support multiple config directories

CIME/XML/archive_base.py

@@ -1,6 +1,7 @@
 """
 Base class for archive files.  This class inherits from generic_xml.py
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.XML.generic_xml import GenericXML
 from CIME.utils import convert_to_type

CIME/XML/batch.py

@@ -4,10 +4,11 @@
 The batch_system type="foo" blocks define most things. Machine-specific overrides
 can be defined by providing a batch_system MACH="mach" block.
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.XML.generic_xml import GenericXML
 from CIME.XML.files import Files
-from CIME.utils import expect
+from CIME.utils import expect, get_config_dir
 
 logger = logging.getLogger(__name__)
 
@@ -45,13 +46,15 @@ def __init__(
         self.batch_system = batch_system
         self.machine = machine
 
-        # Append the contents of $HOME/.cime/config_batch.xml if it exists.
+        # Append the contents of $HOME/get_config_dir()/config_batch.xml if it exists.
         #
         # Also append the contents of a config_batch.xml file in the directory given by
         # extra_machines_dir, if present.
         #
         # This could cause problems if node matches are repeated when only one is expected.
-        infile = os.path.join(os.environ.get("HOME"), ".cime", "config_batch.xml")
+        infile = os.path.join(
+            os.environ.get("HOME"), get_config_dir(), "config_batch.xml"
+        )
         usehome = False
         if os.path.exists(infile):
             GenericXML.read(self, infile)

CIME/XML/component.py

@@ -1,6 +1,7 @@
 """
 Interface to the config_component.xml files.  This class inherits from EntryID.py
 """
+
 from CIME.XML.standard_module_setup import *
 
 from CIME.XML.entry_id import EntryID

CIME/XML/entry_id.py

@@ -3,6 +3,7 @@
 this is an abstract class and is expected to
 be used by other XML interface modules and not directly.
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.utils import expect, convert_to_string, convert_to_type
 from CIME.XML.generic_xml import GenericXML

CIME/XML/env_archive.py

@@ -1,12 +1,15 @@
 """
 Interface to the env_archive.xml file.  This class inherits from EnvBase
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME import utils
 from CIME.XML.archive_base import ArchiveBase
 from CIME.XML.env_base import EnvBase
 
 logger = logging.getLogger(__name__)
+
+
 # pylint: disable=super-init-not-called
 class EnvArchive(ArchiveBase, EnvBase):
     def __init__(self, case_root=None, infile="env_archive.xml", read_only=False):

CIME/XML/env_base.py

@@ -1,6 +1,7 @@
 """
 Base class for env files.  This class inherits from EntryID.py
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.XML.entry_id import EntryID
 from CIME.XML.headers import Headers

CIME/XML/env_batch.py

@@ -16,6 +16,7 @@
     get_logging_options,
     format_time,
     add_flag_to_cmd,
+    get_config_dir,
 )
 from collections import OrderedDict
 import stat, re, math
@@ -632,7 +633,7 @@ def _get_arg_nodes(self, case, bs_nodes):
                     check_paths = [case.get_value("BATCH_SPEC_FILE")]
 
                     user_config_path = os.path.join(
-                        pathlib.Path().home(), ".cime", "config_batch.xml"
+                        pathlib.Path().home(), get_config_dir(), "config_batch.xml"
                     )
 
                     if os.path.exists(user_config_path):

CIME/XML/env_build.py

@@ -1,6 +1,7 @@
 """
 Interface to the env_build.xml file.  This class inherits from EnvBase
 """
+
 from CIME.XML.standard_module_setup import *
 
 from CIME import utils

CIME/XML/env_case.py

@@ -1,6 +1,7 @@
 """
 Interface to the env_case.xml file.  This class inherits from EnvBase
 """
+
 from CIME.XML.standard_module_setup import *
 
 from CIME import utils

CIME/XML/env_mach_pes.py

@@ -1,6 +1,7 @@
 """
 Interface to the env_mach_pes.xml file.  This class inherits from EntryID
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME import utils
 from CIME.XML.env_base import EnvBase

CIME/XML/env_mach_specific.py

@@ -1,6 +1,7 @@
 """
 Interface to the env_mach_specific.xml file.  This class inherits from EnvBase
 """
+
 from CIME.XML.standard_module_setup import *
 
 from CIME.XML.env_base import EnvBase
@@ -11,6 +12,7 @@
 
 logger = logging.getLogger(__name__)
 
+
 # Is not of type EntryID but can use functions from EntryID (e.g
 # get_type) otherwise need to implement own functions and make GenericXML parent class
 class EnvMachSpecific(EnvBase):

