Remove public API of indexing module. (#580)

* Remove public API for indexing module.

* Remove index command from signac.__main__.

* Remove tests for methods and classes that have been removed.

* Remove index from CLI help message.

* Make indexing features adhere to pydocstyle.

* Fix typo.

* Remove index shell test.

doc/api.rst

@@ -162,7 +162,7 @@ Top-level functions
 .. automodule:: signac
     :members:
     :show-inheritance:
-    :exclude-members: Project,Collection,RegexFileCrawler,MainCrawler,MasterCrawler,SignacProjectCrawler,JSONDict,H5Store,H5StoreManager
+    :exclude-members: Project,Collection,JSONDict,H5Store,H5StoreManager
 
 
 Submodules

doc/cli-help.txt

@@ -1,12 +1,12 @@
 usage: signac [-h] [--debug] [--version] [-v] [-y]
-              {init,project,job,statepoint,diff,document,rm,move,clone,index,find,view,schema,shell,sync,import,export,update-cache,config}
+              {init,project,job,statepoint,diff,document,rm,move,clone,find,view,schema,shell,sync,import,export,update-cache,config}
               ...
 
 signac aids in the management, access and analysis of large-scale
 computational investigations.
 
 positional arguments:
-  {init,project,job,statepoint,diff,document,rm,move,clone,index,find,view,schema,shell,sync,import,export,update-cache,config}
+  {init,project,job,statepoint,diff,document,rm,move,clone,find,view,schema,shell,sync,import,export,update-cache,config}
 
 optional arguments:
   -h, --help            show this help message and exit

setup.cfg

@@ -17,7 +17,7 @@ select = E,F,W
 ignore = E123,E126,E203,E226,E241,E704,W503,W504
 
 [pydocstyle]
-match = ^((?!\.sync-zenodo-metadata|setup|benchmark|indexing).)*\.py$
+match = ^((?!\.sync-zenodo-metadata|setup|benchmark).)*\.py$
 match-dir = ^((?!\.|tests|configobj).)*$
 ignore-decorators = "deprecated"
 add-ignore = D105, D107, D203, D204, D213
@@ -35,7 +35,7 @@ omit =
 
 [tool:pytest]
 filterwarnings = 
-	ignore: .*[The indexing module | get_statepoint | Use of.+as key] is deprecated.*: DeprecationWarning
+	ignore: .*[get_statepoint | Use of.+as key] is deprecated.*: DeprecationWarning
 
 [bumpversion:file:setup.py]
 

signac/__init__.py

@@ -12,21 +12,10 @@
 from . import cite, contrib, errors, sync, testing, warnings
 from .contrib import (
     Collection,
-    MainCrawler,
-    MasterCrawler,
     Project,
-    RegexFileCrawler,
-    SignacProjectCrawler,
     TemporaryProject,
-    export,
-    export_one,
-    export_pymongo,
-    export_to_mirror,
-    fetch,
     get_job,
     get_project,
-    index,
-    index_files,
     init_project,
 )
 from .core.h5store import H5Store, H5StoreManager
@@ -56,19 +45,7 @@
     "init_project",
     "get_job",
     "diff_jobs",
-    "fetch",
-    "export_one",
-    "export",
-    "export_to_mirror",
     "Collection",
-    "export_pymongo",
-    "fs",
-    "index_files",
-    "index",
-    "RegexFileCrawler",
-    "MainCrawler",
-    "MasterCrawler",
-    "SignacProjectCrawler",
     "buffered",
     "is_buffered",
     "get_buffer_size",

signac/__main__.py

@@ -29,7 +29,7 @@
 else:
     READLINE = True
 
-from . import Project, get_project, index, init_project
+from . import Project, get_project, init_project
 from .common import config
 from .common.configobj import Section, flatten_errors
 from .contrib.filterparse import parse_filter_arg
@@ -277,16 +277,6 @@ def main_clone(args):
             _print_err(f"Cloned '{job}' to '{dst_project}'.")
 
 
-def main_index(args):
-    """Handle index subcommand."""
-    _print_err(f"Compiling main index for path '{os.path.realpath(args.root)}'...")
-    if args.tags:
-        args.tags = set(args.tags)
-        _print_err("Provided tags: {}".format(", ".join(sorted(args.tags))))
-    for doc in index(root=args.root, tags=args.tags, raise_on_error=args.debug):
-        print(json.dumps(doc))
-
-
 def main_find(args):
     """Handle find subcommand."""
     project = get_project()
@@ -1197,18 +1187,6 @@ def main():
     )
     parser_clone.set_defaults(func=main_clone)
 
-    parser_index = subparsers.add_parser("index")
-    parser_index.add_argument(
-        "root",
-        nargs="?",
-        default=".",
-        help="Specify the root path from where the main index is to be compiled.",
-    )
-    parser_index.add_argument(
-        "-t", "--tags", nargs="+", help="Specify tags for this main index compilation."
-    )
-    parser_index.set_defaults(func=main_index)
-
     parser_find = subparsers.add_parser(
         "find",
         description="""All filter arguments may be provided either directly in JSON
@@ -1486,7 +1464,7 @@ def main():
         "--ignore-times",
         action="store_true",
         dest="deep",
-        help="Never rely on file meta data such as the size or the modification time "
+        help="Never rely on file metadata such as the size or the modification time "
         "when determining file differences.",
     )
     sync_group.add_argument(

signac/contrib/__init__.py

@@ -5,49 +5,17 @@
 
 import logging
 
-from . import indexing
 from .collection import Collection
-from .indexing import (
-    BaseCrawler,
-    JSONCrawler,
-    MainCrawler,
-    MasterCrawler,
-    RegexFileCrawler,
-    SignacProjectCrawler,
-    export,
-    export_one,
-    export_pymongo,
-    export_to_mirror,
-    fetch,
-    fetched,
-    index,
-    index_files,
-)
 from .project import Project, TemporaryProject, get_job, get_project, init_project
 
 logger = logging.getLogger(__name__)
 
 
 __all__ = [
-    "indexing",
     "Project",
     "TemporaryProject",
     "get_project",
     "init_project",
     "get_job",
-    "BaseCrawler",
-    "RegexFileCrawler",
-    "JSONCrawler",
-    "SignacProjectCrawler",
-    "MainCrawler",
-    "MasterCrawler",
-    "fetch",
-    "fetched",
-    "export_one",
-    "export",
-    "export_to_mirror",
-    "export_pymongo",
-    "index_files",
-    "index",
     "Collection",
 ]