[py-icon4py] Modifications for merge of greenline (#834)

* Rebasing * GitHub Action: Apply Pep8-formatting * removing recipes that are builtin to v0.20.1 * Update packages.yaml * removing libxml2 * removing the pypi arg from version() * GitHub Action: Apply Pep8-formatting * Update package.py * GitHub Action: Apply Pep8-formatting * trying Jonas' fixes * updating gt4py min requirements * adding newer py-tabulate * GitHub Action: Apply Pep8-formatting * renaming v to 2.6.2 to avoid patching includes unncessarily * Adding tests to integration_test.py * GitHub Action: Apply Pep8-formatting * Update system_test.py * Update package.py * testing with builtin py-poetry-core * Removing py-poetry-core test * Removing py-poetry-core test * updating serialbox version in system tests * Adding 'Test' suffixes * Update package.py --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: juckerj <[email protected]>
C2SM · Sep 20, 2023 · b7e55db · b7e55db
1 parent c6fc4a6
commit b7e55db
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Showing 13 changed files with 285 additions and 15 deletions.
diff --git a/repos/c2sm/packages/icon/package.py b/repos/c2sm/packages/icon/package.py
@@ -590,6 +590,12 @@ def configure_args(self):
                 self.spec['py-icon4py:atm_dyn_iconam'].headers.directories[0])
             config_vars['LOC_ICON4PY_TOOLS'].append(
                 self.spec['py-icon4py:tools'].headers.directories[0])
+            if self.spec['py-icon4py'].version > Version("0.0.7"):
+                config_vars['LOC_ICON4PY_DIFFUSION'].append(
+                    self.spec['py-icon4py:diffusion'].headers.directories[0])
+                config_vars['LOC_ICON4PY_INTERPOLATION'].append(
+                    self.spec['py-icon4py:interpolation'].headers.
+                    directories[0])
             config_vars['LOC_GRIDTOOLS'].append(
                 self.spec['py-gridtools-cpp:data'].headers.directories[0])
             config_vars['GT4PYNVCFLAGS'] = config_vars['NVCFLAGS']

diff --git a/repos/c2sm/packages/py-ghex/add_origin_install_rpath.patch b/repos/c2sm/packages/py-ghex/add_origin_install_rpath.patch
@@ -0,0 +1,13 @@
+diff --git a/bindings/python/CMakeLists.txt b/bindings/python/CMakeLists.txt
+index 7a69da0..13991c2 100644
+--- a/bindings/python/CMakeLists.txt
++++ b/bindings/python/CMakeLists.txt
+@@ -104,7 +104,7 @@ if(DEFINED SKBUILD_PROJECT_NAME)
+   # set RPaths
+   list(GET CMAKE_PREFIX_PATH 0 scikit_build_core_install_path)
+   set_target_properties(pyghex PROPERTIES 
+-      INSTALL_RPATH "${scikit_build_core_install_path}/ghex/${CMAKE_INSTALL_LIBDIR}")
++      INSTALL_RPATH "$ORIGIN/lib:${scikit_build_core_install_path}/ghex/${CMAKE_INSTALL_LIBDIR}")
+   set_target_properties(ghex PROPERTIES
+       INSTALL_RPATH "${scikit_build_core_install_path}/ghex/${CMAKE_INSTALL_LIBDIR}")
+   if (GHEX_TRANSPORT_BACKEND STREQUAL "LIBFABRIC")
diff --git a/repos/c2sm/packages/py-ghex/package.py b/repos/c2sm/packages/py-ghex/package.py
@@ -0,0 +1,43 @@
+# 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 import *
+
+
+class PyGhex(PythonPackage):
+    """
+    Python bindings for Generic exascale-ready library for halo-exchange operations
+    on variety of grids/meshes.
+    """
+
+    homepage = 'https://github.com/ghex-org/GHEX'
+    url = "https://github.com/ghex-org/GHEX/archive/refs/tags/v0.3.0.tar.gz"
+    git = 'https://github.com/ghex-org/GHEX.git'
+    maintainers = ['boeschf', 'halungge']
+
+    version('0.3.2',
+            commit='4ae0b8031647816cde3a54a856d37d38e7bdb9ac',
+            git=git,
+            submodules=True)
+    version('0.3.1',
+            commit='7ced96a69ab502b0ab0eddc1c0d743e06ccde919',
+            git=git,
+            submodules=True)
+
+    build_directory = 'bindings/python'
+    import_modules = ['ghex', 'ghex.unstructured']
+
+    depends_on("mpi")
+    depends_on('[email protected]:', type=('build', 'run'))
+    depends_on('[email protected] +pyproject', type='build')
+    depends_on('py-pybind11', type=('build', 'run'))
+    depends_on('py-mpi4py', type=('build', 'run'))
+    depends_on('[email protected]:', type='build')
+    depends_on('[email protected]:', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-pytest', type=('build', 'run'))
+
+    patch("add_origin_install_rpath.patch", when="@0.3.1")
diff --git a/repos/c2sm/packages/py-gt4py/package.py b/repos/c2sm/packages/py-gt4py/package.py
@@ -37,11 +37,11 @@ class PyGt4py(PythonPackage):
     depends_on('[email protected]:', type=('build', 'run'))
     depends_on('[email protected]:', type=('build', 'run'))
     depends_on('[email protected]:', type=('build', 'run'))
-    depends_on('py-boltons@20.0.0:', type=('build', 'run'))
-    depends_on('[email protected]:', type=('build', 'run'))
+    depends_on('py-boltons@20.1:', type=('build', 'run'))
+    depends_on('[email protected].1:', type=('build', 'run'))
     depends_on('[email protected]:', type=('build', 'run'))
     depends_on('[email protected]:', type=('build', 'run'))
-    depends_on('[email protected]:', type=('build', 'run'))
+    depends_on('[email protected].0:', type=('build', 'run'))
     depends_on('[email protected]:', type=('build', 'run'))
     depends_on('[email protected]:', type=('build', 'run'))
     depends_on('[email protected]:', type=(
@@ -60,10 +60,10 @@ class PyGt4py(PythonPackage):
     depends_on('[email protected]:2.9.2', type=('build', 'run'))
 
