admixpy 1.0.0__tar.gz

admixpy-1.0.0/CHANGELOG.md

@@ -0,0 +1,21 @@
+# Changelog
+
+All notable changes to AdmixPy are documented in this file.
+
+## 1.0.0 - 2026-08-10
+
+First stable release.
+
+### Features
+
+- Fast whole-dataset f-statistics, qpAdm, and qpWave analysis.
+- f2, Hudson FST, f3, and f4 statistics with block-jackknife uncertainty.
+- qpAdm and qpWave model fitting, rank tests, and qpAdm population-drop models.
+- Direct EIGENSTRAT, PACKEDANCESTRYMAP, TGENO, and SNP-major PLINK input.
+- Precomputed f2 block caches with per-pair SNP counts and FST components.
+- Bounded-memory streaming for direct f3 and f4 workflows.
+- Explicit missing-data, SNP-selection, and pseudohaploid correction options.
+
+### Requirements
+
+- Python 3.10 or newer is required.

admixpy-1.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 system0x7
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

admixpy-1.0.0/MANIFEST.in

@@ -0,0 +1 @@
+include CHANGELOG.md

admixpy-1.0.0/PKG-INFO

@@ -0,0 +1,251 @@
+Metadata-Version: 2.4
+Name: admixpy
+Version: 1.0.0
+Summary: Fast Python implementation of ADMIXTOOLS-style f-statistics, qpadm, and qpwave
+Author: system0x7
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/system0x7/admixpy
+Project-URL: Repository, https://github.com/system0x7/admixpy
+Project-URL: Issues, https://github.com/system0x7/admixpy/issues
+Keywords: population genetics,f-statistics,qpadm,qpwave,admixture
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Dynamic: license-file
+
+# AdmixPy
+
+Fast Python implementation of ADMIXTOOLS-style f-statistics, qpAdm, and qpWave.
+
+> Fast f-statistics, qpAdm, and qpWave in Python.
+
+## Installation
+
+Requires Python 3.10 or newer.
+
+Install the latest release from PyPI:
+
+```bash
+python -m pip install admixpy
+```
+
+Check that the package imports:
+
+```bash
+python -c "import admixpy; print(admixpy.__version__)"
+```
+
+### Installing from source
+
+Create and activate a virtual environment:
+
+```bash
+python3 -m venv venv
+source venv/bin/activate
+```
+
+Install the package from `pyproject.toml`:
+
+```bash
+python -m pip install --upgrade pip
+python -m pip install -e .
+```
+
+### Updating an existing clone
+
+```bash
+cd /path/to/admixpy
+git pull --ff-only
+```
+
+After updating, run the two installation commands in Setup again.
+
+## Alternative
+
+If you only want to install the dependencies without installing the package:
+
+```bash
+python -m pip install -r requirements.txt
+```
+
+## Examples
+
+Supported input layouts include EIGENSTRAT text, packed AncestryMap, TGENO, and
+SNP-major PLINK binary files (`.bed/.bim/.fam`). For `.geno/.snp/.ind` inputs,
+the genotype layout is detected from the file header/size; TGENO can also be provided as `.tgeno/.snp/.ind`.
+
+## Basic API
+
+The main convenience wrappers are:
+
+```python
+admixpy.f2(data, pop1=None, pop2=None, *, unique_only=True,
+           resampling="pairwise_counts", **kwargs)
+admixpy.fst(data, pop1=None, pop2=None, *, unique_only=True,
+            resampling="pairwise_counts", fst_aggregation="block_ratios",
+            **kwargs)
+admixpy.f3(data, pop1=None, pop2=None, pop3=None, *, unique_only=True,
+           resampling="pairwise_counts", verbose=True, **kwargs)
+admixpy.f4(data, pop1, pop2=None, pop3=None, pop4=None, *, comb=True,
+           unique_only=True, afprod=False, verbose=True, **kwargs)
+admixpy.qpwave(data, left, right, ranks=None, left_base=None,
+               right_base=None, rcond=1e-10, diag=0.0, max_nfev=None,
+               verbose=True, **kwargs)
+admixpy.qpadm(data, target, left=None, right=None, sources=None,
+              fudge=0.0001, fudge_twice=False, iterations=20, getcov=True,
+              return_f4=False, return_stats=False, return_cov=False,
