spack/lib/spack/spack/environment/environment.py

# Copyright Spack Project Developers. See COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import collections
import collections.abc
import contextlib
import errno
import os
import pathlib
import re
import shutil
import stat
import urllib.parse
import urllib.request
import warnings
from typing import Any, Dict, Iterable, List, Optional, Sequence, Tuple, Union

import llnl.util.filesystem as fs
import llnl.util.tty as tty
import llnl.util.tty.color as clr
from llnl.util.link_tree import ConflictingSpecsError
from llnl.util.symlink import islink, readlink, symlink

import spack
import spack.caches
import spack.concretize
import spack.config
import spack.deptypes as dt
import spack.error
import spack.filesystem_view as fsv
import spack.hash_types as ht
import spack.paths
import spack.repo
import spack.schema.env
import spack.schema.merged
import spack.spec
import spack.spec_list
import spack.store
import spack.user_environment as uenv
import spack.util.environment
import spack.util.hash
import spack.util.lock as lk
import spack.util.path
import spack.util.spack_json as sjson
import spack.util.spack_yaml as syaml
import spack.util.url
from spack import traverse
from spack.installer import PackageInstaller
from spack.schema.env import TOP_LEVEL_KEY
from spack.spec import Spec
from spack.spec_list import SpecList
from spack.util.path import substitute_path_variables

SpecPair = spack.concretize.SpecPair

#: environment variable used to indicate the active environment
spack_env_var = "SPACK_ENV"

#: environment variable used to indicate the active environment view
spack_env_view_var = "SPACK_ENV_VIEW"

#: currently activated environment
_active_environment: Optional["Environment"] = None


#: default path where environments are stored in the spack tree
default_env_path = os.path.join(spack.paths.var_path, "environments")


#: Name of the input yaml file for an environment
manifest_name = "spack.yaml"


#: Name of the input yaml file for an environment
lockfile_name = "spack.lock"


#: Name of the directory where environments store repos, logs, views, configs
env_subdir_name = ".spack-env"


def env_root_path() -> str:
    """Override default root path if the user specified it"""
    return spack.util.path.canonicalize_path(
        spack.config.get("config:environments_root", default=default_env_path)
    )


def environment_name(path: Union[str, pathlib.Path]) -> str:
    """Human-readable representation of the environment.

    This is the path for directory environments, and just the name
    for managed environments.
    """
    path_str = str(path)
    if path_str.startswith(env_root_path()):
        return os.path.basename(path_str)
    else:
        return path_str


def ensure_no_disallowed_env_config_mods(scopes: List[spack.config.ConfigScope]) -> None:
    for scope in scopes:
        config = scope.get_section("config")
        if config and "environments_root" in config["config"]:
            raise SpackEnvironmentError(
                "Spack environments are prohibited from modifying 'config:environments_root' "
                "because it can make the definition of the environment ill-posed. Please "
                "remove from your environment and place it in a permanent scope such as "
                "defaults, system, site, etc."
            )


def default_manifest_yaml():
    """default spack.yaml file to put in new environments"""
    return """\
# This is a Spack Environment file.
#
# It describes a set of packages to be installed, along with
# configuration settings.
spack:
  # add package specs to the `specs` list
  specs: []
  view: true
  concretizer:
    unify: {}
""".format(
        "true" if spack.config.get("concretizer:unify") else "false"
    )


#: regex for validating enviroment names
valid_environment_name_re = r"^\w[\w-]*$"

#: version of the lockfile format. Must increase monotonically.
lockfile_format_version = 5


READER_CLS = {
    1: spack.spec.SpecfileV1,
    2: spack.spec.SpecfileV1,
    3: spack.spec.SpecfileV2,
    4: spack.spec.SpecfileV3,
    5: spack.spec.SpecfileV4,
}


# Magic names
# The name of the standalone spec list in the manifest yaml
user_speclist_name = "specs"
# The name of the default view (the view loaded on env.activate)
default_view_name = "default"
# Default behavior to link all packages into views (vs. only root packages)
default_view_link = "all"
# The name for any included concrete specs
included_concrete_name = "include_concrete"


def installed_specs():
    """
    Returns the specs of packages installed in the active environment or None
    if no packages are installed.
    """
    env = active_environment()
    hashes = env.all_hashes() if env else None
    return spack.store.STORE.db.query(hashes=hashes)


def valid_env_name(name):
    return re.match(valid_environment_name_re, name)


def validate_env_name(name):
    if not valid_env_name(name):
        raise ValueError(
            (
                "'%s': names must start with a letter, and only contain "
                "letters, numbers, _, and -."
            )
            % name
        )
    return name


def activate(env, use_env_repo=False):
    """Activate an environment.

    To activate an environment, we add its manifest's configuration scope to the
    existing Spack configuration, and we set active to the current environment.

    Arguments:
        env (Environment): the environment to activate
        use_env_repo (bool): use the packages exactly as they appear in the
            environment's repository
    """
    global _active_environment

    # Fail early to avoid ending in an invalid state
    if not isinstance(env, Environment):
        raise TypeError("`env` should be of type {0}".format(Environment.__name__))

    # Check if we need to reinitialize the store due to pushing the configuration
    # below.
    install_tree_before = spack.config.get("config:install_tree")
    upstreams_before = spack.config.get("upstreams")
    env.manifest.prepare_config_scope()
    install_tree_after = spack.config.get("config:install_tree")
    upstreams_after = spack.config.get("upstreams")
    if install_tree_before != install_tree_after or upstreams_before != upstreams_after:
        # Hack to store the state of the store before activation
        env.store_token = spack.store.reinitialize()

    if use_env_repo:
        spack.repo.PATH.put_first(env.repo)

    tty.debug("Using environment '%s'" % env.name)

    # Do this last, because setting up the config must succeed first.
    _active_environment = env


def deactivate():
    """Undo any configuration or repo settings modified by ``activate()``."""
    global _active_environment

    if not _active_environment:
        return

    # If we attached a store token on activation, restore the previous state
    # and consume the token
    if hasattr(_active_environment, "store_token"):
        spack.store.restore(_active_environment.store_token)
        delattr(_active_environment, "store_token")
    _active_environment.manifest.deactivate_config_scope()

    # use _repo so we only remove if a repo was actually constructed
    if _active_environment._repo:
        spack.repo.PATH.remove(_active_environment._repo)

    tty.debug("Deactivated environment '%s'" % _active_environment.name)

    _active_environment = None


def active_environment() -> Optional["Environment"]:
    """Returns the active environment when there is any"""
    return _active_environment


def _root(name):
    """Non-validating version of root(), to be used internally."""
    return os.path.join(env_root_path(), name)


def root(name):
    """Get the root directory for an environment by name."""
    validate_env_name(name)
    return _root(name)


def exists(name):
    """Whether an environment with this name exists or not."""
    return valid_env_name(name) and os.path.isdir(_root(name))


def active(name):
    """True if the named environment is active."""
    return _active_environment and name == _active_environment.name


def is_env_dir(path):
    """Whether a directory contains a spack environment."""
    return os.path.isdir(path) and os.path.exists(os.path.join(path, manifest_name))


def as_env_dir(name_or_dir):
    """Translate an environment name or directory to the environment directory"""
    if is_env_dir(name_or_dir):
        return name_or_dir
    else:
        validate_env_name(name_or_dir)
        if not exists(name_or_dir):
            raise SpackEnvironmentError("no such environment '%s'" % name_or_dir)
        return root(name_or_dir)


def environment_from_name_or_dir(name_or_dir):
    """Get an environment with the supplied name."""
    return Environment(as_env_dir(name_or_dir))


def read(name):
    """Get an environment with the supplied name."""
    validate_env_name(name)
    if not exists(name):
        raise SpackEnvironmentError("no such environment '%s'" % name)
    return Environment(root(name))


def create(
    name: str,
    init_file: Optional[Union[str, pathlib.Path]] = None,
    with_view: Optional[Union[str, pathlib.Path, bool]] = None,
    keep_relative: bool = False,
    include_concrete: Optional[List[str]] = None,
) -> "Environment":
    """Create a managed environment in Spack and returns it.

    A managed environment is created in a root directory managed by this Spack instance, so that
    Spack can keep track of them.

    Files with suffix ``.json`` or ``.lock`` are considered lockfiles. Files with any other name
    are considered manifest files.

    Args:
        name: name of the managed environment
        init_file: either a lockfile, a manifest file, or None
        with_view: whether a view should be maintained for the environment. If the value is a
            string, it specifies the path to the view
        keep_relative: if True, develop paths are copied verbatim into the new environment file,
            otherwise they are made absolute
        include_concrete: list of concrete environment names/paths to be included
    """
    environment_dir = environment_dir_from_name(name, exists_ok=False)
    return create_in_dir(
        environment_dir,
        init_file=init_file,
        with_view=with_view,
        keep_relative=keep_relative,
        include_concrete=include_concrete,
    )


def create_in_dir(
    root: Union[str, pathlib.Path],
    init_file: Optional[Union[str, pathlib.Path]] = None,
    with_view: Optional[Union[str, pathlib.Path, bool]] = None,
    keep_relative: bool = False,
    include_concrete: Optional[List[str]] = None,
) -> "Environment":
    """Create an environment in the directory passed as input and returns it.

    Files with suffix ``.json`` or ``.lock`` are considered lockfiles. Files with any other name
    are considered manifest files.

    Args:
        root: directory where to create the environment.
        init_file: either a lockfile, a manifest file, or None
        with_view: whether a view should be maintained for the environment. If the value is a
            string, it specifies the path to the view
        keep_relative: if True, develop paths are copied verbatim into the new environment file,
            otherwise they are made absolute
        include_concrete: concrete environment names/paths to be included
    """
    initialize_environment_dir(root, envfile=init_file)

    if with_view is None and keep_relative:
        return Environment(root)

    try:
        manifest = EnvironmentManifestFile(root)

        if with_view is not None:
            manifest.set_default_view(with_view)

        if include_concrete is not None:
            set_included_envs_to_env_paths(include_concrete)
            validate_included_envs_exists(include_concrete)
            validate_included_envs_concrete(include_concrete)
            manifest.set_include_concrete(include_concrete)

        manifest.flush()

    except (spack.config.ConfigFormatError, SpackEnvironmentConfigError) as e:
        shutil.rmtree(root)
        raise e

    env = Environment(root)

    if init_file:
        init_file_dir = os.path.abspath(os.path.dirname(init_file))

        if not keep_relative:
            if env.path != init_file_dir:
                # If we are here, we are creating an environment based on an
                # spack.yaml file in another directory, and moreover we want
                # dev paths in this environment to refer to their original
                # locations.
                _rewrite_relative_dev_paths_on_relocation(env, init_file_dir)

    return env


def _rewrite_relative_dev_paths_on_relocation(env, init_file_dir):
    """When initializing the environment from a manifest file and we plan
    to store the environment in a different directory, we have to rewrite
    relative paths to absolute ones."""
    with env:
        dev_specs = spack.config.get("develop", default={}, scope=env.scope_name)
        if not dev_specs:
            return
        for name, entry in dev_specs.items():
            dev_path = substitute_path_variables(entry["path"])
            expanded_path = spack.util.path.canonicalize_path(dev_path, default_wd=init_file_dir)

            # Skip if the expanded path is the same (e.g. when absolute)
            if dev_path == expanded_path:
                continue

            tty.debug("Expanding develop path for {0} to {1}".format(name, expanded_path))

            dev_specs[name]["path"] = expanded_path

        spack.config.set("develop", dev_specs, scope=env.scope_name)

        env._dev_specs = None
        # If we changed the environment's spack.yaml scope, that will not be reflected
        # in the manifest that we read
        env._re_read()


def environment_dir_from_name(name: str, exists_ok: bool = True) -> str:
    """Returns the directory associated with a named environment.

