spack config: new subcommands add/remove (#13920)

spack config add <value>: add nested value value to the configuration scope specified
spack config remove/rm: remove specified configuration from the relevant scope

12 files changed, 718 insertions, 102 deletions

diff --git a/lib/spack/spack/cmd/config.py b/lib/spack/spack/cmd/config.py
index b1a6454555..954d4e4585 100644
--- a/lib/spack/spack/cmd/config.py
+++ b/lib/spack/spack/cmd/config.py
@@ -5,12 +5,14 @@
 
 from __future__ import print_function
 import os
+import re
 
 import llnl.util.tty as tty
 
 import spack.config
+import spack.schema.env
 import spack.environment as ev
-
+import spack.util.spack_yaml as syaml
 from spack.util.editor import editor
 
 description = "get and set configuration options"
@@ -58,24 +60,48 @@ def setup_parser(subparser):
 
     sp.add_parser('list', help='list configuration sections')
 
+    add_parser = sp.add_parser('add', help='add configuration parameters')
+    add_parser.add_argument(
+        'path', nargs='?',
+        help="colon-separated path to config that should be added,"
+        " e.g. 'config:default:true'")
+    add_parser.add_argument(
+        '-f', '--file',
+        help="file from which to set all config values"
+    )
+
+    remove_parser = sp.add_parser('remove', aliases=['rm'],
+                                  help='remove configuration parameters')
+    remove_parser.add_argument(
+        'path',
+        help="colon-separated path to config that should be removed,"
+        " e.g. 'config:default:true'")
+
+    # Make the add parser available later
+    setup_parser.add_parser = add_parser
+
 
 def _get_scope_and_section(args):
     """Extract config scope and section from arguments."""
     scope = args.scope
-    section = args.section
+    section = getattr(args, 'section', None)
+    path = getattr(args, 'path', None)
 
     # w/no args and an active environment, point to env manifest
-    if not args.section:
+    if not section:
         env = ev.get_env(args, 'config edit')
         if env:
             scope = env.env_file_config_scope_name()
 
     # set scope defaults
-    elif not args.scope:
-        if section == 'compilers':
-            scope = spack.config.default_modify_scope()
-        else:
-            scope = 'user'
+    elif not scope:
+        scope = spack.config.default_modify_scope(section)
+
+    # special handling for commands that take value instead of section
+    if path:
+        section = path[:path.find(':')] if ':' in path else path
+        if not scope:
+            scope = spack.config.default_modify_scope(section)
 
     return scope, section
 
@@ -135,11 +161,126 @@ def config_list(args):
     print(' '.join(list(spack.config.section_schemas)))
 
 
+def set_config(args, section, new, scope):
+    if re.match(r'env.*', scope):
+        e = ev.get_env(args, 'config add')
+        e.set_config(section, new)
+    else:
+        spack.config.set(section, new, scope=scope)
+
+
+def config_add(args):
+    """Add the given configuration to the specified config scope
+
+    This is a stateful operation that edits the config files."""
+    if not (args.file or args.path):
+        tty.error("No changes requested. Specify a file or value.")
+        setup_parser.add_parser.print_help()
+        exit(1)
+
+    scope, section = _get_scope_and_section(args)
+
+    # Updates from file
+    if args.file:
+        # Get file as config dict
+        data = spack.config.read_config_file(args.file)
+        if any(k in data for k in spack.schema.env.keys):
+            data = ev.config_dict(data)
+
+        # update all sections from config dict
+        # We have to iterate on keys to keep overrides from the file
+        for section in data.keys():
+            if section in spack.config.section_schemas.keys():
+                # Special handling for compiler scope difference
+                # Has to be handled after we choose a section
+                if scope is None:
+                    scope = spack.config.default_modify_scope(section)
+
+                value = data[section]
+                existing = spack.config.get(section, scope=scope)
+                new = spack.config.merge_yaml(existing, value)
+
+                set_config(args, section, new, scope)
+
+    if args.path:
+        components = spack.config.process_config_path(args.path)
+
+        has_existing_value = True
+        path = ''
+        override = False
+        for idx, name in enumerate(components[:-1]):
+            # First handle double colons in constructing path
+            colon = '::' if override else ':' if path else ''
+            path += colon + name
+            if getattr(name, 'override', False):
+                override = True
+            else:
+                override = False
+
+            # Test whether there is an existing value at this level
+            existing = spack.config.get(path, scope=scope)
+
+            if existing is None:
+                has_existing_value = False
+                # We've nested further than existing config, so we need the
+                # type information for validation to know how to handle bare
+                # values appended to lists.
+                existing = spack.config.get_valid_type(path)
+
+                # construct value from this point down
+                value = syaml.load_config(components[-1])
+                for component in reversed(components[idx + 1:-1]):
+                    value = {component: value}
+                break
+
+        if has_existing_value:
+            path, _, value = args.path.rpartition(':')
+            value = syaml.load_config(value)
+            existing = spack.config.get(path, scope=scope)
+
+        # append values to lists
+        if isinstance(existing, list) and not isinstance(value, list):
+            value = [value]
+
+        # merge value into existing
+        new = spack.config.merge_yaml(existing, value)
+        set_config(args, path, new, scope)
+
+
+def config_remove(args):
+    """Remove the given configuration from the specified config scope
+
+    This is a stateful operation that edits the config files."""
+    scope, _ = _get_scope_and_section(args)
+
+    path, _, value = args.path.rpartition(':')
+    existing = spack.config.get(path, scope=scope)
+
+    if not isinstance(existing, (list, dict)):
+        path, _, value = path.rpartition(':')
+        existing = spack.config.get(path, scope=scope)
+
+    value = syaml.load(value)
+
+    if isinstance(existing, list):
+        values = value if isinstance(value, list) else [value]
+        for v in values:
+            existing.remove(v)
+    elif isinstance(existing, dict):
+        existing.pop(value, None)
+    else:
+        # This should be impossible to reach
+        raise spack.config.ConfigError('Config has nested non-dict values')
+
+    set_config(args, path, existing, scope)
+
+
 def config(parser, args):
-    action = {
-        'get': config_get,
-        'blame': config_blame,
-        'edit': config_edit,
-        'list': config_list,
-    }
+    action = {'get': config_get,
+              'blame': config_blame,
+              'edit': config_edit,
+              'list': config_list,
+              'add': config_add,
+              'rm': config_remove,
+              'remove': config_remove}
     action[args.config_command](args)
diff --git a/lib/spack/spack/cmd/external.py b/lib/spack/spack/cmd/external.py
index f93deaba03..afdd40e2a0 100644
--- a/lib/spack/spack/cmd/external.py
+++ b/lib/spack/spack/cmd/external.py
@@ -186,7 +186,7 @@ def _update_pkg_config(pkg_to_entries, not_buildable):
     cfg_scope = spack.config.default_modify_scope()
     pkgs_cfg = spack.config.get('packages', scope=cfg_scope)
 