+              verbose=True, **kwargs)
+```
+
+The main convenience wrappers are `f2`, `fst`, `f3`, `f4`, `qpwave`, and
+`qpadm`.
+
+`data` can be a supported genotype dataset prefix or precomputed f2 data.
+Population arguments can be strings or lists where the wrapper supports multiple
+combinations. For PLINK `.bed/.bim/.fam` input, population labels are read from
+the FID column of the `.fam` file.
+
+For direct genotype input, `f3`, `f4`, `qpwave`, and `qpadm` default to
+`allsnps=True`, matching the ADMIXTOOLS1-style behavior of estimating each
+statistic from its available SNPs. For precomputed f2 input, `allsnps` defaults
+to `False` and the standard f2-based behavior is used. Pass `allsnps=False` to
+restrict direct-genotype models to SNPs shared across the required populations.
+
+Direct genotype `f3` also defaults to `allsnps=True` and is calculated per SNP.
+By default, its corrected numerator is divided by unbiased target
+heterozygosity. Set `outgroupmode=True` to return the unnormalized f3 numerator;
+that raw mode is directly comparable to f2-derived f3 and to original `qp3Pop`
+outgroup mode after removing the latter's factor of 1000.
+
+| Data | Scope | Recommended setting |
+|---|---|---|
+| Known modern diploid data | All direct genotype statistics | Keep defaults (ploidy auto-detected), or set `adjust_pseudohaploid=False` to force known diploid data |
+| Ancient or mixed-ploidy data | All direct genotype statistics | `adjust_pseudohaploid=True, apply_corr=True` (auto-detected per sample) |
+| ADMIXTOOLS2-normalized direct f3 | f3 only | `outgroupmode=False` (default) |
+| Raw/original outgroup f3 | f3 only | `outgroupmode=True` |
+| Diploid singleton target or repeated source | f3 only | Keep `apply_corr=True`; two called alleles make correction possible |
+| Pseudohaploid singleton used only as a distinct source | f3 only | Allowed with `apply_corr=True` because it occurs linearly |
+| Pseudohaploid singleton target or repeated source | f3 only | Unbiased correction is not possible; affected SNPs are excluded |
+| Intentionally biased singleton estimate | f3 only | `outgroupmode=True, apply_corr=False`; exploratory/legacy |
+| Missingness differs among populations or blocks | f2, FST, f3, and cached f4 | `resampling="pairwise_counts"` (default) |
+| In-memory blocks without SNP counts | Precomputed-block workflows | `resampling="nominal_blocks"`; incomplete on-disk caches must be rebuilt |
+| Maximum available SNPs per combination | Direct f3/f4, qpWave, and qpAdm | `allsnps=True` (direct-genotype default) |
+| Common SNP set across a model | Direct f3/f4, qpWave, and qpAdm | `allsnps=False` |
+| Use only polymorphic sites | Direct f-statistics | `poly_only=True` (drops non-polymorphic sites) |
+
+Direct f3 and f4 genotype calculations (including the f4 calculations
+for qpAdm and qpWave) read the genotype file once by default and hold the
+complete SNP-by-population allele-frequency and count tables in memory. For
+datasets that do not fit comfortably in RAM, set `stream=True` to use two
+bounded-memory passes with 250,000 SNPs per chunk by default. The chunk size
+can be adjusted with `chunk_size`.
+
+Lower-level helpers are also exported for direct use, including allele-frequency
+conversion (`anygeno_to_afs`, `eigenstrat_to_afs`, `plink_to_afs`,
+`packedancestrymap_to_afs`, `tgeno_to_afs`), f2 block IO and access
+(`get_f2`, `read_f2`, `write_f2`), and block/statistical utilities such as
+`iter_geno_to_afs`, `f3_stats_from_geno`, `block_covariance`,
+`jackknife_cov`, `stats_to_loo`, and `est_to_loo`.
+
+### SNP selection, missingness, and small samples
+
+By default, `f2` excludes SNPs with identical allele frequencies in every
