We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
Can't install from tarball on GitHub
```
$ pip install https://github.com/BD2KGenomics/toil/archive/3.14.0.tar.gz
Collecting https://github.com/BD2KGenomics/toil/archive/3.14.0.tar.gz
  Downloading https://github.com/BD2KGenomics/toil/archive/3.14.0.tar.gz
     - 7.0MB 40.4MB/s
    Complete output from command python setup.py egg_info:
    fatal: Not a git repository (or any of the parent directories): .git
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-l5WfLH-build/setup.py", line 152, in <module>
        version = importVersion()
      File "/tmp/pip-l5WfLH-build/setup.py", line 132, in importVersion
        new = version_template.expand_()
      File "version_template.py", line 131, in expand_
        return ''.join("%s = %s\n" % (k, repr(resolve(k))) for k, v in variables.items())
      File "version_template.py", line 131, in <genexpr>
        return ''.join("%s = %s\n" % (k, repr(resolve(k))) for k, v in variables.items())
      File "version_template.py", line 127, in resolve
        v = v()
      File "version_template.py", line 85, in dockerShortTag
        return shortVersion()
      File "version_template.py", line 46, in shortVersion
        return _version(shorten=True)
      File "version_template.py", line 51, in _version
        currentCommit()[:7 if shorten else None],
      File "version_template.py", line 111, in currentCommit
        return check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).split()[0]
      File "/usr/lib/python2.7/subprocess.py", line 223, in check_output
        raise CalledProcessError(retcode, cmd, output=output)
    subprocess.CalledProcessError: Command 'git log --pretty=oneline -n 1 -- $(pwd)' returned non-zero exit status 128
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-l5WfLH-build/
```

