ipyrad2 0.1.9__py3-none-any.whl

ipyrad2/__init__.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env python
+
+from __future__ import annotations
+
+try:
+    from ._version import __version__
+except ImportError:
+    try:
+        from importlib.metadata import PackageNotFoundError, version
+    except Exception:  # pragma: no cover - fallback for very old Pythons
+        from importlib_metadata import PackageNotFoundError, version  # type: ignore
+
+    try:
+        __version__ = version("ipyrad2")
+    except PackageNotFoundError:
+        __version__ = "0.0.0+unknown"

ipyrad2/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.1.9'
+__version_tuple__ = version_tuple = (0, 1, 9)
+
+__commit_id__ = commit_id = 'g0393cec41'

ipyrad2/analysis/__init__.py

@@ -0,0 +1,61 @@
+"""Canonical public surface for phase-1 and phase-2 analysis tools and helpers."""
+
+from importlib import import_module
+
+__all__ = [
+    "Bpp",
+    "LocusExtracter",
+    "PCAFamilyResult",
+    "SNPsExtracter",
+    "SNPsImputer",
+    "VCFToHDF5",
+    "WindowExtracter",
+    "run_admixture_method",
+    "run_bpp_method",
+    "run_dapc_method",
+    "run_locus_extracter",
+    "run_pca_analysis",
+    "run_pca_method",
+    "run_popgen_method",
+    "run_snps_extracter",
+    "run_snmf_method",
+    "run_tsne_analysis",
+    "run_umap_analysis",
+    "run_vcf_to_hdf5",
+    "run_window_extracter",
+]
+
+
+_LAZY_EXPORTS = {
+    "VCFToHDF5": (".converters.vcf_to_hdf5", "VCFToHDF5"),
+    "run_vcf_to_hdf5": (".converters.vcf_to_hdf5", "run_vcf_to_hdf5"),
+    "LocusExtracter": (".extracters.locus_extracter", "LocusExtracter"),
+    "run_locus_extracter": (".extracters.locus_extracter", "run_locus_extracter"),
+    "SNPsExtracter": (".extracters.snps_extracter", "SNPsExtracter"),
+    "run_snps_extracter": (".extracters.snps_extracter", "run_snps_extracter"),
+    "WindowExtracter": (".extracters.window_extracter", "WindowExtracter"),
+    "run_window_extracter": (".extracters.window_extracter", "run_window_extracter"),
+    "SNPsImputer": (".methods.snps_imputer", "SNPsImputer"),
+    "Bpp": (".methods.bpp", "Bpp"),
+    "run_admixture_method": (".methods.admixture", "run_admixture_method"),
+    "run_bpp_method": (".methods.bpp", "run_bpp_method"),
+    "run_dapc_method": (".methods.dapc", "run_dapc_method"),
+    "run_popgen_method": (".methods.popgen", "run_popgen_method"),
+    "run_snmf_method": (".methods.snmf", "run_snmf_method"),
+    "PCAFamilyResult": (".methods.pca", "PCAFamilyResult"),
+    "run_pca_analysis": (".methods.pca", "run_pca_analysis"),
+    "run_pca_method": (".methods.pca", "run_pca_method"),
+    "run_tsne_analysis": (".methods.pca", "run_tsne_analysis"),
+    "run_umap_analysis": (".methods.pca", "run_umap_analysis"),
+}
+
+
+def __getattr__(name: str):
+    """Load heavier or optional analysis helpers lazily."""
+    if name in _LAZY_EXPORTS:
+        module_name, attr_name = _LAZY_EXPORTS[name]
+        module = import_module(module_name, __name__)
+        value = getattr(module, attr_name)
+        globals()[name] = value
+        return value
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

ipyrad2/analysis/converters/__init__.py

@@ -0,0 +1,22 @@
+"""Data-conversion tools for the analysis workflow."""
+
+from importlib import import_module
+
+__all__ = ["VCFToHDF5", "run_vcf_to_hdf5"]
+
+
+_LAZY_EXPORTS = {
+    "VCFToHDF5": (".vcf_to_hdf5", "VCFToHDF5"),
+    "run_vcf_to_hdf5": (".vcf_to_hdf5", "run_vcf_to_hdf5"),
+}
+
+
+def __getattr__(name: str):
+    """Load converter helpers lazily so parser imports stay lightweight."""
+    if name in _LAZY_EXPORTS:
+        module_name, attr_name = _LAZY_EXPORTS[name]
+        module = import_module(module_name, __name__)
+        value = getattr(module, attr_name)
+        globals()[name] = value
+        return value
+    raise AttributeError(name)