    Args:
        name: name of the environment
        exists_ok: if False, raise an error if the environment exists already

    Raises:
        SpackEnvironmentError: if exists_ok is False and the environment exists already
    """
    if not exists_ok and exists(name):
        raise SpackEnvironmentError(f"'{name}': environment already exists at {root(name)}")

    ensure_env_root_path_exists()
    validate_env_name(name)
    return root(name)


def ensure_env_root_path_exists():
    if not os.path.isdir(env_root_path()):
        fs.mkdirp(env_root_path())


def set_included_envs_to_env_paths(include_concrete: List[str]) -> None:
    """If the included environment(s) is the environment name
    it is replaced by the path to the environment

    Args:
        include_concrete: list of env name or path to env"""

    for i, env_name in enumerate(include_concrete):
        if is_env_dir(env_name):
            include_concrete[i] = env_name
        elif exists(env_name):
            include_concrete[i] = root(env_name)


def validate_included_envs_exists(include_concrete: List[str]) -> None:
    """Checks that all of the included environments exist

    Args:
       include_concrete: list of already existing concrete environments to include

    Raises:
        SpackEnvironmentError: if any of the included environments do not exist
    """

    missing_envs = set()

    for i, env_name in enumerate(include_concrete):
        if not is_env_dir(env_name):
            missing_envs.add(env_name)

    if missing_envs:
        msg = "The following environment(s) are missing: {0}".format(", ".join(missing_envs))
        raise SpackEnvironmentError(msg)


def validate_included_envs_concrete(include_concrete: List[str]) -> None:
    """Checks that all of the included environments are concrete

    Args:
        include_concrete: list of already existing concrete environments to include

    Raises:
        SpackEnvironmentError: if any of the included environments are not concrete
    """

    non_concrete_envs = set()

    for env_path in include_concrete:
        if not os.path.exists(Environment(env_path).lock_path):
            non_concrete_envs.add(Environment(env_path).name)

    if non_concrete_envs:
        msg = "The following environment(s) are not concrete: {0}\n" "Please run:".format(
            ", ".join(non_concrete_envs)
        )
        for env in non_concrete_envs:
            msg += f"\n\t`spack -e {env} concretize`"

        raise SpackEnvironmentError(msg)


def all_environment_names():
    """List the names of environments that currently exist."""
    # just return empty if the env path does not exist.  A read-only
    # operation like list should not try to create a directory.
    if not os.path.exists(env_root_path()):
        return []

    candidates = sorted(os.listdir(env_root_path()))
    names = []
    for candidate in candidates:
        yaml_path = os.path.join(_root(candidate), manifest_name)
        if valid_env_name(candidate) and os.path.exists(yaml_path):
            names.append(candidate)
    return names


def all_environments():
    """Generator for all managed Environments."""
    for name in all_environment_names():
        yield read(name)


def _read_yaml(str_or_file):
    """Read YAML from a file for round-trip parsing."""
    try:
        data = syaml.load_config(str_or_file)
    except syaml.SpackYAMLError as e:
        raise SpackEnvironmentConfigError(
            f"Invalid environment configuration detected: {e.message}"
        )

    filename = getattr(str_or_file, "name", None)
    spack.config.validate(data, spack.schema.env.schema, filename)
    return 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)
    spack.config.validate(data, spack.schema.env.schema, filename)
    syaml.dump_config(data, str_or_file, default_flow_style=False)


def _eval_conditional(string):
    """Evaluate conditional definitions using restricted variable scope."""
    valid_variables = spack.spec.get_host_environment()
    valid_variables.update({"re": re, "env": os.environ})
    return eval(string, valid_variables)


def _is_dev_spec_and_has_changed(spec):
    """Check if the passed spec is a dev build and whether it has changed since the
    last installation"""
    # First check if this is a dev build and in the process already try to get
    # the dev_path
    if not spec.variants.get("dev_path", None):
        return False

    # Now we can check whether the code changed since the last installation
    if not spec.installed:
        # Not installed -> nothing to compare against
        return False

    # hook so packages can use to write their own method for checking the dev_path
    # use package so attributes about concretization such as variant state can be
    # utilized
    return spec.package.detect_dev_src_change()


def _error_on_nonempty_view_dir(new_root):
    """Defensively error when the target view path already exists and is not an
    empty directory. This usually happens when the view symlink was removed, but
    not the directory it points to. In those cases, it's better to just error when
    the new view dir is non-empty, since it indicates the user removed part but not
    all of the view, and it likely in an inconsistent state."""
    # Check if the target path lexists
    try:
        st = os.lstat(new_root)
    except (IOError, OSError):
        return

    # Empty directories are fine
    if stat.S_ISDIR(st.st_mode) and len(os.listdir(new_root)) == 0:
        return

    # Anything else is an error
    raise SpackEnvironmentViewError(
        "Failed to generate environment view, because the target {} already "
        "exists or is not empty. To update the view, remove this path, and run "
        "`spack env view regenerate`".format(new_root)
    )


class ViewDescriptor:
    def __init__(
        self,
        base_path,
        root,
        projections={},
        select=[],
        exclude=[],
        link=default_view_link,
        link_type="symlink",
    ):
        self.base = base_path
        self.raw_root = root
        self.root = spack.util.path.canonicalize_path(root, default_wd=base_path)
        self.projections = projections
        self.select = select
        self.exclude = exclude
        self.link_type = fsv.canonicalize_link_type(link_type)
        self.link = link

    def select_fn(self, spec):
        return any(spec.satisfies(s) for s in self.select)

    def exclude_fn(self, spec):
        return not any(spec.satisfies(e) for e in self.exclude)

    def update_root(self, new_path):
        self.raw_root = new_path
        self.root = spack.util.path.canonicalize_path(new_path, default_wd=self.base)

    def __eq__(self, other):
        return all(
            [
                self.root == other.root,
                self.projections == other.projections,
                self.select == other.select,
                self.exclude == other.exclude,
                self.link == other.link,
                self.link_type == other.link_type,
            ]
        )

    def to_dict(self):
        ret = syaml.syaml_dict([("root", self.raw_root)])
        if self.projections:
            ret["projections"] = self.projections
        if self.select:
            ret["select"] = self.select
        if self.exclude:
            ret["exclude"] = self.exclude
        if self.link_type:
            ret["link_type"] = self.link_type
        if self.link != default_view_link:
            ret["link"] = self.link
        return ret

    @staticmethod
    def from_dict(base_path, d):
        return ViewDescriptor(
            base_path,
            d["root"],
            d.get("projections", {}),
            d.get("select", []),
            d.get("exclude", []),
            d.get("link", default_view_link),
            d.get("link_type", "symlink"),
        )

    @property
    def _current_root(self):
        if not islink(self.root):
            return None

        root = readlink(self.root)
        if os.path.isabs(root):
            return root

        root_dir = os.path.dirname(self.root)
        return os.path.join(root_dir, root)

    def _next_root(self, specs):
        content_hash = self.content_hash(specs)
        root_dir = os.path.dirname(self.root)
        root_name = os.path.basename(self.root)
        return os.path.join(root_dir, "._%s" % root_name, content_hash)

    def content_hash(self, specs):
        d = syaml.syaml_dict(
            [
                ("descriptor", self.to_dict()),
                ("specs", [(spec.dag_hash(), spec.prefix) for spec in sorted(specs)]),
            ]
        )
        contents = sjson.dump(d)
        return spack.util.hash.b32_hash(contents)

    def get_projection_for_spec(self, spec):
        """Get projection for spec. This function does not require the view
        to exist on the filesystem."""
        return self._view(self.root).get_projection_for_spec(spec)

    def view(self, new: Optional[str] = None) -> fsv.SimpleFilesystemView:
        """
        Returns a view object for the *underlying* view directory. This means that the
        self.root symlink is followed, and that the view has to exist on the filesystem
        (unless ``new``). This function is useful when writing to the view.

        Raise if new is None and there is no current view

        Arguments:
            new: If a string, create a FilesystemView rooted at that path. Default None. This
                should only be used to regenerate the view, and cannot be used to access specs.
        """
        path = new if new else self._current_root
        if not path:
            # This can only be hit if we write a future bug
            raise SpackEnvironmentViewError(
                f"Attempting to get nonexistent view from environment. View root is at {self.root}"
            )
        return self._view(path)

    def _view(self, root: str) -> fsv.SimpleFilesystemView:
        """Returns a view object for a given root dir."""
        return fsv.SimpleFilesystemView(
            root,
            spack.store.STORE.layout,
            ignore_conflicts=True,
            projections=self.projections,
            link_type=self.link_type,
        )

    def __contains__(self, spec):
        """Is the spec described by the view descriptor

        Note: This does not claim the spec is already linked in the view.
        It merely checks that the spec is selected if a select operation is
        specified and is not excluded if an exclude operator is specified.
        """
        if self.select:
            if not self.select_fn(spec):
                return False

        if self.exclude:
            if not self.exclude_fn(spec):
                return False

        return True

    def specs_for_view(self, concrete_roots: List[Spec]) -> List[Spec]:
        """Flatten the DAGs of the concrete roots, keep only unique, selected, and installed specs
        in topological order from root to leaf."""
        if self.link == "all":
            deptype = dt.LINK | dt.RUN
        elif self.link == "run":
            deptype = dt.RUN
        else:
            deptype = dt.NONE

        specs = traverse.traverse_nodes(
            concrete_roots, order="topo", deptype=deptype, key=traverse.by_dag_hash
        )

        # Filter selected, installed specs
        with spack.store.STORE.db.read_transaction():
            result = [s for s in specs if s in self and s.installed]

        return self._exclude_duplicate_runtimes(result)

    def regenerate(self, concrete_roots: List[Spec]) -> None:
        specs = self.specs_for_view(concrete_roots)

        # To ensure there are no conflicts with packages being installed
        # that cannot be resolved or have repos that have been removed
        # we always regenerate the view from scratch.
        # We will do this by hashing the view contents and putting the view
        # in a directory by hash, and then having a symlink to the real
        # view in the root. The real root for a view at /dirname/basename
        # will be /dirname/._basename_<hash>.
        # This allows for atomic swaps when we update the view

        # cache the roots because the way we determine which is which does
        # not work while we are updating
        new_root = self._next_root(specs)
        old_root = self._current_root

        if new_root == old_root:
            tty.debug(f"View at {self.root} does not need regeneration.")
            return

        _error_on_nonempty_view_dir(new_root)

        # construct view at new_root
        if specs:
            tty.msg(f"Updating view at {self.root}")

        view = self.view(new=new_root)

        root_dirname = os.path.dirname(self.root)
        tmp_symlink_name = os.path.join(root_dirname, "._view_link")

        # Remove self.root if is it an empty dir, since we need a symlink there. Note that rmdir
        # fails if self.root is a symlink.
        try:
            os.rmdir(self.root)
        except (FileNotFoundError, NotADirectoryError):
            pass
        except OSError as e:
            if e.errno == errno.ENOTEMPTY:
                msg = "it is a non-empty directory"
            elif e.errno == errno.EACCES:
                msg = "of insufficient permissions"
            else:
                raise
            raise SpackEnvironmentViewError(
                f"The environment view in {self.root} cannot not be created because {msg}."
            ) from e

        # Create a new view
        try:
            fs.mkdirp(new_root)
            view.add_specs(*specs)

            # create symlink from tmp_symlink_name to new_root
            if os.path.exists(tmp_symlink_name):
                os.unlink(tmp_symlink_name)
            symlink(new_root, tmp_symlink_name)

            # mv symlink atomically over root symlink to old_root
            fs.rename(tmp_symlink_name, self.root)
        except Exception as e:
            # Clean up new view and temporary symlink on any failure.
            try:
                shutil.rmtree(new_root, ignore_errors=True)
                os.unlink(tmp_symlink_name)
            except OSError:
                pass

            # Give an informative error message for the typical error case: two specs, same package
            # project to same prefix.
            if isinstance(e, ConflictingSpecsError):
                spec_a = e.args[0].format(color=clr.get_color_when())
                spec_b = e.args[1].format(color=clr.get_color_when())
                raise SpackEnvironmentViewError(
                    f"The environment view in {self.root} could not be created, "
                    "because the following two specs project to the same prefix:\n"
                    f"    {spec_a}, and\n"
                    f"    {spec_b}.\n"
                    "    To resolve this issue:\n"
                    "        a. use `concretization:unify:true` to ensure there is only one "
                    "package per spec in the environment, or\n"
                    "        b. disable views with `view:false`, or\n"
                    "        c. create custom view projections."
                ) from e
            raise

        # Remove the old root when it's in the same folder as the new root. This guards
        # against removal of an arbitrary path when the original symlink in self.root
        # was not created by the environment, but by the user.
        if (
            old_root
            and os.path.exists(old_root)
            and os.path.samefile(os.path.dirname(new_root), os.path.dirname(old_root))
        ):
            try:
                shutil.rmtree(old_root)
            except (IOError, OSError) as e:
                msg = "Failed to remove old view at %s\n" % old_root
                msg += str(e)
                tty.warn(msg)

    def _exclude_duplicate_runtimes(self, nodes):
        all_runtimes = spack.repo.PATH.packages_with_tags("runtime")
        runtimes_by_name = {}
        for s in nodes:
            if s.name not in all_runtimes:
                continue
            current_runtime = runtimes_by_name.get(s.name, s)
            runtimes_by_name[s.name] = max(current_runtime, s, key=lambda x: x.version)
        return [x for x in nodes if x.name not in all_runtimes or runtimes_by_name[x.name] == x]


def _create_environment(path):
    return Environment(path)


def env_subdir_path(manifest_dir: Union[str, pathlib.Path]) -> str:
    """Path to where the environment stores repos, logs, views, configs.