CIME/XML/env_postprocessing.py

@@ -1,6 +1,7 @@
 """
 Interface to the env_postprocessing.xml file.  This class inherits from EnvBase
 """
+
 from CIME.XML.standard_module_setup import *
 
 from CIME.XML.env_base import EnvBase

CIME/XML/env_run.py

@@ -1,6 +1,7 @@
 """
 Interface to the env_run.xml file.  This class inherits from EnvBase
 """
+
 from CIME.XML.standard_module_setup import *
 
 from CIME.XML.env_base import EnvBase

CIME/XML/env_test.py

@@ -1,6 +1,7 @@
 """
 Interface to the env_test.xml file.  This class inherits from EnvBase
 """
+
 from CIME.XML.standard_module_setup import *
 
 from CIME.XML.env_base import EnvBase

CIME/XML/generic_xml.py

@@ -2,6 +2,7 @@
 Common interface to XML files, this is an abstract class and is expected to
 be used by other XML interface modules and not directly.
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.utils import safe_copy, get_src_root
 
@@ -399,10 +400,12 @@ def get_child(self, name=None, attributes=None, root=None, err_msg=None):
         )
         expect(
             child,
-            err_msg
-            if err_msg
-            else "Expected one child, found None with name '{}' and attribs '{}' in file {}".format(
-                name, attributes, self.filename
+            (
+                err_msg
+                if err_msg
+                else "Expected one child, found None with name '{}' and attribs '{}' in file {}".format(
+                    name, attributes, self.filename
+                )
             ),
         )
         return child
@@ -419,10 +422,12 @@ def get_optional_child(self, name=None, attributes=None, root=None, err_msg=None
 
         expect(
             len(children) <= 1,
-            err_msg
-            if err_msg
-            else "Multiple matches for name '{}' and attribs '{}' in file {}".format(
-                name, attributes, self.filename
+            (
+                err_msg
+                if err_msg
+                else "Multiple matches for name '{}' and attribs '{}' in file {}".format(
+                    name, attributes, self.filename
+                )
             ),
         )
         return children[0] if children else None

CIME/XML/headers.py

@@ -1,6 +1,7 @@
 """
 Interface to the config_headers.xml file.  This class inherits from EntryID.py
 """
+
 from CIME.XML.standard_module_setup import *
 
 from CIME.XML.generic_xml import GenericXML

CIME/XML/inputdata.py

@@ -1,6 +1,7 @@
 """
 Interface to the config_inputdata.xml file.  This class inherits from GenericXML.py
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.XML.generic_xml import GenericXML
 from CIME.XML.files import Files

CIME/XML/machines.py

@@ -5,7 +5,13 @@
 from CIME.XML.standard_module_setup import *
 from CIME.XML.generic_xml import GenericXML
 from CIME.XML.files import Files
-from CIME.utils import CIMEError, expect, convert_to_unknown_type, get_cime_config
+from CIME.utils import (
+    CIMEError,
+    expect,
+    convert_to_unknown_type,
+    get_cime_config,
+    get_config_dir,
+)
 
 import re
 import logging
@@ -99,14 +105,14 @@ def __init__(
 
         GenericXML.__init__(self, infile, schema, read_only=read_only)
 
-        # Append the contents of $HOME/.cime/config_machines.xml if it exists.
+        # Append the contents of $HOME/get_config_dir()/config_machines.xml if it exists.
         #
         # Also append the contents of a config_machines.xml file in the directory given by
         # extra_machines_dir, if present.
         #
         # This could cause problems if node matches are repeated when only one is expected.
         local_infile = os.path.join(
-            os.environ.get("HOME"), ".cime", "config_machines.xml"
+            os.environ.get("HOME"), get_config_dir(), "config_machines.xml"
         )
         logger.debug("Infile: {}".format(local_infile))
 
@@ -349,7 +355,9 @@ def set_machine(self, machine, schema=None):
         if machine == "Query":
             return machine
         elif self.get_version() == 3:
-            machines_file = Path.home() / ".cime" / machine / "config_machines.xml"
+            machines_file = (
+                Path.home() / get_config_dir() / machine / "config_machines.xml"
+            )
 
             if machines_file.exists():
                 GenericXML.read(

CIME/XML/namelist_definition.py

@@ -32,7 +32,6 @@
 
 
 class CaseInsensitiveDict(dict):
-
     """Basic case insensitive dict with strings only keys.
     From https://stackoverflow.com/a/27890005"""
 
@@ -65,7 +64,6 @@ def __setitem__(self, k, v):
 
 
 class NamelistDefinition(EntryID):
-
     """Class representing variable definitions for a namelist.
     This class inherits from `EntryID`, and supports most inherited methods;
     however, `set_value` is unsupported.

