make test temporary directories not in the "test" folder

This prevented the execution of the tests post-installation

pybedtools/test/test_1.py

@@ -1,24 +1,17 @@
 import pybedtools
 import os, difflib, sys
+import tempfile
+
 from pybedtools import featurefuncs
 import pytest
 
 import threading
 import warnings
-from .tfuncs import test_tempdir
 
 unwriteable = "unwriteable"
 
 
-def setup_module():
-    if not os.path.exists(test_tempdir):
-        os.system("mkdir -p %s" % test_tempdir)
-    pybedtools.set_tempdir(test_tempdir)
-
-
 def teardown_module():
-    if os.path.exists(test_tempdir):
-        os.system("rm -r %s" % test_tempdir)
     pybedtools.cleanup()
 
 
@@ -67,7 +60,8 @@ def cleanup_unwriteable():
     """
     if os.path.exists(unwriteable):
         os.system("rm -rf %s" % unwriteable)
-    pybedtools.set_tempdir(test_tempdir)
+    tempfile.tempdir = None
+    pybedtools.set_tempdir(tempfile.gettempdir())
 
 
 def test_interval_index():
@@ -503,6 +497,7 @@ def test_sequence():
     For example, the first 100 bases of a chromosome are defined as
     chromStart=0, chromEnd=100, and span the bases numbered 0-99. """
 
+    test_tempdir = os.path.abspath(tempfile.gettempdir())
     fi = os.path.join(test_tempdir, "test.fasta")
 
     s = """

pybedtools/test/test_cbedtools.py

@@ -5,17 +5,8 @@
 from pybedtools import Interval, IntervalFile
 import pybedtools
 import pytest
-from .tfuncs import test_tempdir
-
-def setup_module():
-    if not os.path.exists(test_tempdir):
-        os.system("mkdir -p %s" % test_tempdir)
-    pybedtools.set_tempdir(test_tempdir)
-
 
 def teardown_module():
-    if os.path.exists(test_tempdir):
-        os.system("rm -r %s" % test_tempdir)
     pybedtools.cleanup()
 
 PATH = os.path.dirname(__file__)

pybedtools/test/test_contrib.py

@@ -7,7 +7,7 @@
 from pybedtools import Interval
 
 # from pybedtools.contrib import Classifier
-from .tfuncs import setup_module, teardown_module, testdir, test_tempdir, unwriteable
+from .tfuncs import teardown_module
 
 # model for gdc.
 # chr2L, starts at 1 and spacing is 10bp.

pybedtools/test/test_gzip_support.py

@@ -4,17 +4,9 @@
 
 import pybedtools
 import gzip
-from .tfuncs import test_tempdir
 
 
-def setup_module():
-    if not os.path.exists(test_tempdir):
-        os.system("mkdir -p %s" % test_tempdir)
-    pybedtools.set_tempdir(test_tempdir)
-
 def teardown_module():
-    if os.path.exists(test_tempdir):
-        os.system("rm -r %s" % test_tempdir)
     pybedtools.cleanup()
 
 def _make_temporary_gzip(bed_filename):

pybedtools/test/test_helpers.py

@@ -1,7 +1,8 @@
 import pybedtools
 import sys
 import os
-from .tfuncs import testdir, test_tempdir
+import tempfile
+from .tfuncs import testdir
 import pytest
 from pathlib import Path
 
@@ -41,6 +42,7 @@ def test_cleanup():
 
     # make a fake tempfile, not created during this pybedtools session
     pybedtools.cleanup()
+    test_tempdir = os.path.abspath(tempfile.gettempdir())
     testfn = Path(test_tempdir) / "pybedtools.TESTING.tmp"
     testfn.parent.mkdir(parents=True, exist_ok=True)
     testfn.touch()

pybedtools/test/test_issues.py

@@ -10,19 +10,10 @@
 
 
 testdir = os.path.dirname(__file__)
-tempdir = os.path.join(os.path.abspath(testdir), "tmp")
 unwriteable = "unwriteable"
 
 
-def setup_module():
-    if not os.path.exists(tempdir):
-        os.system("mkdir -p %s" % tempdir)
-    pybedtools.set_tempdir(tempdir)
-
-
 def teardown_module():
-    if os.path.exists(tempdir):
-        os.system("rm -r %s" % tempdir)
     pybedtools.cleanup()
 
 

pybedtools/test/test_iter.py

@@ -5,17 +5,8 @@
 import os
 import gzip
 import pybedtools
-from .tfuncs import test_tempdir
-
-def setup_module():
-    if not os.path.exists(test_tempdir):
-        os.system("mkdir -p %s" % test_tempdir)
-    pybedtools.set_tempdir(test_tempdir)
-
 
 def teardown_module():
-    if os.path.exists(test_tempdir):
-        os.system("rm -r %s" % test_tempdir)
     pybedtools.cleanup()
 
 yamltestdesc = ["test_cases.yaml"]

pybedtools/test/tfuncs.py

@@ -1,19 +1,9 @@
-import pytest
 import pybedtools
 import os
 
 testdir = os.path.dirname(__file__)
-test_tempdir = os.path.join(os.path.abspath(testdir), "tmp")
 unwriteable = os.path.join(os.path.abspath(testdir), "unwriteable")
 
 
-def setup_module():
-    if not os.path.exists(test_tempdir):
-        os.system("mkdir -p %s" % test_tempdir)
-    pybedtools.set_tempdir(test_tempdir)
-
-
 def teardown_module():
-    if os.path.exists(test_tempdir):
-        os.system("rm -r %s" % test_tempdir)
     pybedtools.cleanup()