    Args:
        manifest_dir:  directory containing the environment manifest file

    Returns:  directory the environment uses to manage its files
    """
    return os.path.join(str(manifest_dir), env_subdir_name)


class Environment:
    """A Spack environment, which bundles together configuration and a list of specs."""

    def __init__(self, manifest_dir: Union[str, pathlib.Path]) -> None:
        """An environment can be constructed from a directory containing a "spack.yaml" file, and
        optionally a consistent "spack.lock" file.

        Args:
            manifest_dir: directory with the "spack.yaml" associated with the environment
        """
        self.path = os.path.abspath(str(manifest_dir))
        self.name = environment_name(self.path)
        self.env_subdir_path = env_subdir_path(self.path)

        self.txlock = lk.Lock(self._transaction_lock_path)

        self._unify = None
        self.new_specs: List[Spec] = []
        self.views: Dict[str, ViewDescriptor] = {}

        #: Specs from "spack.yaml"
        self.spec_lists: Dict[str, SpecList] = {user_speclist_name: SpecList()}
        #: User specs from the last concretization
        self.concretized_user_specs: List[Spec] = []
        #: Roots associated with the last concretization, in order
        self.concretized_order: List[str] = []
        #: Concretized specs by hash
        self.specs_by_hash: Dict[str, Spec] = {}
        #: Repository for this environment (memoized)
        self._repo = None

        #: Environment paths for concrete (lockfile) included environments
        self.included_concrete_envs: List[str] = []
        #: First-level included concretized spec data from/to the lockfile.
        self.included_concrete_spec_data: Dict[str, Dict[str, List[str]]] = {}
        #: User specs from included environments from the last concretization
        self.included_concretized_user_specs: Dict[str, List[Spec]] = {}
        #: Roots from included environments with the last concretization, in order
        self.included_concretized_order: Dict[str, List[str]] = {}
        #: Concretized specs by hash from the included environments
        self.included_specs_by_hash: Dict[str, Dict[str, Spec]] = {}

        #: Previously active environment
        self._previous_active = None
        self._dev_specs = None

        # Load the manifest file contents into memory
        self._load_manifest_file()

    def _load_manifest_file(self):
        """Instantiate and load the manifest file contents into memory."""
        with lk.ReadTransaction(self.txlock):
            self.manifest = EnvironmentManifestFile(self.path, self.name)
            with self.manifest.use_config():
                self._read()

    @property
    def unify(self):
        if self._unify is None:
            self._unify = spack.config.get("concretizer:unify", False)
        return self._unify

    @unify.setter
    def unify(self, value):
        self._unify = value

    def __reduce__(self):
        return _create_environment, (self.path,)

    def _re_read(self):
        """Reinitialize the environment object."""
        self.clear(re_read=True)
        self._load_manifest_file()

    def _read(self):
        self._construct_state_from_manifest()

        if os.path.exists(self.lock_path):
            with open(self.lock_path, encoding="utf-8") as f:
                read_lock_version = self._read_lockfile(f)["_meta"]["lockfile-version"]

            if read_lock_version == 1:
                tty.debug(f"Storing backup of {self.lock_path} at {self._lock_backup_v1_path}")
                shutil.copy(self.lock_path, self._lock_backup_v1_path)

    def write_transaction(self):
        """Get a write lock context manager for use in a `with` block."""
        return lk.WriteTransaction(self.txlock, acquire=self._re_read)

    def _process_definition(self, entry):
        """Process a single spec definition item."""
        when_string = entry.get("when")
        if when_string is not None:
            when = _eval_conditional(when_string)
            assert len([x for x in entry if x != "when"]) == 1
        else:
            when = True
            assert len(entry) == 1

        if when:
            for name, spec_list in entry.items():
                if name == "when":
                    continue
                user_specs = SpecList(name, spec_list, self.spec_lists.copy())
                if name in self.spec_lists:
                    self.spec_lists[name].extend(user_specs)
                else:
                    self.spec_lists[name] = user_specs

    def _process_view(self, env_view: Optional[Union[bool, str, Dict]]):
        """Process view option(s), which can be boolean, string, or None.

        A boolean environment view option takes precedence over any that may
        be included. So ``view: True`` results in the default view only. And
        ``view: False`` means the environment will have no view.

        Args:
            env_view: view option provided in the manifest or configuration
        """

        def add_view(name, values):
            """Add the view with the name and the string or dict values."""
            if isinstance(values, str):
                self.views[name] = ViewDescriptor(self.path, values)
            elif isinstance(values, dict):
                self.views[name] = ViewDescriptor.from_dict(self.path, values)
            else:
                tty.error(f"Cannot add view named {name} for {type(values)} values {values}")

        # If the configuration specifies 'view: False' then we are done
        # processing views. If this is called with the environment's view
        # view (versus an included view), then there are to be NO views.
        if env_view is False:
            return

        # If the configuration specifies 'view: True' then only the default
        # view will be created for the environment and we are done processing
        # views.
        if env_view is True:
            add_view(default_view_name, self.view_path_default)
            return

        # Otherwise, the configuration has a subdirectory or dictionary.
        if isinstance(env_view, str):
            add_view(default_view_name, env_view)
        elif env_view:
            for name, values in env_view.items():
                add_view(name, values)

        # If we reach this point without an explicit view option then we
        # provide the default view.
        if self.views == dict():
            self.views[default_view_name] = ViewDescriptor(self.path, self.view_path_default)

    def _process_concrete_includes(self):
        """Extract and load into memory included concrete spec data."""
        self.included_concrete_envs = self.manifest[TOP_LEVEL_KEY].get(included_concrete_name, [])

        if self.included_concrete_envs:
            if os.path.exists(self.lock_path):
                with open(self.lock_path, encoding="utf-8") as f:
                    data = self._read_lockfile(f)

                if included_concrete_name in data:
                    self.included_concrete_spec_data = data[included_concrete_name]
            else:
                self.include_concrete_envs()

    def _construct_state_from_manifest(self):
        """Set up user specs and views from the manifest file."""
        self.spec_lists = collections.OrderedDict()
        self.views = {}

        for item in spack.config.get("definitions", []):
            self._process_definition(item)

        env_configuration = self.manifest[TOP_LEVEL_KEY]
        spec_list = env_configuration.get(user_speclist_name, [])
        user_specs = SpecList(
            user_speclist_name, [s for s in spec_list if s], self.spec_lists.copy()
        )
        self.spec_lists[user_speclist_name] = user_specs

        self._process_view(spack.config.get("view", True))
        self._process_concrete_includes()

    def all_concretized_user_specs(self) -> List[Spec]:
        """Returns all of the concretized user specs of the environment and
        its included environment(s)."""
        concretized_user_specs = self.concretized_user_specs[:]
        for included_specs in self.included_concretized_user_specs.values():
            for included in included_specs:
                # Don't duplicate included spec(s)
                if included not in concretized_user_specs:
                    concretized_user_specs.append(included)

        return concretized_user_specs

    def all_concretized_orders(self) -> List[str]:
        """Returns all of the concretized order of the environment and
        its included environment(s)."""
        concretized_order = self.concretized_order[:]
        for included_concretized_order in self.included_concretized_order.values():
            for included in included_concretized_order:
                # Don't duplicate included spec(s)
                if included not in concretized_order:
                    concretized_order.append(included)

        return concretized_order

    @property
    def user_specs(self):
        return self.spec_lists[user_speclist_name]

    @property
    def dev_specs(self):
        if not self._dev_specs:
            self._dev_specs = self._read_dev_specs()
        return self._dev_specs

    def _read_dev_specs(self):
        dev_specs = {}
        dev_config = spack.config.get("develop", {})
        for name, entry in dev_config.items():
            local_entry = {"spec": str(entry["spec"])}
            # default path is the spec name
            if "path" not in entry:
                local_entry["path"] = name
            else:
                local_entry["path"] = entry["path"]
            dev_specs[name] = local_entry
        return dev_specs

    @property
    def included_user_specs(self) -> SpecList:
        """Included concrete user (or root) specs from last concretization."""
        spec_list = SpecList()

        if not self.included_concrete_envs:
            return spec_list

        def add_root_specs(included_concrete_specs):
            # add specs from the include *and* any nested includes it may have
            for env, info in included_concrete_specs.items():
                for root_list in info["roots"]:
                    spec_list.add(root_list["spec"])

                if "include_concrete" in info:
                    add_root_specs(info["include_concrete"])

        add_root_specs(self.included_concrete_spec_data)
        return spec_list

    def clear(self, re_read=False):
        """Clear the contents of the environment

        Arguments:
            re_read: If ``True``, do not clear ``new_specs``. This value cannot be read from yaml,
                and needs to be maintained when re-reading an existing environment.
        """
        self.spec_lists = collections.OrderedDict()
        self.spec_lists[user_speclist_name] = SpecList()

        self._dev_specs = {}
        self.concretized_order = []  # roots of last concretize, in order
        self.concretized_user_specs = []  # user specs from last concretize
        self.specs_by_hash = {}  # concretized specs by hash

        self.included_concrete_spec_data = {}  # concretized specs from lockfile of included envs
        self.included_concretized_order = {}  # root specs of the included envs, keyed by env path
        self.included_concretized_user_specs = {}  # user specs from last concretize's included env
        self.included_specs_by_hash = {}  # concretized specs by hash from the included envs

        self.invalidate_repository_cache()
        self._previous_active = None  # previously active environment
        if not re_read:
            # things that cannot be recreated from file
            self.new_specs = []  # write packages for these on write()

        self.manifest.clear()

    @property
    def active(self):
        """True if this environment is currently active."""
        return _active_environment and self.path == _active_environment.path

    @property
    def manifest_path(self):
        """Path to spack.yaml file in this environment."""
        return os.path.join(self.path, manifest_name)

    @property
    def _transaction_lock_path(self):
        """The location of the lock file used to synchronize multiple
        processes updating the same environment.
        """
        return os.path.join(self.env_subdir_path, "transaction_lock")

    @property
    def lock_path(self):
        """Path to spack.lock file in this environment."""
        return os.path.join(self.path, lockfile_name)

    @property
    def _lock_backup_v1_path(self):
        """Path to backup of v1 lockfile before conversion to v2"""
        return self.lock_path + ".backup.v1"

    @property
    def repos_path(self):
        return os.path.join(self.env_subdir_path, "repos")

    @property
    def view_path_default(self):
        # default path for environment views
        return os.path.join(self.env_subdir_path, "view")

    @property
    def repo(self):
        if self._repo is None:
            self._repo = make_repo_path(self.repos_path)
        return self._repo

    @property
    def scope_name(self):
        """Name of the config scope of this environment's manifest file."""
        return self.manifest.scope_name

    def include_concrete_envs(self):
        """Copy and save the included envs' specs internally"""

        root_hash_seen = set()
        concrete_hash_seen = set()
        self.included_concrete_spec_data = {}

        for env_path in self.included_concrete_envs:
            # Check that environment exists
            if not is_env_dir(env_path):
                raise SpackEnvironmentError(f"Unable to find env at {env_path}")

            env = Environment(env_path)
            self.included_concrete_spec_data[env_path] = {"roots": [], "concrete_specs": {}}

