leonarski_fandClaude Opus 4.8
abbee2d4dc
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>
31 lines
1.5 KiB
Markdown
31 lines
1.5 KiB
Markdown
# Large reference test datasets (git-LFS)
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The `[large]` Catch tests in `tests/` run the full analysis/processing pipeline over real
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JUNGFRAU datasets that are too big to keep as ordinary git blobs. They are tracked with
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**git-LFS** (see the `tests/data/*.h5` rule in the top-level `.gitattributes`).
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These files are **not required** to build or to run the normal test suite: every test that
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needs them resolves the path through `jfjoch_test::LargeDataFile()` (`tests/TestData.h`) and
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`SKIP()`s when the file is absent or is still an unfetched LFS pointer. `jfjoch_test` also
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prints, at start-up, whether this directory is populated.
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## Fetching
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```
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git lfs install
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git lfs pull # or: git lfs pull --include "tests/data/*.h5"
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```
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## Datasets
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| File | Dataset | Shipped |
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|----------------------------|-----------------------------------------|-----------|
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| `rotation_master.h5` | protein rotation series (~1800 images) | yes (LFS) |
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`rotation_master.h5` (plus its `_data_NNNNNN.h5` files) is fetched by `git lfs pull` and
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drives `Rugnux_Rotation`. A separate serial dataset is intentionally **not** shipped
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to keep the repository small — the rotation series can be run in serial mode (full analysis
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without rotation indexing) to exercise that path. To add your own dataset, drop the master + its
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data files here as real files (not symlinks, if you intend to commit them via LFS); the master
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references its data files by relative name, so keep them side by side.
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