--- END ISSUE ---

Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
--- BEGIN FILES ---
Path: `version_template.py`
Content:
```
1 # Copyright (C) 2015-2016 Regents of the University of California
2 #
3 # Licensed under the Apache License, Version 2.0 (the "License");
4 # you may not use this file except in compliance with the License.
5 # You may obtain a copy of the License at
6 #
7 #     http://www.apache.org/licenses/LICENSE-2.0
8 #
9 # Unless required by applicable law or agreed to in writing, software
10 # distributed under the License is distributed on an "AS IS" BASIS,
11 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12 # See the License for the specific language governing permissions and
13 # limitations under the License.
14 
15 """This script is a template for src/toil/version.py. Running it without arguments echoes all
16 globals, i.e. module attributes. Constant assignments will be echoed verbatim while callables
17 will be invoked and their result echoed as an assignment using the function name as the left-hand
18 side and the return value of the function as right-hand side. To prevent a module attribute from
19 being echoed, start or end the attribute name with an underscore. To print the value of a single
20 symbol, pass the name of that attribute to the script as a command line argument. You can also
21 import the expand_ function and invoke it directly with either no or exactly one argument."""
22 
23 # Note to maintainers:
24 #
25 #  - don't import at module level unless you want the imported value to be included in the output
26 #  - only import from the Python standard run-time library (you can't have any dependencies)
27 
28 baseVersion = '3.15.0a1'
29 
30 cgcloudVersion = '1.6.0a1.dev393'
31 
32 
33 def version():
34     """
35     A version identifier that includes the full-legth commit SHA1 and an optional suffix to
36     indicate that the working copy is dirty.
37     """
38     return _version()
39 
40 
41 def shortVersion():
42     """
43     A version identifier that includes the abbreviated commit SHA1 and an optional suffix to
44     indicate that the working copy is dirty.
45     """
46     return _version(shorten=True)
47 
48 
49 def _version(shorten=False):
50     return '-'.join(filter(None, [distVersion(),
51                                   currentCommit()[:7 if shorten else None],
52                                   ('dirty' if dirty() else None)]))
53 
54 
55 def distVersion():
56     """
57     The distribution version identifying a published release on PyPI.
58     """
59     from pkg_resources import parse_version
60     build_number = buildNumber()
61     parsedBaseVersion = parse_version(baseVersion)
62     if isinstance(parsedBaseVersion, tuple):
63         raise RuntimeError("Setuptools version 8.0 or newer required. Update by running "
64                            "'pip install setuptools --upgrade'")
65 
66     if build_number is not None and parsedBaseVersion.is_prerelease:
67         return baseVersion + '.dev' + build_number
68     else:
69         return baseVersion
70 
71 
72 def dockerTag():
73     """
74     The primary tag of the Docker image for the appliance. This uniquely identifies the appliance
75     image.
76     """
77     return version()
78 
79 
80 def dockerShortTag():
81     """
82     A secondary, shortened form of :func:`dockerTag` with which to tag the appliance image for
83     convenience.
84     """
85     return shortVersion()
86 
87 
88 def dockerMinimalTag():
89     """
90     A minimal tag with which to tag the appliance image for convenience. Does not include
91     information about the git commit or working copy dirtyness.
92     """
93     return distVersion()
94 
95 
96 dockerRegistry = 'quay.io/ucsc_cgl'
97 
98 dockerName = 'toil'
99 
100 
101 def buildNumber():
102     """
103     The Jenkins build number, if defined, else None.
104     """
105     import os
106     return os.getenv('BUILD_NUMBER')
107 
108 
109 def currentCommit():
110     from subprocess import check_output
111     return check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).split()[0]
112 
113 
114 def dirty():
115     from subprocess import call
116     return 0 != call('(git diff --exit-code '
117                      '&& git diff --cached --exit-code) > /dev/null', shell=True)
118 
119 
120 def expand_(name=None):
121     variables = {k: v for k, v in globals().items()
122                  if not k.startswith('_') and not k.endswith('_')}
123 
124     def resolve(k):
125         v = variables[k]
126         if callable(v):
127             v = v()
128         return v
129 
130     if name is None:
131         return ''.join("%s = %s\n" % (k, repr(resolve(k))) for k, v in variables.items())
132     else:
133         return resolve(name)
134 
135 
136 def _main():
137     import sys
138     sys.stdout.write(expand_(*sys.argv[1:]))
139 
140 
141 if __name__ == '__main__':
142     _main()
143
```
--- END FILES ---

Please first localize the bug based on the issue statement, and then generate a patch according to the `git diff` format fenced by three backticks.

Here is an example:

```diff
diff --git a/examples/server_async.py b/examples/server_async.py
--- a/examples/server_async.py
+++ b/examples/server_async.py
@@ -313,4 +313,4 @@
 
 
 if __name__ == "__main__":
-    asyncio.run(run_async_server("."), debug=True)
+    asyncio.run(run_async_server(), debug=True)
diff --git a/examples/server_sync.py b/examples/server_sync.py
--- a/examples/server_sync.py
+++ b/examples/server_sync.py
@@ -313,5 +313,5 @@
 
 
 if __name__ == "__main__":
-    server = run_sync_server(".")
+    server = run_sync_server()
     server.shutdown()

```

diff --git a/version_template.py b/version_template.py
--- a/version_template.py
+++ b/version_template.py
@@ -108,13 +108,21 @@
 
 def currentCommit():
     from subprocess import check_output
-    return check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).split()[0]
+    try:
+        output = check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).split()[0]
+    except:
+        # Return this we are not in a git environment.
+        return '000'
+    return output
 
 
 def dirty():
     from subprocess import call
-    return 0 != call('(git diff --exit-code '
-                     '&& git diff --cached --exit-code) > /dev/null', shell=True)
+    try:
+        return 0 != call('(git diff --exit-code '
+                         '&& git diff --cached --exit-code) > /dev/null', shell=True)
+    except:
+        return False # In case the git call fails.
 
 
 def expand_(name=None):