            # Copy unique root specs from env
            for root_dict in env._concrete_roots_dict():
                if root_dict["hash"] not in root_hash_seen:
                    self.included_concrete_spec_data[env_path]["roots"].append(root_dict)
                    root_hash_seen.add(root_dict["hash"])

            # Copy unique concrete specs from env
            for dag_hash, spec_details in env._concrete_specs_dict().items():
                if dag_hash not in concrete_hash_seen:
                    self.included_concrete_spec_data[env_path]["concrete_specs"].update(
                        {dag_hash: spec_details}
                    )
                    concrete_hash_seen.add(dag_hash)

            # Copy transitive include data
            transitive = env.included_concrete_spec_data
            if transitive:
                self.included_concrete_spec_data[env_path]["include_concrete"] = transitive

        self._read_lockfile_dict(self._to_lockfile_dict())
        self.write()

    def destroy(self):
        """Remove this environment from Spack entirely."""
        shutil.rmtree(self.path)

    def update_stale_references(self, from_list=None):
        """Iterate over spec lists updating references."""
        if not from_list:
            from_list = next(iter(self.spec_lists.keys()))
        index = list(self.spec_lists.keys()).index(from_list)

        # spec_lists is an OrderedDict to ensure lists read from the manifest
        # are maintainted in order, hence, all list entries after the modified
        # list may refer to the modified list requiring stale references to be
        # updated.
        for i, (name, speclist) in enumerate(
            list(self.spec_lists.items())[index + 1 :], index + 1
        ):
            new_reference = dict((n, self.spec_lists[n]) for n in list(self.spec_lists.keys())[:i])
            speclist.update_reference(new_reference)

    def add(self, user_spec, list_name=user_speclist_name):
        """Add a single user_spec (non-concretized) to the Environment

        Returns:
            (bool): True if the spec was added, False if it was already
                present and did not need to be added

        """
        spec = Spec(user_spec)

        if list_name not in self.spec_lists:
            raise SpackEnvironmentError(f"No list {list_name} exists in environment {self.name}")

        if list_name == user_speclist_name:
            if spec.anonymous:
                raise SpackEnvironmentError("cannot add anonymous specs to an environment")
            elif not spack.repo.PATH.exists(spec.name) and not spec.abstract_hash:
                virtuals = spack.repo.PATH.provider_index.providers.keys()
                if spec.name not in virtuals:
                    msg = "no such package: %s" % spec.name
                    raise SpackEnvironmentError(msg)

        list_to_change = self.spec_lists[list_name]
        existing = str(spec) in list_to_change.yaml_list
        if not existing:
            list_to_change.add(str(spec))
            self.update_stale_references(list_name)
            if list_name == user_speclist_name:
                self.manifest.add_user_spec(str(user_spec))
            else:
                self.manifest.add_definition(str(user_spec), list_name=list_name)

        return bool(not existing)

    def change_existing_spec(
        self,
        change_spec: Spec,
        list_name: str = user_speclist_name,
        match_spec: Optional[Spec] = None,
        allow_changing_multiple_specs=False,
    ):
        """
        Find the spec identified by `match_spec` and change it to `change_spec`.

        Arguments:
            change_spec: defines the spec properties that
                need to be changed. This will not change attributes of the
                matched spec unless they conflict with `change_spec`.
            list_name: identifies the spec list in the environment that
                should be modified
            match_spec: if set, this identifies the spec
                that should be changed. If not set, it is assumed we are
                looking for a spec with the same name as `change_spec`.
        """
        if not (change_spec.name or (match_spec and match_spec.name)):
            raise ValueError(
                "Must specify a spec name to identify a single spec"
                " in the environment that will be changed"
            )
        match_spec = match_spec or Spec(change_spec.name)

        list_to_change = self.spec_lists[list_name]
        if list_to_change.is_matrix:
            raise SpackEnvironmentError(
                "Cannot directly change specs in matrices:"
                " specify a named list that is not a matrix"
            )

        matches = list((idx, x) for idx, x in enumerate(list_to_change) if x.satisfies(match_spec))
        if len(matches) == 0:
            raise ValueError(
                "There are no specs named {0} in {1}".format(match_spec.name, list_name)
            )
        elif len(matches) > 1 and not allow_changing_multiple_specs:
            raise ValueError("{0} matches multiple specs".format(str(match_spec)))

        for idx, spec in matches:
            override_spec = Spec.override(spec, change_spec)
            self.spec_lists[list_name].replace(idx, str(override_spec))
            if list_name == user_speclist_name:
                self.manifest.override_user_spec(str(override_spec), idx=idx)
            else:
                self.manifest.override_definition(
                    str(spec), override=str(override_spec), list_name=list_name
                )
        self.update_stale_references(from_list=list_name)

    def remove(self, query_spec, list_name=user_speclist_name, force=False):
        """Remove specs from an environment that match a query_spec"""
        err_msg_header = (
            f"Cannot remove '{query_spec}' from '{list_name}' definition "
            f"in {self.manifest.manifest_file}"
        )
        query_spec = Spec(query_spec)
        try:
            list_to_change = self.spec_lists[list_name]
        except KeyError as e:
            msg = f"{err_msg_header}, since '{list_name}' does not exist"
            raise SpackEnvironmentError(msg) from e

        if not query_spec.concrete:
            matches = [s for s in list_to_change if s.satisfies(query_spec)]

        else:
            # concrete specs match against concrete specs in the env
            # by dag hash.
            specs_hashes = zip(self.concretized_user_specs, self.concretized_order)
            matches = [s for s, h in specs_hashes if query_spec.dag_hash() == h]

        if not matches:
            raise SpackEnvironmentError(f"{err_msg_header}, no spec matches")

        old_specs = set(self.user_specs)
        new_specs = set()
        for spec in matches:
            if spec not in list_to_change:
                continue
            try:
                list_to_change.remove(spec)
                self.update_stale_references(list_name)
                new_specs = set(self.user_specs)
            except spack.spec_list.SpecListError as e:
                # define new specs list
                new_specs = set(self.user_specs)
                msg = str(e)
                if force:
                    msg += " It will be removed from the concrete specs."
                    # Mock new specs, so we can remove this spec from concrete spec lists
                    new_specs.remove(spec)
                tty.warn(msg)
            else:
                if list_name == user_speclist_name:
                    self.manifest.remove_user_spec(str(spec))
                else:
                    self.manifest.remove_definition(str(spec), list_name=list_name)

        # If force, update stale concretized specs
        for spec in old_specs - new_specs:
            if force and spec in self.concretized_user_specs:
                i = self.concretized_user_specs.index(spec)
                del self.concretized_user_specs[i]

                dag_hash = self.concretized_order[i]
                del self.concretized_order[i]
                del self.specs_by_hash[dag_hash]

    def is_develop(self, spec):
        """Returns true when the spec is built from local sources"""
        return spec.name in self.dev_specs

    def concretize(self, force=False, tests=False):
        """Concretize user_specs in this environment.

        Only concretizes specs that haven't been concretized yet unless
        force is ``True``.

        This only modifies the environment in memory. ``write()`` will
        write out a lockfile containing concretized specs.

        Arguments:
            force (bool): re-concretize ALL specs, even those that were
               already concretized
            tests (bool or list or set): False to run no tests, True to test
                all packages, or a list of package names to run tests for some

        Returns:
            List of specs that have been concretized. Each entry is a tuple of
            the user spec and the corresponding concretized spec.
        """
        if force:
            # Clear previously concretized specs
            self.concretized_user_specs = []
            self.concretized_order = []
            self.specs_by_hash = {}

        # Remove concrete specs that no longer correlate to a user spec
        for spec in set(self.concretized_user_specs) - set(self.user_specs):
            self.deconcretize(spec, concrete=False)

        # If a combined env, check updated spec is in the linked envs
        if self.included_concrete_envs:
            self.include_concrete_envs()

        # Pick the right concretization strategy
        if self.unify == "when_possible":
            return self._concretize_together_where_possible(tests=tests)

        if self.unify is True:
            return self._concretize_together(tests=tests)

        if self.unify is False:
            return self._concretize_separately(tests=tests)

        msg = "concretization strategy not implemented [{0}]"
        raise SpackEnvironmentError(msg.format(self.unify))

    def deconcretize(self, spec: spack.spec.Spec, concrete: bool = True):
        """
        Remove specified spec from environment concretization

        Arguments:
            spec: Spec to deconcretize. This must be a root of the environment
            concrete: If True, find all instances of spec as concrete in the environemnt.
                If False, find a single instance of the abstract spec as root of the environment.
        """
        # spec has to be a root of the environment
        if concrete:
            dag_hash = spec.dag_hash()

            pairs = zip(self.concretized_user_specs, self.concretized_order)
            filtered = [(spec, h) for spec, h in pairs if h != dag_hash]
            # Cannot use zip and unpack two values; it fails if filtered is empty
            self.concretized_user_specs = [s for s, _ in filtered]
            self.concretized_order = [h for _, h in filtered]
        else:
            index = self.concretized_user_specs.index(spec)
            dag_hash = self.concretized_order.pop(index)

            del self.concretized_user_specs[index]

        # If this was the only user spec that concretized to this concrete spec, remove it
        if dag_hash not in self.concretized_order:
            # if we deconcretized a dependency that doesn't correspond to a root, it
            # won't be here.
            if dag_hash in self.specs_by_hash:
                del self.specs_by_hash[dag_hash]

    def _get_specs_to_concretize(
        self,
    ) -> Tuple[List[spack.spec.Spec], List[spack.spec.Spec], List[SpecPair]]:
        """Compute specs to concretize for unify:true and unify:when_possible.

        This includes new user specs and any already concretized specs.

        Returns:
            Tuple of new user specs, user specs to keep, and the specs to concretize.

        """
        # Exit early if the set of concretized specs is the set of user specs
        new_user_specs = list(set(self.user_specs) - set(self.concretized_user_specs))
        kept_user_specs = list(set(self.user_specs) & set(self.concretized_user_specs))
        kept_user_specs += self.included_user_specs
        if not new_user_specs:
            return new_user_specs, kept_user_specs, []

        specs_to_concretize = [(s, None) for s in new_user_specs] + [
            (abstract, concrete)
            for abstract, concrete in self.concretized_specs()
            if abstract in kept_user_specs
        ]
        return new_user_specs, kept_user_specs, specs_to_concretize

    def _concretize_together_where_possible(self, tests: bool = False) -> Sequence[SpecPair]:
        # Avoid cyclic dependency
        import spack.solver.asp

        # Exit early if the set of concretized specs is the set of user specs
        new_user_specs, _, specs_to_concretize = self._get_specs_to_concretize()
        if not new_user_specs:
            return []

        self.concretized_user_specs = []
        self.concretized_order = []
        self.specs_by_hash = {}

        ret = []
        result = spack.concretize.concretize_together_when_possible(
            specs_to_concretize, tests=tests
        )
        for abstract, concrete in result:
            # Only add to the environment if it's from this environment (not included in)
            if abstract in self.user_specs:
                self._add_concrete_spec(abstract, concrete)

            # Return only the new specs
            if abstract in new_user_specs:
                ret.append((abstract, concrete))

        return ret

    def _concretize_together(self, tests: bool = False) -> Sequence[SpecPair]:
        """Concretization strategy that concretizes all the specs
        in the same DAG.
        """
        # Exit early if the set of concretized specs is the set of user specs
        new_user_specs, kept_user_specs, specs_to_concretize = self._get_specs_to_concretize()
        if not new_user_specs:
            return []

        self.concretized_user_specs = []
        self.concretized_order = []
        self.specs_by_hash = {}

        try:
            concretized_specs = spack.concretize.concretize_together(
                specs_to_concretize, tests=tests
            )
        except spack.error.UnsatisfiableSpecError as e:
            # "Enhance" the error message for multiple root specs, suggest a less strict
            # form of concretization.
            if len(self.user_specs) > 1:
                e.message += ". "
                if kept_user_specs:
                    e.message += (
                        "Couldn't concretize without changing the existing environment. "
                        "If you are ok with changing it, try `spack concretize --force`. "
                    )
                e.message += (
                    "You could consider setting `concretizer:unify` to `when_possible` "
                    "or `false` to allow multiple versions of some packages."
                )
            raise

        for abstract, concrete in concretized_specs:
            # Don't add if it's just included
            if abstract in self.user_specs:
                self._add_concrete_spec(abstract, concrete)

