WIP: Move all modules into root namespace.

.pre-commit-config.yaml

@@ -28,6 +28,7 @@ repos:
       - id: pyupgrade
         args:
           - --py38-plus
+        exclude: '_vendor'
   - repo: https://github.com/PyCQA/isort
     rev: '5.10.1'
     hooks:
@@ -40,6 +41,11 @@ repos:
     rev: '4.0.1'
     hooks:
       - id: flake8
+        exclude: |
+          (?x)^(
+            ^signac/_vendor/configobj/|
+            ^signac/_vendor/deprecation/|
+          )
   - repo: https://github.com/PyCQA/pydocstyle
     rev: '6.1.1'
     hooks:
@@ -48,8 +54,8 @@ repos:
           (?x)^(
             ^doc/|
             ^tests/|
-            ^signac/common/configobj/|
-            ^signac/common/deprecation/|
+            ^signac/_vendor/configobj/|
+            ^signac/_vendor/deprecation/|
             ^signac/db/
           )
   - repo: https://github.com/pre-commit/mirrors-mypy

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|benchmark).)*\.py$
-match-dir = ^((?!\.|tests|configobj).)*$
+match-dir = ^((?!\.|tests|_vendor).)*$
 ignore-decorators = "deprecated"
 add-ignore = D105, D107, D203, D204, D213
 
@@ -31,7 +31,7 @@ concurrency = thread,multiprocessing
 parallel = True
 source = signac
 omit = 
-	*/signac/common/configobj/*.py
+	*/signac/_vendor/configobj/*.py
 
 [tool:pytest]
 filterwarnings = 

signac/__init__.py

@@ -9,13 +9,13 @@
 collectively accessible.
 """
 
-from . import contrib, errors, sync, testing
+from . import errors, sync, testing
 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 +29,8 @@
 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 ._vendor.configobj import Section, flatten_errors
 from .diff import diff_jobs
 from .errors import (
     DestinationExistsError,
@@ -44,7 +39,10 @@
     SchemaSyncConflict,
     SyncConflict,
 )
+from .filterparse import parse_filter_arg
+from .import_export import _SchemaPathEvaluationError, export_jobs
 from .sync import DocSync, FileSync
+from .utility import _add_verbosity_argument, _print_err, _query_yes_no, _safe_relpath
 from .version import __version__
 
 MSG_SYNC_SPECIFY_KEY = """
@@ -491,7 +489,7 @@ 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(
@@ -534,7 +532,7 @@ 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 = {}
@@ -637,7 +635,7 @@ def main_update_cache(args):
 # UNCOMMENT THE FOLLOWING BLOCK WHEN THE FIRST MIGRATION IS INTRODUCED.
 # def main_migrate(args):
 #     "Migrate the project's schema to the current schema version."
-#     from .contrib.migration import apply_migrations, _get_config_schema_version
+#     from .migration import apply_migrations, _get_config_schema_version
 #     from packaging import version
 #     from .version import SCHEMA_VERSION
 #     project = get_project(_ignore_schema_version=True)

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

@@ -10,7 +10,7 @@
 from math import isclose
 from numbers import Number
 
-from ..errors import InvalidKeyError
+from .errors import InvalidKeyError
 from .utility import _nested_dicts_to_dotted_keys, _to_hashable
 
 logger = logging.getLogger(__name__)

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

@@ -6,7 +6,7 @@
 import logging
 import os
 
-from .configobj import ConfigObj, ConfigObjError
+from ._vendor.configobj import ConfigObj, ConfigObjError
 from .errors import ConfigError
 from .validate import cfg, get_validator
 

signac/diff.py

@@ -3,7 +3,7 @@
 # This software is licensed under the BSD 3-Clause License.
 """Compute diffs of state points."""
 
-from .contrib.utility import _dotted_dict_to_nested_dicts, _nested_dicts_to_dotted_keys
+from .utility import _dotted_dict_to_nested_dicts, _nested_dicts_to_dotted_keys
 
 
 def diff_jobs(*jobs):
@@ -18,7 +18,7 @@ def diff_jobs(*jobs):
 
     Parameters
     ----------
-    \*jobs : sequence[:class:`~signac.contrib.job.Job`]
+    \*jobs : sequence[:class:`~signac.job.Job`]
         Sequence of jobs to diff.
 
     Returns