Add schema versioning to flow

changelog.txt

@@ -18,6 +18,7 @@ Added
 - Defined validators for the ``fork`` directive (#480).
 - Submission summary now appears in ``FlowProject`` status output, showing the number of queued, running, unknown statuses. (#472, #488).
 - Status overview now shows the number of jobs with incomplete operations and totals for the label overviews (#501).
+- Add schema version to ensure compatibility and enable migrations in future package versions (#504).
 
 Changed
 +++++++

flow/errors.py

@@ -61,3 +61,9 @@ def parse(self, parser):
     def err(self, msg, caller):
         """Raise a template error."""
         raise jinja2.TemplateError(msg)
+
+
+class IncompatibleSchemaVersion(RuntimeError):
+    """The FlowProject's schema version is incompatible with this version of flow."""
+
+    pass

flow/migration/__init__.py

@@ -0,0 +1,113 @@
+# Copyright (c) 2021 The Regents of the University of Michigan
+# All rights reserved.
+# This software is licensed under the BSD 3-Clause License.
+"""Handle migrations of signac schema versions."""
+
+import os
+import sys
+from contextlib import contextmanager
+
+from filelock import FileLock
+from packaging import version
+from signac.common.config import get_config
+
+from flow.util.config import get_config_value
+
+from ..version import SCHEMA_VERSION, __version__
+from .v0_to_v1 import migrate_v0_to_v1
+
+FN_MIGRATION_LOCKFILE = ".FLOW_PROJECT_MIGRATION_LOCK"
+
+
+MIGRATIONS = {
+    ("0", "1"): migrate_v0_to_v1,
+}
+
+
+def _reload_project_config(project):
+    project_reloaded = project.get_project(
+        root=project.root_directory(), search=False, _ignore_flow_schema_version=True
+    )
+    project._config = project_reloaded._config
+
+
+def _update_project_config(project, **kwargs):
+    """Update the project configuration."""
+    for fn in ("signac.rc", ".signacrc"):
+        config = get_config(project.fn(fn))
+        if "project" in config:
+            break
+    else:
+        raise RuntimeError("Unable to determine project configuration file.")
+    config.setdefault("flow", {}).update(kwargs)
+    config.write()
+    _reload_project_config(project)
+
+
+@contextmanager
+def _lock_for_migration(project):
+    lock = FileLock(project.fn(FN_MIGRATION_LOCKFILE))
+    try:
+        with lock:
+            yield
+    finally:
+        try:
+            os.unlink(lock.lock_file)
+        except FileNotFoundError:
+            pass
+
+
+def _collect_migrations(project):
+    schema_version = version.parse(SCHEMA_VERSION)
+
+    def get_config_schema_version():
+        # TODO: The means of getting schema versions will have to change for
+        # flow versions in schema versions > 1 that no longer rely on signac's
+        # configuration file and schema.
+        return version.parse(get_config_value("schema_version", config=project.config))
+
+    if get_config_schema_version() > schema_version:
+        # Project config schema version is newer and therefore not supported.
+        raise RuntimeError(
+            "The signac-flow schema version used by this project is {}, but flow {} "
+            "only supports up to schema version {}. Try updating flow.".format(
+                get_config_schema_version(), __version__, SCHEMA_VERSION
+            )
+        )
+
+    while get_config_schema_version() < schema_version:
+        for (origin, destination), migration in MIGRATIONS.items():
+            if version.parse(origin) == get_config_schema_version():
+                yield (origin, destination), migration
+                break
+        else:
+            raise RuntimeError(
+                "The signac-flow schema version used by this project is {}, but flow {} "
+                "uses schema version {} and does not know how to migrate.".format(
+                    get_config_schema_version(), __version__, schema_version
+                )
+            )
+
+
+def apply_migrations(project):
+    """Apply migrations to a project."""
+    with _lock_for_migration(project):
+        for (origin, destination), migrate in _collect_migrations(project):
+            try:
+                print(
+                    f"Applying migration for version {origin} to {destination}... ",
+                    end="",
+                    file=sys.stderr,
+                )
+                migrate(project)
+            except Exception as e:
+                raise RuntimeError(f"Failed to apply migration {destination}.") from e
+            else:
+                _update_project_config(project, schema_version=destination)
+                print("OK", file=sys.stderr)
+                yield origin, destination
+
+
+__all__ = [
+    "apply_migrations",
+]

