We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
santiy_check_commands doesn't work for ipython


--- END ISSUE ---

Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
--- BEGIN FILES ---
Path: `easybuild/framework/extensioneasyblock.py`
Content:
```
1 ##
2 # Copyright 2013 Ghent University
3 #
4 # This file is part of EasyBuild,
5 # originally created by the HPC team of the University of Ghent (http://ugent.be/hpc).
6 #
7 # http://github.com/hpcugent/easybuild
8 #
9 # EasyBuild is free software: you can redistribute it and/or modify
10 # it under the terms of the GNU General Public License as published by
11 # the Free Software Foundation v2.
12 #
13 # EasyBuild is distributed in the hope that it will be useful,
14 # but WITHOUT ANY WARRANTY; without even the implied warranty of
15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
16 # GNU General Public License for more details.
17 #
18 # You should have received a copy of the GNU General Public License
19 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
20 ##
21 """
22 EasyBuild support for building and installing extensions as actual extensions or as stand-alone modules,
23 implemented as an easyblock
24 
25 @author: Kenneth Hoste (Ghent University)
26 """
27 import copy
28 import os
29 
30 from easybuild.framework.easyblock import EasyBlock
31 from easybuild.framework.easyconfig import CUSTOM
32 from easybuild.framework.extension import Extension
33 from easybuild.tools.filetools import apply_patch, extract_file
34 from easybuild.tools.utilities import remove_unwanted_chars
35 
36 
37 class ExtensionEasyBlock(EasyBlock, Extension):
38     """
39     Install an extension as a separate module, or as an extension.
40 
41     Deriving classes should implement the following functions:
42     * required EasyBlock functions:
43       - configure_step
44       - build_step
45       - install_step
46     * required Extension functions
47       - run
48     """
49 
50     @staticmethod
51     def extra_options(extra_vars=None):
52         """Extra easyconfig parameters specific to ExtensionEasyBlock."""
53 
54         # using [] as default value is a bad idea, so we handle it this way
55         if extra_vars is None:
56             extra_vars = []
57 
58         extra_vars.extend([
59                            ('options', [{}, "Dictionary with extension options.", CUSTOM]),
60                           ])
61         return EasyBlock.extra_options(extra_vars)
62 
63     def __init__(self, *args, **kwargs):
64         """Initialize either as EasyBlock or as Extension."""
65 
66         self.is_extension = False
67 
68         if isinstance(args[0], EasyBlock):
69             Extension.__init__(self, *args, **kwargs)
70             # name and version properties of EasyBlock are used, so make sure name and version are correct
71             self.cfg['name'] = self.ext.get('name', None)
72             self.cfg['version'] = self.ext.get('version', None)
73             self.builddir = self.master.builddir
74             self.installdir = self.master.installdir
75             self.is_extension = True
76             self.unpack_options = None
77         else:
78             EasyBlock.__init__(self, *args, **kwargs)
79             self.options = copy.deepcopy(self.cfg.get('options', {}))  # we need this for Extension.sanity_check_step
80 
81         self.ext_dir = None  # dir where extension source was unpacked
82 
83     def run(self, unpack_src=False):
84         """Common operations for extensions: unpacking sources, patching, ..."""
85 
86         # unpack file if desired
87         if unpack_src:
88             targetdir = os.path.join(self.master.builddir, remove_unwanted_chars(self.name))
89             self.ext_dir = extract_file("%s" % self.src, targetdir, extra_options=self.unpack_options)
90 
91         # patch if needed
92         if self.patches:
93             for patchfile in self.patches:
94                 if not apply_patch(patchfile, self.ext_dir):
95                     self.log.error("Applying patch %s failed" % patchfile)
96 
97     def sanity_check_step(self, exts_filter=None, custom_paths=None, custom_commands=None):
98         """
99         Custom sanity check for extensions, whether installed as stand-alone module or not
100         """
101         if not self.cfg['exts_filter']:
102             self.cfg['exts_filter'] = exts_filter
103         self.log.debug("starting sanity check for extension with filter %s", self.cfg['exts_filter'])
104 
105         if not self.is_extension:
106             # load fake module
107             fake_mod_data = self.load_fake_module(purge=True)
108 
109         # perform sanity check
110         sanity_check_ok = Extension.sanity_check_step(self)
111 
112         if not self.is_extension:
113             # unload fake module and clean up
114             self.clean_up_fake_module(fake_mod_data)
115 
116         if custom_paths or custom_commands:
117             EasyBlock.sanity_check_step(self, custom_paths=custom_paths, custom_commands=custom_commands,
118                 extension=self.is_extension)
119 
120         # pass or fail sanity check
121         if not sanity_check_ok:
122             msg = "Sanity check for %s failed: %s" % (self.name, '; '.join(self.sanity_check_fail_msgs))
123             if self.is_extension:
124                 self.log.warning(msg)
125             else:
126                 self.log.error(msg)
127             return False
128         else:
129             self.log.info("Sanity check for %s successful!" % self.name)
130             return True
131 
132     def make_module_extra(self, extra=None):
133         """Add custom entries to module."""
