Move utility functions closer to usage (#870)

* Inline add_verbosity_arg and remove unnecessary setting.

* Remove verbosity setting exclusive to remove.

* Inline helper function for chunking in update_cache.

signac/__main__.py

@@ -38,7 +38,7 @@
     _locate_config_dir,
     _read_config_file,
 )
-from ._utility import _add_verbosity_argument, _print_err, _query_yes_no, _safe_relpath
+from ._utility import _print_err, _query_yes_no, _safe_relpath
 from ._vendor.configobj import Section, flatten_errors
 from .diff import diff_jobs
 from .errors import (
@@ -222,10 +222,10 @@ def main_remove(args):
             continue
         if args.clear:
             job.clear()
+            logging.info("Cleared f{job_id}")
         else:
             job.remove()
-        if args.verbose:
-            print(job_id)
+            logging.info("Removing f{job_id}")
 
 
 def main_move(args):
@@ -885,7 +885,13 @@ def main():
     parser.add_argument(
         "--version", action="store_true", help="Display the version number and exit."
     )
-    _add_verbosity_argument(parser, default=2)
+    parser.add_argument(
+        "-v",
+        "--verbosity",
+        help="Set level of verbosity.",
+        action="count",
+        default=2,
+    )
     parser.add_argument(
         "-y",
         "--yes",
@@ -1056,12 +1062,6 @@ def main():
         action="store_true",
         help="Request confirmation before attempting to remove/clear each job.",
     )
-    parser_remove.add_argument(
-        "-v",
-        "--verbose",
-        action="store_true",
-        help="Be verbose when removing/clearing files.",
-    )
     parser_remove.set_defaults(func=main_remove)
 
     parser_move = subparsers.add_parser("move")
@@ -1300,7 +1300,6 @@ def main():
         help="Optional: The directory of the project that should be modified for "
         "synchronization, defaults to the local project.",
     )
-    _add_verbosity_argument(parser_sync, default=2)
 
     sync_group = parser_sync.add_argument_group("copy options")
     sync_group.add_argument(

signac/_utility.py

@@ -6,8 +6,6 @@
 import os.path
 import sys
 from collections.abc import Mapping
-from datetime import timedelta
-from time import time
 
 
 def _print_err(*args, **kwargs):
@@ -76,32 +74,6 @@ def _query_yes_no(question, default="yes"):  # pragma: no cover
             print("Please respond with 'yes' or 'no' (or 'y' or 'n').")
 
 
-def _add_verbosity_argument(parser, default=0):
-    """Add a verbosity argument to parser.
-
-    Parameters
-    ----------
-    parser : :class:`argparse.ArgumentParser`
-        The parser to which to add a verbosity argument.
-    default : int
-        The default level, defaults to 0.
-
-    Notes
-    -----
-    The argument is '-v' or '--verbosity'.
-    Add multiple '-v' arguments, e.g. '-vv' or '-vvv' to
-    increase the level of verbosity.
-
-    """
-    parser.add_argument(
-        "-v",
-        "--verbosity",
-        help="Set level of verbosity.",
-        action="count",
-        default=default,
-    )
-
-
 def _mkdir_p(path):
     """Make a new directory, or do nothing if the directory already exists.
 
@@ -119,59 +91,6 @@ def _mkdir_p(path):
         os.makedirs(path, exist_ok=True)
 
