new packages: py-arm-pyart and dependencies (#32579)

* new packages: py-arm-pyart and dependencies

- py-arm-pyart
- py-cylp
- rsl

* Update var/spack/repos/builtin/packages/py-cylp/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Fix dependencies

- xarray is not optional
- pandas is needed
- pylab is needed
  - new package, py-pylab-sdk
- setuptools is needed at run time

* Patch for import of StringIO

* Update var/spack/repos/builtin/packages/py-arm-pyart/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Fix call to `StringIO` in patch

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

5 files changed, 187 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-arm-pyart/StringIO.patch b/var/spack/repos/builtin/packages/py-arm-pyart/StringIO.patch
new file mode 100644
index 0000000000..bd8bc2868f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-arm-pyart/StringIO.patch
@@ -0,0 +1,48 @@
+diff -ru a/pyart/testing/data/make_small_mdv_ppi.py b/pyart/testing/data/make_small_mdv_ppi.py
+--- a/pyart/testing/data/make_small_mdv_ppi.py	2022-07-19 13:06:08.000000000 -0500
++++ b/pyart/testing/data/make_small_mdv_ppi.py	2022-09-10 16:06:38.712279369 -0500
+@@ -6,7 +6,10 @@
+ """
+ 
+ import struct
+-import StringIO
++try:
++    from StringIO import StringIO
++except ImportError:
++    from io import StringIO
+ import gzip
+ 
+ import pyart
+@@ -40,7 +43,7 @@
+ 
+ fdata_str = fdata.astype('uint16').byteswap().tostring()
+ uncompressed_data_size = len(fdata_str)
+-fileobj = StringIO.StringIO()
++fileobj = StringIO()
+ gzipfile = gzip.GzipFile(fileobj=fileobj, mode='w')
+ gzipfile.write(fdata_str)
+ gzipfile.close()
+diff -ru a/pyart/testing/data/make_small_mdv_rhi.py b/pyart/testing/data/make_small_mdv_rhi.py
+--- a/pyart/testing/data/make_small_mdv_rhi.py	2022-07-19 13:06:08.000000000 -0500
++++ b/pyart/testing/data/make_small_mdv_rhi.py	2022-09-10 16:07:12.775303046 -0500
+@@ -6,7 +6,10 @@
+ """
+ 
+ import struct
+-import StringIO
++try:
++    from StringIO import StringIO
++except ImportError:
++    from io import StringIO
+ import gzip
+ 
+ import pyart
+@@ -39,7 +42,7 @@
+ 
+ fdata_str = fdata.astype('uint16').byteswap().tostring()
+ uncompressed_data_size = len(fdata_str)
+-fileobj = StringIO.StringIO()
++fileobj = StringIO()
+ gzipfile = gzip.GzipFile(fileobj=fileobj, mode='w')
+ gzipfile.write(fdata_str)
+ gzipfile.close()
diff --git a/var/spack/repos/builtin/packages/py-arm-pyart/package.py b/var/spack/repos/builtin/packages/py-arm-pyart/package.py
new file mode 100644
index 0000000000..9b07f1f60c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-arm-pyart/package.py
@@ -0,0 +1,71 @@
+# Copyright 2013-2022 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 PyArmPyart(PythonPackage):
+    """Python ARM Radar Toolkit.
+
+    A growing collection of weather radar algorithms and utilities build on top
+    of the Scientific Python stack and distributed under the 3-Clause BSD
+    license. Py-ART is used by the Atmospheric Radiation Measurement (ARM)
+    Climate Research Facility for working with data from a number of
+    precipitation and cloud radars, but has been designed so that it can be
+    used by others in the radar and atmospheric communities to examine,
+    processes, and analyse data from many types of weather radars."""
+
+    homepage = "https://github.com/ARM-DOE/pyart"
+    pypi = "arm_pyart/arm_pyart-1.12.7.tar.gz"
+
+    version("1.12.7", sha256="b7b23ecef270c60b017d94603941f0c117de072a10125c5f58c0685d801f9161")
+
+    variant("cartopy", description="Plot grids on maps", default=False)
+    variant("cylp", description="Linear programming solver", default=False)
+    variant("gdal", description="Output GeoTIFFs from grid objects", default=False)
+    variant("hdf5", description="Support for HDF5 files", default=False)
+    variant("rsl", description="Use RSL library", default=False)
+    variant("wradlib", description="Calculate texture of differential phase field", default=False)
+
+    conflicts("~hdf5", when="+wradlib")
+    conflicts("~gdal", when="+wradlib")
+
+    depends_on("python@3.6:3.10", type=("build", "run"))