-    spack.config._merge_yaml(pkgs_cfg, pkg_to_cfg)
+    spack.config.merge_yaml(pkgs_cfg, pkg_to_cfg)
     spack.config.set('packages', pkgs_cfg, scope=cfg_scope)
 
 
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 445d62d2ab..a3d8101cad 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -56,12 +56,12 @@ import spack.schema.packages
 import spack.schema.modules
 import spack.schema.config
 import spack.schema.upstreams
+import spack.schema.env
 from spack.error import SpackError
 
 # Hacked yaml for configuration files preserves line numbers.
 import spack.util.spack_yaml as syaml
 
-
 #: Dict from section names -> schema for that section
 section_schemas = {
     'compilers': spack.schema.compilers.schema,
@@ -70,9 +70,15 @@ section_schemas = {
     'packages': spack.schema.packages.schema,
     'modules': spack.schema.modules.schema,
     'config': spack.schema.config.schema,
-    'upstreams': spack.schema.upstreams.schema
+    'upstreams': spack.schema.upstreams.schema,
 }
 
+# Same as above, but including keys for environments
+# this allows us to unify config reading between configs and environments
+all_schemas = copy.deepcopy(section_schemas)
+all_schemas.update(dict((key, spack.schema.env.schema)
+                        for key in spack.schema.env.keys))
+
 #: Builtin paths to configuration files in Spack
 configuration_paths = (
     # Default configuration scope is the lowest-level scope. These are
@@ -142,19 +148,21 @@ class ConfigScope(object):
         if section not in self.sections:
             path   = self.get_section_filename(section)
             schema = section_schemas[section]
-            data   = _read_config_file(path, schema)
+            data   = read_config_file(path, schema)
             self.sections[section] = data
         return self.sections[section]
 
     def write_section(self, section):
         filename = self.get_section_filename(section)
         data = self.get_section(section)
-        validate(data, section_schemas[section])
+
+        # We copy data here to avoid adding defaults at write time
+        validate_data = copy.deepcopy(data)
+        validate(validate_data, section_schemas[section])
 
         try:
             mkdirp(self.path)
             with open(filename, 'w') as f:
-                validate(data, section_schemas[section])
                 syaml.dump_config(data, stream=f, default_flow_style=False)
         except (yaml.YAMLError, IOError) as e:
             raise ConfigFileError(
@@ -217,7 +225,7 @@ class SingleFileScope(ConfigScope):
         #   }
         # }
         if self._raw_data is None:
-            self._raw_data = _read_config_file(self.path, self.schema)
+            self._raw_data = read_config_file(self.path, self.schema)
             if self._raw_data is None:
                 return None
 
@@ -376,6 +384,16 @@ class Configuration(object):
         """Non-internal scope with highest precedence."""
         return next(reversed(self.file_scopes), None)
 