        # Return the portion of the return value that is new
        return concretized_specs[: len(new_user_specs)]

    def _concretize_separately(self, tests=False):
        """Concretization strategy that concretizes separately one
        user spec after the other.
        """
        import spack.bootstrap

        # keep any concretized specs whose user specs are still in the manifest
        old_concretized_user_specs = self.concretized_user_specs
        old_concretized_order = self.concretized_order
        old_specs_by_hash = self.specs_by_hash

        self.concretized_user_specs = []
        self.concretized_order = []
        self.specs_by_hash = {}

        for s, h in zip(old_concretized_user_specs, old_concretized_order):
            if s in self.user_specs:
                concrete = old_specs_by_hash[h]
                self._add_concrete_spec(s, concrete, new=False)

        to_concretize = [
            (root, None) for root in self.user_specs if root not in old_concretized_user_specs
        ]
        concretized_specs = spack.concretize.concretize_separately(to_concretize, tests=tests)

        by_hash = {}
        for abstract, concrete in concretized_specs:
            self._add_concrete_spec(abstract, concrete)
            by_hash[concrete.dag_hash()] = concrete

        # Unify the specs objects, so we get correct references to all parents
        self._read_lockfile_dict(self._to_lockfile_dict())

        # Re-attach information on test dependencies
        if tests:
            # This is slow, but the information on test dependency is lost
            # after unification or when reading from a lockfile.
            for h in self.specs_by_hash:
                current_spec, computed_spec = self.specs_by_hash[h], by_hash[h]
                for node in computed_spec.traverse():
                    test_edges = node.edges_to_dependencies(depflag=dt.TEST)
                    for current_edge in test_edges:
                        test_dependency = current_edge.spec
                        if test_dependency in current_spec[node.name]:
                            continue
                        current_spec[node.name].add_dependency_edge(
                            test_dependency.copy(), depflag=dt.TEST, virtuals=current_edge.virtuals
                        )

        return concretized_specs

    @property
    def default_view(self):
        if not self.has_view(default_view_name):
            raise SpackEnvironmentError(f"{self.name} does not have a default view enabled")

        return self.views[default_view_name]

    def has_view(self, view_name: str) -> bool:
        return view_name in self.views

    def update_default_view(self, path_or_bool: Union[str, bool]) -> None:
        """Updates the path of the default view.

        If the argument passed as input is False the default view is deleted, if present. The
        manifest will have an entry "view: false".

        If the argument passed as input is True a default view is created, if not already present.
        The manifest will have an entry "view: true". If a default view is already declared, it
        will be left untouched.

        If the argument passed as input is a path a default view pointing to that path is created,
        if not present already. If a default view is already declared, only its "root" will be
        changed.

        Args:
            path_or_bool: either True, or False or a path
        """
        view_path = self.view_path_default if path_or_bool is True else path_or_bool

        # We don't have the view, and we want to remove it
        if default_view_name not in self.views and path_or_bool is False:
            return

        # We want to enable the view, but we have it already
        if default_view_name in self.views and path_or_bool is True:
            return

        # We have the view, and we want to set it to the same path
        if default_view_name in self.views and self.default_view.root == view_path:
            return

        self.delete_default_view()
        if path_or_bool is False:
            self.views.pop(default_view_name, None)
            self.manifest.remove_default_view()
            return

        # If we had a default view already just update its path,
        # else create a new one and add it to views
        if default_view_name in self.views:
            self.default_view.update_root(view_path)
        else:
            self.views[default_view_name] = ViewDescriptor(self.path, view_path)

        self.manifest.set_default_view(self._default_view_as_yaml())

    def delete_default_view(self) -> None:
        """Deletes the default view associated with this environment."""
        if default_view_name not in self.views:
            return

        try:
            view = pathlib.Path(self.default_view.root)
            shutil.rmtree(view.resolve())
            view.unlink()
        except FileNotFoundError as e:
            msg = f"[ENVIRONMENT] error trying to delete the default view: {str(e)}"
            tty.debug(msg)

    def regenerate_views(self):
        if not self.views:
            tty.debug("Skip view update, this environment does not maintain a view")
            return

        for view in self.views.values():
            view.regenerate(self.concrete_roots())

    def check_views(self):
        """Checks if the environments default view can be activated."""
        try:
            # This is effectively a no-op, but it touches all packages in the
            # default view if they are installed.
            for view_name, view in self.views.items():
                for spec in self.concrete_roots():
                    if spec in view and spec.package and spec.installed:
                        msg = '{0} in view "{1}"'
                        tty.debug(msg.format(spec.name, view_name))

        except (spack.repo.UnknownPackageError, spack.repo.UnknownNamespaceError) as e:
            tty.warn(e)
            tty.warn(
                "Environment %s includes out of date packages or repos. "
                "Loading the environment view will require reconcretization." % self.name
            )

    def _env_modifications_for_view(
        self, view: ViewDescriptor, reverse: bool = False
    ) -> spack.util.environment.EnvironmentModifications:
        try:
            with spack.store.STORE.db.read_transaction():
                installed_roots = [s for s in self.concrete_roots() if s.installed]
            mods = uenv.environment_modifications_for_specs(*installed_roots, view=view)
        except Exception as e:
            # Failing to setup spec-specific changes shouldn't be a hard error.
            tty.warn(
                f"could not {'unload' if reverse else 'load'} runtime environment due "
                f"to {e.__class__.__name__}: {e}"
            )
            return spack.util.environment.EnvironmentModifications()
        return mods.reversed() if reverse else mods

    def add_view_to_env(
        self, env_mod: spack.util.environment.EnvironmentModifications, view: str
    ) -> spack.util.environment.EnvironmentModifications:
        """Collect the environment modifications to activate an environment using the provided
        view. Removes duplicate paths.

        Args:
            env_mod: the environment modifications object that is modified.
            view: the name of the view to activate."""
        descriptor = self.views.get(view)
        if not descriptor:
            return env_mod

        env_mod.extend(uenv.unconditional_environment_modifications(descriptor))
        env_mod.extend(self._env_modifications_for_view(descriptor))

        # deduplicate paths from specs mapped to the same location
        for env_var in env_mod.group_by_name():
            env_mod.prune_duplicate_paths(env_var)

        return env_mod

    def rm_view_from_env(
        self, env_mod: spack.util.environment.EnvironmentModifications, view: str
    ) -> spack.util.environment.EnvironmentModifications:
        """Collect the environment modifications to deactivate an environment using the provided
        view. Reverses the action of ``add_view_to_env``.

        Args:
            env_mod: the environment modifications object that is modified.
            view: the name of the view to deactivate."""
        descriptor = self.views.get(view)
        if not descriptor:
            return env_mod

        env_mod.extend(uenv.unconditional_environment_modifications(descriptor).reversed())
        env_mod.extend(self._env_modifications_for_view(descriptor, reverse=True))

        return env_mod

    def _add_concrete_spec(self, spec, concrete, new=True):
        """Called when a new concretized spec is added to the environment.

        This ensures that all internal data structures are kept in sync.

        Arguments:
            spec (Spec): user spec that resulted in the concrete spec
            concrete (Spec): spec concretized within this environment
            new (bool): whether to write this spec's package to the env
                repo on write()
        """
        assert concrete.concrete

        # when a spec is newly concretized, we need to make a note so
        # that we can write its package to the env repo on write()
        if new:
            self.new_specs.append(concrete)

        # update internal lists of specs
        self.concretized_user_specs.append(spec)

        h = concrete.dag_hash()
        self.concretized_order.append(h)
        self.specs_by_hash[h] = concrete

    def _dev_specs_that_need_overwrite(self):
        """Return the hashes of all specs that need to be reinstalled due to source code change."""
        changed_dev_specs = [
            s
            for s in traverse.traverse_nodes(
                self.concrete_roots(), order="breadth", key=traverse.by_dag_hash
            )
            if _is_dev_spec_and_has_changed(s)
        ]

        # Collect their hashes, and the hashes of their installed parents.
        # Notice: with order=breadth all changed dev specs are at depth 0,
        # even if they occur as parents of one another.
        return [
            spec.dag_hash()
            for depth, spec in traverse.traverse_nodes(
                changed_dev_specs,
                root=True,
                order="breadth",
                depth=True,
                direction="parents",
                key=traverse.by_dag_hash,
            )
            if depth == 0 or spec.installed
        ]

    def _partition_roots_by_install_status(self):
        """Partition root specs into those that do not have to be passed to the
        installer, and those that should be, taking into account development
        specs. This is done in a single read transaction per environment instead
        of per spec."""
        installed, uninstalled = [], []
        with spack.store.STORE.db.read_transaction():
            for concretized_hash in self.all_concretized_orders():
                if concretized_hash in self.specs_by_hash:
                    spec = self.specs_by_hash[concretized_hash]
                else:
                    for env_path in self.included_specs_by_hash.keys():
                        if concretized_hash in self.included_specs_by_hash[env_path]:
                            spec = self.included_specs_by_hash[env_path][concretized_hash]
                            break
                if not spec.installed or (
                    spec.satisfies("dev_path=*") or spec.satisfies("^dev_path=*")
                ):
                    uninstalled.append(spec)
                else:
                    installed.append(spec)
        return installed, uninstalled

    def uninstalled_specs(self):
        """Return root specs that are not installed, or are installed, but
        are development specs themselves or have those among their dependencies."""
        return self._partition_roots_by_install_status()[1]

    def install_all(self, **install_args):
        """Install all concretized specs in an environment.

        Note: this does not regenerate the views for the environment;
        that needs to be done separately with a call to write().

        Args:
            install_args (dict): keyword install arguments
        """
        self.install_specs(None, **install_args)

    def install_specs(self, specs: Optional[List[Spec]] = None, **install_args):
        roots = self.concrete_roots()
        specs = specs if specs is not None else roots

        # Extend the set of specs to overwrite with modified dev specs and their parents
        install_args["overwrite"] = {
            *install_args.get("overwrite", ()),
            *self._dev_specs_that_need_overwrite(),
        }

        # Only environment roots are marked explicit
        install_args["explicit"] = {
            *install_args.get("explicit", ()),
            *(s.dag_hash() for s in roots),
        }

        PackageInstaller([spec.package for spec in specs], **install_args).install()

    def all_specs_generator(self) -> Iterable[Spec]:
        """Returns a generator for all concrete specs"""
        return traverse.traverse_nodes(self.concrete_roots(), key=traverse.by_dag_hash)

    def all_specs(self) -> List[Spec]:
        """Returns a list of all concrete specs"""
        return list(self.all_specs_generator())

    def all_hashes(self):
        """Return hashes of all specs."""
        return [s.dag_hash() for s in self.all_specs_generator()]

    def roots(self):
        """Specs explicitly requested by the user *in this environment*.

        Yields both added and installed specs that have user specs in
        `spack.yaml`.
        """
        concretized = dict(self.concretized_specs())
        for spec in self.user_specs:
            concrete = concretized.get(spec)
            yield concrete if concrete else spec

    def added_specs(self):
        """Specs that are not yet installed.

        Yields the user spec for non-concretized specs, and the concrete
        spec for already concretized but not yet installed specs.
        """
        # use a transaction to avoid overhead of repeated calls
        # to `package.spec.installed`
        with spack.store.STORE.db.read_transaction():
            concretized = dict(self.concretized_specs())
            for spec in self.user_specs:
                concrete = concretized.get(spec)
                if not concrete:
                    yield spec
                elif not concrete.installed:
                    yield concrete

    def concretized_specs(self):
        """Tuples of (user spec, concrete spec) for all concrete specs."""
        for s, h in zip(self.all_concretized_user_specs(), self.all_concretized_orders()):
            if h in self.specs_by_hash:
                yield (s, self.specs_by_hash[h])
            else:
                for env_path in self.included_specs_by_hash.keys():
                    if h in self.included_specs_by_hash[env_path]:
                        yield (s, self.included_specs_by_hash[env_path][h])
                        break

    def concrete_roots(self):
        """Same as concretized_specs, except it returns the list of concrete
        roots *without* associated user spec"""
        return [root for _, root in self.concretized_specs()]

    def get_by_hash(self, dag_hash: str) -> List[Spec]:
        # If it's not a partial hash prefix we can early exit
        early_exit = len(dag_hash) == 32
        matches = []
        for spec in traverse.traverse_nodes(
            self.concrete_roots(), key=traverse.by_dag_hash, order="breadth"
        ):
            if spec.dag_hash().startswith(dag_hash):
                matches.append(spec)
                if early_exit:
                    break
        return matches

    def get_one_by_hash(self, dag_hash):
        """Returns the single spec from the environment which matches the
        provided hash.  Raises an AssertionError if no specs match or if
        more than one spec matches."""
        hash_matches = self.get_by_hash(dag_hash)
        assert len(hash_matches) == 1
        return hash_matches[0]

    def all_matching_specs(self, *specs: spack.spec.Spec) -> List[Spec]:
        """Returns all concretized specs in the environment satisfying any of the input specs"""
        return [
            s
            for s in traverse.traverse_nodes(self.concrete_roots(), key=traverse.by_dag_hash)
            if any(s.satisfies(t) for t in specs)
        ]

    @spack.repo.autospec
    def matching_spec(self, spec):
        """
        Given a spec (likely not concretized), find a matching concretized
        spec in the environment.