+loaded population, while `fst` retains them. This matches the ADMIXTOOLS
+default but means the two statistics can use different SNP sets. Use
+`poly_only=True` to both calls when they should be directly comparable.
+
+AdmixPy uses `resampling="pairwise_counts"` as default for data
+with missing genotypes: each population pair is weighted by the SNP
+observations actually available for that pair. Pairwise `f2` and `fst` result
+tables include `n`. Set `resampling="nominal_blocks"` to reproduce the older
+behavior in which every pair uses nominal block sizes. Raw-genotype f4 with
+`allsnps=True` already uses per-statistic counts on a common SNP intersection.
+Cached pairwise f3/f4 instead defines a pairwise-available estimator and cannot
+reconstruct that common intersection.
+
+FST cache files additionally retain numerator and denominator sums. The
+default `fst_aggregation="block_ratios"` averages stored block estimates.
+Set `fst_aggregation="pooled_components"` to recompute full-data and
+leave-one-block-out FST as ratios of pooled numerator and denominator sums.
+
+Bias-corrected f2 and FST require at least two independent allele observations
+in each population. SNP values with a count below two are excluded with a
+warning when `apply_corr=True`. Setting `apply_corr=False` explicitly requests
+the finite but sampling-biased raw estimate; the Hudson FST denominator remains
+`(p1-p2)^2 + p1(1-p1) + p2(1-p2)` in either mode.
+
+Cache files without real per-pair SNP counts are rejected and must be rebuilt.
+
+Run an f4 statistic from a supported genotype dataset prefix:
+
+```python
+import admixpy
+
+prefix = "/path/to/dataset_prefix"
+
+result = admixpy.f4(
+    prefix,
+    "Mbuti",
+    "Germany_ViesenhaeuserHof_EN",
+    "Sardinian",
+    "French",
+)
+
+print(result)
+```
+
+qpAdm can be run the same way from a Python REPL:
+
+```python
+>>> import admixpy as a
+>>> prefix = "/path/to/dataset_prefix"
+>>> target = "Sardinian"
+>>> left = ["Turkey_N", "Russia_Samara_EBA_Yamnaya", "Luxembourg_Loschbour_Mesolithic", "Iran_GanjDareh_N"]
+>>> right = ["Chimp", "Turkey_Epipaleolithic", "Georgia_KotiasKlde_Mesolithic", "Russia_Vologda_Mesolithic", "Switzerland_Epipaleolithic", "Iran_BeltCave_Mesolithic"]
+>>> res = a.qpadm(prefix, target=target, left=left, right=right)
+>>> res
+QpAdmResult(target='Sardinian')
+
+weights:
+                           left weight     se     z
+                       Turkey_N  0.686  0.013 52.45
+      Russia_Samara_EBA_Yamnaya  0.102  0.012  8.54
+Luxembourg_Loschbour_Mesolithic  0.119 0.0064 18.57
+               Iran_GanjDareh_N  0.094  0.013  7.11
+
+rankdrop:
+f4rank dof   chisq         p  p_nested
+     3   2    0.53     0.769 9.39e-242
+     2   6 1123.16 2.03e-239         0
+     1  12 3317.58         0         0
+     0  20 6849.91         0       NaN
+
+popdrop:
+ pat                                                                    dropped f4rank dof   chisq         p  feasible status
+0000                                                                                 3   2    0.53     0.769      True   PASS
+0001                                                           Iran_GanjDareh_N      2   3   58.58  1.18e-12      True   FAIL
+0010                                            Luxembourg_Loschbour_Mesolithic      2   3   370.2  6.29e-80     False   FAIL
+0100                                                  Russia_Samara_EBA_Yamnaya      2   3   73.09  9.29e-16      True   FAIL
+1000                                                                   Turkey_N      2   3  825.23 1.46e-178     False   FAIL
+ ...
+```
+
+## Citation
+
+AdmixPy implements methods from Patterson et al. (2012) and Maier et al. (2023).
+
+## License
+
+[MIT License](LICENSE) .