+    def highest_precedence_non_platform_scope(self):
+        """Non-internal non-platform scope with highest precedence
+
+        Platform-specific scopes are of the form scope/platform"""
+        generator = reversed(self.file_scopes)
+        highest = next(generator, None)
+        while highest and '/' in highest.name:
+            highest = next(generator, None)
+        return highest
+
     def matching_scopes(self, reg_expr):
         """
         List of all scopes whose names match the provided regular expression.
@@ -435,8 +453,21 @@ class Configuration(object):
         _validate_section_name(section)  # validate section name
         scope = self._validate_scope(scope)  # get ConfigScope object
 
+        # manually preserve comments
+        need_comment_copy = (section in scope.sections and
+                             scope.sections[section] is not None)
+        if need_comment_copy:
+            comments = getattr(scope.sections[section][section],
+                               yaml.comments.Comment.attrib,
+                               None)
+
         # read only the requested section's data.
-        scope.sections[section] = {section: update_data}
+        scope.sections[section] = syaml.syaml_dict({section: update_data})
+        if need_comment_copy and comments:
+            setattr(scope.sections[section][section],
+                    yaml.comments.Comment.attrib,
+                    comments)
+
         scope.write_section(section)
 
     def get_config(self, section, scope=None):
@@ -483,14 +514,17 @@ class Configuration(object):
             if section not in data:
                 continue
 
-            merged_section = _merge_yaml(merged_section, data)
+            merged_section = merge_yaml(merged_section, data)
 
         # no config files -- empty config.
         if section not in merged_section:
-            return {}
+            return syaml.syaml_dict()
 
         # take the top key off before returning.
-        return merged_section[section]
+        ret = merged_section[section]
+        if isinstance(ret, dict):
+            ret = syaml.syaml_dict(ret)
+        return ret
 
     def get(self, path, default=None, scope=None):
         """Get a config section or a single value from one.
@@ -506,14 +540,12 @@ class Configuration(object):
 
         We use ``:`` as the separator, like YAML objects.
     """
-        # TODO: Currently only handles maps. Think about lists if neded.
-        section, _, rest = path.partition(':')
+        # TODO: Currently only handles maps. Think about lists if needed.
+        parts = process_config_path(path)
+        section = parts.pop(0)
 
         value = self.get_config(section, scope=scope)
-        if not rest:
-            return value
 
-        parts = rest.split(':')
         while parts:
             key = parts.pop(0)
             value = value.get(key, default)
@@ -525,21 +557,40 @@ class Configuration(object):
 
         Accepts the path syntax described in ``get()``.
         """
-        parts = _process_config_path(path)
+        if ':' not in path:
+            # handle bare section name as path
+            self.update_config(path, value, scope=scope)
+            return
+
+        parts = process_config_path(path)
         section = parts.pop(0)
 
-        if not parts:
-            self.update_config(section, value, scope=scope)
-        else:
-            section_data = self.get_config(section, scope=scope)
+        section_data = self.get_config(section, scope=scope)
+
+        data = section_data
+        while len(parts) > 1:
+            key = parts.pop(0)
+
+            if _override(key):
+                new = type(data[key])()
+                del data[key]
+            else:
+                new = data[key]
 
-            data = section_data
-            while len(parts) > 1:
-                key = parts.pop(0)
-                data = data[key]
-            data[parts[0]] = value
+            if isinstance(new, dict):
+                # Make it an ordered dict
+                new = syaml.syaml_dict(new)
+                # reattach to parent object
+                data[key] = new
+            data = new
 
-            self.update_config(section, section_data, scope=scope)
+        if _override(parts[0]):
+            data.pop(parts[0], None)
+
+        # update new value
+        data[parts[0]] = value
+
+        self.update_config(section, section_data, scope=scope)
 
     def __iter__(self):
         """Iterate over scopes in this configuration."""
@@ -692,26 +743,53 @@ def _validate_section_name(section):
             % (section, " ".join(section_schemas.keys())))
 
 
-def validate(data, schema, set_defaults=True):
+def validate(data, schema, filename=None):
     """Validate data read in from a Spack YAML file.
 
     Arguments:
         data (dict or list): data read from a Spack YAML file
         schema (dict or list): jsonschema to validate data
-        set_defaults (bool): whether to set defaults based on the schema
 
     This leverages the line information (start_mark, end_mark) stored
     on Spack YAML structures.
     """
     import jsonschema
+    # validate a copy to avoid adding defaults
+    # This allows us to round-trip data without adding to it.
+    test_data = copy.deepcopy(data)
+
+    if isinstance(test_data, yaml.comments.CommentedMap):
+        # HACK to fully copy ruamel CommentedMap that doesn't provide copy
+        # method. Especially necessary for environments
+        setattr(test_data,
+                yaml.comments.Comment.attrib,
+                getattr(data,
+                        yaml.comments.Comment.attrib,
+                        yaml.comments.Comment()))
+
     try:
-        spack.schema.Validator(schema).validate(data)
+        spack.schema.Validator(schema).validate(test_data)
     except jsonschema.ValidationError as e:
-        raise ConfigFormatError(e, data)
+        if hasattr(e.instance, 'lc'):
+            line_number = e.instance.lc.line + 1
+        else:
+            line_number = None
+        raise ConfigFormatError(e, data, filename, line_number)
+    # return the validated data so that we can access the raw data
+    # mostly relevant for environments
+    return test_data
 
