apply black

Author: ctb

tests/conftest.py

@@ -4,8 +4,10 @@
 import pytest
 
 from sourmash_tst_utils import TempDirectory, RunnerContext
+
 sys.stdout = sys.stderr
 
+
 @pytest.fixture
 def runtmp():
     with TempDirectory() as location:

tests/sourmash_tst_utils.py

@@ -1,4 +1,5 @@
 "Various utilities used by sourmash tests."
+
 import sys
 import os
 import tempfile
@@ -13,20 +14,31 @@
 from io import StringIO
 
 
-SIG_FILES = [os.path.join('demo', f) for f in (
-  "SRR2060939_1.sig", "SRR2060939_2.sig", "SRR2241509_1.sig",
-  "SRR2255622_1.sig", "SRR453566_1.sig", "SRR453569_1.sig", "SRR453570_1.sig")
+SIG_FILES = [
+    os.path.join("demo", f)
+    for f in (
+        "SRR2060939_1.sig",
+        "SRR2060939_2.sig",
+        "SRR2241509_1.sig",
+        "SRR2255622_1.sig",
+        "SRR453566_1.sig",
+        "SRR453569_1.sig",
+        "SRR453570_1.sig",
+    )
 ]
 
+
 def get_test_data(filename):
     thisdir = os.path.dirname(__file__)
     return os.path.join(thisdir, "test-data", filename)
 
+
 def get_example_data(filename):
     thisdir = os.path.dirname(__file__)
     return os.path.join(thisdir, "../examples", filename)
 
-def scriptpath(scriptname='sourmash'):
+
+def scriptpath(scriptname="sourmash"):
     """Return the path to the scripts, in both dev and install situations."""
     # note - it doesn't matter what the scriptname is here, as long as
     # it's some script present in this version of sourmash.
@@ -39,15 +51,15 @@ def scriptpath(scriptname='sourmash'):
     if os.path.exists(os.path.join(path, scriptname)):
         return path
 
-    for path in os.environ['PATH'].split(':'):
+    for path in os.environ["PATH"].split(":"):
         if os.path.exists(os.path.join(path, scriptname)):
             return path
 
 
 def _runscript(scriptname):
     """Find & run a script with exec (i.e. not via os.system or subprocess)."""
     namespace = {"__name__": "__main__"}
-    namespace['sys'] = globals()['sys']
+    namespace["sys"] = globals()["sys"]
 
     entry_points = importlib.metadata.entry_points(
         group="console_scripts", name="sourmash"
@@ -58,8 +70,8 @@ def _runscript(scriptname):
     return 0
 
 
-ScriptResults = collections.namedtuple('ScriptResults',
-                                       ['status', 'out', 'err'])
+ScriptResults = collections.namedtuple("ScriptResults", ["status", "out", "err"])
+
 
 def runscript(scriptname, args, **kwargs):
     """Run a Python script using exec().
@@ -75,17 +87,17 @@ def runscript(scriptname, args, **kwargs):
     sysargs.extend(args)
 
     cwd = os.getcwd()
-    in_directory = kwargs.get('in_directory', cwd)
-    fail_ok = kwargs.get('fail_ok', False)
+    in_directory = kwargs.get("in_directory", cwd)
+    fail_ok = kwargs.get("fail_ok", False)
 
     try:
         status = -1
         oldargs = sys.argv
         sys.argv = sysargs
 
         oldin = None
-        if 'stdin_data' in kwargs:
-            oldin, sys.stdin = sys.stdin, StringIO(kwargs['stdin_data'])
+        if "stdin_data" in kwargs:
+            oldin, sys.stdin = sys.stdin, StringIO(kwargs["stdin_data"])
 
         oldout, olderr = sys.stdout, sys.stderr
         sys.stdout = StringIO()
@@ -95,8 +107,8 @@ def runscript(scriptname, args, **kwargs):
         os.chdir(in_directory)
 
         try:
-            print('running:', scriptname, 'in:', in_directory, file=oldout)
-            print('arguments', sysargs, file=oldout)
+            print("running:", scriptname, "in:", in_directory, file=oldout)
+            print("arguments", sysargs, file=oldout)
 
             status = _runscript(scriptname)
         except SystemExit as err:
@@ -123,9 +135,10 @@ def runscript(scriptname, args, **kwargs):
 
     return ScriptResults(status, out, err)
 
+
 class TempDirectory(object):
     def __init__(self):
-        self.tempdir = tempfile.mkdtemp(prefix='sourmashtest_')
+        self.tempdir = tempfile.mkdtemp(prefix="sourmashtest_")
 
     def __enter__(self):
         return self.tempdir
@@ -143,7 +156,7 @@ def __exit__(self, exc_type, exc_value, traceback):
 class SourmashCommandFailed(Exception):
     def __init__(self, msg):
         Exception.__init__(self, msg)
-        self.message = msg 
+        self.message = msg
 
 
 class RunnerContext(object):
@@ -156,32 +169,34 @@ class RunnerContext(object):
 
     You can use the 'output' method to build filenames in my temp directory.
     """
+
     def __init__(self, location):
         self.location = location
         self.last_command = None
         self.last_result = None
 
     def run_sourmash(self, *args, **kwargs):
         "Run the sourmash script with the given arguments."
-        kwargs['fail_ok'] = True
-        if 'in_directory' not in kwargs:
-            kwargs['in_directory'] = self.location
+        kwargs["fail_ok"] = True
+        if "in_directory" not in kwargs:
+            kwargs["in_directory"] = self.location
 
-        cmdlist = ['sourmash']
-        cmdlist.extend(( str(x) for x in args))
+        cmdlist = ["sourmash"]
+        cmdlist.extend((str(x) for x in args))
         self.last_command = " ".join(cmdlist)
-        self.last_result = runscript('sourmash', args, **kwargs)
+        self.last_result = runscript("sourmash", args, **kwargs)
 
         if self.last_result.status:
             raise SourmashCommandFailed(self.last_result.err)
 
         return self.last_result
+
     sourmash = run_sourmash
 
     def run(self, scriptname, *args, **kwargs):
         "Run a script with the given arguments."
-        if 'in_directory' not in kwargs:
-            kwargs['in_directory'] = self.location
+        if "in_directory" not in kwargs:
+            kwargs["in_directory"] = self.location
         self.last_command = " ".join(args)
         self.last_result = runscript(scriptname, args, **kwargs)
         return self.last_result
@@ -199,10 +214,10 @@ def __str__(self):
                 if self.last_result.out:
                     s += "- stdout:\n---\n{}---\n".format(self.last_result.out)
                 else:
-                    s += '(no stdout)\n\n'
+                    s += "(no stdout)\n\n"
                 if self.last_result.err:
                     s += "- stderr:\n---\n{}---\n".format(self.last_result.err)
                 else:
-                    s += '(no stderr)\n'
+                    s += "(no stderr)\n"
 
         return s