admixpy-1.0.0/README.md

@@ -0,0 +1,224 @@
+# AdmixPy
+
+Fast Python implementation of ADMIXTOOLS-style f-statistics, qpAdm, and qpWave.
+
+> Fast f-statistics, qpAdm, and qpWave in Python.
+
+## Installation
+
+Requires Python 3.10 or newer.
+
+Install the latest release from PyPI:
+
+```bash
+python -m pip install admixpy
+```
+
+Check that the package imports:
+
+```bash
+python -c "import admixpy; print(admixpy.__version__)"
+```
+
+### Installing from source
+
+Create and activate a virtual environment:
+
+```bash
+python3 -m venv venv
+source venv/bin/activate
+```
+
+Install the package from `pyproject.toml`:
+
+```bash
+python -m pip install --upgrade pip
+python -m pip install -e .
+```
+
+### Updating an existing clone
+
+```bash
+cd /path/to/admixpy
+git pull --ff-only
+```
+
+After updating, run the two installation commands in Setup again.
+
+## Alternative
+
+If you only want to install the dependencies without installing the package:
+
+```bash
+python -m pip install -r requirements.txt
+```
+
+## Examples
+
+Supported input layouts include EIGENSTRAT text, packed AncestryMap, TGENO, and
+SNP-major PLINK binary files (`.bed/.bim/.fam`). For `.geno/.snp/.ind` inputs,
+the genotype layout is detected from the file header/size; TGENO can also be provided as `.tgeno/.snp/.ind`.
+
+## Basic API
+
+The main convenience wrappers are:
+
+```python
+admixpy.f2(data, pop1=None, pop2=None, *, unique_only=True,
+           resampling="pairwise_counts", **kwargs)
+admixpy.fst(data, pop1=None, pop2=None, *, unique_only=True,
+            resampling="pairwise_counts", fst_aggregation="block_ratios",
+            **kwargs)
+admixpy.f3(data, pop1=None, pop2=None, pop3=None, *, unique_only=True,
+           resampling="pairwise_counts", verbose=True, **kwargs)
+admixpy.f4(data, pop1, pop2=None, pop3=None, pop4=None, *, comb=True,
+           unique_only=True, afprod=False, verbose=True, **kwargs)
+admixpy.qpwave(data, left, right, ranks=None, left_base=None,
+               right_base=None, rcond=1e-10, diag=0.0, max_nfev=None,
+               verbose=True, **kwargs)
+admixpy.qpadm(data, target, left=None, right=None, sources=None,
+              fudge=0.0001, fudge_twice=False, iterations=20, getcov=True,
+              return_f4=False, return_stats=False, return_cov=False,
+              verbose=True, **kwargs)
+```
+
+The main convenience wrappers are `f2`, `fst`, `f3`, `f4`, `qpwave`, and
+`qpadm`.
+
+`data` can be a supported genotype dataset prefix or precomputed f2 data.
+Population arguments can be strings or lists where the wrapper supports multiple
+combinations. For PLINK `.bed/.bim/.fam` input, population labels are read from
+the FID column of the `.fam` file.
+
+For direct genotype input, `f3`, `f4`, `qpwave`, and `qpadm` default to
+`allsnps=True`, matching the ADMIXTOOLS1-style behavior of estimating each
+statistic from its available SNPs. For precomputed f2 input, `allsnps` defaults
+to `False` and the standard f2-based behavior is used. Pass `allsnps=False` to
+restrict direct-genotype models to SNPs shared across the required populations.
+
+Direct genotype `f3` also defaults to `allsnps=True` and is calculated per SNP.
+By default, its corrected numerator is divided by unbiased target
+heterozygosity. Set `outgroupmode=True` to return the unnormalized f3 numerator;
+that raw mode is directly comparable to f2-derived f3 and to original `qp3Pop`
+outgroup mode after removing the latter's factor of 1000.
+
+| Data | Scope | Recommended setting |
+|---|---|---|
+| Known modern diploid data | All direct genotype statistics | Keep defaults (ploidy auto-detected), or set `adjust_pseudohaploid=False` to force known diploid data |
+| Ancient or mixed-ploidy data | All direct genotype statistics | `adjust_pseudohaploid=True, apply_corr=True` (auto-detected per sample) |
+| ADMIXTOOLS2-normalized direct f3 | f3 only | `outgroupmode=False` (default) |
+| Raw/original outgroup f3 | f3 only | `outgroupmode=True` |
+| Diploid singleton target or repeated source | f3 only | Keep `apply_corr=True`; two called alleles make correction possible |
+| Pseudohaploid singleton used only as a distinct source | f3 only | Allowed with `apply_corr=True` because it occurs linearly |
+| Pseudohaploid singleton target or repeated source | f3 only | Unbiased correction is not possible; affected SNPs are excluded |
+| Intentionally biased singleton estimate | f3 only | `outgroupmode=True, apply_corr=False`; exploratory/legacy |
+| Missingness differs among populations or blocks | f2, FST, f3, and cached f4 | `resampling="pairwise_counts"` (default) |
+| In-memory blocks without SNP counts | Precomputed-block workflows | `resampling="nominal_blocks"`; incomplete on-disk caches must be rebuilt |
+| Maximum available SNPs per combination | Direct f3/f4, qpWave, and qpAdm | `allsnps=True` (direct-genotype default) |
