py-functionalizer: new package to replace spykfunc (#2480)

Author: matz-e

bluebrain/deployment/environments/applications_hpc.yaml

@@ -13,6 +13,7 @@ spack:
           - py-archive-advisor
           - py-basalt
           - py-brain-indexer
+          - py-functionalizer
           - py-mvdtool
           - py-neurodamus
           - py-pytouchreader
@@ -47,9 +48,10 @@ spack:
     - parquet-converters
     - py-archive-advisor
     - py-brain-indexer
+    - py-functionalizer
     - py-neurodamus
     - py-pytouchreader
-    - spykfunc
+    - spykfunc@0.19.0
     - spykfunc@0.18.7
     - steps
     - synapsetool

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

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright 2013-2020 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 PyFunctionalizer(PythonPackage):
+    """Functionalizer - Spark functionalizer developed by Blue Brain Project, EPFL"""
+
+    homepage = "https://github.com/BlueBrain/functionalizer"
+    pypi = "functionalizer/functionalizer-1.0.0.tar.gz"
+
+    version("1.0.0", sha256="c62754fcf41e29729386c23cefb0dd57b449ac27c0b47ba5e2e4b2776c517494")
+
+    depends_on("py-cmake", type="build")
+    depends_on("py-ninja", type="build")
+    depends_on("py-scikit-build-core+pyproject", type="build")
+    depends_on("py-setuptools-scm", type="build")
+
+    depends_on("spark+hadoop@3.0.0:", type="run")
+    depends_on("hadoop@3:", type="run")
+
+    depends_on("py-docopt", type=("build", "run"))
+    depends_on("py-future", type=("build", "run"))
+    depends_on("py-fz-td-recipe@0.2:", type=("build", "run"))
+    # h5py needed for morphologies before, and to supplement libSONATA due
+    # to missing API functionality
+    depends_on("py-h5py", type=("build", "run"))
+    depends_on("py-hdfs", type=("build", "run"))
+    depends_on("py-jprops", type=("build", "run"))
+    depends_on("py-libsonata@0.1.17:", type=("build", "run"))
+    depends_on("py-lxml", type=("build", "run"))
+    depends_on("py-morphio", type=("build", "run"))
+    depends_on("py-mpi4py", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-packaging", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("py-pyarrow+dataset+parquet@3.0.0:", type=("build", "run"))
+    depends_on("py-pyspark@3.0.0:", type=("build", "run"))
+
+    def setup_run_environment(self, env):
+        env.set("SPARK_HOME", self.spec["spark"].prefix)
+        env.set("HADOOP_HOME", self.spec["hadoop"].prefix)

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

@@ -15,10 +15,10 @@ class Spykfunc(PythonPackage):
 
     submodules = True
 
-    version("develop", branch="main")
+    version("develop", branch="main", deprecated=True)
     version("0.19.0", tag="v0.19.0")
     version("0.18.7", tag="v0.18.7")
-    version("0.18.6", tag="v0.18.6")
+    version("0.18.6", tag="v0.18.6", deprecated=True)
 
     depends_on("cmake", type="build")
     depends_on("ninja", type="build")