{"golden_diff": "diff --git a/version_template.py b/version_template.py\n--- a/version_template.py\n+++ b/version_template.py\n@@ -108,13 +108,21 @@\n \n def currentCommit():\n     from subprocess import check_output\n-    return check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).split()[0]\n+    try:\n+        output = check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).split()[0]\n+    except:\n+        # Return this we are not in a git environment.\n+        return '000'\n+    return output\n \n \n def dirty():\n     from subprocess import call\n-    return 0 != call('(git diff --exit-code '\n-                     '&& git diff --cached --exit-code) > /dev/null', shell=True)\n+    try:\n+        return 0 != call('(git diff --exit-code '\n+                         '&& git diff --cached --exit-code) > /dev/null', shell=True)\n+    except:\n+        return False # In case the git call fails.\n \n \n def expand_(name=None):\n", "issue": "Can't install from tarball on GitHub\n```\r\n$ pip install https://github.com/BD2KGenomics/toil/archive/3.14.0.tar.gz\r\nCollecting https://github.com/BD2KGenomics/toil/archive/3.14.0.tar.gz\r\n  Downloading https://github.com/BD2KGenomics/toil/archive/3.14.0.tar.gz\r\n     - 7.0MB 40.4MB/s\r\n    Complete output from command python setup.py egg_info:\r\n    fatal: Not a git repository (or any of the parent directories): .git\r\n    Traceback (most recent call last):\r\n      File \"<string>\", line 1, in <module>\r\n      File \"/tmp/pip-l5WfLH-build/setup.py\", line 152, in <module>\r\n        version = importVersion()\r\n      File \"/tmp/pip-l5WfLH-build/setup.py\", line 132, in importVersion\r\n        new = version_template.expand_()\r\n      File \"version_template.py\", line 131, in expand_\r\n        return ''.join(\"%s = %s\\n\" % (k, repr(resolve(k))) for k, v in variables.items())\r\n      File \"version_template.py\", line 131, in <genexpr>\r\n        return ''.join(\"%s = %s\\n\" % (k, repr(resolve(k))) for k, v in variables.items())\r\n      File \"version_template.py\", line 127, in resolve\r\n        v = v()\r\n      File \"version_template.py\", line 85, in dockerShortTag\r\n        return shortVersion()\r\n      File \"version_template.py\", line 46, in shortVersion\r\n        return _version(shorten=True)\r\n      File \"version_template.py\", line 51, in _version\r\n        currentCommit()[:7 if shorten else None],\r\n      File \"version_template.py\", line 111, in currentCommit\r\n        return check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).split()[0]\r\n      File \"/usr/lib/python2.7/subprocess.py\", line 223, in check_output\r\n        raise CalledProcessError(retcode, cmd, output=output)\r\n    subprocess.CalledProcessError: Command 'git log --pretty=oneline -n 1 -- $(pwd)' returned non-zero exit status 128\r\n    \r\n    ----------------------------------------\r\nCommand \"python setup.py egg_info\" failed with error code 1 in /tmp/pip-l5WfLH-build/\r\n```\n", "before_files": [{"content": "# Copyright (C) 2015-2016 Regents of the University of California\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n#     http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicable law or agreed to in writing, software\n# distributed under the License is distributed on an \"AS IS\" BASIS,\n# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n# See the License for the specific language governing permissions and\n# limitations under the License.\n\n\"\"\"This script is a template for src/toil/version.py. Running it without arguments echoes all\nglobals, i.e. module attributes. Constant assignments will be echoed verbatim while callables\nwill be invoked and their result echoed as an assignment using the function name as the left-hand\nside and the return value of the function as right-hand side. To prevent a module attribute from\nbeing echoed, start or end the attribute name with an underscore. To print the value of a single\nsymbol, pass the name of that attribute to the script as a command line argument. You can also\nimport the expand_ function and invoke it directly with either no or exactly one argument.