CIME/XML/pes.py

@@ -1,6 +1,7 @@
 """
 Interface to the config_pes.xml file.  This class inherits from GenericXML.py
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.XML.generic_xml import GenericXML
 from CIME.XML.files import Files

CIME/XML/pio.py

@@ -1,6 +1,7 @@
 """
 Class for config_pio files .  This class inherits from EntryID.py
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.XML.entry_id import EntryID
 from CIME.XML.files import Files

CIME/XML/postprocessing.py

@@ -5,7 +5,7 @@
 from CIME.XML.standard_module_setup import *
 from CIME.XML.entry_id import EntryID
 from CIME.XML.files import Files
-from CIME.utils import expect
+from CIME.utils import expect, get_config_dir
 
 logger = logging.getLogger(__name__)
 
@@ -31,10 +31,10 @@ def __init__(self, infile=None, files=None):
 
         EntryID.__init__(self, infile, schema=schema)
 
-        # Append the contents of $HOME/.cime/config_postprocessing.xml if it exists
+        # Append the contents of $HOME/get_config_dir()/config_postprocessing.xml if it exists
         # This could cause problems if node matchs are repeated when only one is expected
         infile = os.path.join(
-            os.environ.get("HOME"), ".cime", "config_postprocessing.xml"
+            os.environ.get("HOME"), get_config_dir(), "config_postprocessing.xml"
         )
         if os.path.exists(infile):
             EntryID.read(self, infile)

CIME/XML/stream.py

@@ -3,6 +3,7 @@
 
 stream files predate cime and so do not conform to entry id format
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.XML.generic_xml import GenericXML
 from CIME.XML.files import Files

CIME/XML/test_reporter.py

@@ -2,6 +2,7 @@
 Interface to the testreporter xml.  This class inherits from GenericXML.py
 
 """
+
 # pylint: disable=import-error
 import urllib.parse
 import urllib.request

CIME/XML/testlist.py

@@ -35,6 +35,7 @@
 
 - workflow: adds a workflow to the test
 """
+
 from CIME.XML.standard_module_setup import *
 
 from CIME.XML.generic_xml import GenericXML

CIME/XML/tests.py

@@ -1,6 +1,7 @@
 """
 Interface to the config_tests.xml file.  This class inherits from GenericEntry
 """
+
 from CIME.XML.standard_module_setup import *
 
 from CIME.XML.generic_xml import GenericXML

CIME/XML/testspec.py

@@ -1,6 +1,7 @@
 """
 Interface to the testspec.xml file.  This class inherits from generic_xml.py
 """
+
 from CIME.XML.standard_module_setup import *
 
 from CIME.XML.generic_xml import GenericXML

CIME/XML/workflow.py

@@ -5,7 +5,7 @@
 from CIME.XML.standard_module_setup import *
 from CIME.XML.generic_xml import GenericXML
 from CIME.XML.files import Files
-from CIME.utils import expect
+from CIME.utils import expect, get_config_dir
 
 logger = logging.getLogger(__name__)
 
@@ -25,9 +25,11 @@ def __init__(self, infile=None, files=None):
 
         GenericXML.__init__(self, infile, schema=schema)
 
-        # Append the contents of $HOME/.cime/config_workflow.xml if it exists
+        # Append the contents of $HOME/get_config_dir()/config_workflow.xml if it exists
         # This could cause problems if node matchs are repeated when only one is expected
-        infile = os.path.join(os.environ.get("HOME"), ".cime", "config_workflow.xml")
+        infile = os.path.join(
+            os.environ.get("HOME"), get_config_dir(), "config_workflow.xml"
+        )
         if os.path.exists(infile):
             GenericXML.read(self, infile)
 

CIME/build_scripts/buildlib.pio

@@ -105,7 +105,11 @@ def buildlib(bldroot, installpath, case):
     elif pio_version == 1:
         cmake_opts = '"-D GENF90_PATH=$CIMEROOT/CIME/non_py/externals/genf90 "'
     else:
-        cmake_opts = '"-D GENF90_PATH=' + srcroot + '/libraries/parallelio/scripts/ "'
+        cmake_opts = (
+            '"-DCMAKE_POLICY_VERSION_MINIMUM=3.5 -D GENF90_PATH='
+            + srcroot
+            + '/libraries/parallelio/scripts/ "'
+        )
 
     stdargs = get_standard_makefile_args(case, shared_lib=True)
 

CIME/tests/test_sys_bless_tests_results.py

@@ -214,5 +214,5 @@ def test_rebless_namelist(self):
 
         # Basic namelist compare should now pass again
         self._create_test(compargs)
-
-        self.verify_perms(self._baseline_area)
+        if self._config.test_mode == "e3sm":
+            self.verify_perms(self._baseline_area)