stfc / alc-dls-exafs / 27427257496
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Extract paths (#70)

* WIP Refactor to use HDF5 files to store the FEFF otuput including path information

Storing all the paths for all the frames/sites generates a very large number of files. This approach organises and compresses that output into an easy-to-transport single archive file. HDF5 was chosen as it's flexible saves the FeffConfig metadata also) and is already a dependency from larch.

Also added the option to filter out hydrogens as they typically don't contribute to EXAFS and can cause some issue with FEFF.

* feat: add curved-wave amplitude ratio (cw_ratio) path filtering

Parse FEFF's files.dat to extract the curved-wave chi amplitude ratio
for each scattering path and thread it through the full pipeline:

- feff_utils: add parse_files_dat() to read cw_ratio from files.dat
- hdf5_store: store and read cw_ratio as an HDF5 attribute per path
- exafs_data: add cw_ratio field to PathContribution; average across
  samples in PathAggregator.finalize(); add filter_path_contributions()
  utility (filters by min_cw_ratio threshold and/or top_n cap, preserving
  r_eff ordering among survivors)
- cli: add --min-cw-ratio option to both `analyze` and `pipeline` commands
- tests: add TestParseFilesDat and TestFilterPathContributions
- scripts: add pack_output_to_hdf5.py to import an existing
  pipeline_output/ tree into HDF5 without re-running FEFF
- README: document HDF5 output mode and the pack script

* change all return sites and unpack sites of (chi, k) → (k, chi) to match the documented convention.

* feat: store raw FEFF parameters and MD-averaged path contributions in HDF5

- `PathContribution` gains `amp`, `pha`, `lam`, `rep`, `k_param` (raw FEFF
  params for on-the-fly chi recomputation), `source_frames`, `source_sites`
  (MD provenance), and `contribution_pct`; `PathAggregator` averages and
  populates all new fields
- `iter_path_contributions` yields `(path_key, info, frame_index, site_index)`
  4-tuples; all call sites updated to unpac... (continued)

1883 of 3737 relevant lines covered (50.39%)

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Coverage Regressions

Lines Coverage ∆ File
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288
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 -3.19% feff_utils.py
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 -15.79% pipeline.py
Jobs
ID Job ID Ran Files Coverage
1 run-3.13 - 27427257496.1 11
50.39
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2 run-3.11 - 27427257496.2 11
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3 run-3.12 - 27427257496.3 11
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4 run-3.10 - 27427257496.4 11
50.39
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Source Files on build 27427257496