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f71fa950bb5ffba1f6bd6d0459af50d8b167c73e2e7ca6cdac466814a883b759 data_raw_protein_20260517T175654Z_chunk_001.tar.zst |
95bb3fb79bab0a29f53301506da939ae63d628b216b1621b8283743ccaa10dc1 data_raw_protein_20260517T175654Z_chunk_002.tar.zst |
cef6b270b98836adcf822cc76a9055c960ebb4f9184592f3fe58e296b8df672c data_raw_protein_20260517T175654Z_chunk_003.tar.zst |
918dde227ab5e6737f52ce9ec9a6c1dfc44e5a7d60346a44fc97947af55fb8b1 data_raw_protein_20260517T175654Z_chunk_004.tar.zst |
data/raw/protein/9606.protein.aliases.v12.0.txt.gz |
data/raw/protein/9606.protein.links.v12.0.txt.gz |
data/raw/protein/esm3 |
data/raw/protein/esmc |
hoptf/data/MANIFEST.json:164: "canonical_path": "data/raw/protein/esmc/esmc-600m-2024-12", |
hoptf/data/MANIFEST.json:172: "indexed_path": "data/raw/protein/esm3/esm3-sm-open-v1", |
hoptf/data/MANIFEST.json:173: "canonical_path": "data/raw/protein/esm3/esm3-sm-open-v1", |
hoptf/v2/scripts/generate_esmc.py:15:DEFAULT_SNAPSHOT_ROOT = Path("data/raw/protein/esmc") |
hoptf/v2/planning/2026-05-16_larger_variant_panel_experiment.md:172: --snapshot-dir data/raw/protein/esmc/esmc-600m-2024-12 \ |
src/mantra/embeddings/tests/PYTEST_SMOKE_ARTIFACT_ESMC.json:9: "/home/machina/MANTRA/data/raw/protein/esmc/MANIFEST.json", |
src/mantra/embeddings/tests/TEST_SMOKE_CONTRACT_ESMC.json:11: "/home/machina/MANTRA/data/raw/protein/esmc/MANIFEST.json", |
src/mantra/embeddings/tests/PYTEST_SMOKE_ARTIFACT_ESM3.json:9: "/home/machina/MANTRA/data/raw/protein/esm3/MANIFEST.json", |
src/mantra/embeddings/tests/test_generate_esm3.py:75: smoke_path(REPO_ROOT / "data/raw/protein/esm3/MANIFEST.json", recorder=recorder) |
src/mantra/embeddings/tests/TEST_SMOKE_CONTRACT_ESM3.json:11: "/home/machina/MANTRA/data/raw/protein/esm3/MANIFEST.json", |
src/mantra/embeddings/tests/test_generate_esmc.py:86: smoke_path(REPO_ROOT / "data/raw/protein/esmc/MANIFEST.json", recorder=recorder) |
sota5/runs/full_with_priors/artifacts/PRIOR_BUILD_MANIFEST.json:44: "/home/machina/MANTRA/data/raw/protein/esm3/esm3-sm-open-v1" |
sota5/runs/full_with_priors/artifacts/PRIOR_BUILD_MANIFEST.json:64: "/home/machina/MANTRA/data/raw/protein/esmc" |
FINAL/source/src/mantra/embeddings/tests/PYTEST_SMOKE_ARTIFACT_ESMC.json:9: "/home/machina/MANTRA/data/raw/protein/esmc/MANIFEST.json", |
FINAL/source/src/mantra/embeddings/tests/TEST_SMOKE_CONTRACT_ESMC.json:11: "/home/machina/MANTRA/data/raw/protein/esmc/MANIFEST.json", |
FINAL/source/src/mantra/embeddings/tests/PYTEST_SMOKE_ARTIFACT_ESM3.json:9: "/home/machina/MANTRA/data/raw/protein/esm3/MANIFEST.json", |
FINAL/source/src/mantra/embeddings/tests/test_generate_esm3.py:75: smoke_path(REPO_ROOT / "data/raw/protein/esm3/MANIFEST.json", recorder=recorder) |
FINAL/source/src/mantra/embeddings/tests/TEST_SMOKE_CONTRACT_ESM3.json:11: "/home/machina/MANTRA/data/raw/protein/esm3/MANIFEST.json", |
FINAL/source/src/mantra/embeddings/tests/test_generate_esmc.py:86: smoke_path(REPO_ROOT / "data/raw/protein/esmc/MANIFEST.json", recorder=recorder) |
data/raw/protein/esm3/README.md:13:- Local target: `data/raw/protein/esm3/esm3-sm-open-v1/` |
data/raw/protein/esm3/README.md:27: --local-dir data/raw/protein/esm3/esm3-sm-open-v1 \ |
data/raw/protein/esm3/README.md:38:python -m pip install -r data/raw/protein/esm3/requirements-esm3.txt |
data/raw/protein/esm3/MANIFEST.json:5: "local_root": "data/raw/protein/esm3", |
data/raw/protein/esm3/MANIFEST.json:16: "command_log": "data/raw/protein/esm3/esm3-sm-open-v1/download.log", |
data/raw/protein/esm3/MANIFEST.json:112: "data/raw/protein/esm3/README.md", |
data/raw/protein/esm3/MANIFEST.json:113: "data/raw/protein/esm3/MANIFEST.json", |