flow/migration/v0_to_v1.py

@@ -0,0 +1,46 @@
+# Copyright (c) 2021 The Regents of the University of Michigan
+# All rights reserved.
+# This software is licensed under the BSD 3-Clause License.
+"""Migrate from schema version 0 to version 1.
+
+This migration is a null-migration that serves as a template
+for future migrations and testing purposes.
+"""
+
+
+def migrate_v0_to_v1(project):
+    """Migrate from schema version 0 to version 1."""
+    pass  # nothing to do here, serves purely as an example
+
+
+def migrate_v1_to_v2(project):
+    """Migrate from schema version 1 to version 2."""
+    # TODO: This migration is not yet implemented, but this comment documents
+    # what this function will need to do. There are a few different scenarios
+    # that must be accounted for:
+    # 1. User updates signac before flow. In this case, signac's config API may
+    #    already have changed, and we cannot rely on it. Therefore, we need add
+    #    configobj as an optional requirement for flow rather than relying on
+    #    signac's config API (it's available on PyPI). Alternatively, we could
+    #    bundle configobj like we do in signac, but I don't want to commit to
+    #    that long term so that would at best be a short term solution (say for
+    #    one or two flow releases) and then after that we tell users who
+    #    haven't migrated to just `pip install configobj`. Then, this function
+    #    can rely on the fact that in signac schema version one the config
+    #    information is stored in signac.rc using the known schema and operate
+    #    accordingly to pull it.
+    # 2. User updates signac and attempts to migrate before migrating flow
+    #    schema. In this case, `signac migrate` should error and tell the user
+    #    to update flow and run `flow migrate` first. This can be accomplished
+    #    by having the v1->v2 migration in signac check for the presence of the
+    #    "flow" key in the config and error if it is present.  We will
+    #    introduce the flow v1->v2 migration before signac's to ensure that
+    #    this be possible.
+    # 3. Users update signac and create a new project, but still use an old
+    #    version of flow that has errors trying to access signac config
+    #    information. This case should fail fast, and we'll just have to inform
+    #    such users that they need to upgrade flow.
+    #
+    # Once a FlowProject has migrated to schema version 2, it is decoupled from
+    # signac's internal schema and should not have any further problems.
+    pass

flow/project.py

@@ -33,13 +33,15 @@
 import signac
 from deprecation import deprecated
 from jinja2 import TemplateNotFound as Jinja2TemplateNotFound
+from packaging import version
 from signac.contrib.filterparse import parse_filter_arg
 from tqdm.auto import tqdm
 
 from .aggregates import _aggregator, _get_aggregate_id
 from .environment import get_environment
 from .errors import (
     ConfigKeyError,
+    IncompatibleSchemaVersion,
     NoSchedulerError,
     SubmitError,
     TemplateError,
@@ -63,7 +65,7 @@
     switch_to_directory,
 )
 from .util.translate import abbreviate, shorten
-from .version import __version__
+from .version import SCHEMA_VERSION, __version__
 
 logger = logging.getLogger(__name__)
 
@@ -1424,9 +1426,20 @@ def hello(job):
 
     """
 
-    def __init__(self, config=None, environment=None, entrypoint=None):
+    def __init__(
+        self,
+        config=None,
+        environment=None,
+        entrypoint=None,
+        _ignore_flow_schema_version=False,
+    ):
         super().__init__(config=config)
 
+        # This internal constructor parameter exists solely for the purpose of
+        # allowing reloads of the project during migration.
+        if not _ignore_flow_schema_version:
+            self._check_flow_schema_compatibility()
+
         # Associate this class with a compute environment.
         self._environment = environment or get_environment()
 
@@ -1454,6 +1467,39 @@ def __init__(self, config=None, environment=None, entrypoint=None):
         self._group_to_aggregate_store = _bidict()
         self._register_groups()
 
+    def _check_flow_schema_compatibility(self):
+        """Check whether this project's data schema is compatible with this version.
+
+        Raises
+        ------
+        :class:`~flow.errors.IncompatibleSchemaVersion`
+            If the schema version is incompatible.
+
+        """
+        schema_version = version.parse(SCHEMA_VERSION)
+        config_schema_version = version.parse(
+            flow_config.get_config_value("schema_version", config=self.config)
+        )
+        if config_schema_version > schema_version:
+            # Project config schema version is newer and therefore not supported.
+            raise IncompatibleSchemaVersion(
+                "The signac-flow schema version used by this project is '{}', but flow {} "
+                "only supports up to schema version '{}'. Try updating flow.".format(
+                    config_schema_version, __version__, schema_version
+                )
+            )
+        elif config_schema_version < schema_version:
+            raise IncompatibleSchemaVersion(
+                "The flow schema version used by this project is '{}', but flow {} "
+                "requires schema version '{}'. Please use '$ flow migrate' to "
+                "irreversibly migrate this project's schema to the supported "
+                "version.".format(config_schema_version, __version__, schema_version)
+            )
+        else:  # identical and therefore compatible
+            logger.debug(
+                f"The project's schema version {config_schema_version} is supported."
+            )
+
     def _setup_template_environment(self):
         """Set up the jinja2 template environment.
 
