import pytest
import os
from SCNIC.general import simulate_correls
from SCNIC.between_correls import between_correls


@pytest.fixture()
def args():
    class Arguments(object):
        def __init__(self):
            self.table1 = "table1.biom"
            self.table2 = "table2.biom"
            self.output = "out_dir"
            self.correl_method = "spearman"
            self.p_adjust = "bh"
            self.min_sample = None
            self.min_p = None
            self.min_r = None
            self.sparcc_filter = False
            self.force = False
            self.procs = 1

    return Arguments()


def test_between_correls(args, tmpdir):
    table1 = simulate_correls()
    table2 = simulate_correls()
    loc = tmpdir.mkdir("with_correls_test")
    table1.to_json("madebyme", open(str(loc)+"/table1.biom", 'w'))
    table2.to_json("madebyme", open(str(loc) + "/table2.biom", 'w'))
    os.chdir(str(loc))
    between_correls(args)
    files = os.listdir(str(loc)+'/out_dir')
    assert "correls.txt" in files
    assert "crossnet.gml" in files

import pytest
import os
from SCNIC.general import simulate_correls
from SCNIC.between_correls import between_correls


@pytest.fixture()
def args():
    class Arguments(object):
        def __init__(self):
            self.table1 = "table1.biom"
            self.table2 = "table2.biom"
            self.output = "out_dir"
            self.correl_method = "spearman"
            self.p_adjust = "bh"
            self.min_sample = None
            self.min_p = None
            self.min_r = None
            self.sparcc_filter = True
            self.force = False
            self.procs = 1

    return Arguments()


def test_between_correls(args, tmpdir):
    table1 = simulate_correls()
    table2 = simulate_correls()
    loc = tmpdir.mkdir("with_correls_test")
    table1.to_json("madebyme", open(str(loc)+"/table1.biom", 'w'))
    table2.to_json("madebyme", open(str(loc) + "/table2.biom", 'w'))
    os.chdir(str(loc))
    between_correls(args)
    files = os.listdir(str(loc)+'/out_dir')
    assert "correls.txt" in files
    assert "crossnet.gml" in files

Add module.py test and modify some others for better coverage. Remove files not used.
Add module.py test and modify some others for better coverage.
Remove files not used.
