[DATALAD RUNCMD] run codespell throughout fixing additional new typos…

… automagically

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

README.md

@@ -182,7 +182,7 @@ udocker tag centos/centos8  mycentos/centos8:arm64
 
 Create a container from a pulled image, assign a name to the created
 container and run it. A created container can be run multiple times
-until it is explicitely removed.
+until it is explicitly removed.
 
 ```bash
 udocker create --name=myfed  fedora:29

tests/unit/test_elfpatcher.py

@@ -34,7 +34,7 @@ def test_01__init(self, mock_path, mock_hinfo):
         mock_path.return_value = "/some_contdir"
         mock_hinfo.uid = "1000"
         elfp = ElfPatcher(self.local, self.contid)
-        self.assertTrue(mock_path.callled)
+        self.assertTrue(mock_path.called)
         self.assertEqual(elfp._uid, "1000")
 
     @patch('udocker.helper.elfpatcher.FileUtil.find_exec')

udocker/cli.py

@@ -104,7 +104,7 @@ def _check_imagerepo(self, imagerepo, def_imagerepo=None):
 
     def _set_repository(self, registry_url, index_url=None,
                         imagerepo=None, http_proxy=None):
-        """Select docker respository"""
+        """Select docker repository"""
         transport = "https:"
         if http_proxy:
             self.dockerioapi.set_proxy(http_proxy)

udocker/cmdparser.py

@@ -65,7 +65,7 @@ def missing_options(self):
 
     def get(self, opt_name, opt_where="CMD_OPT", opt_multiple=False):
         """Get the value of a command line option --xyz=
-        multiple=true  multiple occurences of option can be present
+        multiple=true  multiple occurrences of option can be present
         """
         if opt_where == "CMD":
             return self._argv_split["CMD"]

udocker/config.py

@@ -46,7 +46,7 @@ class Config(object):
     conf['tmpdir'] = os.getenv("TMPDIR", "/tmp")    # for tmp files only
 
     # defaults for container execution
-    conf['cmd'] = ["bash", "-i"]  # Comand to execute
+    conf['cmd'] = ["bash", "-i"]  # Command to execute
 
     # default path for executables
     conf['root_path'] = "/usr/sbin:/sbin:/usr/bin:/bin"
@@ -110,7 +110,7 @@ class Config(object):
                                        "/usr/lib", )
     conf['lib_dirs_list_append'] = (".", )
 
-    # fakechroot access files, used to circunvent openmpi init issues
+    # fakechroot access files, used to circumvent openmpi init issues
     conf['access_files'] = ("/sys/class/infiniband", "/dev/open-mx",
                             "/dev/myri0", "/dev/myri1", "/dev/myri2",
                             "/dev/myri3", "/dev/myri4", "/dev/myri5",

udocker/engine/base.py

@@ -43,7 +43,7 @@ class ExecutionEngineCommon(object):
     opt["user"] = ""                 # User to run in the container
     opt["cwd"] = ""                  # Default dir in the container
     opt["entryp"] = ""               # Container entrypoint
-    opt["cmd"] = []                  # Comand to execute
+    opt["cmd"] = []                  # Command to execute
     opt["hostname"] = ""             # Hostname TBD
     opt["domain"] = ""               # Host domainname TBD
     opt["volfrom"] = []              # Mount vol from container TBD

udocker/engine/fakechroot.py

@@ -137,7 +137,7 @@ def _get_volume_bindings(self):
 
     def _get_access_filesok(self):
         """
-        Circunvent mpi init issues when calling access()
+        Circumvent mpi init issues when calling access()
         A list of certain existing files is provided
         """
         file_list = []

udocker/tools.py

@@ -202,7 +202,7 @@ def _install(self, tarball_file):
             for tar_in in tfile.getmembers():
                 if tar_in.name.startswith("udocker_dir/bin/"):
                     tar_in.name = os.path.basename(tar_in.name)
