe/bluepyefe-2.2.18.tar.gz"
     git = "https://github.com/BlueBrain/BluePyEfe.git"
 
+    version("2.3.6", sha256="e52117372c41bfa3796e7a340d04b9c4b14f9ebcaacb9d36e947f3d041eb7e35")
     version("2.2.18", sha256="bfb50c6482433ec2ffb4b65b072d2778bd89ae50d92dd6830969222aabb30275")
 
     depends_on("py-setuptools", type="build")
@@ -25,8 +26,7 @@ class PyBluepyefe(PythonPackage):
     depends_on("py-efel", type=("build", "run"))
     depends_on("py-scipy", type=("build", "run"))
     depends_on("py-h5py", type=("build", "run"))
-    depends_on("py-igor", type=("build", "run"))
+    depends_on("py-igor2", type=("build", "run"), when="@2.3.6:")
 
-    def setup_run_environment(self, env):
-        env.set("NEURON_INIT_MPI", "0")
-        env.unset("PMI_RANK")
+    depends_on("py-numpy@:1.23", type=("build", "run"), when="@2.2.18")
+    depends_on("py-igor", type=("build", "run"), when="@2.2.18")
\ No newline at end of file

packages/py-bluepymm/package.py

@@ -14,15 +14,12 @@ class PyBluepymm(PythonPackage):
     homepage = "https://github.com/BlueBrain/BluePyMM"
     pypi = "bluepymm/bluepymm-0.7.49.tar.gz"
 
+    version("0.8.7", sha256="f0e5d4e113b19f71398d0796d5182f322c48c2ab07793ce8d0e4771a251914ab")
     version("0.7.65", sha256="024b009decd8d967b3b885421196d53670e3c0a6b75aaaa55559f148b0b0d7d4")
 
     depends_on("py-setuptools", type="build")
     depends_on("py-bluepyopt", type="run")
     depends_on("py-matplotlib", type="run")
-    # The below dependency should disappear once
-    # the matplotlib package is fixed
-    # not needed with EBRAINS python version:
-    # depends_on("py-backports-functools-lru-cache", type="run", when="^python@:3.3.99")
     depends_on("py-pandas", type="run")
     depends_on("py-numpy", type="run")
     depends_on("py-ipyparallel", type="run")

packages/py-bluepyopt/package.py

@@ -15,35 +15,26 @@ class PyBluepyopt(PythonPackage):
     pypi = "bluepyopt/bluepyopt-1.9.27.tar.gz"
 
     # NOTE : while adding new release check pmi_rank.patch compatibility
-    version("1.13.86", sha256="37b4abcc4a53ed5af50fa0b3bc4d0003332b7f2f2b6e4d9f0b9de8638254e753")
-    version("1.10.38", sha256="fb1411c6a8fbfac52d36b837225bae882fd6524acfb4d0580189312ef3c1cfcc")
-    version("1.9.37", sha256="4399af71de48b288832e92f0de73c431bf88d6e76e2c4ea250c3b38fb38a45a8")
-    version("1.9.27", sha256="4cce15b92b32311c808cae5e005b664deb6e8dc5df4ca13ea7b59252ae346522")
-    version("1.8.68", sha256="b9d432840aab89d4863c935d3dc604816441eba02d731422b92056cee751ca9c")
-    version("1.6.56", sha256="1c57c91465ca4b947fe157692e7004a3e6df02e4151e3dc77a8831382a8f1ab9")
-    version("1.8.68", sha256="b9d432840aab89d4863c935d3dc604816441eba02d731422b92056cee751ca9c")
-    version("1.9.12", sha256="7b623ab9168f460a85d952719ca5249248fc95e6f7a02658b0673b2baa0a8fc6")
+    version("1.14.4", sha256="7567fd736053250ca06030f67ad93c607b100c2b98df8dc588c26b64cb3e171c")
 
     # patch required to avoid hpe-mpi linked mechanism library
-    patch("pmi_rank.patch", when="@1.9.27:")
+    patch("pmi_rank.patch")
 
-    variant("neuron", default=True, description="Use BluePyOpt together with NEURON")
+    variant("scoop", default=False, description="Use BluePyOpt together with py-scoop")
 
