Clean up utility functions. (#597)

* Clean up utility functions.

* Add missing test case for dotted keys function where values are empty dicts.

signac/__main__.py

@@ -1696,8 +1696,7 @@ def main():
 
     parser_update_cache = subparsers.add_parser(
         "update-cache",
-        description="""Use this command to update the project's persistent state point cache.
-This feature is still experimental and may be removed in future versions.""",
+        description="Use this command to update the project's persistent state point cache.",
     )
     parser_update_cache.set_defaults(func=main_update_cache)
 

signac/contrib/project.py

@@ -41,7 +41,7 @@
 from .indexing import _SignacProjectCrawler
 from .job import Job
 from .schema import ProjectSchema, _collect_by_type
-from .utility import _mkdir_p, _nested_dicts_to_dotted_keys, split_and_print_progress
+from .utility import _mkdir_p, _nested_dicts_to_dotted_keys, _split_and_print_progress
 
 logger = logging.getLogger(__name__)
 
@@ -1801,7 +1801,7 @@ def _update_in_memory_cache(self):
             def _add(_id):
                 self._sp_cache[_id] = self._get_statepoint_from_workspace(_id)
 
-            to_add_chunks = split_and_print_progress(
+            to_add_chunks = _split_and_print_progress(
                 iterable=list(to_add),
                 num_chunks=max(1, min(100, int(len(to_add) / 1000))),
                 write=logger.info,

signac/contrib/utility.py

@@ -6,18 +6,14 @@
 import logging
 import os
 import sys
-import tarfile
-import zipfile
 from collections.abc import Mapping
-from contextlib import contextmanager
 from datetime import timedelta
-from tempfile import TemporaryDirectory
 from time import time
 
 logger = logging.getLogger(__name__)
 
 
-def query_yes_no(question, default="yes"):
+def query_yes_no(question, default="yes"):  # pragma: no cover
     """Ask a yes/no question via input() and return their answer.
 
     "question" is a string that is presented to the user.
@@ -150,7 +146,7 @@ def _mkdir_p(path):
         os.makedirs(path, exist_ok=True)
 
 
-def split_and_print_progress(iterable, num_chunks=10, write=None, desc="Progress: "):
+def _split_and_print_progress(iterable, num_chunks=10, write=None, desc="Progress: "):
     """Split the progress and prints it.
 
     Parameters
@@ -201,39 +197,6 @@ def split_and_print_progress(iterable, num_chunks=10, write=None, desc="Progress
         yield iterable
 
 
-@contextmanager
-def _extract(filename):
-    """Extract zipfile and tarfile.
-
-    Parameters
-    ----------
-    filename : str
-        Name of zipfile/tarfile to extract.
-
-    Yields
-    ------
-    str
-        Path to the extracted directory.
-
-    Raises
-    ------
-    RuntimeError
-        When the provided file is neither a zipfile nor a tarfile.
-
-    """
-    with TemporaryDirectory() as tmpdir:
-        if zipfile.is_zipfile(filename):
-            with zipfile.ZipFile(filename) as file:
-                file.extractall(tmpdir)
-                yield tmpdir
-        elif tarfile.is_tarfile(filename):
-            with tarfile.open(filename) as file:
-                file.extractall(path=tmpdir)
-                yield tmpdir
-        else:
-            raise RuntimeError(f"Unknown file type: '{filename}'.")
-
-
 def _dotted_dict_to_nested_dicts(dotted_dict, delimiter_nested="."):
     """Convert dotted keys in the state point dict to a nested dict.
 

tests/test_project.py

@@ -809,8 +809,9 @@ def test_schema(self):
         for i in range(10):
             self.project.open_job(
                 {
-                    "const": 0,
+                    "const1": 0,
                     "const2": {"const3": 0},
+                    "const4": {},
                     "a": i,
                     "b": {"b2": i},
                     "c": [i if i % 2 else None, 0, 0],
@@ -821,8 +822,18 @@ def test_schema(self):
             ).init()
 
         s = self.project.detect_schema()
-        assert len(s) == 9
-        for k in "const", "const2.const3", "a", "b.b2", "c", "d", "e.e2", "f.f2":
+        assert len(s) == 10
+        for k in (
+            "const1",
+            "const2.const3",
+            "const4",
+            "a",
+            "b.b2",
+            "c",
+            "d",
+            "e.e2",
+            "f.f2",
+        ):
             assert k in s
             if "." in k:
                 with pytest.warns(FutureWarning):
@@ -836,10 +847,9 @@ def test_schema(self):
         assert s.format() == str(s)
         s = self.project.detect_schema(exclude_const=True)
         assert len(s) == 7
-        assert "const" not in s
-        with pytest.warns(FutureWarning):
-            assert ("const2", "const3") not in s
+        assert "const1" not in s
         assert "const2.const3" not in s
+        assert "const4" not in s
         assert type not in s["e"]
 
     def test_schema_subset(self):