@@ -2497,7 +2543,9 @@ def print_status(
                 "eligible_jobs_max_lines"
             )
 
-        status_parallelization = self.config["flow"]["status_parallelization"]
+        status_parallelization = flow_config.get_config_value(
+            "status_parallelization", config=self.config
+        )
 
         # initialize jinja2 template environment and necessary filters
         template_environment = self._template_environment()
@@ -4349,7 +4397,9 @@ def _main_status(self, args):
             # Use small offset to account for overhead with few jobs
             delta_t = (time.time() - start - 0.5) / max(length_jobs, 1)
             config_key = "status_performance_warn_threshold"
-            warn_threshold = flow_config.get_config_value(config_key)
+            warn_threshold = flow_config.get_config_value(
+                config_key, config=self.config
+            )
             if not args["profile"] and delta_t > warn_threshold >= 0:
                 print(
                     "WARNING: "

flow/util/config.py

@@ -2,18 +2,19 @@
 # All rights reserved.
 # This software is licensed under the BSD 3-Clause License.
 """Contains logic for working with flow related information stored in the signac config."""
-from signac.common import config
+import signac.common.config
 
 from ..errors import ConfigKeyError
 
 # Monkeypatch the signac config spec to include flow-specific fields.
-config.cfg += """
+signac.common.config.cfg += """
 [flow]
 import_packaged_environments = boolean()
 status_performance_warn_threshold = float(default=0.2)
 show_traceback = boolean()
-eligible_jobs_max_lines = int(default=10)
+eligible_jobs_max_lines = integer(default=10)
 status_parallelization = string(default='none')
+schema_version = string(default='1')
 """
 
 
@@ -24,7 +25,7 @@ class _GetConfigValueNoneType:
 _GET_CONFIG_VALUE_NONE = _GetConfigValueNoneType()
 
 
-def require_config_value(key, ns=None, default=_GET_CONFIG_VALUE_NONE):
+def require_config_value(key, ns=None, default=_GET_CONFIG_VALUE_NONE, config=None):
     """Request a value from the user's configuration, failing if not available.
 
     Parameters
@@ -36,6 +37,10 @@ def require_config_value(key, ns=None, default=_GET_CONFIG_VALUE_NONE):
     default
         A default value in case the key cannot be found
         within the user's configuration.
+    config
+        The config to pull from. If ``None``, uses
+        :func:`~signac.common.config.load_config` to acquire one
+        (Default value = None).
 
     Returns
     -------
@@ -49,11 +54,13 @@ def require_config_value(key, ns=None, default=_GET_CONFIG_VALUE_NONE):
         and no default value is provided.
 
     """
+    config = config or signac.common.config.load_config()
+
     try:
         if ns is None:
-            return config.load_config()["flow"][key]
+            return config["flow"][key]
         else:
-            return config.load_config()["flow"][ns][key]
+            return config["flow"][ns][key]
     except KeyError:
         if default is _GET_CONFIG_VALUE_NONE:
             k = str(key) if ns is None else f"{ns}.{key}"
@@ -62,7 +69,7 @@ def require_config_value(key, ns=None, default=_GET_CONFIG_VALUE_NONE):
             return default
 
 
-def get_config_value(key, ns=None, default=None):
+def get_config_value(key, ns=None, default=None, config=None):
     """Request a value from the user's configuration.
 
     Parameters
@@ -74,11 +81,13 @@ def get_config_value(key, ns=None, default=None):
     default
         A default value returned if the key cannot be found within the user
         configuration.
+    config
+        The config to pull from (Default value = None).
 
     Returns
     -------
     object
         The value if found, None if not found.
 
     """
-    return require_config_value(key=key, ns=ns, default=default)
+    return require_config_value(key=key, ns=ns, default=default, config=config)

flow/version.py

@@ -5,4 +5,6 @@
 
 __version__ = "0.13.0"
 
-__all__ = ["__version__"]
+SCHEMA_VERSION = "1"
+
+__all__ = ["__version__", "SCHEMA_VERSION"]

requirements.txt

@@ -3,3 +3,5 @@ jinja2>=2.10
 cloudpickle>=1.1.1
 deprecation>=2.0.0
 tqdm>=4.48.1
+filelock~=3.0
+packaging>=15.0

requirements/requirements-test.txt

@@ -3,3 +3,5 @@ coverage==5.5
 pytest-cov==2.11.1
 pytest==6.2.2
 ruamel.yaml==0.17.2
+filelock~=3.0
+packaging>=15.0