     depends_on("py-setuptools", type="build")
-    depends_on("py-numpy", type=("build", "run"))
-    depends_on("py-pandas", type=("build", "run"))
-    depends_on("py-deap", type=("build", "run"))
-    depends_on("py-deap@1.3.3:", type=("build","run"), when="@1.13.86:")
-    depends_on("py-efel", type=("build", "run"))
+    depends_on("py-numpy@1.6:", type=("build", "run"))
+    depends_on("py-pandas@0.18:", type=("build", "run"))
+    depends_on("py-deap@1.3.3:", type=("build", "run"))
+    depends_on("py-efel@2.13:", type=("build", "run"))
     depends_on("py-ipyparallel", type=("build", "run"))
-    depends_on("py-pickleshare", type=("build", "run"))
-    depends_on("py-jinja2", type=("build", "run"))
+    depends_on("py-pickleshare@0.7.3:", type=("build", "run"))
+    depends_on("py-jinja2@2.8:", type=("build", "run"))
     depends_on("py-future", type=("build", "run"))
-    depends_on("py-pebble@4.3.10:", type=("build", "run"))
-    depends_on("py-scoop@0.7:", type=("build", "run"), when="@:1.9.37")
-    depends_on("neuron", type=("build", "run"), when="+neuron")
+    depends_on("py-pebble@4.6:", type=("build", "run"))
+    depends_on("py-scoop@0.7:", type=("build", "run"), when="+scoop")
+    depends_on("neuron@7.4:", type=("build", "run"))
 
     def setup_run_environment(self, env):
         env.unset("PMI_RANK")
         env.set("NEURON_INIT_MPI", "0")
-        env.prepend_path("PATH", self.spec["py-ipyparallel"].prefix.bin)

packages/py-efel/package.py

@@ -21,8 +21,11 @@ class PyEfel(PythonPackage):
     homepage = "https://github.com/BlueBrain/eFEL"
     pypi = "efel/efel-3.0.80.tar.gz"
 
-    version("4.0.4", sha256="258c506776df609edc799338fd773e78f0f0315fd6f3e2f969478bda401a8894")
+    version("5.5.7", sha256="28fdd07ccb027c8a35823d3ff4c407b3704a7023754eec6110674825dc7b749d")
+    version("5.2.0", sha256="ed2c5efe22a4c703a4d9e47775b939009e1456713ac896898ebabf177c60b1dc")
 
     depends_on("py-setuptools", type="build")
-    depends_on("py-numpy", type="run")
-    depends_on("py-six", type="run")
+
+    depends_on("py-neo@0.5.2:", type=("build", "run"))
+    depends_on("py-typing-extensions@4.8:", type=("build", "run"))
+    depends_on("py-numpy@1.6:", type=("build", "run"))

packages/py-igor2/package.py

+# Copyright 2013-2024 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 *
+
+
+# begin EBRAINS: package is backported from Spack develop (b70cb60)
+class PyIgor2(PythonPackage):
+    """igor2: interface for reading binary IGOR files."""
+
+    # pypi only has no sdist
+    homepage = "https://github.com/AFM-analysis/igor2"
+    url = "https://pypi.io/packages/py3/i/igor2/igor2-0.5.3-py3-none-any.whl"
+
+    license("LGPL-3.0-or-later")
+
+    version(
+        "0.5.3",
+        sha256="bb7b54a5926ec640e0e9176f46e0dd88ad956fec2d17ba3b0a7687eba82cefee",
+        expand=False,
+    )
+
+    depends_on("python@3.8:3", type=("build", "run"))
+    depends_on("py-numpy@1.25.1:", type=("build", "run"))
+# end EBRAINS

packages/py-libsonata/package.py

@@ -15,27 +15,22 @@ class PyLibsonata(PythonPackage):
     git = "https://github.com/BlueBrain/libsonata.git"
     pypi = "libsonata/libsonata-0.1.14.tar.gz"
 