-                    Msg().out("Debug: extrating", tar_in.name, l=Msg.DBG)
+                    Msg().out("Debug: extracting", tar_in.name, l=Msg.DBG)
                     tfile.extract(tar_in, self.localrepo.bindir)
             FileUtil(self.localrepo.bindir).rchmod(stat.S_IRUSR |
                                                    stat.S_IWUSR |
@@ -212,15 +212,15 @@ def _install(self, tarball_file):
             for tar_in in tfile.getmembers():
                 if tar_in.name.startswith("udocker_dir/lib/"):
                     tar_in.name = os.path.basename(tar_in.name)
-                    Msg().out("Debug: extrating", tar_in.name, l=Msg.DBG)
+                    Msg().out("Debug: extracting", tar_in.name, l=Msg.DBG)
                     tfile.extract(tar_in, self.localrepo.libdir)
             FileUtil(self.localrepo.libdir).rchmod()
 
             FileUtil(self.localrepo.docdir).rchmod()
             for tar_in in tfile.getmembers():
                 if tar_in.name.startswith("udocker_dir/doc/"):
                     tar_in.name = os.path.basename(tar_in.name)
-                    Msg().out("Debug: extrating", tar_in.name, l=Msg.DBG)
+                    Msg().out("Debug: extracting", tar_in.name, l=Msg.DBG)
                     tfile.extract(tar_in, self.localrepo.docdir)
             FileUtil(self.localrepo.docdir).rchmod()
             tfile.close()

udocker/utils/fileutil.py

@@ -598,7 +598,7 @@ def find_file_in_dir(self, image_list):
         return ""
 
     def _link_change_apply(self, new_l_path, f_path, force):
-        """Actually apply the link convertion"""
+        """Actually apply the link conversion"""
         p_path = os.path.realpath(os.path.dirname(f_path))
         if force and not os.access(p_path, os.W_OK):
             os.chmod(p_path, stat.S_IMODE(os.stat(p_path).st_mode) | stat.S_IWUSR)
@@ -610,7 +610,7 @@ def _link_change_apply(self, new_l_path, f_path, force):
             os.symlink(new_l_path, f_path)
 
     def _link_set(self, f_path, orig_path, root_path, force):
-        """Convertion to container specific symbolic link"""
+        """Conversion to container specific symbolic link"""
         l_path = os.readlink(f_path)
         if not l_path.startswith("/"):
             return False
@@ -635,7 +635,7 @@ def _link_set(self, f_path, orig_path, root_path, force):
         return False
 
     def _link_restore(self, f_path, orig_path, root_path, force):
-        """Convertion for host specific symbolic link"""
+        """Conversion for host specific symbolic link"""
         l_path = os.readlink(f_path)
         new_l_path = ""
         if not l_path.startswith("/"):
@@ -663,7 +663,7 @@ def links_conv(self, force=False, to_container=True, orig_path=""):
         root_path = os.path.realpath(self.filename)
         links = []
         if not self._is_safe_prefix(root_path):
-            Msg().err("Error: links convertion outside of directory tree: ",
+            Msg().err("Error: links conversion outside of directory tree: ",
                       root_path)
 
             return None

udocker/utils/uenv.py

@@ -102,7 +102,7 @@ def extend(self, envlist):
         return self
 
     def extendif(self, envlist):
-        """Extend Uenv environment with list of key=val if key non-existant"""
+        """Extend Uenv environment with list of key=val if key non-existent"""
         if isinstance(envlist, (list)):
             for envstr in envlist:
                 self.appendif(envstr)

utils/build_tarball.sh

@@ -20,7 +20,7 @@
 
 # The tarball containing the build binaries for udocker is
 # maintained separately and has its own version. Each release of
-# udocker requires a tarball that is equal or greather than a given
+# udocker requires a tarball that is equal or greater than a given
 # base version.
 # i.e. udocker 1.3.0 requires a tarball >= 1.2.8