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Author SHA1 Message Date
kemal f571ad8a2e v2 methylation QC validated on minfiDataEPIC and against sesame (K-026) 
beta r 0.99998 vs sesame 1.28.1 (max |dbeta| 0.011), detection calls 99.1% identical,
noob within 0.5% median; replicate r 0.997; all 21 control metrics pass. Spec deviations
recorded (5-field control lines, pOOBAH formula, minfi sheet keys). User guide section.
 2026-09-29 00:41:54 +01:00
kemal 26c8a0cf40 Release 1.1.0: compiled kernels (P9) and packaging (P10)
ci / test (3.12) (push) Failing after 10s
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ci / test (3.13) (push) Failing after 15s
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2026-09-28 23:56:39 +01:00
kemal b11c3706ac P10 complete: packaging verified on fresh x86_64 and aarch64 VMs 
Wheels (pure + manylinux_2_28 kernels), sdist, Docker image and conda packages built and
installed on fresh Ubuntu 24.04 machines; 225 unit tests pass against the installed
package; the tutorial runs with pip (with and without kernels); GTC/VCF content digests are
identical across pip, Docker and conda on both architectures and equal to the Pi's run.
docs/validation/P10.md; guide: install from wheels, Docker, conda; exit code 141.
 2026-09-28 23:53:59 +01:00
kemal adf6acd2d0 P9 complete: compiled kernels validated (byte-identical, 78-80 GSA samples/min/core), scaling report 
Graviton3 c7g.8xlarge, 360 GSE165845 arrays: 360/360 GTCs identical between the Rust
kernels and the pure-Python paths; 1 worker 78-80 samples/min (pure Python 29.6).
Scaling 1->8 workers efficiency 0.87-0.90; above that the 125 MB/s gp3 disk caps the
run (~620 samples/min) and, on a RAM disk, a fixed per-worker start-up cost limits a
360-sample batch to efficiency 0.48 at 32 workers (K-025). Worker state is pickled once.
docs/validation/P9.md, result JSONs, guide/README/CHANGELOG updates.
 2026-09-28 22:32:48 +01:00
kemal f11b39b5a3 v1.0.0: user guide, examples, changelog
ci / test (3.12) (push) Failing after 11s
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docs/user_guide.md (install, inputs, complete run, commands, presets, QC, outputs,
accuracy, limitations, troubleshooting), examples/gsa_demo.sh (end-to-end run on the
public GSA demo, verified on the Pi), examples/sample_sheet.csv, CHANGELOG.md; version 1.0.0.
 2026-09-28 20:38:24 +01:00