        The matching spec does not have to be installed in the environment,
        but must be concrete (specs added with `spack add` without an
        intervening `spack concretize` will not be matched).

        If there is a single root spec that matches the provided spec or a
        single dependency spec that matches the provided spec, then the
        concretized instance of that spec will be returned.

        If multiple root specs match the provided spec, or no root specs match
        and multiple dependency specs match, then this raises an error
        and reports all matching specs.
        """
        env_root_to_user = {root.dag_hash(): user for user, root in self.concretized_specs()}
        root_matches, dep_matches = [], []

        for env_spec in traverse.traverse_nodes(
            specs=[root for _, root in self.concretized_specs()],
            key=traverse.by_dag_hash,
            order="breadth",
        ):
            if not env_spec.satisfies(spec):
                continue

            # If the spec is concrete, then there is no possibility of multiple matches,
            # and we immediately return the single match
            if spec.concrete:
                return env_spec

            # Distinguish between environment roots and deps. Specs that are both
            # are classified as environment roots.
            user_spec = env_root_to_user.get(env_spec.dag_hash())
            if user_spec:
                root_matches.append((env_spec, user_spec))
            else:
                dep_matches.append(env_spec)

        # No matching spec
        if not root_matches and not dep_matches:
            return None

        # Single root spec, any number of dep specs => return root spec.
        if len(root_matches) == 1:
            return root_matches[0][0]

        if not root_matches and len(dep_matches) == 1:
            return dep_matches[0]

        # More than one spec matched, and either multiple roots matched or
        # none of the matches were roots
        # If multiple root specs match, it is assumed that the abstract
        # spec will most-succinctly summarize the difference between them
        # (and the user can enter one of these to disambiguate)
        fmt_str = "{hash:7}  " + spack.spec.DEFAULT_FORMAT
        color = clr.get_color_when()
        match_strings = [
            f"Root spec {abstract.format(color=color)}\n  {concrete.format(fmt_str, color=color)}"
            for concrete, abstract in root_matches
        ]
        match_strings.extend(
            f"Dependency spec\n  {s.format(fmt_str, color=color)}" for s in dep_matches
        )
        matches_str = "\n".join(match_strings)

        raise SpackEnvironmentError(
            f"{spec} matches multiple specs in the environment {self.name}: \n{matches_str}"
        )

    def removed_specs(self):
        """Tuples of (user spec, concrete spec) for all specs that will be
        removed on next concretize."""
        needed = set()
        for s, c in self.concretized_specs():
            if s in self.user_specs:
                for d in c.traverse():
                    needed.add(d)

        for s, c in self.concretized_specs():
            for d in c.traverse():
                if d not in needed:
                    yield d

    def _get_environment_specs(self, recurse_dependencies=True):
        """Returns the specs of all the packages in an environment.

        If these specs appear under different user_specs, only one copy
        is added to the list returned.
        """
        specs = [self.specs_by_hash[h] for h in self.all_concretized_orders()]
        if recurse_dependencies:
            specs.extend(
                traverse.traverse_nodes(
                    specs, root=False, deptype=("link", "run"), key=traverse.by_dag_hash
                )
            )

        return specs

    def _concrete_specs_dict(self):
        concrete_specs = {}
        for s in traverse.traverse_nodes(self.specs_by_hash.values(), key=traverse.by_dag_hash):
            spec_dict = s.node_dict_with_hashes(hash=ht.dag_hash)
            # Assumes no legacy formats, since this was just created.
            spec_dict[ht.dag_hash.name] = s.dag_hash()
            concrete_specs[s.dag_hash()] = spec_dict

            if s.build_spec is not s:
                for d in s.build_spec.traverse():
                    build_spec_dict = d.node_dict_with_hashes(hash=ht.dag_hash)
                    build_spec_dict[ht.dag_hash.name] = d.dag_hash()
                    concrete_specs[d.dag_hash()] = build_spec_dict

        return concrete_specs

    def _concrete_roots_dict(self):
        hash_spec_list = zip(self.concretized_order, self.concretized_user_specs)
        return [{"hash": h, "spec": str(s)} for h, s in hash_spec_list]

    def _to_lockfile_dict(self):
        """Create a dictionary to store a lockfile for this environment."""
        concrete_specs = self._concrete_specs_dict()
        root_specs = self._concrete_roots_dict()

        spack_dict = {"version": spack.spack_version}
        spack_commit = spack.get_spack_commit()
        if spack_commit:
            spack_dict["type"] = "git"
            spack_dict["commit"] = spack_commit
        else:
            spack_dict["type"] = "release"

        # this is the lockfile we'll write out
        data = {
            # metadata about the format
            "_meta": {
                "file-type": "spack-lockfile",
                "lockfile-version": lockfile_format_version,
                "specfile-version": spack.spec.SPECFILE_FORMAT_VERSION,
            },
            # spack version information
            "spack": spack_dict,
            # users specs + hashes are the 'roots' of the environment
            "roots": root_specs,
            # Concrete specs by hash, including dependencies
            "concrete_specs": concrete_specs,
        }

        if self.included_concrete_envs:
            data[included_concrete_name] = self.included_concrete_spec_data

        return data

    def _read_lockfile(self, file_or_json):
        """Read a lockfile from a file or from a raw string."""
        lockfile_dict = sjson.load(file_or_json)
        self._read_lockfile_dict(lockfile_dict)
        return lockfile_dict

    def set_included_concretized_user_specs(
        self,
        env_name: str,
        env_info: Dict[str, Dict[str, Any]],
        included_json_specs_by_hash: Dict[str, Dict[str, Any]],
    ) -> Dict[str, Dict[str, Any]]:
        """Sets all of the concretized user specs from included environments
        to include those from nested included environments.

        Args:
           env_name: the name (technically the path) of the included environment
           env_info: included concrete environment data
           included_json_specs_by_hash: concrete spec data keyed by hash

        Returns: updated specs_by_hash
        """
        self.included_concretized_order[env_name] = []
        self.included_concretized_user_specs[env_name] = []

        def add_specs(name, info, specs_by_hash):
            # Add specs from the environment as well as any of its nested
            # environments.
            for root_info in info["roots"]:
                self.included_concretized_order[name].append(root_info["hash"])
                self.included_concretized_user_specs[name].append(Spec(root_info["spec"]))
            if "concrete_specs" in info:
                specs_by_hash.update(info["concrete_specs"])

            if included_concrete_name in info:
                for included_name, included_info in info[included_concrete_name].items():
                    if included_name not in self.included_concretized_order:
                        self.included_concretized_order[included_name] = []
                        self.included_concretized_user_specs[included_name] = []
                    add_specs(included_name, included_info, specs_by_hash)

        add_specs(env_name, env_info, included_json_specs_by_hash)
        return included_json_specs_by_hash

    def _read_lockfile_dict(self, d):
        """Read a lockfile dictionary into this environment."""
        self.specs_by_hash = {}
        self.included_specs_by_hash = {}
        self.included_concretized_user_specs = {}
        self.included_concretized_order = {}

        roots = d["roots"]
        self.concretized_user_specs = [Spec(r["spec"]) for r in roots]
        self.concretized_order = [r["hash"] for r in roots]
        json_specs_by_hash = d["concrete_specs"]
        included_json_specs_by_hash = {}

        if included_concrete_name in d:
            for env_name, env_info in d[included_concrete_name].items():
                included_json_specs_by_hash.update(
                    self.set_included_concretized_user_specs(
                        env_name, env_info, included_json_specs_by_hash
                    )
                )

        current_lockfile_format = d["_meta"]["lockfile-version"]
        try:
            reader = READER_CLS[current_lockfile_format]
        except KeyError:
            msg = (
                f"Spack {spack.__version__} cannot read the lockfile '{self.lock_path}', using "
                f"the v{current_lockfile_format} format."
            )
            if lockfile_format_version < current_lockfile_format:
                msg += " You need to use a newer Spack version."
            raise SpackEnvironmentError(msg)

        first_seen, self.concretized_order = self.filter_specs(
            reader, json_specs_by_hash, self.concretized_order
        )

        for spec_dag_hash in self.concretized_order:
            self.specs_by_hash[spec_dag_hash] = first_seen[spec_dag_hash]

        if any(self.included_concretized_order.values()):
            first_seen = {}

            for env_name, concretized_order in self.included_concretized_order.items():
                filtered_spec, self.included_concretized_order[env_name] = self.filter_specs(
                    reader, included_json_specs_by_hash, concretized_order
                )
                first_seen.update(filtered_spec)

            for env_path, spec_hashes in self.included_concretized_order.items():
                self.included_specs_by_hash[env_path] = {}
                for spec_dag_hash in spec_hashes:
                    self.included_specs_by_hash[env_path].update(
                        {spec_dag_hash: first_seen[spec_dag_hash]}
                    )

    def filter_specs(self, reader, json_specs_by_hash, order_concretized):
        # Track specs by their lockfile key.  Currently spack uses the finest
        # grained hash as the lockfile key, while older formats used the build
        # hash or a previous incarnation of the DAG hash (one that did not
        # include build deps or package hash).
        specs_by_hash = {}

        # Track specs by their DAG hash, allows handling DAG hash collisions
        first_seen = {}

        # First pass: Put each spec in the map ignoring dependencies
        for lockfile_key, node_dict in json_specs_by_hash.items():
            spec = reader.from_node_dict(node_dict)
            if not spec._hash:
                # in v1 lockfiles, the hash only occurs as a key
                spec._hash = lockfile_key
            specs_by_hash[lockfile_key] = spec

        # Second pass: For each spec, get its dependencies from the node dict
        # and add them to the spec, including build specs
        for lockfile_key, node_dict in json_specs_by_hash.items():
            name, data = reader.name_and_data(node_dict)
            for _, dep_hash, deptypes, _, virtuals in reader.dependencies_from_node_dict(data):
                specs_by_hash[lockfile_key]._add_dependency(
                    specs_by_hash[dep_hash], depflag=dt.canonicalize(deptypes), virtuals=virtuals
                )

            if "build_spec" in node_dict:
                _, bhash, _ = reader.extract_build_spec_info_from_node_dict(node_dict)
                specs_by_hash[lockfile_key]._build_spec = specs_by_hash[bhash]

        # Traverse the root specs one at a time in the order they appear.
        # The first time we see each DAG hash, that's the one we want to
        # keep.  This is only required as long as we support older lockfile
        # formats where the mapping from DAG hash to lockfile key is possibly
        # one-to-many.

        for lockfile_key in order_concretized:
            for s in specs_by_hash[lockfile_key].traverse():
                if s.dag_hash() not in first_seen:
                    first_seen[s.dag_hash()] = s

        # Now make sure concretized_order and our internal specs dict
        # contains the keys used by modern spack (i.e. the dag_hash
        # that includes build deps and package hash).

        order_concretized = [specs_by_hash[h_key].dag_hash() for h_key in order_concretized]

        return first_seen, order_concretized

    def write(self, regenerate: bool = True) -> None:
        """Writes an in-memory environment to its location on disk.

        Write out package files for each newly concretized spec.  Also
        regenerate any views associated with the environment and run post-write
        hooks, if regenerate is True.