+
+    depends_on("py-setuptools", type=("build", "run"))
+    depends_on("py-setuptools-scm@6.2:", type="build")
+
+    depends_on("py-cython", type="build")
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-netcdf4", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
+    depends_on("py-pooch", type=("build", "run"))
+    depends_on("py-cftime", type=("build", "run"))
+    depends_on("py-fsspec", type=("build", "run"))
+    depends_on("py-s3fs", type=("build", "run"))
+    depends_on("py-xarray@0.21.1:", type=("build", "run"))
+
+    # These are not listed but needed due to being imported in a python file
+    depends_on("py-pandas", type="run")
+    depends_on("py-pylab-sdk", type="run")
+
+    # Dependencies for variants
+    depends_on("py-cartopy", type="run", when="+cartopy")
+    depends_on("py-cylp", type="run", when="+cylp")
+    depends_on("gdal+python", type="run", when="+gdal")
+    depends_on("py-h5py", type="run", when="+hdf5")
+    depends_on("rsl", type=("build", "run"), when="+rsl")
+    depends_on("py-wradlib", type="run", when="+wradlib")
+
+    patch("StringIO.patch")
+
+    def setup_build_environment(self, env):
+        if "+rsl" in self.spec:
+            env.set("RSL_PATH", self.spec["rsl"].prefix)
+        else:
+            # set RSL_PATH to empty to make sure RSL is not picked up from a
+            # non-spack install in /usr/local
+            env.set("RSL_PATH", "")
diff --git a/var/spack/repos/builtin/packages/py-cylp/package.py b/var/spack/repos/builtin/packages/py-cylp/package.py
new file mode 100644
index 0000000000..b3d96d686a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cylp/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2022 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 PyCylp(PythonPackage):
+    """A Python interface for CLP, CBC, and CGL.
+
+    CyLP is a Python interface to COIN-OR’s Linear and mixed-integer program
+    solvers (CLP, CBC, and CGL). CyLP’s unique feature is that you can use it
+    to alter the solution process of the solvers from within Python."""
+
+    homepage = "https://github.com/coin-or/cylp"
+    pypi = "cylp/cylp-0.91.5.tar.gz"
+
+    version("0.91.5", sha256="d68ab1dde125be60abf45c8fd9edd24ab880c8144ad881718ddfa01ff6674c77")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-cython@:2", type="build")
+
+    depends_on("py-numpy@1.5:", type=("build", "run"))
+    depends_on("py-scipy@0.10.0:", type=("build", "run"))
+
+    depends_on("cbc")
diff --git a/var/spack/repos/builtin/packages/py-pylab-sdk/package.py b/var/spack/repos/builtin/packages/py-pylab-sdk/package.py
new file mode 100644
index 0000000000..5984d55cd1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pylab-sdk/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2022 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 PyPylabSdk(PythonPackage):
+    """A development kit that collects simple utilities."""
+
+    homepage = "https://github.com/PyLabCo/pylab-sdk"
+    pypi = "pylab-sdk/pylab-sdk-1.3.2.tar.gz"
+
+    version("1.3.2", sha256="ea53e97fec45ea15f65bd53da6b25dc16a9accf3a7f5decbaa970592d760148d")
+
+    depends_on("python@3:", type=("build", "run"))
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-requests", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/rsl/package.py b/var/spack/repos/builtin/packages/rsl/package.py
new file mode 100644
index 0000000000..b6719d71f0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rsl/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2022 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 Rsl(AutotoolsPackage):
+    """This library is an object oriented programming environment for writing
+    software applicable to all RADAR data related to the TRMM GV effort."""
+
+    homepage = "https://trmm-fc.gsfc.nasa.gov/trmm_gv/software/rsl/"
+    url = "https://trmm-fc.gsfc.nasa.gov/trmm_gv/software/rsl/software/rsl-v1.50.tar.gz"
+
+    version("1.50", sha256="9e4e3fe45eb1e4aebea63255d4956b00eb69527044a83f182cde1b43510bd342")
+
+    depends_on("bzip2")
+    depends_on("jpeg")
+    depends_on("zlib")