genomicsem 0.1.0__tar.gz

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Files changed (80) hide show
  1. genomicsem-0.1.0/Cargo.toml +59 -0
  2. genomicsem-0.1.0/PKG-INFO +14 -0
  3. genomicsem-0.1.0/bindings/python/src/rust/Cargo.lock +2394 -0
  4. genomicsem-0.1.0/bindings/python/src/rust/Cargo.toml +23 -0
  5. genomicsem-0.1.0/bindings/python/src/rust/src/conversions.rs +149 -0
  6. genomicsem-0.1.0/bindings/python/src/rust/src/lib.rs +2053 -0
  7. genomicsem-0.1.0/crates/gsem/Cargo.toml +35 -0
  8. genomicsem-0.1.0/crates/gsem/README.md +62 -0
  9. genomicsem-0.1.0/crates/gsem/src/gwas/add_snps.rs +119 -0
  10. genomicsem-0.1.0/crates/gsem/src/gwas/common_factor.rs +140 -0
  11. genomicsem-0.1.0/crates/gsem/src/gwas/gc_correction.rs +123 -0
  12. genomicsem-0.1.0/crates/gsem/src/gwas/mod.rs +6 -0
  13. genomicsem-0.1.0/crates/gsem/src/gwas/multi_snp.rs +400 -0
  14. genomicsem-0.1.0/crates/gsem/src/gwas/q_snp.rs +56 -0
  15. genomicsem-0.1.0/crates/gsem/src/gwas/user_gwas.rs +431 -0
  16. genomicsem-0.1.0/crates/gsem/src/io/column_detect.rs +330 -0
  17. genomicsem-0.1.0/crates/gsem/src/io/gwas_reader.rs +268 -0
  18. genomicsem-0.1.0/crates/gsem/src/io/hdl_reader.rs +105 -0
  19. genomicsem-0.1.0/crates/gsem/src/io/ld_reader.rs +155 -0
  20. genomicsem-0.1.0/crates/gsem/src/io/mod.rs +88 -0
  21. genomicsem-0.1.0/crates/gsem/src/io/sumstats_reader.rs +358 -0
  22. genomicsem-0.1.0/crates/gsem/src/io/twas_reader.rs +138 -0
  23. genomicsem-0.1.0/crates/gsem/src/io/writer.rs +44 -0
  24. genomicsem-0.1.0/crates/gsem/src/lib.rs +17 -0
  25. genomicsem-0.1.0/crates/gsem/src/main.rs +2279 -0
  26. genomicsem-0.1.0/crates/gsem/src/munge/allele.rs +103 -0
  27. genomicsem-0.1.0/crates/gsem/src/munge/mod.rs +112 -0
  28. genomicsem-0.1.0/crates/gsem/src/munge/qc.rs +315 -0
  29. genomicsem-0.1.0/crates/gsem/src/plot/manhattan.rs +222 -0
  30. genomicsem-0.1.0/crates/gsem/src/plot/mod.rs +194 -0
  31. genomicsem-0.1.0/crates/gsem/src/plot/qq.rs +100 -0
  32. genomicsem-0.1.0/crates/gsem/src/plot/scree.rs +197 -0
  33. genomicsem-0.1.0/crates/gsem/src/stats/enrich.rs +143 -0
  34. genomicsem-0.1.0/crates/gsem/src/stats/gls.rs +93 -0
  35. genomicsem-0.1.0/crates/gsem/src/stats/mod.rs +4 -0
  36. genomicsem-0.1.0/crates/gsem/src/stats/parallel_analysis.rs +202 -0
  37. genomicsem-0.1.0/crates/gsem/src/stats/simulation.rs +166 -0
  38. genomicsem-0.1.0/crates/gsem/src/sumstats.rs +706 -0
  39. genomicsem-0.1.0/crates/gsem/tests/r_validation.rs +983 -0
  40. genomicsem-0.1.0/crates/gsem-ldsc/Cargo.toml +27 -0
  41. genomicsem-0.1.0/crates/gsem-ldsc/benches/ldsc_bench.rs +76 -0
  42. genomicsem-0.1.0/crates/gsem-ldsc/src/annot_reader.rs +347 -0
  43. genomicsem-0.1.0/crates/gsem-ldsc/src/covariance.rs +108 -0
  44. genomicsem-0.1.0/crates/gsem-ldsc/src/error.rs +16 -0
  45. genomicsem-0.1.0/crates/gsem-ldsc/src/hdl.rs +693 -0
  46. genomicsem-0.1.0/crates/gsem-ldsc/src/heritability.rs +102 -0
  47. genomicsem-0.1.0/crates/gsem-ldsc/src/jackknife.rs +151 -0
  48. genomicsem-0.1.0/crates/gsem-ldsc/src/liability.rs +103 -0
  49. genomicsem-0.1.0/crates/gsem-ldsc/src/lib.rs +374 -0
  50. genomicsem-0.1.0/crates/gsem-ldsc/src/regression.rs +150 -0
  51. genomicsem-0.1.0/crates/gsem-ldsc/src/stratified.rs +810 -0
  52. genomicsem-0.1.0/crates/gsem-ldsc/src/weights.rs +110 -0
  53. genomicsem-0.1.0/crates/gsem-matrix/Cargo.toml +20 -0
  54. genomicsem-0.1.0/crates/gsem-matrix/benches/matrix_bench.rs +66 -0
  55. genomicsem-0.1.0/crates/gsem-matrix/src/error.rs +19 -0
  56. genomicsem-0.1.0/crates/gsem-matrix/src/lib.rs +11 -0
  57. genomicsem-0.1.0/crates/gsem-matrix/src/near_pd.rs +216 -0
  58. genomicsem-0.1.0/crates/gsem-matrix/src/smooth.rs +127 -0
  59. genomicsem-0.1.0/crates/gsem-matrix/src/vech.rs +123 -0
  60. genomicsem-0.1.0/crates/gsem-sem/Cargo.toml +23 -0
  61. genomicsem-0.1.0/crates/gsem-sem/benches/sem_bench.rs +83 -0
  62. genomicsem-0.1.0/crates/gsem-sem/src/commonfactor.rs +243 -0
  63. genomicsem-0.1.0/crates/gsem-sem/src/delta.rs +15 -0
  64. genomicsem-0.1.0/crates/gsem-sem/src/error.rs +19 -0
  65. genomicsem-0.1.0/crates/gsem-sem/src/estimator.rs +567 -0
  66. genomicsem-0.1.0/crates/gsem-sem/src/fit_indices.rs +128 -0
  67. genomicsem-0.1.0/crates/gsem-sem/src/jacobian.rs +400 -0
  68. genomicsem-0.1.0/crates/gsem-sem/src/lib.rs +106 -0
  69. genomicsem-0.1.0/crates/gsem-sem/src/model.rs +339 -0
  70. genomicsem-0.1.0/crates/gsem-sem/src/q_factor.rs +282 -0
  71. genomicsem-0.1.0/crates/gsem-sem/src/reorder.rs +106 -0
  72. genomicsem-0.1.0/crates/gsem-sem/src/rgmodel.rs +346 -0
  73. genomicsem-0.1.0/crates/gsem-sem/src/sandwich.rs +44 -0
  74. genomicsem-0.1.0/crates/gsem-sem/src/syntax.rs +433 -0
  75. genomicsem-0.1.0/crates/gsem-sem/src/write_model.rs +179 -0
  76. genomicsem-0.1.0/genomicsem/__init__.py +9 -0
  77. genomicsem-0.1.0/genomicsem/_enrich.py +182 -0
  78. genomicsem-0.1.0/genomicsem/_pa_ldsc.py +139 -0
  79. genomicsem-0.1.0/genomicsem/_sim.py +63 -0
  80. genomicsem-0.1.0/pyproject.toml +20 -0
genomicsem-0.1.0/Cargo.toml ADDED
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+ [workspace]
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+ members = [
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+ "crates/gsem-matrix",
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+ "crates/gsem-ldsc",
