Remove sample identities from the repository; document the rule
Datasets may be confidential; sample names and measured unit cells committed to the repo can leak outside the group working on them. Scrub existing occurrences and add a "No sample identities in the repository" section to CLAUDE.md (forbidden: sample/dataset names, internal codes, measured cells tied to a sample; fine: space group / lattice / twinning descriptors). - Comments: replace internal dataset codes and protein names with the crystallographic situation they illustrate (centred vs pseudo-symmetric, holohedral, cubic, F-cubic/hexagonal, ...). - Docs: same, in the analysis/writer/stream references and example configs. - Tests: rename sample-named identifiers, TEST_CASE names, file prefixes and asserted labels to neutral crystallographic names (e.g. tetragonal_uc); behaviour unchanged. Reduce the CrystFEL reference PDB to a bare CRYST1 cell file (cell.pdb) and rename the reference data file. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This commit is contained in:
@@ -20,10 +20,10 @@ git lfs pull # or: git lfs pull --include "tests/data/*.h5"
|
||||
|
||||
| File | Dataset | Shipped |
|
||||
|----------------------------|-----------------------------------------|-----------|
|
||||
| `lyso_rotation_master.h5` | lysozyme rotation series (~1800 images) | yes (LFS) |
|
||||
| `rotation_master.h5` | protein rotation series (~1800 images) | yes (LFS) |
|
||||
|
||||
`lyso_rotation_master.h5` (plus its `_data_NNNNNN.h5` files) is fetched by `git lfs pull` and
|
||||
drives `Rugnux_LysoRotation`. A separate serial dataset is intentionally **not** shipped
|
||||
`rotation_master.h5` (plus its `_data_NNNNNN.h5` files) is fetched by `git lfs pull` and
|
||||
drives `Rugnux_Rotation`. A separate serial dataset is intentionally **not** shipped
|
||||
to keep the repository small — the rotation series can be run in serial mode (full analysis
|
||||
without rotation indexing) to exercise that path. To add your own dataset, drop the master + its
|
||||
data files here as real files (not symlinks, if you intend to commit them via LFS); the master
|
||||
|
||||
Reference in New Issue
Block a user