Move all modules into root namespace. (#868)

* Move all modules into root namespace.

* Update changelog.

* Use a single global exclude for pre-commit.

* Move internal modules into new _internal subpackage.

* Move internal modules back to top level.

* Clean up exclusions.

Co-authored-by: Carl Simon Adorf <carl.simon.adorf@gmail.com>
Co-authored-by: Vyas Ramasubramani <vyasr@nvidia.com>
Co-authored-by: Vyas Ramasubramani <vyas.ramasubramani@gmail.com>

.pre-commit-config.yaml

@@ -1,11 +1,7 @@
 ci:
   autoupdate_schedule: quarterly
 
-exclude: |
-  (?x)^(
-    ^signac/common/configobj/|
-    ^signac/common/deprecation/
-  )
+exclude: ^signac/_vendor/.*
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -48,9 +44,6 @@ repos:
           (?x)^(
             ^doc/|
             ^tests/|
-            ^signac/common/configobj/|
-            ^signac/common/deprecation/|
-            ^signac/db/
           )
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: 'v0.981'

changelog.txt

@@ -32,6 +32,7 @@ Changed
  - The prefix argument to ``$ signac view`` is now optional and can be provided with ``-p/--prefix`` (#653, #774).
  - Tests are run with ``xfail_strict = True`` (#850).
  - Detection of an invalid config will raise an error rather than a debug log (#855).
+ - The package namespace has been flattened so that most functionality is directly available in the ``signac`` namespace (#756, #868).
 
 Removed
 +++++++

doc/api.rst

@@ -51,7 +51,7 @@ The JobsCursor class
 ====================
 .. _python-api-jobscursor:
 
-.. currentmodule:: signac.contrib.project
+.. currentmodule:: signac.project
 
 .. rubric:: Attributes
 
@@ -72,7 +72,7 @@ The Job class
 
 .. _python-api-job:
 
-.. currentmodule:: signac.contrib.job
+.. currentmodule:: signac.job
 
 .. rubric:: Attributes
 
@@ -110,7 +110,7 @@ The Job class
 The JSONDict
 ============
 
-This class implements the interface for the job's :attr:`~signac.contrib.job.Job.statepoint` and :attr:`~signac.contrib.job.Job.document` attributes, but can also be used on its own.
+This class implements the interface for the job's :attr:`~signac.job.Job.statepoint` and :attr:`~signac.job.Job.document` attributes, but can also be used on its own.
 
 .. autoclass:: JSONDict
     :members:
@@ -120,7 +120,7 @@ This class implements the interface for the job's :attr:`~signac.contrib.job.Job
 The H5Store
 ===========
 
-This class implements the interface to the job's :attr:`~signac.contrib.job.Job.data` attribute, but can also be used on its own.
+This class implements the interface to the job's :attr:`~signac.job.Job.data` attribute, but can also be used on its own.
 
 .. autoclass:: H5Store
     :members:
@@ -130,7 +130,7 @@ This class implements the interface to the job's :attr:`~signac.contrib.job.Job.
 The H5StoreManager
 ==================
 
-This class implements the interface to the job's :attr:`~signac.contrib.job.Job.stores` attribute, but can also be used on its own.
+This class implements the interface to the job's :attr:`~signac.job.Job.stores` attribute, but can also be used on its own.
 
 .. autoclass:: H5StoreManager
     :members:

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.black]
 target-version = ['py38']
 include = '\.pyi?$'
-exclude = '''
+force-exclude = '''
 (
   /(
       \.eggs
@@ -11,11 +11,11 @@ exclude = '''
     | \.venv
     | build
     | dist
-    | signac/common/configobj
+    | _vendor
   )/
 )
 '''
 
 [tool.isort]
 profile = 'black'
-skip_glob = 'signac/common/configobj/*'
+skip_glob = 'signac/_vendor/*'

setup.cfg

@@ -12,13 +12,13 @@ python-tag = py3
 
 [flake8]
 max-line-length = 100
-exclude = configobj
+exclude = _vendor
 select = E,F,W
 ignore = E123,E126,E203,E226,E241,E704,W503,W504
 
 [pydocstyle]
 match = ^((?!\.sync-zenodo-metadata|setup).)*\.py$
-match-dir = ^((?!\.|tests|configobj).)*$
+match-dir = ^((?!\.|tests|_vendor).)*$
 ignore-decorators = "deprecated"
 add-ignore = D105, D107, D203, D204, D213
 
@@ -31,8 +31,7 @@ concurrency = thread,multiprocessing
 parallel = True
 source = signac
 omit = 
-	*/signac/common/configobj/*.py
-	*/signac/common/deprecation/*.py
+	*/signac/_vendor/*
 
 [tool:pytest]
 xfail_strict = True

signac/__init__.py

@@ -9,13 +9,13 @@
 collectively accessible.
 """
 
-from . import contrib, errors, sync
+from . import errors, sync
 from ._synced_collections.backends.collection_json import (
     BufferedJSONAttrDict as JSONDict,
 )
-from .contrib import Project, TemporaryProject, get_job, get_project, init_project
-from .core.h5store import H5Store, H5StoreManager
 from .diff import diff_jobs
+from .h5store import H5Store, H5StoreManager
+from .project import Project, TemporaryProject, get_job, get_project, init_project
 from .version import __version__
 
