├── .gitignore ├── .readthedocs.yaml ├── .travis.yml ├── LICENSE ├── README.md ├── conda ├── build.sh ├── conda_build_config.yaml ├── deploy.sh └── meta.yaml ├── docs ├── Makefile ├── api.rst ├── conf.py ├── index.rst ├── installation.rst ├── introduction.rst ├── parallel.rst ├── requirements.txt └── tutorial.ipynb ├── momi ├── __init__.py ├── compute_sfs.py ├── concatenate_datasets.py ├── confidence_region.py ├── convolution.c ├── convolution.pyx ├── data │ ├── __init__.py │ ├── compressed_counts.py │ ├── configurations.py │ ├── convert.py │ ├── sfs.py │ ├── snps.py │ └── tensor.py ├── demo_model.py ├── demo_plotter.py ├── demography.py ├── einsum2 │ ├── __init__.py │ ├── einsum2.py │ ├── parallel_matmul.c │ └── parallel_matmul.pyx ├── events.py ├── extract_sfs.py ├── likelihood.py ├── math_functions.py ├── moran_model.py ├── optimizers.py ├── read_vcf.py ├── sfs_stats.py ├── size_history.py ├── util.py ├── w_matrix.c └── w_matrix.pyx ├── setup.py └── test ├── .gitignore ├── check_parallel.ipy ├── check_parallel.sh ├── demo_plot └── test_demo_plot.py ├── demo_utils.py ├── einsum2 ├── profile_einsum2.sh ├── test_einsum2.py └── time_einsum2.ipy ├── test_autograd.py ├── test_covariance.py ├── test_dadi_folded_2pop.sfs ├── test_dadi_unfolded_2pop.sfs ├── test_data_structure.py ├── test_demography.py ├── test_inference.py ├── test_likelihood.py ├── test_moran_model.py ├── test_msprime.py ├── test_new_wmatrix.py ├── test_normalizing_constant.py ├── test_rank1tensor.py ├── test_read_vcf.py ├── test_sfs.pickle ├── test_sfs.py ├── test_size_history.py ├── test_stochastic_gradient.py ├── test_subsample.py └── test_tmrca.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/popgenmethods/momi2/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- 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