Pull jcsda-emc libs and repos out of spack fork

setup.sh

@@ -17,5 +17,31 @@ SPACK_STACK_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && p
 export SPACK_STACK_DIR
 echo "Setting environment variable SPACK_STACK_DIR to ${SPACK_STACK_DIR}"
 
-source ${SPACK_STACK_DIR}/spack/share/spack/setup-env.sh
+source ${SPACK_STACK_DIR:?}/spack/share/spack/setup-env.sh
 echo "Sourcing spack environment ${SPACK_STACK_DIR}/spack/share/spack/setup-env.sh"
+
+libpath=${SPACK_STACK_DIR}/spack-ext/lib/jcsda-emc/spack-stack
+if [ -d ${libpath}/stack/cmd ]; then
+  spack config --scope defaults add "config:extensions:$libpath"
+else
+  echo "FATAL ERROR: Could not find spack-stack extensions in ${libpath}"
+  return 1
+fi
+
+# Register the jcsda-emc repos
+msg1="Added repo with namespace"
+msg2="Repository is already registered with Spack"
+for repo in jcsda-emc jcsda-emc-bundles; do
+  repodir=${SPACK_STACK_DIR}/spack-ext/repos/$repo
+  othererrors=$( ( spack repo add $repodir --scope defaults |& grep -v -e "$msg1" -e "$msg2" ) || true )
+  if [ $(echo "$othererrors" | grep -c .) -ne 0 ]; then
+    echo "$othererrors"
+    return 2
+  fi
+  if [ ! -d $repodir ]; then
+    echo "FATAL ERROR: Repo directory $repodir does not exist!"
+    return 3
+  fi
+done
+
+echo "spack-stack extensions and repos are registered"

spack-ext/lib/jcsda-emc/spack-stack/pytest.ini

@@ -0,0 +1,9 @@
+# content of pytest.ini
+[pytest]
+addopts = --durations=20 -ra
+testpaths = tests
+markers =
+  db: tests that require creating a DB
+  network: tests that require access to the network
+  maybeslow: tests that may be slow (e.g. access a lot the filesystem, etc.)
+  regression: tests that fix a reported bug

spack-ext/lib/jcsda-emc/spack-stack/stack/cmd/stack.py

@@ -0,0 +1,40 @@
+import os
+
+from spack.extensions.stack.cmd.stack_cmds.create import (
+    setup_create_parser,
+    stack_create,
+)
+from spack.extensions.stack.cmd.stack_cmds.setup_meta_modules import (
+    setup_meta_modules_parser,
+    stack_setup_meta_modules,
+)
+from spack.extensions.stack.stack_paths import stack_path
+
+description = "Create spack-stack environment"
+section = "spack-stack"
+level = "long"
+
+
+default_env_name = 'default'
+default_env_path = os.path.join(stack_path(), 'envs')
+default_packages = os.path.join(stack_path(),
+                                'configs', 'common', 'packages.yaml')
+container_path = os.path.join(stack_path(), 'configs' 'containers')
+
+
+def setup_parser(subparser):
+    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='stack_command')
+    create_parser = sp.add_parser('create',
+                                  help='Create spack-stack environment or container.')
+    meta_modules_parser = sp.add_parser('setup-meta-modules',
+                                        help='Create lmod/lua or tcl/tk meta-modules')
+    setup_create_parser(create_parser)
+    setup_meta_modules_parser(meta_modules_parser)
+
+
+# Main command that calls subcommands
+def stack(parser, args):
+    if args.stack_command == 'create':
+        stack_create(parser, args)
+    if args.stack_command == 'setup-meta-modules':
+        stack_setup_meta_modules(parser, args)

