Add package py-devito and it's dependencies (#31495)

* [py-devito] Add package

Also add dependencies:
- py-nbval
- py-cgen
- py-codepy
- py-contexttimer
- py-pyrevolve

* [py-devito] Fix some typos

* [py-devito] Fix: include examples directory

Upstream issue: https://github.com/devitocodes/devito/issues/1954

* [py-devito] clean up

* [py-devito] clean up dependency packages

* [py-devito] flake8: line too long

* Address @adamjstewart comments

* Make flake8 happy

Co-authored-by: Stephen Sachs <stesachs@amazon.com>

6 files changed, 192 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-cgen/package.py b/var/spack/repos/builtin/packages/py-cgen/package.py
new file mode 100644
index 0000000000..9d93d21fa7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cgen/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 PyCgen(PythonPackage):
+    """cgen offers a simple abstract syntax tree for C and related languages
+    (C++/CUDA/OpenCL) to allow structured code generation from Python.
+    """
+
+    homepage = "https://documen.tician.de/cgen/"
+    pypi     = "cgen/cgen-2020.1.tar.gz"
+
+    version('2020.1', sha256='4ec99d0c832d9f95f5e51dd18a629ad50df0b5464ce557ef42c6e0cd9478bfcf')
+
+    depends_on('py-pytools@2015.1.2:', type=('build', 'run'))
+    depends_on('py-numpy@1.6:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-codepy/package.py b/var/spack/repos/builtin/packages/py-codepy/package.py
new file mode 100644
index 0000000000..4f5ba19a3b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-codepy/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 PyCodepy(PythonPackage):
+    """CodePy is a C metaprogramming toolkit for Python.
+
+    It handles two aspects of metaprogramming:
+    - Generating C source code.
+    - Compiling this source code and dynamically loading it into the Python interpreter.
+    """
+
+    homepage = "https://documen.tician.de/codepy/"
+    pypi     = "codepy/codepy-2019.1.tar.gz"
+
+    version('2019.1', sha256='384f22c37fe987c0ca71951690c3c2fd14dacdeddbeb0fde4fd01cd84859c94e')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pytools@2015.1.2:', type=('build', 'run'))
+    depends_on('py-numpy@1.6:', type=('build', 'run'))
+    depends_on('py-appdirs@1.4.0:', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-cgen', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-contexttimer/package.py b/var/spack/repos/builtin/packages/py-contexttimer/package.py
new file mode 100644
index 0000000000..24164747e0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-contexttimer/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 PyContexttimer(PythonPackage):
+    """A timer as a context manager.
+
+    contexttimer provides you with a couple of utilities to quickly measure the
+    execution time of a code block or a function.
+    """
+
+    homepage = "https://github.com/brouberol/contexttimer"
+    pypi     = "contexttimer/contexttimer-0.3.3.tar.gz"
+
+    version('0.3.3', sha256='35a1efd389af3f1ca509f33ff23e17d98b66c8fde5ba2a4eb8a8b7fa456598a5')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-devito/package.py b/var/spack/repos/builtin/packages/py-devito/package.py
new file mode 100644
index 0000000000..13f1050d59
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-devito/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 PyDevito(PythonPackage):
+    """Devito is a Python package to implement optimized stencil computation.
+
+    (e.g., finite differences, image processing, machine learning) from high-level
+    symbolic problem definitions. Devito builds on SymPy and employs automated code
+    generation and just-in-time compilation to execute optimized computational kernels
+    on several computer platforms, including CPUs, GPUs, and clusters thereof.
+    """
+
+    homepage = "https://www.devitoproject.org/"
+    pypi     = "devito/devito-4.6.2.tar.gz"
+
+    version('4.6.2', sha256='39c2210a192ad69953b4f8d93440ffd72b07d739c4fe2290e2b182adfb7e143f')
+
+    variant('mpi', default=False, description='Enable MPI support')
+    variant('matplotlib', default=False, description='Enable matplolib support')
+    variant('ipyparallel', default=False, description='Enable ipyparallel support')