 
-def _split_and_print_progress(iterable, num_chunks=10, write=None, desc="Progress: "):
-    """Split the progress and prints it.
-
-    Parameters
-    ----------
-    iterable : list
-        List of values to be chunked.
-    num_chunks : int, optional
-        Number of chunks to split the given iterable (Default value = 10).
-    write : callable, optional
-        Callable used to log messages. If None, ``print`` is used (Default
-        value = None).
-    desc : str, optional
-        Prefix of message to log (Default value = 'Progress: ').
-
-    Yields
-    ------
-    iterable
-
-    Raises
-    ------
-    ValueError
-        If num_chunks <= 0.
-
-    """
-    if num_chunks <= 0:
-        raise ValueError("num_chunks must be a positive integer.")
-    if write is None:
-        write = print
-    if num_chunks > 1:
-        N = len(iterable)
-        len_chunk = int(N / num_chunks)
-        intervals = []
-        show_est = False
-        for i in range(num_chunks - 1):
-            if i:
-                msg = f"{desc}{100 * i / num_chunks:3.0f}%"
-                if intervals:
-                    mean_interval = sum(intervals) / len(intervals)
-                    est_remaining = int(mean_interval * (num_chunks - i))
-                    if est_remaining > 10 or show_est:
-                        show_est = True
-                        msg += f" (ETR: {timedelta(seconds=est_remaining)}h)"
-                write(msg)
-            start = time()
-            yield iterable[i * len_chunk : (i + 1) * len_chunk]
-            intervals.append(time() - start)
-        yield iterable[(i + 1) * len_chunk :]
-        write(f"{desc}100%")
-    else:
-        yield iterable
-
-
 def _dotted_dict_to_nested_dicts(dotted_dict, delimiter_nested="."):
     """Convert dotted keys in the state point dict to a nested dict.
 

signac/project.py

@@ -15,6 +15,7 @@
 from collections import defaultdict
 from collections.abc import Iterable
 from contextlib import contextmanager
+from datetime import timedelta
 from itertools import groupby
 from multiprocessing.pool import ThreadPool
 from tempfile import TemporaryDirectory
@@ -30,7 +31,7 @@
 )
 from ._search_indexer import _SearchIndexer
 from ._synced_collections.backends.collection_json import BufferedJSONAttrDict
-from ._utility import _mkdir_p, _nested_dicts_to_dotted_keys, _split_and_print_progress
+from ._utility import _mkdir_p, _nested_dicts_to_dotted_keys
 from .errors import (
     DestinationExistsError,
     IncompatibleSchemaVersion,
@@ -50,6 +51,59 @@
 JOB_ID_REGEX = re.compile(f"[a-f0-9]{{{JOB_ID_LENGTH}}}")
 
 
+def _split_and_print_progress(iterable, num_chunks=10, write=None, desc="Progress: "):
+    """Split the progress and prints it.
+
+    Parameters
+    ----------
+    iterable : list
+        List of values to be chunked.
+    num_chunks : int, optional
+        Number of chunks to split the given iterable (Default value = 10).
+    write : callable, optional
+        Callable used to log messages. If None, ``print`` is used (Default
+        value = None).
+    desc : str, optional
+        Prefix of message to log (Default value = 'Progress: ').
+
+    Yields
+    ------
+    iterable
+
+    Raises
+    ------
+    ValueError
+        If num_chunks <= 0.
+
+    """
+    if num_chunks <= 0:
+        raise ValueError("num_chunks must be a positive integer.")
+    if write is None:
+        write = print
+    if num_chunks > 1:
+        N = len(iterable)
+        len_chunk = int(N / num_chunks)
+        intervals = []
+        show_est = False
+        for i in range(num_chunks - 1):
+            if i:
+                msg = f"{desc}{100 * i / num_chunks:3.0f}%"
+                if intervals:
+                    mean_interval = sum(intervals) / len(intervals)
+                    est_remaining = int(mean_interval * (num_chunks - i))
+                    if est_remaining > 10 or show_est:
+                        show_est = True
+                        msg += f" (ETR: {timedelta(seconds=est_remaining)}h)"
+                write(msg)
+            start = time.time()
+            yield iterable[i * len_chunk : (i + 1) * len_chunk]
+            intervals.append(time.time() - start)
+        yield iterable[(i + 1) * len_chunk :]
+        write(f"{desc}100%")
+    else:
+        yield iterable
+
+
 class _ProjectConfig(_Config):
     r"""Extends the project config to make it immutable.