Default console logging to stdout instead of stderr

[tomaskontrimas]

Fixes #326

[Copilot]

Pull request overview

This PR updates SkyLLH’s logging configuration so console output defaults to stdout (instead of stderr), aligning with issue #326. It also includes a broad set of Ruff-driven refactors and a dataset-registry update that changes how IceTracks-DR2 is resolved.

Changes:

• Default console logging stream switched from sys.stderr to sys.stdout.
• Dataset sample registry updated so 'IceTracks-DR2' points to the 14-year v2.0 release (with explicit -v1/-v2 aliases), and deprecated sample-name support is removed.
• Repo-wide style/cleanup refactors (dict/list literals, exception narrowing, small loop simplifications) + CI/pre-commit Ruff version updates and documentation updates.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/publicdata_ps/test_time_integrated_ps_dr2.py	Adds DR2 (14-year) integration-style analysis tests via skyllh.create_datasets('IceTracks-DR2').
tests/publicdata_ps/test_time_integrated_ps_dr1.py	Minor test tweak (full_output=True).
tests/core/test_weights.py	Refactor: dict() → {}.
tests/core/test_storage.py	Refactor dict literals; simplify __str__ test.
tests/core/test_signal_generator.py	Narrows expected exception in uninitialized-generator test.
tests/core/test_logging.py	Refactor handler flush suppression; comment updated (stderr → stream).
tests/core/test_dataset.py	Removes deprecated sample-name behavior tests and related imports.
skyllh/scripting/argparser.py	Refactor: dict() → {}.
skyllh/i3/pdfratio.py	Refactor: dict() → {}.
skyllh/i3/pdf.py	Refactor: return empty dict {}.
skyllh/i3/detsigyield.py	Refactor: dict literals + dict() → {}.
skyllh/i3/dataset.py	Refactor: dict() → {}.
skyllh/i3/backgroundpdf.py	Refactor: return empty dict {}.
skyllh/datasets/i3/TestData.py	Refactor dict literals for version qualifiers and kwargs.
skyllh/datasets/i3/PublicData_14y_ps.py	Refactor dict literals for version qualifiers and kwargs.
skyllh/datasets/i3/PublicData_14y_ps_v2.py	New DR2 v2.0 dataset module; repoints origin to Dataverse version 2.0.
skyllh/datasets/i3/PublicData_10y_ps.py	Refactor dict literals for version qualifiers and kwargs.
skyllh/datasets/i3/init.py	Replaces deprecation-aware registry with plain dict; adds DR2 v2 mapping + aliases.
skyllh/datasets/datasets.py	Removes deprecation-aware registry; create_datasets no longer remaps deprecated names.
skyllh/core/utils/trials.py	Refactor dict literal construction.
skyllh/core/utils/multidimgridpdf.py	Refactor: dict comprehension.
skyllh/core/utils/analysis.py	Tightens optional dependency import handling (except ImportError).
skyllh/core/trialdata.py	Refactor: iterate dict .values() instead of .items() throwaway key.
skyllh/core/times.py	Removes redundant pass from abstract method body (docstring-only body remains).
skyllh/core/test_statistic.py	Removes redundant pass from abstract method body (docstring-only body remains).
skyllh/core/storage.py	Refactors registry/dict comprehensions; micro-optimizes row fill loop.
skyllh/core/source_hypo_grouping.py	Refactor: list() → [].
skyllh/core/smoothing.py	Removes redundant pass from abstract method body (docstring-only body remains).
skyllh/core/signalpdf.py	Refactor: return empty dict {}; refactor empty grads dict.
skyllh/core/signal_generator.py	Refactor dict literals; keeps default list-of-dicts initialization pattern.
skyllh/core/signal_generation.py	Removes redundant pass from abstract method bodies (docstring-only bodies remain).
skyllh/core/services.py	Refactor: dict() → {}.
skyllh/core/scrambling.py	Removes redundant pass from abstract method body (docstring-only body remains).
skyllh/core/pdfratio.py	Removes redundant pass from abstract method bodies (docstring-only bodies remain).
skyllh/core/pdf.py	Refactor: empty dict returns; list/range simplifications; empty grads dict.
skyllh/core/parameters.py	Refactor dict comprehensions and initializations.
skyllh/core/minimizers/iminuit.py	Refactor: tuple()/dict() → ()/{} defaults.
skyllh/core/minimizer.py	Refactor: tuple()/dict() → ()/{} defaults; removes redundant pass in abstract methods.
skyllh/core/math.py	Removes redundant pass from abstract method body (docstring-only body remains).
skyllh/core/logging.py	Behavior change: default console stream now sys.stdout; docstring updated accordingly.
skyllh/core/llhratio.py	Removes redundant pass from abstract method bodies (docstring-only bodies remain).
skyllh/core/interpolate.py	Removes redundant pass from abstract method body (docstring-only body remains).
skyllh/core/flux_model.py	Removes redundant pass from abstract method bodies (docstring-only bodies remain); small max() simplification.
skyllh/core/event_selection.py	return None → bare return (still returns None); removes redundant pass in abstract method.
skyllh/core/detsigyield.py	Removes redundant pass from abstract methods; return None → bare return (still None).
skyllh/core/dataset.py	Removes redundant pass in exception classes; narrows except to OSError; refactors dict/list initializations and iterations.
skyllh/core/backgroundpdf.py	Refactor: empty grads dict.
skyllh/core/background_generator.py	Removes redundant pass from abstract method bodies; refactor default kwargs dict.
skyllh/core/background_generation.py	Removes redundant pass from abstract method bodies.
skyllh/core/analysis.py	Refactor default kwargs dicts; removes redundant pass from abstract methods.
skyllh/analyses/i3/publicdata_ps/utils.py	Corrects exception type: ValueError → TypeError for invalid flux argument type.
skyllh/analyses/i3/publicdata_ps/time_dependent_ps.py	Refactor argument tuple/dict construction.
skyllh/analyses/i3/publicdata_ps/signalpdf.py	Refactor: empty grads dict.
skyllh/analyses/i3/publicdata_ps/signal_generator.py	Refactor: dict comprehension for record-array construction.
skyllh/analyses/i3/publicdata_ps/scripts/mceq_atm_bkg.py	Refactor: dict() → {}.
skyllh/analyses/i3/publicdata_ps/backgroundpdf.py	Corrects exception type: ValueError → TypeError; improves docstring; refactor empty grads dict.
skyllh/init.py	Narrows exception for multiprocessing start method; uses module logger instead of root warning.
pyproject.toml	Adds ruff>=0.16 to dev extras; adds per-file ignores for dataset-module naming rule.
doc/sphinx/tutorials/index.rst	Documents that 'IceTracks-DR2' now refers to DR2 v2.0; adds explicit v1/v2 naming note.
doc/sphinx/conf.py	Modernizes year calculation (timezone-aware) and simplifies autodoc exclude-members formatting.
.pre-commit-config.yaml	Updates Ruff pre-commit hook version to v0.16.3.
.github/workflows/ci.yml	Pins pip install "ruff>=0.16"; bumps repository cache key to v2.

Suppressed comments (1)

tests/core/test_logging.py:64

• The PR changes the default console stream from stderr to stdout, but test_console_handlers currently overwrites handler streams before making any assertion about the default. Adding an assertion that the installed StreamHandler targets sys.stdout would make this change regression-tested.

        # Redirect current console stream to test stream.
        for logger_name in ('skyllh', self.user_logger_name):
            lg = logging.getLogger(logger_name)
            for handler in lg.handlers:
                if isinstance(handler, logging.StreamHandler):

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