+    variant('pandas', default=False, description='Enable pandas support')
+
+    depends_on('py-pip@9.0.1:', type='build')
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-numpy@1.16:', type=('build', 'run'))
+    depends_on('py-sympy@1.7:1.9', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-flake8@2.1.0:', type=('build', 'run'))
+    depends_on('py-nbval', type=('build', 'run'))
+    depends_on('py-cached-property', type=('build', 'run'))
+    depends_on('py-psutil@5.1.0:5', type=('build', 'run'))
+    depends_on('py-py-cpuinfo@:8', type=('build', 'run'))
+    depends_on('py-cgen@2020.1:', type=('build', 'run'))
+    depends_on('py-codepy@2019.1:', type=('build', 'run'))
+    depends_on('py-click@:8', type=('build', 'run'))
+    depends_on('py-codecov', type=('build', 'run'))
+    depends_on('py-multidict', type=('build', 'run'))
+    depends_on('py-anytree@2.4.3:2.8', type=('build', 'run'))
+    depends_on('py-pyrevolve@2.1.3:', type=('build', 'run'))
+    depends_on('py-distributed@:2022.2', type=('build', 'run'))
+    depends_on('py-pytest@3.6:6', type=('build', 'run'))
+    depends_on('py-pytest-runner', type=('build', 'run'))
+    depends_on('py-pytest-cov', type=('build', 'run'))
+
+    # requirements-mpi.tct
+    depends_on('py-mpi4py', type=('build', 'run'), when='+mpi')
+
+    # requirements-optional.txt
+    depends_on('py-matplotlib', type=('build', 'run'), when='+matplotlib')
+    depends_on('py-ipyparallel', type=('build', 'run'), when='+ipyparallel')
+    depends_on('py-pandas', type=('build', 'run'), when='+pandas')
+
+    depends_on('mpi', type=('build', 'run'))
+
+    depends_on('intel-parallel-studio', type='run', when='%intel@:2021.1.1')
+    depends_on('intel-oneapi-compilers', type='run', when='%intel@2021.1.2:')
+
+    @run_before('install')
+    def add_examples_dir(self):
+        # Add file `__init__py` to examples/ so it is picked up by setuptools
+        touch('examples/__init__.py')
+
+    def setup_run_environment(self, env):
+        # Make benchmark.py available
+        env.prepend_path('DEVITO_HOME', self.prefix)
diff --git a/var/spack/repos/builtin/packages/py-nbval/package.py b/var/spack/repos/builtin/packages/py-nbval/package.py
new file mode 100644
index 0000000000..f4eac48a89
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-nbval/package.py
@@ -0,0 +1,29 @@
+# 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 PyNbval(PythonPackage):
+    """Py.test plugin for validating Jupyter notebooks.
+
+    The plugin adds functionality to py.test to recognise and collect Jupyter notebooks.
+    The intended purpose of the tests is to determine whether execution of the stored
+    inputs match the stored outputs of the .ipynb file. Whilst also ensuring that the
+    notebooks are running without errors.
+    """
+
+    homepage = "https://github.com/computationalmodelling/nbval"
+    pypi     = "nbval/nbval-0.9.6.tar.gz"
+
+    version('0.9.6', sha256='cfefcd2ef66ee2d337d0b252c6bcec4023384eb32e8b9e5fcc3ac80ab8cd7d40')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pytest@2.8:', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-jupyter-client', type=('build', 'run'))
+    depends_on('py-nbformat', type=('build', 'run'))
+    depends_on('py-ipykernel', type=('build', 'run'))
+    depends_on('py-coverage', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pyrevolve/package.py b/var/spack/repos/builtin/packages/py-pyrevolve/package.py
new file mode 100644
index 0000000000..02786929ed
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyrevolve/package.py
@@ -0,0 +1,23 @@
+# 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 PyPyrevolve(PythonPackage):
+    """PyRevolve.
+
+    Python wrapper for Revolve: https://dl.acm.org/doi/10.1145/347837.347846
+    """
+
+    homepage = "https://github.com/devitocodes/pyrevolve"
+    pypi     = "pyrevolve/pyrevolve-2.2.tar.gz"
+
+    version('2.2', sha256='b49aea5cd6c520ac5fcd1d25fa23fe2c5502741d2965f3eee10be067e7b0efb4')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-contexttimer', type=('build', 'run'))
+    depends_on('py-cython@0.17:', type='build')
+    depends_on('py-versioneer', type='build')