 
-def _read_config_file(filename, schema):
-    """Read a YAML configuration file."""
+def read_config_file(filename, schema=None):
+    """Read a YAML configuration file.
+
+    User can provide a schema for validation. If no schema is provided,
+    we will infer the schema from the top-level key."""
+    # Dev: Inferring schema and allowing it to be provided directly allows us
+    # to preserve flexibility in calling convention (don't need to provide
+    # schema when it's not necessary) while allowing us to validate against a
+    # known schema when the top-level key could be incorrect.
+
     # Ignore nonexisting files.
     if not os.path.exists(filename):
         return None
@@ -729,9 +807,16 @@ def _read_config_file(filename, schema):
             data = syaml.load_config(f)
 
         if data:
+            if not schema:
+                key = next(iter(data))
+                schema = all_schemas[key]
             validate(data, schema)
         return data
 
+    except StopIteration:
+        raise ConfigFileError(
+            "Config file is empty or is not a valid YAML dict: %s" % filename)
+
     except MarkedYAMLError as e:
         raise ConfigFileError(
             "Error parsing yaml%s: %s" % (str(e.context_mark), e.problem))
@@ -772,13 +857,40 @@ def _mark_internal(data, name):
     return d
 
 
-def _merge_yaml(dest, source):
+def get_valid_type(path):
+    """Returns an instance of a type that will pass validation for path.
+
+    The instance is created by calling the constructor with no arguments.
+    If multiple types will satisfy validation for data at the configuration
+    path given, the priority order is ``list``, ``dict``, ``str``, ``bool``,
+    ``int``, ``float``.
+    """
+    components = process_config_path(path)
+    section = components[0]
+    for type in (list, syaml.syaml_dict, str, bool, int, float):
+        try:
+            ret = type()
+            test_data = ret
+            for component in reversed(components):
+                test_data = {component: test_data}
+            validate(test_data, section_schemas[section])
+            return ret
+        except (ConfigFormatError, AttributeError):
+            # This type won't validate, try the next one
+            # Except AttributeError because undefined behavior of dict ordering
+            # in python 3.5 can cause the validator to raise an AttributeError
+            # instead of a ConfigFormatError.
+            pass
+    raise ConfigError("Cannot determine valid type for path '%s'." % path)
+
+
+def merge_yaml(dest, source):
     """Merges source into dest; entries in source take precedence over dest.
 
     This routine may modify dest and should be assigned to dest, in
     case dest was None to begin with, e.g.:
 
-       dest = _merge_yaml(dest, source)
+       dest = merge_yaml(dest, source)
 
     Config file authors can optionally end any attribute in a dict
     with `::` instead of `:`, and the key will override that of the
@@ -793,6 +905,7 @@ def _merge_yaml(dest, source):
 
     # Source list is prepended (for precedence)
     if they_are(list):
+        # Make sure to copy ruamel comments
         dest[:] = source + [x for x in dest if x not in source]
         return dest
 
@@ -805,9 +918,10 @@ def _merge_yaml(dest, source):
             if _override(sk) or sk not in dest:
                 # if sk ended with ::, or if it's new, completely override
                 dest[sk] = copy.copy(sv)
+                # copy ruamel comments manually
             else:
                 # otherwise, merge the YAML
-                dest[sk] = _merge_yaml(dest[sk], source[sk])
+                dest[sk] = merge_yaml(dest[sk], source[sk])
 
             # this seems unintuitive, but see below. We need this because
             # Python dicts do not overwrite keys on insert, and we want
@@ -837,7 +951,7 @@ def _merge_yaml(dest, source):
 # Process a path argument to config.set() that may contain overrides ('::' or
 # trailing ':')
 #
-def _process_config_path(path):
+def process_config_path(path):
     result = []
     if path.startswith(':'):
         raise syaml.SpackYAMLError("Illegal leading `:' in path `{0}'".
@@ -861,13 +975,20 @@ def _process_config_path(path):
 #
 # Settings for commands that modify configuration
 #
-def default_modify_scope():
+def default_modify_scope(section='config'):
     """Return the config scope that commands should modify by default.
 
     Commands that modify configuration by default modify the *highest*
     priority scope.
+
+    Arguments:
+        section (boolean): Section for which to get the default scope.
+            If this is not 'compilers', a general (non-platform) scope is used.
     """
-    return spack.config.config.highest_precedence_scope().name
+    if section == 'compilers':
+        return spack.config.config.highest_precedence_scope().name
+    else:
+        return spack.config.config.highest_precedence_non_platform_scope().name
 
 
 def default_list_scope():
@@ -894,17 +1015,17 @@ class ConfigFormatError(ConfigError):
     """Raised when a configuration format does not match its schema."""
 
