mmore500

mmore500

mmore500

from datetime import datetime, timedelta
import itertools as it
import typing

from matplotlib import pyplot as plt
from matplotlib import text as mpl_text
import numpy as np
import outset as otst
import opytional as opyt
import pandas as pd

mmore500

* text eol=lf filter=cleanWhitespace

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mkdir -p ~/.cloudshell/
touch ~/.cloudshell/no-apt-get-warning

sudo apt-get update -y
sudo apt-get install -y aptitude
sudo aptitude install -y libgdal-dev libproj-dev r-base
sudo Rscript -e "install.packages(c('codetools', 'dplyr', 'gen3sis', 'gdistance', 'ggplot2', 'Matrix', 'raster', 'rgdal'))"

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def _estimate_rank_of_mrca_between_unbiased(
    first: HereditaryStratigraphicColumn,
    second: HereditaryStratigraphicColumn,
) -> typing.Optional[float]:
    ranks_of_retained_commonality_between = [
        *iter_ranks_of_retained_commonality_between_generic(first, second)
    ]
    if not ranks_of_retained_commonality_between:
        return None

mmore500

import typing

import numpy as np
import pandas as pd

from ..._auxiliary_lib import indices_of_unique
from ._compile_phylogeny_from_lineage_iters import (
    compile_phylogeny_from_lineage_iters,
)

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// cppimport
#include <memory>

#include <pybind11/pybind11.h>

namespace py = pybind11;


struct PerfectBacktrackHandleNative {
  py::object parent;

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import collections
import typing


class PerfectBacktrackDatabase:
    """Breadcrumb for perfectly backtracking a phylogenetic chain of descent.

    Because only backwards references are held, Python garbage collection takes
    care of pruning away extinct lineages.
    """

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    arr = pop_df.to_numpy()
    split = np.split(
        arr[:, 2],
        np.unique(arr[:, [0, 1]], axis=0, return_index=True)[1][1:],
    )
    pos = 0
    for group in split:
        # minimizing operations on group_df gives >50% speedup
        genome_lookup = group
        tournament_rosters = np.random.randint(