\"\"\"\n\n# Note to maintainers:\n#\n#  - don't import at module level unless you want the imported value to be included in the output\n#  - only import from the Python standard run-time library (you can't have any dependencies)\n\nbaseVersion = '3.15.0a1'\n\ncgcloudVersion = '1.6.0a1.dev393'\n\n\ndef version():\n    \"\"\"\n    A version identifier that includes the full-legth commit SHA1 and an optional suffix to\n    indicate that the working copy is dirty.\n    \"\"\"\n    return _version()\n\n\ndef shortVersion():\n    \"\"\"\n    A version identifier that includes the abbreviated commit SHA1 and an optional suffix to\n    indicate that the working copy is dirty.\n    \"\"\"\n    return _version(shorten=True)\n\n\ndef _version(shorten=False):\n    return '-'.join(filter(None, [distVersion(),\n                                  currentCommit()[:7 if shorten else None],\n                                  ('dirty' if dirty() else None)]))\n\n\ndef distVersion():\n    \"\"\"\n    The distribution version identifying a published release on PyPI.\n    \"\"\"\n    from pkg_resources import parse_version\n    build_number = buildNumber()\n    parsedBaseVersion = parse_version(baseVersion)\n    if isinstance(parsedBaseVersion, tuple):\n        raise RuntimeError(\"Setuptools version 8.0 or newer required. Update by running \"\n                           \"'pip install setuptools --upgrade'\")\n\n    if build_number is not None and parsedBaseVersion.is_prerelease:\n        return baseVersion + '.dev' + build_number\n    else:\n        return baseVersion\n\n\ndef dockerTag():\n    \"\"\"\n    The primary tag of the Docker image for the appliance. This uniquely identifies the appliance\n    image.\n    \"\"\"\n    return version()\n\n\ndef dockerShortTag():\n    \"\"\"\n    A secondary, shortened form of :func:`dockerTag` with which to tag the appliance image for\n    convenience.\n    \"\"\"\n    return shortVersion()\n\n\ndef dockerMinimalTag():\n    \"\"\"\n    A minimal tag with which to tag the appliance image for convenience. Does not include\n    information about the git commit or working copy dirtyness.\n    \"\"\"\n    return distVersion()\n\n\ndockerRegistry = 'quay.io/ucsc_cgl'\n\ndockerName = 'toil'\n\n\ndef buildNumber():\n    \"\"\"\n    The Jenkins build number, if defined, else None.\n    \"\"\"\n    import os\n    return os.getenv('BUILD_NUMBER')\n\n\ndef currentCommit():\n    from subprocess import check_output\n    return check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).split()[0]\n\n\ndef dirty():\n    from subprocess import call\n    return 0 != call('(git diff --exit-code '\n                     '&& git diff --cached --exit-code) > /dev/null', shell=True)\n\n\ndef expand_(name=None):\n    variables = {k: v for k, v in globals().items()\n                 if not k.startswith('_') and not k.endswith('_')}\n\n    def resolve(k):\n        v = variables[k]\n        if callable(v):\n            v = v()\n        return v\n\n    if name is None:\n        return ''.join(\"%s = %s\\n\" % (k, repr(resolve(k))) for k, v in variables.items())\n    else:\n        return resolve(name)\n\n\ndef _main():\n    import sys\n    sys.stdout.write(expand_(*sys.argv[1:]))\n\n\nif __name__ == '__main__':\n    _main()\n", "path": "version_template.py"}], "after_files": [{"content": "# Copyright (C) 2015-2016 Regents of the University of California\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n#     http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicable law or agreed to in writing, software\n# distributed under the License is distributed on an \"AS IS\" BASIS,\n# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n# See the License for the specific language governing permissions and\n# limitations under the License.