     def __init__(self, validation_error, data, filename=None, line=None):
+        # spack yaml has its own file/line marks -- try to find them
+        # we prioritize these over the inputs
+        mark = self._get_mark(validation_error, data)
+        if mark:
+            filename = mark.name
+            line = mark.line + 1
+
         self.filename = filename  # record this for ruamel.yaml
 
+        # construct location
         location = '<unknown file>'
-
-        # spack yaml has its own file/line marks -- try to find them
-        if not filename and not line:
-            mark = self._get_mark(validation_error, data)
-            if mark:
-                filename = mark.name
-                line = mark.line + 1
-
         if filename:
             location = '%s' % filename
         if line is not None:
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 1b9df358f4..bc9730e490 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -80,9 +80,6 @@ valid_environment_name_re = r'^\w[\w-]*$'
 #: version of the lockfile format. Must increase monotonically.
 lockfile_format_version = 2
 
-#: legal first keys in the spack.yaml manifest file
-env_schema_keys = ('spack', 'env')
-
 # Magic names
 # The name of the standalone spec list in the manifest yaml
 user_speclist_name = 'specs'
@@ -366,7 +363,7 @@ def create(name, init_file=None, with_view=None):
 
 def config_dict(yaml_data):
     """Get the configuration scope section out of an spack.yaml"""
-    key = spack.config.first_existing(yaml_data, env_schema_keys)
+    key = spack.config.first_existing(yaml_data, spack.schema.env.keys)
     return yaml_data[key]
 
 
@@ -392,42 +389,19 @@ def all_environments():
         yield read(name)
 
 
-def validate(data, filename=None):
-    # validating changes data by adding defaults. Return validated data
-    validate_data = copy.deepcopy(data)
-    # HACK to fully copy ruamel CommentedMap that doesn't provide copy method
-    import ruamel.yaml as yaml
-    setattr(
-        validate_data,
-        yaml.comments.Comment.attrib,
-        getattr(data, yaml.comments.Comment.attrib, yaml.comments.Comment())
-    )
-
-    import jsonschema
-    try:
-        spack.schema.Validator(spack.schema.env.schema).validate(validate_data)
-    except jsonschema.ValidationError as e:
-        if hasattr(e.instance, 'lc'):
-            line_number = e.instance.lc.line + 1
-        else:
-            line_number = None
-        raise spack.config.ConfigFormatError(
-            e, data, filename, line_number)
-    return validate_data
-
-
 def _read_yaml(str_or_file):
     """Read YAML from a file for round-trip parsing."""
     data = syaml.load_config(str_or_file)
     filename = getattr(str_or_file, 'name', None)
-    default_data = validate(data, filename)
+    default_data = spack.config.validate(
+        data, spack.schema.env.schema, filename)
     return (data, default_data)
 
 
 def _write_yaml(data, str_or_file):
     """Write YAML to a file preserving comments and dict order."""
     filename = getattr(str_or_file, 'name', None)
-    validate(data, filename)
+    spack.config.validate(data, spack.schema.env.schema, filename)
     syaml.dump_config(data, str_or_file, default_flow_style=False)
 
 
@@ -815,12 +789,21 @@ class Environment(object):
         return spack.config.SingleFileScope(config_name,
                                             self.manifest_path,
                                             spack.schema.env.schema,
-                                            [env_schema_keys])
+                                            [spack.schema.env.keys])
 
     def config_scopes(self):
         """A list of all configuration scopes for this environment."""
         return self.included_config_scopes() + [self.env_file_config_scope()]
 
+    def set_config(self, path, value):
+        """Set configuration for this environment"""
+        yaml = config_dict(self.yaml)
+        keys = spack.config.process_config_path(path)
+        for key in keys[:-1]:
+            yaml = yaml[key]
+        yaml[keys[-1]] = value
+        self.write()
+
     def destroy(self):
         """Remove this environment from Spack entirely."""
         shutil.rmtree(self.path)
@@ -1501,8 +1484,12 @@ class Environment(object):
                         del yaml_dict[key]
 
         # if all that worked, write out the manifest file at the top level
-        # Only actually write if it has changed or was never written
-        changed = self.yaml != self.raw_yaml
+        # (we used to check whether the yaml had changed and not write it out
+        # if it hadn't. We can't do that anymore because it could be the only
+        # thing that changed is the "override" attribute on a config dict,
+        # which would not show up in even a string comparison between the two
+        # keys).
+        changed = not yaml_equivalent(self.yaml, self.raw_yaml)
         written = os.path.exists(self.manifest_path)
         if changed or not written:
             self.raw_yaml = copy.deepcopy(self.yaml)
@@ -1529,6 +1516,39 @@ class Environment(object):
             activate(self._previous_active)
 