     depends_on('[email protected]:', when="@1.1.3:", type=('build', 'run'))
-    depends_on('[email protected]:', type=('build', 'run'))
-    depends_on('py-typing-extensions@4.5:', type=('build', 'run'))
+    depends_on('[email protected].10:', type=('build', 'run'))
+    depends_on('py-typing-extensions@4.2:4.6', type=('build', 'run'))
     depends_on('[email protected]:', type=('build', 'run'))
-    depends_on('[email protected]:', type=('build', 'run'))
+    depends_on('[email protected]:3.0.9', type=('build', 'run'))
     depends_on('[email protected]:', type=('build', 'run'))
 
     # Python dependencies from requirements-dev.txt

diff --git a/repos/c2sm/packages/py-icon4py/package.py b/repos/c2sm/packages/py-icon4py/package.py
@@ -41,6 +41,21 @@ class PyIcon4py(PythonPackage):
     depends_on('py-pytest', type=('build', 'run'))
     depends_on('[email protected]:', type=('build', 'run'))
 
+    depends_on('[email protected]:', when='@0.0.8:', type=('build', 'run'))
+    depends_on('py-netcdf4', when='@0.0.8:', type=('build', 'run'))
+    depends_on('[email protected]%gcc', when='@0.0.8:', type=('build', 'run'))
+    depends_on('[email protected]%nvhpc',
+               when='@0.0.8:',
+               type=('build', 'run'))
+    depends_on('[email protected]:', when='@0.0.8:', type=('build', 'run'))
+    depends_on('py-pytz', when='@0.0.8:', type=('build', 'run'))
+    depends_on('[email protected]', when='@0.0.8:', type=('build', 'run'))
+    depends_on('py-wget', when='@0.0.8:', type=('build', 'run'))
+    depends_on('[email protected] +python',
+               when='@0.0.8:',
+               type=('build', 'run'))
+    depends_on('py-pytest-mpi', when='@0.0.8:', type='build')
+
     # cmake in unit-tests needs this path
     def setup_build_environment(self, env):
         env.set("CMAKE_INCLUDE_PATH", self.spec['boost'].prefix.include)
@@ -50,8 +65,10 @@ def test(self):
         super().test()
 
         # unit tests
-        python('-m', 'pytest', '-v', '-s', '-n', 'auto', '--cov',
-               '--cov-append')
+        if 'py-pytest-mpi' in self.spec:
+            python('-m', 'pytest', '--with-mpi', '-v', '-s')
+        else:
+            python('-m', 'pytest', '-v', '-s', '-n', 'auto')
 
     @property
     def headers(self):
@@ -76,10 +93,16 @@ def headers(self):
                 'atm_dyn_iconam': 'dycore',
                 'tools': 'icon4pytools'
             },
-            ver('=main'): {
+            ver('=0.0.7'): {
                 'atm_dyn_iconam': 'dycore',
                 'tools': 'icon4pytools'
-            }
+            },
+            ver('=main'): {
+                'atm_dyn_iconam': 'dycore',
+                'tools': 'icon4pytools',
+                'diffusion': 'diffusion/stencils',
+                'interpolation': 'interpolation/stencils',
+            },
         }
 