134 
135         txt = EasyBlock.make_module_extra(self)
136         if not extra is None:
137             txt += extra
138         return txt
139
```
--- 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/easybuild/framework/extensioneasyblock.py b/easybuild/framework/extensioneasyblock.py
--- a/easybuild/framework/extensioneasyblock.py
+++ b/easybuild/framework/extensioneasyblock.py
@@ -113,7 +113,7 @@
             # unload fake module and clean up
             self.clean_up_fake_module(fake_mod_data)
 
-        if custom_paths or custom_commands:
+        if custom_paths or self.cfg['sanity_check_paths'] or custom_commands or self.cfg['sanity_check_commands']:
             EasyBlock.sanity_check_step(self, custom_paths=custom_paths, custom_commands=custom_commands,
                 extension=self.is_extension)

{"golden_diff": "diff --git a/easybuild/framework/extensioneasyblock.py b/easybuild/framework/extensioneasyblock.py\n--- a/easybuild/framework/extensioneasyblock.py\n+++ b/easybuild/framework/extensioneasyblock.py\n@@ -113,7 +113,7 @@\n             # unload fake module and clean up\n             self.clean_up_fake_module(fake_mod_data)\n \n-        if custom_paths or custom_commands:\n+        if custom_paths or self.cfg['sanity_check_paths'] or custom_commands or self.cfg['sanity_check_commands']:\n             EasyBlock.sanity_check_step(self, custom_paths=custom_paths, custom_commands=custom_commands,\n                 extension=self.is_extension)\n", "issue": "santiy_check_commands doesn't work for ipython\n\n", "before_files": [{"content": "##\n# Copyright 2013 Ghent University\n#\n# This file is part of EasyBuild,\n# originally created by the HPC team of the University of Ghent (http://ugent.be/hpc).\n#\n# http://github.com/hpcugent/easybuild\n#\n# EasyBuild is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as published by\n# the Free Software Foundation v2.\n#\n# EasyBuild is distributed in the hope that it will be useful,\n# but WITHOUT ANY WARRANTY; without even the implied warranty of\n# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n# GNU General Public License for more details.\n#\n# You should have received a copy of the GNU General Public License\n# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.\n##\n\"\"\"\nEasyBuild support for building and installing extensions as actual extensions or as stand-alone modules,\nimplemented as an easyblock\n\n@author: Kenneth Hoste (Ghent University)\n\"\"\"\nimport copy\nimport os\n\nfrom easybuild.framework.easyblock import EasyBlock\nfrom easybuild.framework.easyconfig import CUSTOM\nfrom easybuild.framework.extension import Extension\nfrom easybuild.tools.filetools import apply_patch, extract_file\nfrom easybuild.tools.utilities import remove_unwanted_chars\n\n\nclass ExtensionEasyBlock(EasyBlock, Extension):\n    \"\"\"\n    Install an extension as a separate module, or as an extension.\n\n    Deriving classes should implement the following functions:\n    * required EasyBlock functions:\n      - configure_step\n      - build_step\n      - install_step\n    * required Extension functions\n      - run\n    \"\"\"\n\n    @staticmethod\n    def extra_options(extra_vars=None):\n        \"\"\"Extra easyconfig parameters specific to ExtensionEasyBlock.\"\"\"\n\n        # using [] as default value is a bad idea, so we handle it this way\n        if extra_vars is None:\n            extra_vars = []\n\n        extra_vars.extend([\n                           ('options', [{}, \"Dictionary with extension options.\", CUSTOM]),\n                          ])\n        return EasyBlock.extra_options(extra_vars)\n\n    def __init__(self, *args, **kwargs):\n        \"\"\"Initialize either as EasyBlock or as Extension.\"\"\"\n\n        self.is_extension = False\n\n        if isinstance(args[0], EasyBlock):\n            Extension.__init__(self, *args, **kwargs)\n            # name and version properties of EasyBlock are used, so make sure name and version are correct\n            self.cfg['name'] = self.ext.get('name', None)\n            self.cfg['version'] = self.ext.get('version', None)\n            self.builddir = self.master.builddir\n            self.installdir = self.master.installdir\n            self.is_extension = True\n            self.unpack_options = None\n        else:\n            EasyBlock.