fix: make the progress flag match its help text

PQAnalysis/analysis/rdf/rdf.py

@@ -21,7 +21,7 @@
 from PQAnalysis.utils.progress import tqdm
 
 # local absolute imports
-from PQAnalysis.config import with_progress_bar
+from PQAnalysis import config
 from PQAnalysis.types import Np1DNumberArray, PositiveInt, PositiveReal
 from PQAnalysis.core import distance, Cell, Cells
 from PQAnalysis.traj import (
@@ -873,7 +873,7 @@ def _calculate_bins(self):
         for frame in tqdm(
             itertools.chain([self.first_frame], self.frame_generator),
             total=self.n_frames,
-            disable=not with_progress_bar
+            disable=not config.with_progress_bar
         ):
             for i, reference_index in enumerate(self.reference_indices):
 
@@ -953,7 +953,7 @@ def _calculate_bins_raw(self):
         for values, cell in tqdm(
             self._raw_reader.raw_frame_generator(),
             total=self.n_frames,
-            disable=not with_progress_bar):
+            disable=not config.with_progress_bar):
 
             counter += 1
 

PQAnalysis/cli/_argument_parser.py

@@ -195,7 +195,10 @@ def _parse_progress(self):
         The progress argument is an optional argument and defaults to True.
         """
         super().add_argument(
-            '--progress', action='store_false', help='Show progress bar.'
+            '--progress',
+            action=argparse.BooleanOptionalAction,
+            default=True,
+            help='Show progress bar.'
         )
 
     def _parse_version(self):

tests/analysis/rdf/test_rdf.py

@@ -1,6 +1,9 @@
+import sys
+
 import numpy as np
 import pytest
 
+from PQAnalysis import config
 from PQAnalysis.analysis.rdf.exceptions import RDFError
 from PQAnalysis.analysis import RDF
 from PQAnalysis.traj import Trajectory
@@ -298,6 +301,31 @@ def test__add_to_bins():
 
 
 
+def test_progress_bar_binds_config_at_call_time(monkeypatch):
+    # config.with_progress_bar is set by the CLI after the module
+    # import, so it must be read at call time, not bound by value
+    # at import time
+    captured = {}
+
+    def fake_tqdm(iterable, **kwargs):
+        captured.update(kwargs)
+        return iterable
+
+    rdf_module = sys.modules[RDF.__module__]
+    monkeypatch.setattr(rdf_module, "tqdm", fake_tqdm)
+
+    monkeypatch.setattr(config, "with_progress_bar", False)
+    RDF(_make_no_intra_trajectory(), ["H"], ["C"], delta_r=0.5, n_bins=5).run()
+    assert captured["disable"] is True
+
+    captured.clear()
+
+    monkeypatch.setattr(config, "with_progress_bar", True)
+    RDF(_make_no_intra_trajectory(), ["H"], ["C"], delta_r=0.5, n_bins=5).run()
+    assert captured["disable"] is False
+
+
+
 class TestRDF:
 
     def test__init__type_checking(self, caplog):

tests/cli/test_main.py

@@ -78,3 +78,35 @@ def test_argcomplete_is_loaded_only_for_shell_completion(monkeypatch):
 
     assert calls == [parser]
     assert args.progress is True
+
+
+
+@pytest.mark.parametrize(
+    ("flags", "expected"),
+    [
+        ([], True),
+        (["--progress"], True),
+        (["--no-progress"], False),
+    ],
+)
+def test_progress_flag_matches_its_help_text(monkeypatch, flags, expected):
+    # --progress used to be a store_false flag, so passing it hid the
+    # progress bar although its help text reads "Show progress bar."
+    monkeypatch.setattr(argument_parser, "print_header", lambda: None)
+    monkeypatch.setattr(
+        argument_parser.config,
+        "with_progress_bar",
+        argument_parser.config.with_progress_bar,
+    )
+
+    parser = argument_parser._ArgumentParser(prog="pqanalysis-test")
+    root_logger = argument_parser.logging.getLogger()
+    original_level = root_logger.level
+
+    try:
+        args = parser.parse_args([*flags, "--log-file", "off"])
+    finally:
+        root_logger.setLevel(original_level)
+
+    assert args.progress is expected
+    assert argument_parser.config.with_progress_bar is expected