-    submodules = True
-
-    version("develop", branch="master", get_full_repo=True)
-    version("0.1.23", sha256="815aac5bdaa5d025b5f3558ac4d3acb9ebcb070594109af4c0844f47ec701c1d")
-    version("0.1.22", sha256="4adbb32ed2fac5d3c74bde03a5e2adb319724d324318a2a7dc2ef3c30f817b2c")
-    version("0.1.21", sha256="5b280d82cb21a745d9cdb736c00446e0209494c21d2d17a2c878fabf23a08b68")
-    version("0.1.20", sha256="f2e63a26dcf045bb7424e236e12f9b9ef8c46c356e953d26555f313f5763651e")
-    version("0.1.18", sha256="1b13728cbffbcb74cc864c7bc186e568945e25c260f732ffa872437c081fd9b4")
-    version("0.1.17", sha256="d122dd9fce82c8ce1621746ed9029e7db0d319fb94f6a737fb14f572f632f7b4")
-    version("0.1.16", sha256="49ced56992ba8be8aa6638525e8078b7e3ce0d5c05c34ee90746cab02bb5185a")
-    version("0.1.15", sha256="8c7c509db692b482cba5b0453579747db5a981ce5b3c13da96b14ae0332a6e81")
-    version("0.1.14", sha256="a5c75df1c3ef6fac10d92fb6781643e0834e5c35debe77693686dab8bfcf221f")
-    version("0.1.13", sha256="8263938e49b501c477f626b4c25e0c74e91152268830c69aabc96eeb263c6eea")
-    version("0.1.12", sha256="f0fa0f3b129d28e41b337ce2c39c3604990752de8e485327ec9df3bf0360e9c1")
-    version("0.1.11", sha256="95f302818971fec3f19ef18febd5c31c580490692138c8e4fe3534104d88b5e0")
-    version("0.1.10", sha256="7ef9f911f7ea31da5ff5306d8372ec194d223850aede0878ac2a921ce049bbb2")
-
-    depends_on("cmake@3.3:", type="build")
-    depends_on("hdf5")
-    depends_on("py-pybind11")
-
-    depends_on("py-numpy@1.17:", type=("build", "run"))
-    depends_on("py-setuptools", type="build", when="@0.1:")
-    depends_on("py-setuptools-scm", type="build", when="@0.1:")
+    maintainers("tristan0x")
+
+    version("master", branch="master")
+    version("0.1.25", sha256="b332efa718123ee265263e1583a5998eaa945a13b8a22903873764cf1d8173fa")
+
+    depends_on("catch2@2.13:", type="test")
+    depends_on("cmake@3.16:", type="build")
+    depends_on("fmt@7.1:")
+    depends_on("hdf5@1.14:")
+    depends_on("highfive@2.9:")
+    depends_on("nlohmann-json@3.9.1")
+    depends_on("py-pybind11@2.11.0:")
+
+    depends_on("py-numpy@1.17.3:", type=("build", "run"))
+    depends_on("py-setuptools@42:", type="build", when="@0.1:")
+    depends_on("py-setuptools-scm@3.4:", type="build", when="@0.1:")
+
+    def patch(self):
+        filter_file("-DEXTLIB_FROM_SUBMODULES=ON", "-DEXTLIB_FROM_SUBMODULES=OFF", "setup.py")

packages/py-morph-tool/package.py

@@ -15,26 +15,27 @@ class PyMorphTool(PythonPackage):
     git = "https://github.com/BlueBrain/morph-tool.git"
     pypi = "morph-tool/morph-tool-2.9.1.tar.gz"
 
-    version("develop", branch="master")
+    version("master", branch="master")
     version("2.9.1", sha256="305e9456c8047726588b23dfa070eb95ccbe5573e9fea3e0a83dc93eacdf61dc")
     version("2.9.0", sha256="c60d4010e17ddcc3f53c864c374fffee05713c8f8fd2ba4eed7706041ce1fa47")
 
-    variant("neuron", default=False, description="Enable additional neuron support")
+    variant("nrn", default=False, description="Enable additional neuron support")
+    variant("plot", default=False, description="Enable additional plotly support")
+    variant("parallel", default=False, description="Enable additional parallel support")
 
-    depends_on("py-setuptools", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-setuptools-scm", type="build")
 
     depends_on("py-click@6.7:", type=("build", "run"))
     depends_on("py-deprecation@2.1.0:", type=("build", "run"))
     depends_on("py-more-itertools@8.6.0:", type=("build", "run"))
+    depends_on("py-morphio@3", type=("build", "run"))
+    depends_on("py-neurom@3", type=("build", "run"))
     depends_on("py-numpy@1.14:", type=("build", "run"))
     depends_on("py-pandas@1.0.3:", type=("build", "run"))
-    depends_on("py-xmltodict@0.12:", type=("build", "run"))
+    depends_on("py-xmltodict@0.12.0:", type=("build", "run"))
 
-    depends_on("py-plotly@4.1:", type=("build", "run"))
-    depends_on("py-dask@2.19:", type=("build", "run"))
-    depends_on("neuron+python@7.8:", type=("build", "run"))
-    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@3.3.6:3,develop", type=("build", "run"), when="@2.9.1:")
-    depends_on("py-morphio@3.0:3,develop", type=("build", "run"), when="@2.9.0")
+    depends_on("py-plotly@4.1.0:", type=("build", "run"), when="+plot")
+    depends_on("py-dask+bag@2.19.0:", type=("build", "run"), when="+parallel")
+    depends_on("neuron+python@7.8:", type=("build", "run"), when="+nrn")
+    depends_on("py-bluepyopt@1.9.37:", type=("build", "run"), when="+nrn")

packages/py-morphio/package.py

@@ -5,6 +5,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import sys
+
 from spack.package import *
 
 
@@ -15,21 +17,16 @@ class PyMorphio(PythonPackage):
     git = "https://github.com/BlueBrain/MorphIO.git"
     pypi = "morphio/MorphIO-3.3.2.tar.gz"
 