__init__(self, *args, **kwargs)\n            self.options = copy.deepcopy(self.cfg.get('options', {}))  # we need this for Extension.sanity_check_step\n\n        self.ext_dir = None  # dir where extension source was unpacked\n\n    def run(self, unpack_src=False):\n        \"\"\"Common operations for extensions: unpacking sources, patching, ...\"\"\"\n\n        # unpack file if desired\n        if unpack_src:\n            targetdir = os.path.join(self.master.builddir, remove_unwanted_chars(self.name))\n            self.ext_dir = extract_file(\"%s\" % self.src, targetdir, extra_options=self.unpack_options)\n\n        # patch if needed\n        if self.patches:\n            for patchfile in self.patches:\n                if not apply_patch(patchfile, self.ext_dir):\n                    self.log.error(\"Applying patch %s failed\" % patchfile)\n\n    def sanity_check_step(self, exts_filter=None, custom_paths=None, custom_commands=None):\n        \"\"\"\n        Custom sanity check for extensions, whether installed as stand-alone module or not\n        \"\"\"\n        if not self.cfg['exts_filter']:\n            self.cfg['exts_filter'] = exts_filter\n        self.log.debug(\"starting sanity check for extension with filter %s\", self.cfg['exts_filter'])\n\n        if not self.is_extension:\n            # load fake module\n            fake_mod_data = self.load_fake_module(purge=True)\n\n        # perform sanity check\n        sanity_check_ok = Extension.sanity_check_step(self)\n\n        if not self.is_extension:\n            # unload fake module and clean up\n            self.clean_up_fake_module(fake_mod_data)\n\n        if custom_paths or custom_commands:\n            EasyBlock.sanity_check_step(self, custom_paths=custom_paths, custom_commands=custom_commands,\n                extension=self.is_extension)\n\n        # pass or fail sanity check\n        if not sanity_check_ok:\n            msg = \"Sanity check for %s failed: %s\" % (self.name, '; '.join(self.sanity_check_fail_msgs))\n            if self.is_extension:\n                self.log.warning(msg)\n            else:\n                self.log.error(msg)\n            return False\n        else:\n            self.log.info(\"Sanity check for %s successful!\" % self.name)\n            return True\n\n    def make_module_extra(self, extra=None):\n        \"\"\"Add custom entries to module.\"\"\"\n\n        txt = EasyBlock.make_module_extra(self)\n        if not extra is None:\n            txt += extra\n        return txt\n", "path": "easybuild/framework/extensioneasyblock.py"}], "after_files": [{"content": "##\n# Copyright 2013 Ghent University\n#\n# This file is part of EasyBuild,\n# originally created by the HPC team of the University of Ghent (http://ugent.be/hpc).\n#\n# http://github.com/hpcugent/easybuild\n#\n# EasyBuild is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as published by\n# the Free Software Foundation v2.\n#\n# EasyBuild is distributed in the hope that it will be useful,\n# but WITHOUT ANY WARRANTY; without even the implied warranty of\n# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n# GNU General Public License for more details.\n#\n# You should have received a copy of the GNU General Public License\n# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.\n##\n\"\"\"\nEasyBuild support for building and installing extensions as actual extensions or as stand-alone modules,\nimplemented as an easyblock\n\n@author: Kenneth Hoste (Ghent University)\n\"\"\"\nimport copy\nimport os\n\nfrom easybuild.framework.easyblock import EasyBlock\nfrom easybuild.framework.easyconfig import CUSTOM\nfrom easybuild.framework.extension import Extension\nfrom easybuild.tools.filetools import apply_patch, extract_file\nfrom easybuild.tools.utilities import remove_unwanted_chars\n\n\nclass ExtensionEasyBlock(EasyBlock, Extension):\n    \"\"\"\n    Install an extension as a separate module, or as an extension.