Merge pull request #243 from xylar/update-to-0.5.0-alpha.1

Update to v0.5.0-alpha.1

deploy/bootstrap.py

@@ -563,11 +563,13 @@ def _build_conda_env(options, activate_base):
                             mpi_prefix=mpi_prefix,
                             include_mache=not local_mache)
 
-        for package in ['esmf', 'geometric_features', 'mache', 'metis', 'moab',
+        for package in ['esmf', 'geometric_features', 'mache', 'metis',
                         'mpas_tools', 'netcdf_c', 'netcdf_fortran', 'otps',
                         'parallelio', 'pnetcdf']:
             replacements[package] = config.get('deploy', package)
 
+        replacements['moab'] = config.get('deploy', 'conda_moab')
+
         spec_file = template.render(**replacements)
 
         spec_filename = f'spec-file-{conda_mpi}.txt'
@@ -868,7 +870,7 @@ def _build_spack_libs_env(options, compiler, mpi, env_vars):  # noqa: C901
     cmake = config.get('deploy', 'cmake')
     lapack = config.get('deploy', 'lapack')
     metis = config.get('deploy', 'metis')
-    moab = config.get('deploy', 'moab')
+    moab = config.get('deploy', 'spack_moab')
     parmetis = config.get('deploy', 'parmetis')
     petsc = config.get('deploy', 'petsc')
     scorpio = config.get('deploy', 'scorpio')
@@ -1179,6 +1181,8 @@ def _update_permissions(options, directories):  # noqa: C901
     # os.walk()
     for directory in directories:
         dir_stat = _safe_stat(directory)
+        if dir_stat is None:
+            continue
 
         perm = dir_stat.st_mode & mask
 
@@ -1218,6 +1222,8 @@ def _update_permissions(options, directories):  # noqa: C901
                 directory = os.path.join(root, directory)
 
                 dir_stat = _safe_stat(directory)
+                if dir_stat is None:
+                    continue
 
                 if dir_stat.st_uid != new_uid:
                     # current user doesn't own this dir so let's move on
@@ -1242,6 +1248,8 @@ def _update_permissions(options, directories):  # noqa: C901
                     pass
                 file_name = os.path.join(root, file_name)
                 file_stat = _safe_stat(file_name)
+                if file_stat is None:
+                    continue
 
                 if file_stat.st_uid != new_uid:
                     # current user doesn't own this file so let's move on
@@ -1339,7 +1347,7 @@ def _safe_rmtree(path):
 
 @_ignore_file_errors
 def _safe_stat(path):
-    os.stat(path)
+    return os.stat(path)
 
 
 def _discover_machine(quiet=False):

deploy/conda-dev-spec.template

@@ -1,8 +1,5 @@
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-
 # Base
-python>=3.9,<=3.12
+python>=3.9,<3.13
 antimeridian
 cartopy
 cartopy_offlinedata

deploy/default.cfg

@@ -20,26 +20,27 @@ python = 3.12
 mpi = nompi
 
 # versions of conda packages
-geometric_features = 1.2.0
-mache = 1.24.0
-mpas_tools = 0.34.1
+geometric_features = 1.5.0
+mache = 1.27.0
+conda_moab = 5.5.1
+mpas_tools = 0.36.0
 otps = 2021.10
-parallelio = 2.6.2
+parallelio = 2.6.3
 
 # versions of conda or spack packages (depending on machine type)
-esmf = 8.6.1
+esmf = 8.7.0
 metis = 5.1.0
-moab = 5.5.1
 netcdf_c = 4.9.2
 netcdf_fortran = 4.6.1
 pnetcdf = 1.13.0
 
 # versions of spack packages
-albany = develop
+albany = developcompass-2024-03-13
 # cmake newer than 3.23.0 needed for Trilinos
 cmake = 3.23.0:
-hdf5 = 1.14.1
+hdf5 = 1.14.3
 lapack = 3.9.1
+spack_moab = master
 parmetis = 4.0.3
 petsc = 3.19.1
-scorpio = 1.4.2
+scorpio = 1.6.5

polaris/version.py

@@ -1 +1 @@
-__version__ = '0.4.0-alpha.2'
+__version__ = '0.5.0-alpha.1'

pyproject.toml

@@ -69,7 +69,7 @@ requires = ["setuptools>=60"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools.packages.find]
-exclude = ["docs*", "conda*"]
+exclude = ["deploy*", "docs*", "e3sm_submodules*", "licenses*", "utils*"]
 
 [tool.setuptools.dynamic]
 version = { attr = "polaris.version.__version__" }