 
+def yaml_equivalent(first, second):
+    """Returns whether two spack yaml items are equivalent, including overrides
+    """
+    if isinstance(first, dict):
+        return isinstance(second, dict) and _equiv_dict(first, second)
+    elif isinstance(first, list):
+        return isinstance(second, list) and _equiv_list(first, second)
+    else:  # it's a string
+        return isinstance(second, six.string_types) and first == second
+
+
+def _equiv_list(first, second):
+    """Returns whether two spack yaml lists are equivalent, including overrides
+    """
+    if len(first) != len(second):
+        return False
+    return all(yaml_equivalent(f, s) for f, s in zip(first, second))
+
+
+def _equiv_dict(first, second):
+    """Returns whether two spack yaml dicts are equivalent, including overrides
+    """
+    if len(first) != len(second):
+        return False
+    same_values = all(yaml_equivalent(fv, sv)
+                      for fv, sv in zip(first.values(), second.values()))
+    same_keys_with_same_overrides = all(
+        fk == sk and getattr(fk, 'override', False) == getattr(sk, 'override',
+                                                               False)
+        for fk, sk in zip(first.keys(), second.keys()))
+    return same_values and same_keys_with_same_overrides
+
+
 def display_specs(concretized_specs):
     """Displays the list of specs returned by `Environment.concretize()`.
 
diff --git a/lib/spack/spack/schema/env.py b/lib/spack/spack/schema/env.py
index 907abc5c9a..6ead76416b 100644
--- a/lib/spack/spack/schema/env.py
+++ b/lib/spack/spack/schema/env.py
@@ -13,6 +13,8 @@ from llnl.util.lang import union_dicts
 import spack.schema.merged
 import spack.schema.projections
 
+#: legal first keys in the schema
+keys = ('spack', 'env')
 
 spec_list_schema = {
     'type': 'array',
diff --git a/lib/spack/spack/test/cmd/config.py b/lib/spack/spack/test/cmd/config.py
index 82a9d814ea..6dbf50676d 100644
--- a/lib/spack/spack/test/cmd/config.py
+++ b/lib/spack/spack/test/cmd/config.py
@@ -2,7 +2,7 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
+import pytest
 import os
 
 from llnl.util.filesystem import mkdirp
@@ -12,6 +12,7 @@ import spack.environment as ev
 from spack.main import SpackCommand
 
 config = SpackCommand('config')
+env = SpackCommand('env')
 
 
 def test_get_config_scope(mock_low_high_config):
@@ -46,7 +47,7 @@ repos:
 
 def test_config_edit():
     """Ensure `spack config edit` edits the right paths."""
-    dms = spack.config.default_modify_scope()
+    dms = spack.config.default_modify_scope('compilers')
     dms_path = spack.config.config.scopes[dms].path
     user_path = spack.config.config.scopes['user'].path
 
