atop's `-P PRC` output inserts the clock-tick rate (HZ=100) between the
`state` and `utime` columns. Both the Python parser and the native C
aggregator read that constant as utime for every record, charging a flat
1 CPU-second per record — so cpu_seconds collapsed to pid_count and
short-lived fork-storm commands (xset, dd, chronyc) topped the CPU table
(xset showed 67h). The old test fixtures lacked the HZ field, so code and
tests agreed on the bug.
- _parse_prc / atop_agg.c: read utime/stime past the HZ field (after+2/+3,
tokens[10]/[11]); bump the length guards accordingly
- restore C/atop_agg (deleted in 89b4f59) under linux_configuration/C/,
where the build path resolves; corrected test fixtures to include HZ
- _atop_agg_binary: fall back to the Python parser when the C source tree
is gone instead of trusting an orphaned cached binary
- add regression tests proving HZ is not summed as CPU
- bundle the in-progress since-last-report multi-day aggregation (segments,
-b/-e bounding, persisted state, window merging) and its tests/conftest
- meta: gate linux_configuration/tests in pytest_changed_packages.py
Verified by running usage_report.py --date 20260604: Top CPU now led by
SkyrimSE; xset/dd/chronyc fall to ~0. C unit tests + full pytest suite green.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- Move all linux_configuration scripts into two semantic categories:
- single_use/: scripts run once manually (fresh install, fixes, setup)
- periodic_background/: scripts run by systemd timers or daemons
- Preserve existing subdirectory structure within each category
- Fix lib/common.sh source paths for new directory depths
- Fix CONFIG_DIR depth in setup_periodic_system.sh and check_and_enable_services.sh
- Update all references in tests, fresh-install/main.sh, nix modules, and docs
- Fix check_polling_antipatterns.sh false positives (||, regex |, case patterns, jq strings)
- Fix pre-existing mypy exclusion path and type annotations for moved tools/ directory
- Rewrite check_polling_antipatterns.sh using awk (no bash regex loops); add require_serial: true
- Move pyproject.toml, .pre-commit-config.yaml, requirements.txt, run.sh,
lint_python.sh, .fvmrc into meta/ with root symlinks preserving tool
auto-discovery.
- Combine requirements.txt + requirements-dev.txt into meta/requirements.txt
(single sorted source of truth).
- Remove setup.sh, .binary-allowlist, C/ (no native code remains),
python_pkg/{split,pdfCentered,geo_data}, scripts/check_c_cpp_build_files.sh.
- Drop clang-format/cppcheck/flawfinder/check-c-cpp-build-files hooks and
archived path excludes from pre-commit config.
- Add .secret-patterns to .gitignore and untrack it (sensitive content;
full history purge is a follow-up step).