        Args:
            regenerate: regenerate views and run post-write hooks as well as writing if True.
        """
        self.manifest_uptodate_or_warn()
        if self.specs_by_hash or self.included_concrete_envs:
            self.ensure_env_directory_exists(dot_env=True)
            self.update_environment_repository()
            self.manifest.flush()
            # Write the lock file last. This is useful for Makefiles
            # with `spack.lock: spack.yaml` rules, where the target
            # should be newer than the prerequisite to avoid
            # redundant re-concretization.
            self.update_lockfile()
        else:
            self.ensure_env_directory_exists(dot_env=False)
            with fs.safe_remove(self.lock_path):
                self.manifest.flush()

        if regenerate:
            self.regenerate_views()

        self.new_specs.clear()

    def update_lockfile(self) -> None:
        with fs.write_tmp_and_move(self.lock_path, encoding="utf-8") as f:
            sjson.dump(self._to_lockfile_dict(), stream=f)

    def ensure_env_directory_exists(self, dot_env: bool = False) -> None:
        """Ensure that the root directory of the environment exists

        Args:
            dot_env: if True also ensures that the <root>/.env directory exists
        """
        fs.mkdirp(self.path)
        if dot_env:
            fs.mkdirp(self.env_subdir_path)

    def update_environment_repository(self) -> None:
        """Updates the repository associated with the environment."""
        for spec in traverse.traverse_nodes(self.new_specs):
            if not spec.concrete:
                raise ValueError("specs passed to environment.write() must be concrete!")

            self._add_to_environment_repository(spec)

    def _add_to_environment_repository(self, spec_node: Spec) -> None:
        """Add the root node of the spec to the environment repository"""
        repository_dir = os.path.join(self.repos_path, spec_node.namespace)
        repository = spack.repo.create_or_construct(repository_dir, spec_node.namespace)
        pkg_dir = repository.dirname_for_package_name(spec_node.name)
        fs.mkdirp(pkg_dir)
        spack.repo.PATH.dump_provenance(spec_node, pkg_dir)

    def manifest_uptodate_or_warn(self):
        """Emits a warning if the manifest file is not up-to-date."""
        if not is_latest_format(self.manifest_path):
            ver = ".".join(str(s) for s in spack.spack_version_info[:2])
            msg = (
                'The environment "{}" is written to disk in a deprecated format. '
                "Please update it using:\n\n"
                "\tspack env update {}\n\n"
                "Note that versions of Spack older than {} may not be able to "
                "use the updated configuration."
            )
            warnings.warn(msg.format(self.name, self.name, ver))

    def _default_view_as_yaml(self):
        """This internal function assumes the default view is set"""
        path = self.default_view.raw_root
        if (
            self.default_view == ViewDescriptor(self.path, self.view_path_default)
            and len(self.views) == 1
        ):
            return True

        if self.default_view == ViewDescriptor(self.path, path) and len(self.views) == 1:
            return path

        return self.default_view.to_dict()

    def invalidate_repository_cache(self):
        self._repo = None

    def __enter__(self):
        self._previous_active = _active_environment
        activate(self)
        return self

    def __exit__(self, exc_type, exc_val, exc_tb):
        deactivate()
        if self._previous_active:
            activate(self._previous_active)


def yaml_equivalent(first, second) -> bool:
    """Returns whether two spack yaml items are equivalent, including overrides"""
    # YAML has timestamps and dates, but we don't use them yet in schemas
    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)
    elif isinstance(first, bool):
        return isinstance(second, bool) and first is second
    elif isinstance(first, int):
        return isinstance(second, int) and first == second
    elif first is None:
        return second is None
    else:  # it's a string
        return isinstance(second, str) 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(specs):
    """Displays a list of specs traversed breadth-first, covering nodes, with install status.

    Args:
        specs (list): list of specs
    """
    tree_string = spack.spec.tree(
        specs,
        format=spack.spec.DISPLAY_FORMAT,
        hashes=True,
        hashlen=7,
        status_fn=spack.spec.Spec.install_status,
        key=traverse.by_dag_hash,
    )
    print(tree_string)


def make_repo_path(root):
    """Make a RepoPath from the repo subdirectories in an environment."""
    path = spack.repo.RepoPath(cache=spack.caches.MISC_CACHE)

    if os.path.isdir(root):
        for repo_root in os.listdir(root):
            repo_root = os.path.join(root, repo_root)

            if not os.path.isdir(repo_root):
                continue

            repo = spack.repo.from_path(repo_root)
            path.put_last(repo)

    return path


def manifest_file(env_name_or_dir):
    """Return the absolute path to a manifest file given the environment
    name or directory.

    Args:
        env_name_or_dir (str): either the name of a valid environment
            or a directory where a manifest file resides

    Raises:
        AssertionError: if the environment is not found
    """
    env_dir = None
    if is_env_dir(env_name_or_dir):
        env_dir = os.path.abspath(env_name_or_dir)
    elif exists(env_name_or_dir):
        env_dir = os.path.abspath(root(env_name_or_dir))

    assert env_dir, "environment not found [env={0}]".format(env_name_or_dir)
    return os.path.join(env_dir, manifest_name)


def update_yaml(manifest, backup_file):
    """Update a manifest file from an old format to the current one.

    Args:
        manifest (str): path to a manifest file
        backup_file (str): file where to copy the original manifest

    Returns:
        True if the manifest was updated, False otherwise.

    Raises:
        AssertionError: in case anything goes wrong during the update
    """
    # Check if the environment needs update
    with open(manifest, encoding="utf-8") as f:
        data = syaml.load(f)

    top_level_key = _top_level_key(data)
    needs_update = spack.schema.env.update(data[top_level_key])
    if not needs_update:
        msg = "No update needed [manifest={0}]".format(manifest)
        tty.debug(msg)
        return False

    # Copy environment to a backup file and update it
    msg = (
        'backup file "{0}" already exists on disk. Check its content '
        "and remove it before trying to update again."
    )
    assert not os.path.exists(backup_file), msg.format(backup_file)

    shutil.copy(manifest, backup_file)
    with open(manifest, "w", encoding="utf-8") as f:
        syaml.dump_config(data, f)
    return True


def _top_level_key(data):
    """Return the top level key used in this environment

    Args:
        data (dict): raw yaml data of the environment

    Returns:
        Either 'spack' or 'env'
    """
    msg = 'cannot find top level attribute "spack" or "env"' "in the environment"
    assert any(x in data for x in ("spack", "env")), msg
    if "spack" in data:
        return "spack"
    return "env"


def is_latest_format(manifest):
    """Return False if the manifest file exists and is not in the latest schema format.

    Args:
        manifest (str): manifest file to be analyzed
    """
    try:
        with open(manifest, encoding="utf-8") as f:
            data = syaml.load(f)
    except (OSError, IOError):
        return True
    top_level_key = _top_level_key(data)
    changed = spack.schema.env.update(data[top_level_key])
    return not changed


@contextlib.contextmanager
def no_active_environment():
    """Deactivate the active environment for the duration of the context. Has no
    effect when there is no active environment."""
    env = active_environment()
    try:
        deactivate()
        yield
    finally:
        # TODO: we don't handle `use_env_repo` here.
        if env:
            activate(env)


def initialize_environment_dir(
    environment_dir: Union[str, pathlib.Path], envfile: Optional[Union[str, pathlib.Path]]
) -> None:
    """Initialize an environment directory starting from an envfile.

    Files with suffix .json or .lock are considered lockfiles. Files with any other name
    are considered manifest files.

    Args:
        environment_dir: directory where the environment should be placed
        envfile: manifest file or lockfile used to initialize the environment

    Raises:
        SpackEnvironmentError: if the directory can't be initialized
    """
    environment_dir = pathlib.Path(environment_dir)
    target_lockfile = environment_dir / lockfile_name
    target_manifest = environment_dir / manifest_name
    if target_manifest.exists():
        msg = f"cannot initialize environment, {target_manifest} already exists"
        raise SpackEnvironmentError(msg)

    if target_lockfile.exists():
        msg = f"cannot initialize environment, {target_lockfile} already exists"
        raise SpackEnvironmentError(msg)

    def _ensure_env_dir():
        try:
            environment_dir.mkdir(parents=True, exist_ok=True)
        except FileExistsError as e:
            msg = f"cannot initialize the environment, '{environment_dir}' already exists"
            raise SpackEnvironmentError(msg) from e

    if envfile is None:
        _ensure_env_dir()
        target_manifest.write_text(default_manifest_yaml())
        return

    envfile = pathlib.Path(envfile)
    if not envfile.exists() or not envfile.is_file():
        msg = f"cannot initialize environment, {envfile} is not a valid file"
        raise SpackEnvironmentError(msg)

    _ensure_env_dir()

    # When we have a lockfile we should copy that and produce a consistent default manifest
    if str(envfile).endswith(".lock") or str(envfile).endswith(".json"):
        shutil.copy(envfile, target_lockfile)
        # This constructor writes a spack.yaml which is consistent with the root
        # specs in the spack.lock
        try:
            EnvironmentManifestFile.from_lockfile(environment_dir)
        except Exception as e:
            msg = f"cannot initialize environment, '{environment_dir}' from lockfile"
            raise SpackEnvironmentError(msg) from e
        return

    shutil.copy(envfile, target_manifest)

    # Copy relative path includes that live inside the environment dir
    try:
        manifest = EnvironmentManifestFile(environment_dir)
    except Exception as e:
        msg = f"cannot initialize environment, '{environment_dir}' from manifest"
        raise SpackEnvironmentError(msg) from e
    else:
        includes = manifest[TOP_LEVEL_KEY].get("include", [])
        for include in includes:
            if os.path.isabs(include):
                continue

            abspath = pathlib.Path(os.path.normpath(environment_dir / include))
            if not abspath.is_relative_to(environment_dir):
                # Warn that we are not copying relative path
                msg = "Spack will not copy relative include path from outside environment"
                msg += f" directory: {include}"
                tty.warn(msg)
                continue

            orig_abspath = os.path.normpath(envfile.parent / include)
            shutil.copy(orig_abspath, abspath)


class EnvironmentManifestFile(collections.abc.Mapping):
    """Manages the in-memory representation of a manifest file, and its synchronization
    with the actual manifest on disk.
    """

    @staticmethod
    def from_lockfile(manifest_dir: Union[pathlib.Path, str]) -> "EnvironmentManifestFile":
        """Returns an environment manifest file compatible with the lockfile already present in
        the environment directory.

        This function also writes a spack.yaml file that is consistent with the spack.lock
        already existing in the directory.

        Args:
             manifest_dir: directory containing the manifest and lockfile
        """
        # TBD: Should this be the abspath?
        manifest_dir = pathlib.Path(manifest_dir)
        lockfile = manifest_dir / lockfile_name
        with lockfile.open("r", encoding="utf-8") as f:
            data = sjson.load(f)
        user_specs = data["roots"]

        default_content = manifest_dir / manifest_name
        default_content.write_text(default_manifest_yaml())
        manifest = EnvironmentManifestFile(manifest_dir)
        for item in user_specs:
            manifest.add_user_spec(item["spec"])
        manifest.flush()
        return manifest

    def __init__(self, manifest_dir: Union[pathlib.Path, str], name: Optional[str] = None) -> None:
        self.manifest_dir = pathlib.Path(manifest_dir)
        self.name = name or str(manifest_dir)
        self.manifest_file = self.manifest_dir / manifest_name
        self.scope_name = f"env:{self.name}"
        self.config_stage_dir = os.path.join(env_subdir_path(manifest_dir), "config")

        #: Configuration scopes associated with this environment. Note that these are not
        #: invalidated by a re-read of the manifest file.
        self._config_scopes: Optional[List[spack.config.ConfigScope]] = None

        if not self.manifest_file.exists():
            msg = f"cannot find '{manifest_name}' in {self.manifest_dir}"
            raise SpackEnvironmentError(msg)

        with self.manifest_file.open(encoding="utf-8") as f:
            self.yaml_content = _read_yaml(f)

        self.changed = False

    def _all_matches(self, user_spec: str) -> List[str]:
        """Maps the input string to the first equivalent user spec in the manifest,
        and returns it.