spack-ext/lib/jcsda-emc/spack-stack/stack/cmd/stack_cmds/create.py

@@ -0,0 +1,246 @@
+import logging
+import os
+import shutil
+from sys import platform
+
+import llnl.util.tty as tty
+
+from spack.extensions.stack.container_env import StackContainer
+from spack.extensions.stack.stack_env import StackEnv, stack_path
+
+description = "Create spack-stack environment (environment or container)"
+section = "spack-stack"
+level = "long"
+
+default_env_name = "default"
+default_env_path = stack_path("envs")
+
+
+def default_site():
+    if platform == "linux" or platform == "linux2":
+        return "linux.default"
+    elif platform == "darwin":
+        return "macos.default"
+
+
+def site_help():
+    _, site_dirs, _ = next(os.walk(stack_path("configs", "sites")))
+    help_string = 'Pre-configured platform, or "default" for an empty site.yaml.'
+    help_string += os.linesep
+    help_string += 'Defaults to "default" if no arg is given'
+    help_string += os.linesep
+    help_string += "Available options are: "
+    help_string += os.linesep
+    for site in site_dirs:
+        help_string += "\t" + site + os.linesep
+    return help_string
+
+
+def template_help():
+    _, template_dirs, _ = next(os.walk(stack_path("configs", "templates")))
+    help_string = "Environment template" + os.linesep
+    help_string += "Default to an empty spack.yaml" + os.linesep
+    help_string += "Available options are: " + os.linesep
+    for template in template_dirs:
+        help_string += "\t" + template + os.linesep
+    return help_string
+
+
+def container_config_help():
+    _, _, container_configs = next(os.walk(stack_path("configs", "containers")))
+    # Exclude files like "README.md"
+    container_configs = [x for x in container_configs if x.endswith(".yaml")]
+    help_string = "Pre-configured container." + os.linesep
+    help_string += "Available options are: " + os.linesep
+    for config in container_configs:
+        help_string += "\t" + config.rstrip(".yaml") + os.linesep
+    return help_string
+
+
+def container_specs_help():
+    _, _, specs_lists = next(os.walk(stack_path("configs", "containers", "specs")))
+    help_string = "List of specs to build in container." + os.linesep
+    help_string += "Available options are: " + os.linesep
+    for specs_list in specs_lists:
+        help_string += "\t" + specs_list.rstrip(".yaml") + os.linesep
+    return help_string
+
+
+def setup_common_parser_args(subparser):
+    """Shared CLI args for container and environment subcommands"""
+
+    subparser.add_argument(
+        "--overwrite",
+        action="store_true",
+        required=False,
+        default=False,
+        help="Overwrite existing environment if it exists." " Warning this is dangerous.",
+    )
+
+
+def setup_ctr_parser(subparser):
+    """create container-specific parsing options"""
+
+    subparser.add_argument("--container", required=True, help=container_config_help())
+
+    subparser.add_argument("--specs", required=True, help=container_specs_help())
+
+    subparser.add_argument(
+        "--dir",
+        type=str,
+        required=False,
+        default=default_env_path,
+        help="Environment will be placed in <dir>/container/."
+        " Default is {}/container/.".format(default_env_path),
+    )
+
+    setup_common_parser_args(subparser)
+
+
+def setup_env_parser(subparser):
+    """create environment-specific parsing options"""
+    setup_common_parser_args(subparser)
+
+    subparser.add_argument(
+        "--dir",
+        type=str,
+        required=False,
+        default=default_env_path,
+        help="Environment will be placed in <dir>/<env-name>/."
+        " Default is {}/<env-name>/.".format(default_env_path),
+    )
+
+    subparser.add_argument(
+        "--name",
+        type=str,
+        required=False,
+        default=None,
+        help="Environment name, defaults to <template>.<site>",
+    )
+
+    subparser.add_argument(
+        "--template",
+        type=str,
+        required=False,
+        dest="template",
+        default="empty",
+        help=template_help(),
+    )
+
+    subparser.add_argument(
+        "--packages",
+        type=str,
+        required=False,
+        default=None,
+        help="Base packages.yaml, use to override common packages.yaml.",
+    )
+
+    subparser.add_argument(
+        "--upstream",
+        nargs="*",
+        action="append",
+        help="Include upstream environment (/path/to/spack-stack-x.y.z/envs/unified-env/install)",
+    )
+
+    subparser.add_argument(
+        "--modulesys",
+        type=str,
+        choices=["lmod", "tcl"],
+        help="Override choice of tcl vs. lmod config (default is based on site config)",
+    )
+
+    subparser.add_argument(
+        "--site", type=str, required=False, default=default_site(), help=site_help()
+    )
+
+    subparser.add_argument(
+        "--prefix",
+        type=str,
+        required=False,
+        default=None,
+        help="""Install prefix for spack packages and
+                modules (not the spack environment).""",
+    )
+
+    subparser.add_argument(
+        "--modify-pkg",
+        action="append",
+        help="Modify selected package and place in an environment-specific repository",
+    )
+
+
+def setup_create_parser(subparser):
+    sp = subparser.add_subparsers(metavar="SUBCOMMAND", dest="env_type")
+
+    env_parser = sp.add_parser("env", help="Create local Spack environment")
+    ctr_parser = sp.add_parser("ctr", help="Create container.")
+
+    setup_env_parser(env_parser)
+
+    setup_ctr_parser(ctr_parser)
+
+
+def container_create(args):
+    """Create pre-configured container"""
+
+    container = StackContainer(args.container, args.dir, args.specs)
+
+    env_dir = container.env_dir
+    if os.path.exists(env_dir):
+        if args.overwrite:
+            tty.msg("Env {} exists. Overwriting...".format(env_dir))
+            shutil.rmtree(env_dir)
+        else:
+            raise Exception("Env: {} already exists".format(env_dir))
+
+    container.write()
+    tty.msg("Created container {}".format(env_dir))
+
+
+def dict_from_args(args):
+    dict = {}
+    dict["site"] = args.site
+    dict["template"] = args.template
+    dict["name"] = args.name
+    dict["install_prefix"] = args.prefix
+    dict["base_packages"] = args.packages
+    dict["dir"] = args.dir
+    dict["upstreams"] = args.upstream
+    dict["modulesys"] = args.modulesys
+    dict["modifypkg"] = args.modify_pkg
+
+    return dict
+
+
+def env_create(args):
+    """Create pre-configured Spack environment.
+
+    Args: args
+
+    Returns:
+
+    """
+
+    stack_settings = dict_from_args(args)
+    stack_env = StackEnv(**stack_settings)
+
+    env_dir = stack_env.env_dir()
+    if os.path.exists(env_dir):
+        if args.overwrite:
+            tty.msg("Environment {} exists. Overwriting...".format(env_dir))
+            shutil.rmtree(env_dir)
+        else:
+            raise Exception("Environment: {} already exists".format(env_dir))
+
+    logging.debug("Creating environment from command-line args")
+    stack_env = StackEnv(**stack_settings)
+    stack_env.write()
+    stack_env.check_umask()
+    tty.msg("Created environment {}".format(env_dir))
+
+
+def stack_create(parser, args):
+    if args.env_type == "env":
+        env_create(args)
+    elif args.env_type == "ctr":
+        container_create(args)

spack-ext/lib/jcsda-emc/spack-stack/stack/cmd/stack_cmds/setup_meta_modules.py

@@ -0,0 +1,14 @@
+from spack.extensions.stack.meta_modules import setup_meta_modules
+
+description = "Create meta-modules"
+section = "spack-stack"
+level = "long"
+
+
+# Add potential arguments to setup-meta-modules
+def setup_meta_modules_parser(subparser):
+    pass
+
+
+def stack_setup_meta_modules(parser, args):
+    setup_meta_modules()