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+ "crates/gsem-sem",
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+ "crates/gsem",
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+ ]
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+ resolver = "2"
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+
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+ [workspace.package]
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+ version = "0.1.0"
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+ edition = "2024"
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+ license = "GPL-3.0"
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+ repository = "https://github.com/PoHsuanLai/gsem"
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+
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+ [workspace.dependencies]
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+ # Core math
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+ faer = "0.24"
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+ statrs = "0.18"
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+
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+ # Parallelism
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+ rayon = "1.10"
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+
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+ # Serialization
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+ serde = { version = "1", features = ["derive"] }
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+ serde_json = "1"
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+
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+ # Error handling
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+ thiserror = "2"
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+ anyhow = "1"
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+
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+ # Logging
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+ log = "0.4"
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+ env_logger = "0.11"
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+
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+ # I/O
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+ flate2 = "1.1"
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+
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+ # CLI
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+ clap = { version = "4", features = ["derive"] }
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+ indicatif = "0.18"
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+
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+ # Plotting (SVG-only to avoid system deps)
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+ plotters = { version = "0.3", default-features = false, features = ["svg_backend", "line_series", "area_series"] }
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+
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+ # Random
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+ rand = "0.10"
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+ rand_distr = "0.6"
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+
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+ # Testing & Benchmarking
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+ approx = "0.5"
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+ criterion = { version = "0.8", features = ["html_reports"] }
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+ tempfile = "3"
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+
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+ # Internal crates
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+ gsem-matrix = { version = "0.1.0", path = "crates/gsem-matrix" }
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+ gsem-ldsc = { version = "0.1.0", path = "crates/gsem-ldsc" }
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+ gsem-sem = { version = "0.1.0", path = "crates/gsem-sem" }
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+ gsem = { version = "0.1.0", path = "crates/gsem" }
genomicsem-0.1.0/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: genomicsem
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+ Version: 0.1.0
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+ Requires-Dist: numpy>=1.20
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+ Requires-Dist: factor-analyzer>=0.4 ; extra == 'all'
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+ Requires-Dist: matplotlib>=3.5 ; extra == 'all'
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+ Requires-Dist: factor-analyzer>=0.4 ; extra == 'fa'
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+ Requires-Dist: matplotlib>=3.5 ; extra == 'plot'
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+ Provides-Extra: all
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+ Provides-Extra: fa
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+ Provides-Extra: plot
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+ Summary: Rust-accelerated Genomic Structural Equation Modeling
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+ License: GPL-3.0
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+ Requires-Python: >=3.9