diff --git a/deploy/bootstrap.py b/deploy/bootstrap.py
index 61d0c837a..6781d108b 100755
--- a/deploy/bootstrap.py
+++ b/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):
diff --git a/deploy/conda-dev-spec.template b/deploy/conda-dev-spec.template
index 718240d6c..084b772d4 100644
--- a/deploy/conda-dev-spec.template
+++ b/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
diff --git a/deploy/default.cfg b/deploy/default.cfg
index 9ac940c4f..90cc5cad5 100644
--- a/deploy/default.cfg
+++ b/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
diff --git a/e3sm_submodules/E3SM-Project b/e3sm_submodules/E3SM-Project
index ae514946f..67ae4d5d7 160000
--- a/e3sm_submodules/E3SM-Project
+++ b/e3sm_submodules/E3SM-Project
@@ -1 +1 @@
-Subproject commit ae514946f348917eaa3c23405447642a843f8436
+Subproject commit 67ae4d5d770e97ecf689aae239500de428d7153b
diff --git a/e3sm_submodules/MALI-Dev b/e3sm_submodules/MALI-Dev
index e23c40196..114c37340 160000
--- a/e3sm_submodules/MALI-Dev
+++ b/e3sm_submodules/MALI-Dev
@@ -1 +1 @@
-Subproject commit e23c401962f26fa2a9aee62eff3f54004aa759b0
+Subproject commit 114c37340c75a4c86e8d53e8bd042ffe37faf6c0
diff --git a/e3sm_submodules/Omega b/e3sm_submodules/Omega
index c80c46dd2..8247b3712 160000
--- a/e3sm_submodules/Omega
+++ b/e3sm_submodules/Omega
@@ -1 +1 @@
-Subproject commit c80c46dd200c6deb643d50354093b60b92374c83
+Subproject commit 8247b3712c50d90da5e7ce68dbc7284ce3445b76
diff --git a/polaris/version.py b/polaris/version.py
index 339472a8c..7a35f4197 100644
--- a/polaris/version.py
+++ b/polaris/version.py
@@ -1 +1 @@
-__version__ = '0.4.0-alpha.2'
+__version__ = '0.5.0-alpha.1'
diff --git a/pyproject.toml b/pyproject.toml
index bef85afa2..c6cd82e41 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -62,7 +62,7 @@ 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__" }