CathodeX/dvc.lock at main · Kernel-Guard/CathodeX · GitHub

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schema: '2.0'
stages:
  calibrate:
    cmd: python scripts/05b_conformal_calibrate.py --val-predictions
      data/predictions/ensemble_soap_loco_test.parquet --output-dir
      data/calibration
    deps:
    - path: data/predictions/ensemble_soap_loco_test.parquet
      hash: md5
      md5: 5e603af1fb43e9c4c37e651a873722df
      size: 146139
    - path: scripts/05b_conformal_calibrate.py
      hash: md5
      md5: 79331fbed0b1b17d10a3f17418911e46
      size: 2663
    outs:
    - path: data/calibration/conformal_params.json
      hash: md5
      md5: 59b6803872211d0ffb66c8d9dd78b12e
      size: 256
  evaluate:
    cmd: python scripts/09_evaluate_predictions.py --input
      data/predictions/ensemble_soap_loco_test.parquet --conformal-params
      data/calibration/conformal_params.json --output
      data/reports/model_validation/model_validation_report.json
    deps:
    - path: data/calibration/conformal_params.json
      hash: md5
      md5: 59b6803872211d0ffb66c8d9dd78b12e
      size: 256
    - path: data/predictions/ensemble_soap_loco_test.parquet
      hash: md5
      md5: 5e603af1fb43e9c4c37e651a873722df
      size: 146139
    - path: scripts/09_evaluate_predictions.py
      hash: md5
      md5: 8983297fe7ae4bd07f374b89d03ede7b
      size: 5782
    outs:
    - path: data/reports/model_validation/model_validation_report.json
      hash: md5
      md5: 91c3c738075e948f6092d95f4a2040ed
      size: 887
  generate_manifest:
    cmd: python scripts/08_generate_artifact_manifest.py --artifact-dir
      artifacts/models/mace_ensemble_v1 --output
      data/reports/artifact_manifest.json
    deps:
    - path: artifacts/models/mace_ensemble_v1/
      hash: md5
      md5: 39847678bedd3d6866eb48ef73dc0a13.dir
      size: 111049058
      nfiles: 17
    - path: scripts/08_generate_artifact_manifest.py
      hash: md5
      md5: 228897f44819de8d847aee9203fad71f
      size: 3402
    outs:
    - path: data/reports/artifact_manifest.json
      hash: md5
      md5: 533e5ac5c4dfa2786fa0a5a97a343841
      size: 3564
  validate_release:
    cmd: python scripts/12_validate_release.py --input
      data/predictions/ensemble_soap_loco_test.parquet --conformal-params
      data/calibration/conformal_params.json --output
      data/reports/model_validation/release_validation.json
    deps:
    - path: data/reports/artifact_manifest.json
      hash: md5
      md5: 533e5ac5c4dfa2786fa0a5a97a343841
      size: 3564
    - path: data/reports/model_validation/model_validation_report.json
      hash: md5
      md5: 91c3c738075e948f6092d95f4a2040ed
      size: 887
    - path: scripts/12_validate_release.py
      hash: md5
      md5: 9fe662e72a333bd2eddf1057611b5360
      size: 4524
    outs:
    - path: data/reports/model_validation/release_validation.json
      hash: md5
      md5: ba44da791885bea8754bd8f7fcae3c02
      size: 1278
  fetch:
    cmd: python scripts/00_fetch_mp.py --config configs/dataset_mp.yaml
    deps:
    - path: configs/dataset_mp.yaml
      hash: md5
      md5: 2c8d3690b95dd6dfb6e7d84c33142ea6
      size: 1425
    - path: scripts/00_fetch_mp.py
      hash: md5
      md5: d401f923e4ab81269f0a0d4e31786a74
      size: 2943
    params:
      configs/dataset_mp.yaml:
        dataset:
          name: mp_cathodes_v1
          raw_dir: data/raw/mp
          interim_dir: data/interim/mp
          processed_dir: data/processed/mp
          splits_dir: data/splits/mp
          reports_dir: data/reports/mp
        filters:
          require_elements:
          - Li
          - O
          require_any_transition_metals:
          - Fe
          - Mn
          - Co
          - Ni
          - Ti
          - V
          - Cr
          exclude_elements:
          - F
          - Cl
          - Br
          - I
          - S
          - Se
          min_atoms: 5
          max_atoms: 80
          require_3d_periodic: true
          allow_partial_occupancy: false
        mp:
          api_key_env: MP_API_KEY
          base_url: https://api.materialsproject.org/
          timeout_sec: 60
          max_retries: 5
          page_size: 500
    outs:
    - path: data/raw/mp/raw_mp_cathodes_v1.parquet
      hash: md5
      md5: 677ee1831ea63c9d2965577b52f2caaf
      size: 18636967
  cache_structures:
    cmd: python scripts/02b_cache_structures.py --config configs/dataset_mp.yaml
    deps:
    - path: data/raw/mp/raw_mp_cathodes_v1.parquet
      hash: md5
      md5: 677ee1831ea63c9d2965577b52f2caaf
      size: 18636967
    - path: scripts/02b_cache_structures.py
      hash: md5
      md5: f155a16bf5e57a332d81961c990eba54
      size: 3389
    outs:
    - path: data/processed/mp/structures/
      hash: md5
      md5: ea98f115c863574b55a3e6250f3c1881.dir
      size: 16773422
      nfiles: 11378
  build_graphs:
    cmd: python scripts/02_build_graph_cache.py --config configs/dataset_mp.yaml
    deps:
    - path: data/raw/mp/raw_mp_cathodes_v1.parquet
      hash: md5
      md5: 677ee1831ea63c9d2965577b52f2caaf
      size: 18636967
    - path: scripts/02_build_graph_cache.py
      hash: md5
      md5: 5092805ba7212374bd95f98da85d91ca
      size: 10533
    params:
      configs/dataset_mp.yaml:
        graph:
          neighbor_cutoff_angstrom: 8.0
          max_neighbors: 12
          rbf_bins: 41
          rbf_gamma: 10.0
          use_voronoi_features: false
          use_angle_features: false
          cache_format: parquet
          cache_key: cif_hash
    outs:
    - path: data/interim/mp/graphs/
      hash: md5
      md5: 49bfa16075f7cdf70838015cf2d49ed1.dir
      size: 345366141
      nfiles: 11377
    - path: data/processed/mp/processed_mp_cathodes_v1.parquet
      hash: md5
      md5: e2dc550f4c66349a9b6dcece69a6664a
      size: 656138
  make_splits:
    cmd: python scripts/03a_make_soap_loco_splits.py
    deps:
    - path: data/processed/mp/processed_mp_cathodes_v1.parquet
      hash: md5
      md5: e2dc550f4c66349a9b6dcece69a6664a
      size: 656138
    - path: scripts/03a_make_soap_loco_splits.py
      hash: md5
      md5: 83c3778af681e3d5e1d2a334169894d1
      size: 8253
    params:
      configs/dataset_mp.yaml:
        splits:
          method: chemistry_cluster
          train_frac: 0.7
          val_frac: 0.15
          test_frac: 0.15
          random_seed: 42
          clustering:
            fingerprint: composition
            n_clusters: 200
            min_cluster_size: 50
          leakage_checks:
            enforce_no_shared_cif_hash: true
            enforce_no_shared_cluster_id: true
    outs:
    - path: data/splits/mp/splits_mp_cathodes_v1_soap-loco.json
      hash: md5
      md5: 038105a7e0b99526eb5e6fc1c197fe7e
      size: 315058