 # Alias some properties related to buffering into the signac namespace.
@@ -27,7 +27,6 @@
 
 __all__ = [
     "__version__",
-    "contrib",
     "errors",
     "sync",
     "Project",

signac/__main__.py

@@ -29,13 +29,9 @@
 else:
     READLINE = True
 
-from . import get_project, init_project
-from .common import config
-from .common.configobj import Section, flatten_errors
-from .contrib.filterparse import parse_filter_arg
-from .contrib.import_export import _SchemaPathEvaluationError, export_jobs
-from .contrib.utility import _add_verbosity_argument, _print_err, _query_yes_no
-from .core.utility import _safe_relpath
+from . import config, get_project, init_project
+from ._utility import _add_verbosity_argument, _print_err, _query_yes_no, _safe_relpath
+from ._vendor.configobj import Section, flatten_errors
 from .diff import diff_jobs
 from .errors import (
     DestinationExistsError,
@@ -44,6 +40,8 @@
     SchemaSyncConflict,
     SyncConflict,
 )
+from .filterparse import parse_filter_arg
+from .import_export import _SchemaPathEvaluationError, export_jobs
 from .sync import DocSync, FileSync
 from .version import __version__
 
@@ -486,7 +484,7 @@ def _sig(st):
 
 
 def _main_import_interactive(project, origin, args):
-    from .contrib.import_export import _prepare_import_into_project
+    from .import_export import _prepare_import_into_project
 
     if args.move:
         raise ValueError(
@@ -529,7 +527,7 @@ def _main_import_interactive(project, origin, args):
 
 
 def _main_import_non_interactive(project, origin, args):
-    from .contrib.import_export import _prepare_import_into_project
+    from .import_export import _prepare_import_into_project
 
     try:
         paths = {}
@@ -631,7 +629,7 @@ def main_update_cache(args):
 
 def main_migrate(args):
     """Migrate the project's schema to the current schema version."""
-    from .contrib.migration import _get_config_schema_version, apply_migrations
+    from .migration import _get_config_schema_version, apply_migrations
     from .version import SCHEMA_VERSION
 
     root = args.root_directory if args.root_directory else os.getcwd()

signac/core/dict_manager.py → signac/_dict_manager.py

@@ -8,7 +8,7 @@
 import re
 import uuid
 
-from .utility import _safe_relpath
+from ._utility import _safe_relpath
 
 
 class _DictManager:

signac/contrib/_searchindexer.py → signac/_search_indexer.py

@@ -10,8 +10,8 @@
 from math import isclose
 from numbers import Number
 
-from ..errors import InvalidKeyError
-from .utility import _nested_dicts_to_dotted_keys, _to_hashable
+from ._utility import _nested_dicts_to_dotted_keys, _to_hashable
+from .errors import InvalidKeyError
 
 logger = logging.getLogger(__name__)
 

signac/contrib/utility.py → signac/_utility.py

@@ -1,22 +1,33 @@
 # Copyright (c) 2017 The Regents of the University of Michigan
 # All rights reserved.
 # This software is licensed under the BSD 3-Clause License.
-"""Utilities for signac."""
+"""Utility functions."""
 
-import logging
-import os
+import os.path
 import sys
 from collections.abc import Mapping
 from datetime import timedelta
 from time import time
 
-logger = logging.getLogger(__name__)
-
 
 def _print_err(*args, **kwargs):
     print(*args, file=sys.stderr, **kwargs)
 
 
+def _safe_relpath(path):
+    """Attempt to make a relative path, or return the original path.
+
+    This is useful for logging and representing objects, where an absolute path
+    may be very long.
+    """
+    try:
+        return os.path.relpath(path)
+    except ValueError:
+        # Windows cannot find relative paths across drives, so show the
+        # original path instead.
+        return path
+
+
 def _query_yes_no(question, default="yes"):  # pragma: no cover
     """Ask a yes/no question via input() and return their answer.
 

signac/common/config.py → signac/config.py

@@ -6,8 +6,8 @@
 import logging
 import os
 
-from .configobj import ConfigObj, ConfigObjError
-from .configobj.validate import Validator
+from ._vendor.configobj import ConfigObj, ConfigObjError
+from ._vendor.configobj.validate import Validator
 from .errors import ConfigError
 
 logger = logging.getLogger(__name__)
@@ -36,9 +36,9 @@ def _raise_if_older_schema(root):
     IncompatibleSchemaVersion
         If the project uses an older schema version that requires migration.
     """
-    from ..contrib.errors import IncompatibleSchemaVersion
-    from ..contrib.migration import _get_config_schema_version
-    from ..version import SCHEMA_VERSION, __version__
+    from .errors import IncompatibleSchemaVersion
+    from .migration import _get_config_schema_version
+    from .version import SCHEMA_VERSION, __version__
 
     schema_version = int(SCHEMA_VERSION)