old_contents: import pytest
  from SCNIC.module import make_modules, collapse_modules, write_modules_to_dir
  import os
  import glob
  from biom.table import Table
  import numpy as np
  from scipy.spatial.distance import squareform
  
  
  @pytest.fixture()
  def biom_table1():
      arr = np.array([[250,   0, 100, 446,   75],
                      [  0,   0,   1,   1,    2],
                      [  2,   2,   2,   2,    2],
                      [100, 100, 500,   1, 1000],
                      [500,   5,   0,  50,  100]])
      obs_ids = ["otu_%s" % i for i in range(5)]
      samp_ids = ["samp_%s" % i for i in range(5)]
      return Table(arr, obs_ids, samp_ids)
  
  
  @pytest.fixture()
  def dist1():
      dist = np.array([[0.0, .05, 0.2, 1.0, 1.0],
                       [.05, 0.0, 0.2, 1.0, 1.0],
                       [0.2, 0.2, 0.0, 1.0, 1.0],
                       [1.0, 1.0, 1.0, 0.0, 0.7],
                       [1.0, 1.0, 1.0, 0.7, 0.0]])
      return squareform(dist)
  
  
  @pytest.fixture()
  def obs_ids1():
      obs_ids = ["otu_%s" % i for i in range(5)]
      return obs_ids
  
  
  @pytest.fixture()
  def modules1(dist1, obs_ids1):
      return make_modules(dist1, min_dist=.21, obs_ids=obs_ids1)
  
  
  def test_make_modules(modules1):
      assert len(modules1) == 1
      assert np.sum([len(i) for i in modules1]) == 3
  
  
  def test_collapse_modules(biom_table1, modules1):
      coll_table = collapse_modules(biom_table1, modules1)
      assert coll_table.shape[0] == biom_table1.shape[0]-2
      assert coll_table.shape[1] == biom_table1.shape[1]
      assert coll_table.sum() == biom_table1.sum()
      assert np.array_equal(coll_table.sum(axis="sample"), biom_table1.sum(axis="sample"))
      # set since order doesn't matter
      assert frozenset(coll_table.sum(axis="observation")) == frozenset(np.array([885, 1701, 655]))
  
  
  def test_write_modules_to_dir(biom_table1, modules1, tmpdir):
      tempdir = tmpdir.mkdir("mods")
      os.chdir(str(tempdir))
      write_modules_to_dir(biom_table1, modules1)
      os.chdir("modules")
      fnames = glob.glob(str(tempdir)+"/modules/*.biom")
      assert len(fnames) == len(modules1)
  
new_contents: import pytest
  from SCNIC.module_analysis import make_modules, collapse_modules, write_modules_to_dir
  import os
  import glob
  from biom.table import Table
  import numpy as np
  from scipy.spatial.distance import squareform
  
  
  @pytest.fixture()
  def biom_table1():
      arr = np.array([[250,   0, 100, 446,   75],
                      [  0,   0,   1,   1,    2],
                      [  2,   2,   2,   2,    2],
                      [100, 100, 500,   1, 1000],
                      [500,   5,   0,  50,  100]])
      obs_ids = ["otu_%s" % i for i in range(5)]
      samp_ids = ["samp_%s" % i for i in range(5)]
      return Table(arr, obs_ids, samp_ids)
  
  
  @pytest.fixture()
  def dist1():
      dist = np.array([[0.0, .05, 0.2, 1.0, 1.0],
                       [.05, 0.0, 0.2, 1.0, 1.0],
                       [0.2, 0.2, 0.0, 1.0, 1.0],
                       [1.0, 1.0, 1.0, 0.0, 0.7],
                       [1.0, 1.0, 1.0, 0.7, 0.0]])
      return squareform(dist)
  
  
  @pytest.fixture()
  def obs_ids1():
      obs_ids = ["otu_%s" % i for i in range(5)]
      return obs_ids
  
  
  @pytest.fixture()
  def modules1(dist1, obs_ids1):
      return make_modules(dist1, min_dist=.21, obs_ids=obs_ids1)
  
  
  def test_make_modules(modules1):
      assert len(modules1) == 1
      assert np.sum([len(i) for i in modules1]) == 3
  
  
  def test_collapse_modules(biom_table1, modules1):
      coll_table = collapse_modules(biom_table1, modules1)
      assert coll_table.shape[0] == biom_table1.shape[0]-2
      assert coll_table.shape[1] == biom_table1.shape[1]
      assert coll_table.sum() == biom_table1.sum()
      assert np.array_equal(coll_table.sum(axis="sample"), biom_table1.sum(axis="sample"))
      # set since order doesn't matter
      assert frozenset(coll_table.sum(axis="observation")) == frozenset(np.array([885, 1701, 655]))
  
  
  def test_write_modules_to_dir(biom_table1, modules1, tmpdir):
      tempdir = tmpdir.mkdir("mods")
      os.chdir(str(tempdir))
      write_modules_to_dir(biom_table1, modules1)
      os.chdir("modules")
      fnames = glob.glob(str(tempdir)+"/modules/*.biom")
      assert len(fnames) == len(modules1)
  
subject: Fix tests broken by bad import from previous commit.