leonarski_fandClaude Opus 5
deb8572812
- Site config: site.example.json is committed; the local site.json (git-ignored) or $JFJOCH_BATTERY_SITE / --site names this machine's paths and the private manifest. Data roots are the arms' own directories, so copying them and editing the site config moves the battery. - Run states: manifest records the runner's pid; a run is complete, running, aborted (Ctrl-C/SIGTERM, or `abort RUN`) or unfinished. compare and report refuse a run that did not finish unless --allow-incomplete, and the report says so. - `list` shows runs and their state; `run` defaults its label to the rugnux version and its baseline to the site's persisted one; a baseline must be complete and of the same privacy as the run; a private report cannot be written into the repo. - XDS reference d_min: when the finest shell of XDS's table has no significant CC1/2, XDS merged past its own signal (no resolution cut, or a cut at the detector edge) and its limit is the detector's reach. The reference is then where XDS's CC1/2 falls through 0.30 (rugnux's own target), and that is also the range forced on rugnux. The manifest keeps XDS's limit (dmin_xds) and the rule (dmin_rule). Forcing the old 1.08 A on the weak insulin set turned rugnux's I23 into I222 (ISa 12.5); forced at the derived 1.81 A it is I23 again (ISa 18.0). Changed in the inhouse arm: insu_I_weak 1.08 -> 1.81, lyso_half_image 0.80 -> 2.60, cytc_eiger 2.04 -> 2.27, lyso_strong 1.18 -> 1.24; every other inhouse limit stands. - inhouse.json follows the directory rename (ids and inputs, data root /home/data/inhouse); `remap` applies such a rename and keeps the old ids as aliases, so runs from before it still compare set by set. - Optional open-arm model check (model_check.py, when present): R-free of the deposited model against each merge, recorded and plotted. - results.json has a fixed, documented row schema (results_schema 1); the HTML report gains inline-SVG plots (verdicts per arm, d_min and R-free ratios per set). - README.md: arms, data layout and provenance, prerequisites, running, run directory, results schema, report, comparing, protocol, adding datasets. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
48 lines
1.6 KiB
Plaintext
48 lines
1.6 KiB
Plaintext
cmake-build-debug/
|
|
cmake-build-release/
|
|
build*/
|
|
python-client/
|
|
openapi-generator-cli.jar
|
|
|
|
# make_doc.sh: rendered HTML (default output dir) and the throw-away venv it builds in. The venv is
|
|
# normally deleted at the end, but stays behind when the build fails.
|
|
public/
|
|
tmp_venv/
|
|
|
|
# gen_python_client.sh: the built sdist/wheel.
|
|
/dist/
|
|
|
|
# output dirs of the retired rugnux_vs_xds.py, still lying around in older working trees
|
|
rugnux_cmp*/
|
|
|
|
# rugnux_anomalous.py ANODE work dir, when the config does not point it at the data
|
|
rugnux_anomalous*/
|
|
!rugnux_anomalous.py
|
|
|
|
# Processing output and the data it came from. These are USER DATA: a merged .mtz/.cif or a model
|
|
# carries a sample's measured unit cell, and its filename usually carries the sample's name - neither
|
|
# of which may enter this repository (see CLAUDE.md). They accumulate in the working tree while
|
|
# testing, so keep them un-addable rather than relying on everyone typing the right paths.
|
|
*.mtz
|
|
*.cif
|
|
*.pdb
|
|
*.hkl
|
|
*_image.dat
|
|
|
|
# Test fixtures are checked in deliberately; add them with an explicit path.
|
|
!tests/**
|
|
|
|
# CMake configures GitInfo.cpp.in into the BINARY dir; a copy here is only ever the residue of an
|
|
# in-source configure, and a stale one shipped a wrong version string once already.
|
|
common/GitInfo.cpp
|
|
|
|
# Review reports, work plans and investigation notes. They are working material for one task, they
|
|
# go stale the moment the code moves, and Sphinx would publish anything left under docs/.
|
|
docs/review/
|
|
|
|
# Python bytecode (tools/battery and the root scripts)
|
|
__pycache__/
|
|
|
|
# tools/battery: the local site config (paths of this machine, private manifest); site.example.json is the template
|
|
tools/battery/site.json
|