+| Common SNP set across a model | Direct f3/f4, qpWave, and qpAdm | `allsnps=False` |
+| Use only polymorphic sites | Direct f-statistics | `poly_only=True` (drops non-polymorphic sites) |
+
+Direct f3 and f4 genotype calculations (including the f4 calculations
+for qpAdm and qpWave) read the genotype file once by default and hold the
+complete SNP-by-population allele-frequency and count tables in memory. For
+datasets that do not fit comfortably in RAM, set `stream=True` to use two
+bounded-memory passes with 250,000 SNPs per chunk by default. The chunk size
+can be adjusted with `chunk_size`.
+
+Lower-level helpers are also exported for direct use, including allele-frequency
+conversion (`anygeno_to_afs`, `eigenstrat_to_afs`, `plink_to_afs`,
+`packedancestrymap_to_afs`, `tgeno_to_afs`), f2 block IO and access
+(`get_f2`, `read_f2`, `write_f2`), and block/statistical utilities such as
+`iter_geno_to_afs`, `f3_stats_from_geno`, `block_covariance`,
+`jackknife_cov`, `stats_to_loo`, and `est_to_loo`.
+
+### SNP selection, missingness, and small samples
+
+By default, `f2` excludes SNPs with identical allele frequencies in every
+loaded population, while `fst` retains them. This matches the ADMIXTOOLS
+default but means the two statistics can use different SNP sets. Use
+`poly_only=True` to both calls when they should be directly comparable.
+
+AdmixPy uses `resampling="pairwise_counts"` as default for data
+with missing genotypes: each population pair is weighted by the SNP
+observations actually available for that pair. Pairwise `f2` and `fst` result
+tables include `n`. Set `resampling="nominal_blocks"` to reproduce the older
+behavior in which every pair uses nominal block sizes. Raw-genotype f4 with
+`allsnps=True` already uses per-statistic counts on a common SNP intersection.
+Cached pairwise f3/f4 instead defines a pairwise-available estimator and cannot
+reconstruct that common intersection.
+
+FST cache files additionally retain numerator and denominator sums. The
+default `fst_aggregation="block_ratios"` averages stored block estimates.
+Set `fst_aggregation="pooled_components"` to recompute full-data and
+leave-one-block-out FST as ratios of pooled numerator and denominator sums.
+
+Bias-corrected f2 and FST require at least two independent allele observations
+in each population. SNP values with a count below two are excluded with a
+warning when `apply_corr=True`. Setting `apply_corr=False` explicitly requests
+the finite but sampling-biased raw estimate; the Hudson FST denominator remains
+`(p1-p2)^2 + p1(1-p1) + p2(1-p2)` in either mode.
+
+Cache files without real per-pair SNP counts are rejected and must be rebuilt.
+
+Run an f4 statistic from a supported genotype dataset prefix:
+
+```python
+import admixpy
+
+prefix = "/path/to/dataset_prefix"
+
+result = admixpy.f4(
+    prefix,
+    "Mbuti",
+    "Germany_ViesenhaeuserHof_EN",
+    "Sardinian",
+    "French",
+)
+
+print(result)
+```
+
+qpAdm can be run the same way from a Python REPL:
+
+```python
+>>> import admixpy as a
+>>> prefix = "/path/to/dataset_prefix"
+>>> target = "Sardinian"
+>>> left = ["Turkey_N", "Russia_Samara_EBA_Yamnaya", "Luxembourg_Loschbour_Mesolithic", "Iran_GanjDareh_N"]
+>>> right = ["Chimp", "Turkey_Epipaleolithic", "Georgia_KotiasKlde_Mesolithic", "Russia_Vologda_Mesolithic", "Switzerland_Epipaleolithic", "Iran_BeltCave_Mesolithic"]
+>>> res = a.qpadm(prefix, target=target, left=left, right=right)
+>>> res
+QpAdmResult(target='Sardinian')
+
+weights:
+                           left weight     se     z
+                       Turkey_N  0.686  0.013 52.45
+      Russia_Samara_EBA_Yamnaya  0.102  0.012  8.54
+Luxembourg_Loschbour_Mesolithic  0.119 0.0064 18.57
+               Iran_GanjDareh_N  0.094  0.013  7.11
+
+rankdrop:
+f4rank dof   chisq         p  p_nested
+     3   2    0.53     0.769 9.39e-242
+     2   6 1123.16 2.03e-239         0
+     1  12 3317.58         0         0
+     0  20 6849.91         0       NaN
+
+popdrop:
+ pat                                                                    dropped f4rank dof   chisq         p  feasible status
+0000                                                                                 3   2    0.53     0.769      True   PASS
+0001                                                           Iran_GanjDareh_N      2   3   58.58  1.18e-12      True   FAIL
+0010                                            Luxembourg_Loschbour_Mesolithic      2   3   370.2  6.29e-80     False   FAIL
+0100                                                  Russia_Samara_EBA_Yamnaya      2   3   73.09  9.29e-16      True   FAIL
+1000                                                                   Turkey_N      2   3  825.23 1.46e-178     False   FAIL
+ ...
+```
+
+## Citation
+
+AdmixPy implements methods from Patterson et al. (2012) and Maier et al. (2023).
+
+## License
+
+[MIT License](LICENSE) .