-    version("develop", branch="master", submodules=True)
-    version("unifurcation", branch="unifurcation", submodules=True)
+    version("master", branch="master", submodules=True)
 
     version("3.3.6", sha256="0f2e55470d92a3d89f2141ae905ee104fd16257b93dafb90682d90171de2f4e6")
-    version("3.3.5", sha256="9e6cfebaea32080131b2b08a4a32dfbe92b18427a3e557861e27c4131f7542ac")
-    version("3.3.4", sha256="b70c6884e9b835560501f798c75c9cc7eaf3162cba1d930b5a9b854bb9ea60dc")
-    version("3.3.3", sha256="f6d91970cfd734b2e5fb8f9239a0bfa00519fe082dd8e403e4cc204dbdf0a9fa")
-    version("3.3.2", sha256="fc961defbfbfb3f11360954fb3ec51373eaff25b154fa31d6b31decca6937780")
-    version("3.1.1", sha256="ad9f0e363f09f03c6eda54f5f3b006d204236677d2f2c9675421e0441033a503")
-    version("2.7.1", sha256="3f3e2229da85e874527775fce080f712b6dc287edc44b90b6de35d17b34badff")
-
-    depends_on("py-setuptools", type="build")
+
+    depends_on("py-setuptools@24.2:", type="build")
     depends_on("py-setuptools-scm", type="build")
 
     depends_on("ninja", type="build")
     depends_on("cmake@3.2:", type="build")
-    depends_on("py-numpy@1.14.1:", type="run")
-    depends_on("hdf5")
+    depends_on("py-numpy@1.14.1:", type=("build", "run"))
+    depends_on("py-h5py@3", when="platform=windows", type=("build", "run"))
+    if sys.platform != "win32":
+        depends_on("hdf5")

packages/py-neurom/package.py

@@ -15,23 +15,23 @@ class PyNeurom(PythonPackage):
     git = "https://github.com/BlueBrain/NeuroM.git"
     pypi = "neurom/neurom-2.2.1.tar.gz"
 
-    version("develop", branch="master")
-    version("3.2.2", sha256="bc442cf5193289b893a66d5e541868f84bb120b03395b03ce2423c19729b92de")
+    version("master", branch="master")
+    version("3.2.4", sha256="a584e0979b54deee906dd716ea90de20773e20b527d83960d0fe655b0905eb4a")
 
     variant("plotly", default=False, description="Enable plotly support")
 
-    depends_on("py-setuptools@0.42:", type=("build", "run"))
+    depends_on("py-setuptools@42:", type=("build", "run"))
     depends_on("py-setuptools-scm", type="build")
-    depends_on("py-wheel", type="build")
+    depends_on("python@3.8:", type=("build", "run"))
 
     depends_on("py-click@7.0:", type=("build", "run"))
+    depends_on("py-matplotlib@3.2.1:", type=("build", "run"))
+    depends_on("py-morphio@3.3.6:", type=("build", "run"))
     depends_on("py-numpy@1.8.0:", type=("build", "run"))
+    depends_on("py-pandas@1.0.5:", type=("build", "run"))
     depends_on("py-pyyaml@3.10:", type=("build", "run"))
-    depends_on("py-tqdm@4.8.4:", type=("build", "run"))
-    depends_on("py-matplotlib@3.2.1:", type=("build", "run"))
     depends_on("py-scipy@1.2.0:", type=("build", "run"))
+    depends_on("py-tqdm@4.8.4:", type=("build", "run"))
+
     depends_on("py-plotly@3.6.0:", type=("build", "run"), when="+plotly")
     depends_on("py-psutil@5.5.1:", type=("build", "run"), when="+plotly")
-
-    depends_on("py-morphio@3.1.1:", type=("build", "run"))
-    depends_on("py-pandas@1.0.5:", type=("build", "run"))

spack.yaml

@@ -16,13 +16,13 @@ spack:
     - nest@3.7 +sonata
     - neuron@8.2.3 +mpi
     - jaxsnn@8.0-a4
-    - py-bluepyefe@2.2.18
-    - py-bluepymm@0.7.65
-    - py-bluepyopt@1.13.86
+    - py-bluepyefe@2.3.6
+    - py-bluepymm@0.8.7
+    - py-bluepyopt@1.14.4
     - py-bsb@4.0.0a57
     - py-ebrains-drive@0.5.1
     - py-ebrains-kg-core@0.9.15
-    - py-efel@4.0.4
+    - py-efel@5.5.7
     - py-elephant@1.1.0
     - py-fairgraph@0.11.1
     - py-frites@0.4.4
@@ -33,11 +33,11 @@ spack:
     - py-lfpy@2.3
     - py-lfpykit@0.5.1
     - py-libneuroml@0.4.1
-    - py-libsonata@0.1.23
+    - py-libsonata@0.1.25
     - py-neo@0.13.0
     - py-nestml@7.0.1
     - py-netpyne@1.0.5
-    - py-neurom@3.2.2
+    - py-neurom@3.2.4
     - py-neuror@1.6.4
     - py-pynn@0.12.2 +mpi
     - py-pyunicore@0.15.0