data/raw/protein/esm3/MANIFEST.json:114: "data/raw/protein/esm3/esm3-sm-open-v1/DOWNLOAD_STARTED_UTC.txt", |
data/raw/protein/esm3/MANIFEST.json:115: "data/raw/protein/esm3/esm3-sm-open-v1/download.log" |
data/processed/embeddings/registry/MIGRATION_LOG.md:63:- Raw model provenance remains under `data/raw/protein/esm3/`. |
data/processed/embeddings/registry/MIGRATION_LOG.md:73:- Added sequestered raw ESM-C snapshots under `data/raw/protein/esmc/`. |
sota5/scripts/source_build/02_build_priors.py:105: canonical_protein_root = repo_path("data/raw/protein") |
src/mantra/embeddings/generate_esmc.py:17:DEFAULT_SNAPSHOT_ROOT = Path("data/raw/protein/esmc") |
FINAL/source/src/mantra/embeddings/generate_esm3.py:15:DEFAULT_SNAPSHOT_DIR = Path("data/raw/protein/esm3/esm3-sm-open-v1") |
FINAL/source/src/mantra/embeddings/generate_esm3.py:220: snapshot_manifest = Path("data/raw/protein/esm3/MANIFEST.json") |
FINAL/source/src/mantra/embeddings/generate_esmc.py:17:DEFAULT_SNAPSHOT_ROOT = Path("data/raw/protein/esmc") |
src/mantra/embeddings/generate_esm3.py:15:DEFAULT_SNAPSHOT_DIR = Path("data/raw/protein/esm3/esm3-sm-open-v1") |
src/mantra/embeddings/generate_esm3.py:220: snapshot_manifest = Path("data/raw/protein/esm3/MANIFEST.json") |
data/processed/embeddings/registry/protein_sequence/README.md:7:The ESM-3 raw snapshot is sequestered under `data/raw/protein/esm3/esm3-sm-open-v1/`. The processed embedding generator is: |
data/processed/embeddings/registry/protein_sequence/README.md:29:The ESM-C raw snapshots are sequestered under `data/raw/protein/esmc/`: |
data/processed/embeddings/registry/protein_sequence/source_gene_artifacts/tf_atlas_morf_isoforms_esmc_600m/tf_atlas_morf_isoforms_esmc_600m_mean_non_special.meta.json:7: "snapshot_dir": "data/raw/protein/esmc/esmc-600m-2024-12", |
data/processed/embeddings/registry/protein_sequence/source_gene_artifacts/tf_atlas_morf_isoforms_esmc_600m/scripts/generate_esmc.py:17:DEFAULT_SNAPSHOT_ROOT = Path("data/raw/protein/esmc") |
data/processed/embeddings/registry/protein_sequence/source_gene_artifacts/tf_atlas_raw_direct_esmc_600m/tf_atlas_raw_direct_esmc_600m_mean_non_special.meta.json:7: "snapshot_dir": "data/raw/protein/esmc/esmc-600m-2024-12", |
data/processed/embeddings/registry/protein_sequence/source_gene_artifacts/tf_atlas_morf_isoforms_esmc_600m/MANIFEST.json:40: "snapshot_dir": "data/raw/protein/esmc/esmc-600m-2024-12", |
data/processed/embeddings/registry/protein_sequence/source_gene_artifacts/esm3_sm_open_v1/esm3_sm_open_v1_mean_non_special_smoke1.meta.json:6: "snapshot_dir": "data/raw/protein/esm3/esm3-sm-open-v1", |
data/processed/embeddings/registry/protein_sequence/source_gene_artifacts/tf_atlas_raw_direct_esmc_600m/scripts/generate_esmc.py:17:DEFAULT_SNAPSHOT_ROOT = Path("data/raw/protein/esmc") |
data/processed/embeddings/registry/protein_sequence/source_gene_artifacts/esmc_300m_2024_12/esmc_300m_2024_12_mean_non_special_smoke1.meta.json:7: "snapshot_dir": "data/raw/protein/esmc/esmc-300m-2024-12", |
data/processed/embeddings/registry/protein_sequence/source_gene_artifacts/esmc_600m_2024_12/esmc_600m_2024_12_mean_non_special_smoke1.meta.json:7: "snapshot_dir": "data/raw/protein/esmc/esmc-600m-2024-12", |
data/processed/embeddings/registry/protein_sequence/source_gene_artifacts/tf_atlas_raw_direct_esmc_600m/MANIFEST.json:35: "snapshot_dir": "data/raw/protein/esmc/esmc-600m-2024-12", |
data/raw/protein |
data/raw/protein/9606.protein.aliases.v12.0.txt.gz |
data/raw/protein/9606.protein.links.v12.0.txt.gz |
data/raw/protein/esm3 |
data/raw/protein/esmc |
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