@@ -97,3 +98,308 @@ def test_config_list():
     output = config('list')
     assert 'compilers' in output
     assert 'packages' in output
+
+
+def test_config_add(mutable_empty_config):
+    config('add', 'config:dirty:true')
+    output = config('get', 'config')
+
+    assert output == """config:
+  dirty: true
+"""
+
+
+def test_config_add_list(mutable_empty_config):
+    config('add', 'config:template_dirs:test1')
+    config('add', 'config:template_dirs:[test2]')
+    config('add', 'config:template_dirs:test3')
+    output = config('get', 'config')
+
+    assert output == """config:
+  template_dirs:
+  - test3
+  - test2
+  - test1
+"""
+
+
+def test_config_add_override(mutable_empty_config):
+    config('--scope', 'site', 'add', 'config:template_dirs:test1')
+    config('add', 'config:template_dirs:[test2]')
+    output = config('get', 'config')
+
+    assert output == """config:
+  template_dirs:
+  - test2
+  - test1
+"""
+
+    config('add', 'config::template_dirs:[test2]')
+    output = config('get', 'config')
+
+    assert output == """config:
+  template_dirs:
+  - test2
+"""
+
+
+def test_config_add_override_leaf(mutable_empty_config):
+    config('--scope', 'site', 'add', 'config:template_dirs:test1')
+    config('add', 'config:template_dirs:[test2]')
+    output = config('get', 'config')
+
+    assert output == """config:
+  template_dirs:
+  - test2
+  - test1
+"""
+
+    config('add', 'config:template_dirs::[test2]')
+    output = config('get', 'config')
+
+    assert output == """config:
+  'template_dirs:':
+  - test2
+"""
+
+
+def test_config_add_update_dict(mutable_empty_config):
+    config('add', 'packages:all:compiler:[gcc]')
+    config('add', 'packages:all:version:1.0.0')
+    output = config('get', 'packages')
+
+    expected = """packages:
+  all:
+    compiler: [gcc]
+    version:
+    - 1.0.0
+"""
+
+    assert output == expected
+
+
+def test_config_add_ordered_dict(mutable_empty_config):
+    config('add', 'mirrors:first:/path/to/first')
+    config('add', 'mirrors:second:/path/to/second')
+    output = config('get', 'mirrors')
+
+    assert output == """mirrors:
+  first: /path/to/first
+  second: /path/to/second
+"""
+
+
+def test_config_add_invalid_fails(mutable_empty_config):
+    config('add', 'packages:all:variants:+debug')
+    with pytest.raises(
+        (spack.config.ConfigFormatError, AttributeError)
+    ):
+        config('add', 'packages:all:True')
+
+
+def test_config_add_from_file(mutable_empty_config, tmpdir):
+    contents = """spack:
+  config:
+    dirty: true
+"""
+
+    file = str(tmpdir.join('spack.yaml'))
+    with open(file, 'w') as f:
+        f.write(contents)
+    config('add', '-f', file)
+    output = config('get', 'config')
+
+    assert output == """config:
+  dirty: true
+"""
+
+
+def test_config_add_from_file_multiple(mutable_empty_config, tmpdir):
+    contents = """spack:
+  config:
+    dirty: true
+    template_dirs: [test1]
+"""
+
+    file = str(tmpdir.join('spack.yaml'))
+    with open(file, 'w') as f:
+        f.write(contents)
+    config('add', '-f', file)
+    output = config('get', 'config')
+
+    assert output == """config:
+  dirty: true
+  template_dirs: [test1]
+"""
+
+
+def test_config_add_override_from_file(mutable_empty_config, tmpdir):
+    config('--scope', 'site', 'add', 'config:template_dirs:test1')
+    contents = """spack:
+  config::
+    template_dirs: [test2]
+"""
+
+    file = str(tmpdir.join('spack.yaml'))
+    with open(file, 'w') as f:
+        f.write(contents)
+    config('add', '-f', file)
+    output = config('get', 'config')
+
+    assert output == """config:
+  template_dirs: [test2]
+"""
+
+
+def test_config_add_override_leaf_from_file(mutable_empty_config, tmpdir):
+    config('--scope', 'site', 'add', 'config:template_dirs:test1')
+    contents = """spack:
+  config:
+    template_dirs:: [test2]
+"""
+
+    file = str(tmpdir.join('spack.yaml'))
+    with open(file, 'w') as f:
+        f.write(contents)
+    config('add', '-f', file)
+    output = config('get', 'config')
+
+    assert output == """config:
+  'template_dirs:': [test2]
+"""
+
+
+def test_config_add_update_dict_from_file(mutable_empty_config, tmpdir):
+    config('add', 'packages:all:compiler:[gcc]')
+
+    # contents to add to file
+    contents = """spack:
+  packages:
+    all:
+      version:
+      - 1.0.0
+"""
+
+    # create temp file and add it to config
+    file = str(tmpdir.join('spack.yaml'))
+    with open(file, 'w') as f:
+        f.write(contents)
+    config('add', '-f', file)
+
+    # get results
+    output = config('get', 'packages')
+
+    expected = """packages:
+  all:
+    compiler: [gcc]
+    version:
+    - 1.0.0
+"""
+
+    assert output == expected
+
+
+def test_config_add_invalid_file_fails(tmpdir):
+    # contents to add to file
+    # invalid because version requires a list
+    contents = """spack:
+  packages:
+    all:
+      version: 1.0.0
+"""
+
+    # create temp file and add it to config
+    file = str(tmpdir.join('spack.yaml'))
+    with open(file, 'w') as f:
+        f.write(contents)
+
+    with pytest.raises(
+        (spack.config.ConfigFormatError)
+    ):
+        config('add', '-f', file)
+
+
+def test_config_remove_value(mutable_empty_config):
+    config('add', 'config:dirty:true')
+    config('remove', 'config:dirty:true')
+    output = config('get', 'config')
+
+    assert output == """config: {}
+"""
+
+
+def test_config_remove_alias_rm(mutable_empty_config):
+    config('add', 'config:dirty:true')
+    config('rm', 'config:dirty:true')
+    output = config('get', 'config')
+
+    assert output == """config: {}
+"""
+
+
+def test_config_remove_dict(mutable_empty_config):
+    config('add', 'config:dirty:true')
+    config('rm', 'config:dirty')
+    output = config('get', 'config')
+
+    assert output == """config: {}
+"""
+
+
+def test_remove_from_list(mutable_empty_config):
+    config('add', 'config:template_dirs:test1')
+    config('add', 'config:template_dirs:[test2]')
+    config('add', 'config:template_dirs:test3')
+    config('remove', 'config:template_dirs:test2')
+    output = config('get', 'config')
+
+    assert output == """config:
+  template_dirs:
+  - test3
+  - test1
+"""
+
+
+def test_remove_list(mutable_empty_config):
+    config('add', 'config:template_dirs:test1')
+    config('add', 'config:template_dirs:[test2]')
+    config('add', 'config:template_dirs:test3')
+    config('remove', 'config:template_dirs:[test2]')
+    output = config('get', 'config')
+
+    assert output == """config:
+  template_dirs:
+  - test3
+  - test1
+"""
+
+
+def test_config_add_to_env(mutable_empty_config, mutable_mock_env_path):
+    env = ev.create('test')
+    with env:
+        config('add', 'config:dirty:true')
+        output = config('get')
+
+    expected = ev.default_manifest_yaml
+    expected += """  config:
+    dirty: true
+
+"""
+    assert output == expected
+
+
+def test_config_remove_from_env(mutable_empty_config, mutable_mock_env_path):
+    env('create', 'test')
+
+    with ev.read('test'):
+        config('add', 'config:dirty:true')
+
+    with ev.read('test'):
+        config('rm', 'config:dirty')
+        output = config('get')
+
+    expected = ev.default_manifest_yaml
+    expected += """  config: {}
+
+"""
+    assert output == expected
diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py
index 8212db6c21..88132e8672 100644
--- a/lib/spack/spack/test/config.py
+++ b/lib/spack/spack/test/config.py
@@ -576,7 +576,7 @@ def get_config_error(filename, schema, yaml_string):
 