        Args:
            user_spec: user spec to be found

        Raises:
            ValueError: if no equivalent match is found
        """
        result = []
        for yaml_spec_str in self.configuration["specs"]:
            if Spec(yaml_spec_str) == Spec(user_spec):
                result.append(yaml_spec_str)

        if not result:
            raise ValueError(f"cannot find a spec equivalent to {user_spec}")

        return result

    def add_user_spec(self, user_spec: str) -> None:
        """Appends the user spec passed as input to the list of root specs.

        Args:
            user_spec: user spec to be appended
        """
        self.configuration.setdefault("specs", []).append(user_spec)
        self.changed = True

    def remove_user_spec(self, user_spec: str) -> None:
        """Removes the user spec passed as input from the list of root specs

        Args:
            user_spec: user spec to be removed

        Raises:
            SpackEnvironmentError: when the user spec is not in the list
        """
        try:
            for key in self._all_matches(user_spec):
                self.configuration["specs"].remove(key)
        except ValueError as e:
            msg = f"cannot remove {user_spec} from {self}, no such spec exists"
            raise SpackEnvironmentError(msg) from e
        self.changed = True

    def clear(self) -> None:
        """Clear all user specs from the list of root specs"""
        self.configuration["specs"] = []
        self.changed = True

    def override_user_spec(self, user_spec: str, idx: int) -> None:
        """Overrides the user spec at index idx with the one passed as input.

        Args:
            user_spec: new user spec
            idx: index of the spec to be overridden

        Raises:
            SpackEnvironmentError: when the user spec cannot be overridden
        """
        try:
            self.configuration["specs"][idx] = user_spec
        except ValueError as e:
            msg = f"cannot override {user_spec} from {self}"
            raise SpackEnvironmentError(msg) from e
        self.changed = True

    def set_include_concrete(self, include_concrete: List[str]) -> None:
        """Sets the included concrete environments in the manifest to the value(s) passed as input.

        Args:
            include_concrete: list of already existing concrete environments to include
        """
        self.configuration[included_concrete_name] = []

        for env_path in include_concrete:
            self.configuration[included_concrete_name].append(env_path)

        self.changed = True

    def add_definition(self, user_spec: str, list_name: str) -> None:
        """Appends a user spec to the first active definition matching the name passed as argument.

        Args:
            user_spec: user spec to be appended
            list_name: name of the definition where to append

        Raises:
            SpackEnvironmentError: is no valid definition exists already
        """
        defs = self.configuration.get("definitions", [])
        msg = f"cannot add {user_spec} to the '{list_name}' definition, no valid list exists"

        for idx, item in self._iterate_on_definitions(defs, list_name=list_name, err_msg=msg):
            item[list_name].append(user_spec)
            break

        self.changed = True

    def remove_definition(self, user_spec: str, list_name: str) -> None:
        """Removes a user spec from an active definition that matches the name passed as argument.

        Args:
            user_spec: user spec to be removed
            list_name: name of the definition where to remove the spec from

        Raises:
            SpackEnvironmentError: if the user spec cannot be removed from the list,
                or the list does not exist
        """
        defs = self.configuration.get("definitions", [])
        msg = (
            f"cannot remove {user_spec} from the '{list_name}' definition, "
            f"no valid list exists"
        )

        for idx, item in self._iterate_on_definitions(defs, list_name=list_name, err_msg=msg):
            try:
                item[list_name].remove(user_spec)
                break
            except ValueError:
                pass

        self.changed = True

    def override_definition(self, user_spec: str, *, override: str, list_name: str) -> None:
        """Overrides a user spec from an active definition that matches the name passed
        as argument.

        Args:
            user_spec: user spec to be overridden
            override: new spec to be used
            list_name: name of the definition where to override the spec

        Raises:
            SpackEnvironmentError: if the user spec cannot be overridden
        """
        defs = self.configuration.get("definitions", [])
        msg = f"cannot override {user_spec} with {override} in the '{list_name}' definition"

        for idx, item in self._iterate_on_definitions(defs, list_name=list_name, err_msg=msg):
            try:
                sub_index = item[list_name].index(user_spec)
                item[list_name][sub_index] = override
                break
            except ValueError:
                pass

        self.changed = True

    def _iterate_on_definitions(self, definitions, *, list_name, err_msg):
        """Iterates on definitions, returning the active ones matching a given name."""

        def extract_name(_item):
            names = list(x for x in _item if x != "when")
            assert len(names) == 1, f"more than one name in {_item}"
            return names[0]

        for idx, item in enumerate(definitions):
            name = extract_name(item)
            if name != list_name:
                continue

            condition_str = item.get("when", "True")
            if not _eval_conditional(condition_str):
                continue

            yield idx, item
        else:
            raise SpackEnvironmentError(err_msg)

    def set_default_view(self, view: Union[bool, str, pathlib.Path, Dict[str, str]]) -> None:
        """Sets the default view root in the manifest to the value passed as input.

        Args:
            view: If the value is a string or a path, it specifies the path to the view. If
                True the default view is used for the environment, if False there's no view.
        """
        if isinstance(view, dict):
            self.configuration["view"][default_view_name].update(view)
            self.changed = True
            return

        if not isinstance(view, bool):
            view = str(view)

        self.configuration["view"] = view
        self.changed = True

    def remove_default_view(self) -> None:
        """Removes the default view from the manifest file"""
        view_data = self.configuration.get("view")
        if isinstance(view_data, collections.abc.Mapping):
            self.configuration["view"].pop(default_view_name)
            self.changed = True
            return

        self.set_default_view(view=False)

    def flush(self) -> None:
        """Synchronizes the object with the manifest file on disk."""
        if not self.changed:
            return

        with fs.write_tmp_and_move(os.path.realpath(self.manifest_file)) as f:
            _write_yaml(self.yaml_content, f)
        self.changed = False

    @property
    def configuration(self):
        """Return the dictionaries in the pristine YAML, without the top level attribute"""
        return self.yaml_content[TOP_LEVEL_KEY]

    def __len__(self):
        return len(self.yaml_content)

    def __getitem__(self, key):
        return self.yaml_content[key]

    def __iter__(self):
        return iter(self.yaml_content)

    def __str__(self):
        return str(self.manifest_file)

    @property
    def included_config_scopes(self) -> List[spack.config.ConfigScope]:
        """List of included configuration scopes from the manifest.

        Scopes are listed in the YAML file in order from highest to
        lowest precedence, so configuration from earlier scope will take
        precedence over later ones.

        This routine returns them in the order they should be pushed onto
        the internal scope stack (so, in reverse, from lowest to highest).

        Returns: Configuration scopes associated with the environment manifest

        Raises:
            SpackEnvironmentError: if the manifest includes a remote file but
                no configuration stage directory has been identified
        """
        scopes: List[spack.config.ConfigScope] = []

        # load config scopes added via 'include:', in reverse so that
        # highest-precedence scopes are last.
        includes = self[TOP_LEVEL_KEY].get("include", [])
        missing = []
        for i, config_path in enumerate(reversed(includes)):
            # allow paths to contain spack config/environment variables, etc.
            config_path = substitute_path_variables(config_path)
            include_url = urllib.parse.urlparse(config_path)

            # If scheme is not valid, config_path is not a url
            # of a type Spack is generally aware
            if spack.util.url.validate_scheme(include_url.scheme):
                # Transform file:// URLs to direct includes.
                if include_url.scheme == "file":
                    config_path = urllib.request.url2pathname(include_url.path)

                # Any other URL should be fetched.
                elif include_url.scheme in ("http", "https", "ftp"):
                    # Stage any remote configuration file(s)
                    staged_configs = (
                        os.listdir(self.config_stage_dir)
                        if os.path.exists(self.config_stage_dir)
                        else []
                    )
                    remote_path = urllib.request.url2pathname(include_url.path)
                    basename = os.path.basename(remote_path)
                    if basename in staged_configs:
                        # Do NOT re-stage configuration files over existing
                        # ones with the same name since there is a risk of
                        # losing changes (e.g., from 'spack config update').
                        tty.warn(
                            "Will not re-stage configuration from {0} to avoid "
                            "losing changes to the already staged file of the "
                            "same name.".format(remote_path)
                        )

                        # Recognize the configuration stage directory
                        # is flattened to ensure a single copy of each
                        # configuration file.
                        config_path = self.config_stage_dir
                        if basename.endswith(".yaml"):
                            config_path = os.path.join(config_path, basename)
                    else:
                        staged_path = spack.config.fetch_remote_configs(
                            config_path, str(self.config_stage_dir), skip_existing=True
                        )
                        if not staged_path:
                            raise SpackEnvironmentError(
                                "Unable to fetch remote configuration {0}".format(config_path)
                            )
                        config_path = staged_path

                elif include_url.scheme:
                    raise ValueError(
                        f"Unsupported URL scheme ({include_url.scheme}) for "
                        f"environment include: {config_path}"
                    )

            # treat relative paths as relative to the environment
            if not os.path.isabs(config_path):
                config_path = os.path.join(self.manifest_dir, config_path)
                config_path = os.path.normpath(os.path.realpath(config_path))

            if os.path.isdir(config_path):
                # directories are treated as regular ConfigScopes
                config_name = f"env:{self.name}:{os.path.basename(config_path)}"
                tty.debug(f"Creating DirectoryConfigScope {config_name} for '{config_path}'")
                scopes.append(spack.config.DirectoryConfigScope(config_name, config_path))
            elif os.path.exists(config_path):
                # files are assumed to be SingleFileScopes
                config_name = f"env:{self.name}:{config_path}"
                tty.debug(f"Creating SingleFileScope {config_name} for '{config_path}'")
                scopes.append(
                    spack.config.SingleFileScope(
                        config_name, config_path, spack.schema.merged.schema
                    )
                )
            else:
                missing.append(config_path)
                continue

        if missing:
            msg = "Detected {0} missing include path(s):".format(len(missing))
            msg += "\n   {0}".format("\n   ".join(missing))
            raise spack.config.ConfigFileError(msg)

        return scopes

    @property
    def env_config_scopes(self) -> List[spack.config.ConfigScope]:
        """A list of all configuration scopes for the environment manifest. On the first call this
        instantiates all the scopes, on subsequent calls it returns the cached list."""
        if self._config_scopes is not None:
            return self._config_scopes
        scopes: List[spack.config.ConfigScope] = [
            *self.included_config_scopes,
            spack.config.SingleFileScope(
                self.scope_name,
                str(self.manifest_file),
                spack.schema.env.schema,
                yaml_path=[TOP_LEVEL_KEY],
            ),
        ]
        ensure_no_disallowed_env_config_mods(scopes)
        self._config_scopes = scopes
        return scopes

    def prepare_config_scope(self) -> None:
        """Add the manifest's scopes to the global configuration search path."""
        for scope in self.env_config_scopes:
            spack.config.CONFIG.push_scope(scope)
        spack.config.CONFIG.ensure_scope_ordering()

    def deactivate_config_scope(self) -> None:
        """Remove any of the manifest's scopes from the global config path."""
        for scope in self.env_config_scopes:
            spack.config.CONFIG.remove_scope(scope.name)
        spack.config.CONFIG.ensure_scope_ordering()

    @contextlib.contextmanager
    def use_config(self):
        """Ensure only the manifest's configuration scopes are global."""
        with no_active_environment():
            self.prepare_config_scope()
            yield
            self.deactivate_config_scope()


def environment_path_scopes(name: str, path: str) -> Optional[List[spack.config.ConfigScope]]:
    """Retrieve the suitably named environment path scopes

    Arguments:
        name: configuration scope name
        path: path to configuration file(s)

    Returns: list of environment scopes, if any, or None
    """
    if exists(path):  # managed environment
        manifest = EnvironmentManifestFile(root(path))
    elif is_env_dir(path):  # anonymous environment
        manifest = EnvironmentManifestFile(path)
    else:
        return None

    for scope in manifest.env_config_scopes:
        scope.name = f"{name}:{scope.name}"
        scope.writable = False

    return manifest.env_config_scopes


class SpackEnvironmentError(spack.error.SpackError):
    """Superclass for all errors to do with Spack environments."""


class SpackEnvironmentViewError(SpackEnvironmentError):
    """Class for errors regarding view generation."""


class SpackEnvironmentConfigError(SpackEnvironmentError):
    """Class for Spack environment-specific configuration errors."""