\n\n    Deriving classes should implement the following functions:\n    * required EasyBlock functions:\n      - configure_step\n      - build_step\n      - install_step\n    * required Extension functions\n      - run\n    \"\"\"\n\n    @staticmethod\n    def extra_options(extra_vars=None):\n        \"\"\"Extra easyconfig parameters specific to ExtensionEasyBlock.\"\"\"\n\n        # using [] as default value is a bad idea, so we handle it this way\n        if extra_vars is None:\n            extra_vars = []\n\n        extra_vars.extend([\n                           ('options', [{}, \"Dictionary with extension options.\", CUSTOM]),\n                          ])\n        return EasyBlock.extra_options(extra_vars)\n\n    def __init__(self, *args, **kwargs):\n        \"\"\"Initialize either as EasyBlock or as Extension.\"\"\"\n\n        self.is_extension = False\n\n        if isinstance(args[0], EasyBlock):\n            Extension.__init__(self, *args, **kwargs)\n            # name and version properties of EasyBlock are used, so make sure name and version are correct\n            self.cfg['name'] = self.ext.get('name', None)\n            self.cfg['version'] = self.ext.get('version', None)\n            self.builddir = self.master.builddir\n            self.installdir = self.master.installdir\n            self.is_extension = True\n            self.unpack_options = None\n        else:\n            EasyBlock.__init__(self, *args, **kwargs)\n            self.options = copy.deepcopy(self.cfg.get('options', {}))  # we need this for Extension.sanity_check_step\n\n        self.ext_dir = None  # dir where extension source was unpacked\n\n    def run(self, unpack_src=False):\n        \"\"\"Common operations for extensions: unpacking sources, patching, ...\"\"\"\n\n        # unpack file if desired\n        if unpack_src:\n            targetdir = os.path.join(self.master.builddir, remove_unwanted_chars(self.name))\n            self.ext_dir = extract_file(\"%s\" % self.src, targetdir, extra_options=self.unpack_options)\n\n        # patch if needed\n        if self.patches:\n            for patchfile in self.patches:\n                if not apply_patch(patchfile, self.ext_dir):\n                    self.log.error(\"Applying patch %s failed\" % patchfile)\n\n    def sanity_check_step(self, exts_filter=None, custom_paths=None, custom_commands=None):\n        \"\"\"\n        Custom sanity check for extensions, whether installed as stand-alone module or not\n        \"\"\"\n        if not self.cfg['exts_filter']:\n            self.cfg['exts_filter'] = exts_filter\n        self.log.debug(\"starting sanity check for extension with filter %s\", self.cfg['exts_filter'])\n\n        if not self.is_extension:\n            # load fake module\n            fake_mod_data = self.load_fake_module(purge=True)\n\n        # perform sanity check\n        sanity_check_ok = Extension.sanity_check_step(self)\n\n        if not self.is_extension:\n            # unload fake module and clean up\n            self.clean_up_fake_module(fake_mod_data)\n\n        if custom_paths or self.cfg['sanity_check_paths'] or custom_commands or self.cfg['sanity_check_commands']:\n            EasyBlock.sanity_check_step(self, custom_paths=custom_paths, custom_commands=custom_commands,\n                extension=self.is_extension)\n\n        # pass or fail sanity check\n        if not sanity_check_ok:\n            msg = \"Sanity check for %s failed: %s\" % (self.name, '; '.join(self.sanity_check_fail_msgs))\n            if self.is_extension:\n                self.log.warning(msg)\n            else:\n                self.log.error(msg)\n            return False\n        else:\n            self.log.info(\"Sanity check for %s successful!\" % self.name)\n            return True\n\n    def make_module_extra(self, extra=None):\n        \"\"\"Add custom entries to module.\"\"\"\n\n        txt = EasyBlock.make_module_extra(self)\n        if not extra is None:\n            txt += extra\n        return txt\n", "path": "easybuild/framework/extensioneasyblock.py"}]}