     # parse and return error, or fail.
     try:
-        spack.config._read_config_file(filename, schema)
+        spack.config.read_config_file(filename, schema)
     except spack.config.ConfigFormatError as e:
         return e
     else:
diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py
index 8bd8deadce..1efdd6ba95 100644
--- a/lib/spack/spack/test/conftest.py
+++ b/lib/spack/spack/test/conftest.py
@@ -375,6 +375,19 @@ def linux_os():
 
 
 @pytest.fixture(scope='session')
+def default_config():
+    """Isolates the default configuration from the user configs.
+
+    This ensures we can test the real default configuration without having
+    tests fail when the user overrides the defaults that we test against."""
+    defaults_path = os.path.join(spack.paths.etc_path, 'spack', 'defaults')
+    defaults_scope = spack.config.ConfigScope('defaults', defaults_path)
+    defaults_config = spack.config.Configuration(defaults_scope)
+    with use_configuration(defaults_config):
+        yield defaults_config
+
+
+@pytest.fixture(scope='session')
 def configuration_dir(tmpdir_factory, linux_os):
     """Copies mock configuration files in a temporary directory. Returns the
     directory path.
@@ -436,6 +449,19 @@ def mutable_config(tmpdir_factory, configuration_dir):
         yield cfg
 
 
+@pytest.fixture(scope='function')
+def mutable_empty_config(tmpdir_factory, configuration_dir):
+    """Empty configuration that can be modified by the tests."""
+    mutable_dir = tmpdir_factory.mktemp('mutable_config').join('tmp')
+
+    cfg = spack.config.Configuration(
+        *[spack.config.ConfigScope(name, str(mutable_dir.join(name)))
+          for name in ['site', 'system', 'user']])
+
+    with use_configuration(cfg):
+        yield cfg
+
+
 @pytest.fixture()
 def mock_low_high_config(tmpdir):
     """Mocks two configuration scopes: 'low' and 'high'."""
diff --git a/lib/spack/spack/test/container/cli.py b/lib/spack/spack/test/container/cli.py
index 8e5403f072..f9b3b43f83 100644
--- a/lib/spack/spack/test/container/cli.py
+++ b/lib/spack/spack/test/container/cli.py
@@ -9,8 +9,8 @@ import spack.main
 containerize = spack.main.SpackCommand('containerize')
 
 
-def test_command(configuration_dir, capsys):
+def test_command(default_config, container_config_dir, capsys):
     with capsys.disabled():
-        with fs.working_dir(configuration_dir):
+        with fs.working_dir(container_config_dir):
             output = containerize()
     assert 'FROM spack/ubuntu-bionic' in output
diff --git a/lib/spack/spack/test/container/conftest.py b/lib/spack/spack/test/container/conftest.py
index 802b34c5f8..65a89b0748 100644
--- a/lib/spack/spack/test/container/conftest.py
+++ b/lib/spack/spack/test/container/conftest.py
@@ -39,5 +39,5 @@ def config_dumper(tmpdir):
 
 
 @pytest.fixture()
-def configuration_dir(minimal_configuration, config_dumper):
+def container_config_dir(minimal_configuration, config_dumper):
     return config_dumper(minimal_configuration)
diff --git a/lib/spack/spack/test/container/docker.py b/lib/spack/spack/test/container/docker.py
index fbdc085828..f75ae7de2a 100644
--- a/lib/spack/spack/test/container/docker.py
+++ b/lib/spack/spack/test/container/docker.py
@@ -42,7 +42,7 @@ def test_packages(minimal_configuration):
     assert p.list == pkgs
 
 
-def test_ensure_render_works(minimal_configuration):
+def test_ensure_render_works(minimal_configuration, default_config):
     # Here we just want to ensure that nothing is raised
     writer = writers.create(minimal_configuration)
     writer()
diff --git a/lib/spack/spack/test/container/singularity.py b/lib/spack/spack/test/container/singularity.py
index 445a119f6c..ab342cacec 100644
--- a/lib/spack/spack/test/container/singularity.py
+++ b/lib/spack/spack/test/container/singularity.py
@@ -13,7 +13,7 @@ def singularity_configuration(minimal_configuration):
     return minimal_configuration
 
 
-def test_ensure_render_works(singularity_configuration):
+def test_ensure_render_works(default_config, singularity_configuration):
     container_config = singularity_configuration['spack']['container']
     assert container_config['format'] == 'singularity'
     # Here we just want to ensure that nothing is raised