# Copyright 2009 by Tiago Antao <tiagoantao@gmail.com>.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Tests for GenePop easy-controller."""

import os
import unittest
import warnings

from Bio import BiopythonDeprecationWarning
from Bio import MissingExternalDependencyError

with warnings.catch_warnings():
    warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
    from Bio.PopGen.GenePop.EasyController import EasyController

# Tests genepop related code for easy contorller. Note: this requires genepop
# test_PopGen_GenePop_nodepend tests code that does not require genepop

found = False
for path in os.environ["PATH"].split(os.pathsep):
    try:
        for filename in os.listdir(path):
            if filename.startswith("Genepop"):
                found = True
    except OSError:
        pass  # Path doesn't exist - correct to pass
if not found:
    raise MissingExternalDependencyError(
        "Install GenePop if you want to use Bio.PopGen.GenePop."
    )


cur_dir = os.path.abspath(".")  # Tests directory


class AppTest(unittest.TestCase):
    """Tests genepop execution via biopython using EasyController."""

    def setUp(self):
        """Change working directory."""
        # Genepop likes to be on the directory where the file is.
        os.chdir("PopGen")
        self.ctrl = EasyController("big.gen")

    def tearDown(self):
        """Restore working directory."""
        os.chdir(cur_dir)

    def test_basic_info(self):
        """Test basic info."""
        pops, loci = self.ctrl.get_basic_info()
        self.assertEqual(len(pops), 10)
        self.assertEqual(len(loci), 37)

    def test_get_heterozygosity_info(self):
        """Test heterozygosity info."""
        hz_info = self.ctrl.get_heterozygosity_info(0, "Locus2")
        self.assertEqual(hz_info[1], 24)
        self.assertEqual(hz_info[3], 7)

    def test_get_alleles(self):
        """Test get alleles."""
        # Returns keys of a dict, so order is Python implementation dependent
        self.assertCountEqual(self.ctrl.get_alleles(0, "Locus3"), [3, 20])

    def test_get_alleles_all_pops(self):
        """Test get alleles for all populations."""
        self.assertEqual(self.ctrl.get_alleles_all_pops("Locus4"), [1, 3])

    def test_get_fis(self):
        """Test get Fis."""
        alleles, overall = self.ctrl.get_fis(0, "Locus2")
        self.assertEqual(alleles[3][0], 55)
        self.assertEqual(overall[0], 62)

    def test_get_allele_frequency(self):
        """Test allele frequency."""
        tot_genes, alleles = self.ctrl.get_allele_frequency(0, "Locus2")
        self.assertEqual(tot_genes, 62)
        self.assertLess(abs(alleles[20] - 0.113), 0.05)

    def test_get_genotype_count(self):
        """Test genotype count."""
        self.assertEqual(len(self.ctrl.get_genotype_count(0, "Locus2")), 3)

    def test_estimate_nm(self):
        """Test Nm estimation."""
        nms = self.ctrl.estimate_nm()
        self.assertEqual(nms[0], 28.0)

    def test_hwe_excess(self):
        """Test Hardy-Weinberg Equilibrium."""
        hwe_excess = self.ctrl.test_hw_pop(0, "excess")
        self.assertEqual(hwe_excess["Locus1"], (0.4955, None, -0.16, -0.1623, 5))

    # These tests are frequently failing, possibly due to a Genepop problem.
    #    def test_get_avg_fst_pair_locus(self):
    #        """Test get average Fst for pairwise pops on a locus."""
    #        self.assertEqual(len(self.ctrl.get_avg_fst_pair_locus("Locus4")), 45)
    #
    #    def test_get_avg_fst_pair(self):
    #        """Test get pairwise Fst."""
    #        pop_fis =  self.ctrl.get_avg_fst_pair()
    #        self.assertEqual(len(pop_fis), 45)

    def test_get_avg_fis(self):
        """Test average Fis."""
        self.ctrl.get_avg_fis()

    def test_get_multilocus_f_stats(self):
        """Test multilocus F stats."""
        mf = self.ctrl.get_multilocus_f_stats()
        self.assertEqual(len(mf), 3)
        self.assertLess(mf[0], 0.1)

    def test_get_f_stats(self):
        """Test F stats."""
        fs = self.ctrl.get_f_stats("Locus2")
        self.assertEqual(len(fs), 5)
        self.assertLess(fs[0], 0)


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)