\n\n\"\"\"This script is a template for src/toil/version.py. Running it without arguments echoes all\nglobals, i.e. module attributes. Constant assignments will be echoed verbatim while callables\nwill be invoked and their result echoed as an assignment using the function name as the left-hand\nside and the return value of the function as right-hand side. To prevent a module attribute from\nbeing echoed, start or end the attribute name with an underscore. To print the value of a single\nsymbol, pass the name of that attribute to the script as a command line argument. You can also\nimport the expand_ function and invoke it directly with either no or exactly one argument.\"\"\"\n\n# Note to maintainers:\n#\n#  - don't import at module level unless you want the imported value to be included in the output\n#  - only import from the Python standard run-time library (you can't have any dependencies)\n\nbaseVersion = '3.15.0a1'\n\ncgcloudVersion = '1.6.0a1.dev393'\n\n\ndef version():\n    \"\"\"\n    A version identifier that includes the full-legth commit SHA1 and an optional suffix to\n    indicate that the working copy is dirty.\n    \"\"\"\n    return _version()\n\n\ndef shortVersion():\n    \"\"\"\n    A version identifier that includes the abbreviated commit SHA1 and an optional suffix to\n    indicate that the working copy is dirty.\n    \"\"\"\n    return _version(shorten=True)\n\n\ndef _version(shorten=False):\n    return '-'.join(filter(None, [distVersion(),\n                                  currentCommit()[:7 if shorten else None],\n                                  ('dirty' if dirty() else None)]))\n\n\ndef distVersion():\n    \"\"\"\n    The distribution version identifying a published release on PyPI.\n    \"\"\"\n    from pkg_resources import parse_version\n    build_number = buildNumber()\n    parsedBaseVersion = parse_version(baseVersion)\n    if isinstance(parsedBaseVersion, tuple):\n        raise RuntimeError(\"Setuptools version 8.0 or newer required. Update by running \"\n                           \"'pip install setuptools --upgrade'\")\n\n    if build_number is not None and parsedBaseVersion.is_prerelease:\n        return baseVersion + '.dev' + build_number\n    else:\n        return baseVersion\n\n\ndef dockerTag():\n    \"\"\"\n    The primary tag of the Docker image for the appliance. This uniquely identifies the appliance\n    image.\n    \"\"\"\n    return version()\n\n\ndef dockerShortTag():\n    \"\"\"\n    A secondary, shortened form of :func:`dockerTag` with which to tag the appliance image for\n    convenience.\n    \"\"\"\n    return shortVersion()\n\n\ndef dockerMinimalTag():\n    \"\"\"\n    A minimal tag with which to tag the appliance image for convenience. Does not include\n    information about the git commit or working copy dirtyness.\n    \"\"\"\n    return distVersion()\n\n\ndockerRegistry = 'quay.io/ucsc_cgl'\n\ndockerName = 'toil'\n\n\ndef buildNumber():\n    \"\"\"\n    The Jenkins build number, if defined, else None.\n    \"\"\"\n    import os\n    return os.getenv('BUILD_NUMBER')\n\n\ndef currentCommit():\n    from subprocess import check_output\n    try:\n        output = check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).split()[0]\n    except:\n        # Return this we are not in a git environment.\n        return '000'\n    return output\n\n\ndef dirty():\n    from subprocess import call\n    try:\n        return 0 != call('(git diff --exit-code '\n                         '&& git diff --cached --exit-code) > /dev/null', shell=True)\n    except:\n        return False # In case the git call fails.\n\n\ndef expand_(name=None):\n    variables = {k: v for k, v in globals().items()\n                 if not k.startswith('_') and not k.endswith('_')}\n\n    def resolve(k):\n        v = variables[k]\n        if callable(v):\n            v = v()\n        return v\n\n    if name is None:\n        return ''.join(\"%s = %s\\n\" % (k, repr(resolve(k))) for k, v in variables.items())\n    else:\n        return resolve(name)\n\n\ndef _main():\n    import sys\n    sys.stdout.write(expand_(*sys.argv[1:]))\n\n\nif __name__ == '__main__':\n    _main()\n", "path": "version_template.py"}]}