         if len(query_parameters) > 1:
@@ -143,8 +166,14 @@ def install(self, pkg, spec, prefix):
         elif self.spec.version == ver('=0.0.4') or self.spec.version == ver(
                 '=0.0.5'):
             build_dirs = ['common', 'atm_dyn_iconam', 'tools']
-        else:
+        elif self.spec.version == ver('=0.0.6') or self.spec.version == ver(
+                '=0.0.7'):
             build_dirs = ['tools', 'model/atmosphere/dycore', 'model/common/']
+        else:
+            build_dirs = [
+                'tools', 'model/atmosphere/dycore',
+                'model/atmosphere/diffusion', 'model/driver', 'model/common/'
+            ]
 
         for dir in build_dirs:
             with fs.working_dir(os.path.join(self.build_directory, dir)):

diff --git a/repos/c2sm/packages/py-isort/package.py b/repos/c2sm/packages/py-isort/package.py
@@ -0,0 +1,38 @@
+# 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 *
+from spack.pkg.builtin.py_isort import PyIsort as SpackPyIsort
+
+
+class PyIsort(SpackPyIsort):
+    """A Python utility / library to sort Python imports."""
+
+    homepage = "https://github.com/timothycrosley/isort"
+    pypi = "isort/isort-4.2.15.tar.gz"
+
+    version("5.12.0",
+            sha256=
+            "8bef7dde241278824a6d83f44a544709b065191b95b6e50894bdc722fcba0504")
+    version("5.10.1",
+            sha256=
+            "e8443a5e7a020e9d7f97f1d7d9cd17c88bcb3bc7e218bf9cf5095fe550be2951")
+
+    variant("colors",
+            default=False,
+            description="Install colorama for --color support")
+
+    depends_on("[email protected]:", when="@5.12:", type=("build", "run"))
+    depends_on("[email protected]:3", when="@5:5.10", type=("build", "run"))
+    depends_on("py-poetry-core@1:", type="build")
+    depends_on("[email protected]:",
+               when="+colors @5.12:",
+               type=("build", "run"))
+    depends_on("[email protected]:0.4",
+               when="+colors @:5.11",
+               type=("build", "run"))
+
+    # https://github.com/PyCQA/isort/issues/2077
+    conflicts("^[email protected]:", when="@:5.11.4")
diff --git a/repos/c2sm/packages/py-pytest-mpi/package.py b/repos/c2sm/packages/py-pytest-mpi/package.py
@@ -0,0 +1,22 @@
+# 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 import *
+
+
+class PyPytestMpi(PythonPackage):
+    """pytest_mpi is a plugin for pytest providing some useful tools when running tests under MPI,
+    and testing MPI-related code."""
+
+    homepage = "https://pytest-mpi.readthedocs.io"
+    pypi = "pytest-mpi/pytest-mpi-0.6.tar.gz"
+
+    maintainers = ['halungge']
+
+    version('0.6',
+            sha256=
+            '09b3cd3511f8f3cd4d205f54d4a7223724fed0ab68b872ed1123d312152325a9')
+
+    depends_on('py-setuptools', type='build')
diff --git a/repos/c2sm/packages/py-scikit-build-core/package.py b/repos/c2sm/packages/py-scikit-build-core/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2023 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 *
+from spack.pkg.builtin.py_scikit_build_core import PyScikitBuildCore as SpackPyScikitBuildCore
+
+
+class PyScikitBuildCore(SpackPyScikitBuildCore):
+    """scikit-build-core is a doubly improved build system generator
+    for CPython C/C++/Fortran/Cython extensions. It features several
+    improvements over the classic scikit-build build system generator."""
+
+    version("0.5.0",
+            sha256=
+            "a42a95029b34b5cf892855342d9b9445c774cb797fcb24c8fc4c2fb42b18dfca")
diff --git a/repos/c2sm/packages/py-tabulate/package.py b/repos/c2sm/packages/py-tabulate/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2023 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 *
+from spack.pkg.builtin.py_tabulate import PyTabulate as SpackPyTabulate
+
+
+class PyTabulate(SpackPyTabulate):
+    """Pretty-print tabular data"""
+
+    version("0.8.10",
+            sha256=
+            "6c57f3f3dd7ac2782770155f3adb2db0b1a269637e42f27599925e64b114f519")
diff --git a/repos/c2sm/packages/serialbox/package.py b/repos/c2sm/packages/serialbox/package.py
@@ -0,0 +1,15 @@
+from spack.package import *
+from spack.pkg.builtin.serialbox import Serialbox as SpackSerialbox
+
+
+class Serialbox(SpackSerialbox):
+    """See upstream package.
+    Adding version to make compatible with numpy 1.24
+    """
+    git = 'https://github.com/GridTools/serialbox.git'
+    maintainers = ['halungge', 'skosukhin']
+
+    version('2.6.2',
+            commit='88ac4e4dfc824953d068fe63c8e7b3dd9560a914',
+            git=git,
+            submodules=True)
diff --git a/requirements.txt b/requirements.txt
@@ -1,3 +1,3 @@
 requests
 pytest-xdist
-pyyaml
+pyyaml