admixpy-1.0.0/admixpy/__init__.py

@@ -0,0 +1,126 @@
+__version__ = "1.0.0"
+
+from .fstats import (
+    BlockStats,
+    F2Blocks,
+    F4BlockCache,
+    F4ModelCache,
+    QpAdmResult,
+    QpWaveStats,
+    afs_to_f2_blocks,
+    block_covariance,
+    est_to_loo,
+    f2,
+    f2_from_geno,
+    f3,
+    f3_from_f2,
+    f3_stats_from_geno,
+    f4,
+    f4_model_cache,
+    f4_from_f2,
+    f4_stats,
+    f4_stats_from_geno,
+    format_fstats,
+    fst,
+    get_f2,
+    jackknife_cov,
+    jack_vec_stats,
+    mats_to_aparr,
+    mats_to_ctarr,
+    mats_to_f2arr,
+    qpdstat,
+    qp3pop,
+    qpadm,
+    qpadm_fit,
+    qpadm_multi,
+    qpadm_popdrop,
+    qpadm_rankdrop,
+    qpadm_weights,
+    qpwave,
+    qpwave_f4stats,
+    qpwave_multi,
+    qpwave_ranktest,
+    read_f2,
+    stats_to_loo,
+    write_f2,
+)
+from .genotypes import (
+    AfData,
+    anygeno_to_afs,
+    detect_geno_format,
+    discard_from_aftable,
+    eigenstrat_to_afs,
+    get_block_lengths,
+    is_polymorphic,
+    iter_geno_to_afs,
+    packedancestrymap_to_afs,
+    plink_to_afs,
+    read_eigenstrat,
+    read_ind,
+    read_packedancestrymap,
+    read_plink,
+    read_snp,
+    tgeno_to_afs,
+)
+
+__all__ = [
+    "__version__",
+    "AfData",
+    "BlockStats",
+    "F2Blocks",
+    "F4BlockCache",
+    "F4ModelCache",
+    "QpAdmResult",
+    "QpWaveStats",
+    "afs_to_f2_blocks",
+    "anygeno_to_afs",
+    "block_covariance",
+    "detect_geno_format",
+    "discard_from_aftable",
+    "eigenstrat_to_afs",
+    "est_to_loo",
+    "f2",
+    "f2_from_geno",
+    "f3",
+    "f3_from_f2",
+    "f3_stats_from_geno",
+    "f4",
+    "f4_model_cache",
+    "f4_from_f2",
+    "f4_stats",
+    "f4_stats_from_geno",
+    "format_fstats",
+    "fst",
+    "get_block_lengths",
+    "get_f2",
+    "is_polymorphic",
+    "iter_geno_to_afs",
+    "jackknife_cov",
+    "jack_vec_stats",
+    "mats_to_aparr",
+    "mats_to_ctarr",
+    "mats_to_f2arr",
+    "qpdstat",
+    "qp3pop",
+    "qpadm",
+    "qpadm_fit",
+    "qpadm_multi",
+    "qpadm_popdrop",
+    "qpadm_rankdrop",
+    "qpadm_weights",
+    "qpwave",
+    "qpwave_f4stats",
+    "qpwave_multi",
+    "qpwave_ranktest",
+    "packedancestrymap_to_afs",
+    "plink_to_afs",
+    "read_eigenstrat",
+    "read_f2",
+    "read_ind",
+    "read_packedancestrymap",
+    "read_plink",
+    "read_snp",
+    "stats_to_loo",
+    "tgeno_to_afs",
+    "write_f2",
+]