{
    "file_diffs": [
        {
            "old_file_content": "# emacs: -*- mode: python; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-\n# ex: set sts=4 ts=4 sw=4 noet:\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n#\n#   See COPYING file distributed along with the datalad package for the\n#   copyright and license terms.\n#\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n\"\"\"\n\"\"\"\n\n__docformat__ = 'restructuredtext'\n\nimport argparse\nimport os\nimport re\nimport sys\nimport gzip\nimport warnings\nfrom tempfile import NamedTemporaryFile\nfrom textwrap import wrap\n\nfrom ..cmd import WitlessRunner as Runner\nfrom ..log import is_interactive\nfrom ..utils import (\n    ensure_unicode,\n    getpwd,\n    unlink,\n)\nfrom ..version import __version__\nfrom ..dochelpers import exc_str\n\nfrom logging import getLogger\nlgr = getLogger('datalad.cmdline')\n\n\nclass HelpAction(argparse.Action):\n    def __call__(self, parser, namespace, values, option_string=None):\n        # Lets use the manpage on mature systems but only for subcommands --\n        # --help should behave similar to how git does it:\n        # regular --help for \"git\" but man pages for specific commands.\n        # It is important since we do discover all subcommands from entry\n        # points at run time and thus any static manpage would like be out of\n        # date\n        interactive = is_interactive()\n        if interactive \\\n                and option_string == '--help' \\\n                and ' ' in parser.prog:  # subcommand\n            try:\n                import subprocess\n                # get the datalad manpage to use\n                manfile = os.environ.get('MANPATH', '/usr/share/man') \\\n                    + '/man1/{0}.1.gz'.format(parser.prog.replace(' ', '-'))\n                # extract version field from the manpage\n                if not os.path.exists(manfile):\n                    raise IOError(\"manfile is not found\")\n                with gzip.open(manfile) as f:\n                    man_th = [line for line in f if line.startswith(b\".TH\")][0]\n                man_version = man_th.split(b' ')[-1].strip(b\" '\\\"\\t\\n\").decode('utf-8')\n\n                # don't show manpage if man_version not equal to current datalad_version\n                if __version__ != man_version:\n                    raise ValueError\n                subprocess.check_call(\n                    'man %s 2> /dev/null' % manfile,\n                    shell=True)\n                sys.exit(0)\n            except (subprocess.CalledProcessError, IOError, OSError, IndexError, ValueError) as e:\n                lgr.debug(\"Did not use manpage since %s\", exc_str(e))\n        if option_string == '-h':\n            usage = parser.format_usage()\n            ucomps = re.match(\n                r'(?P<pre>.*){(?P<cmds>.*)}(?P<post>....*)',\n                usage,\n                re.DOTALL)\n            if ucomps:\n                ucomps = ucomps.groupdict()\n                indent_level = len(ucomps['post']) - len(ucomps['post'].lstrip())\n                usage = '{pre}{{{cmds}}}{post}'.format(\n                    pre=ucomps['pre'],\n                    cmds='\\n'.join(wrap(\n                        ', '.join(sorted(c.strip() for c in ucomps['cmds'].split(','))),\n                        break_on_hyphens=False,\n                        subsequent_indent=' ' * indent_level)),\n                    post=ucomps['post'],\n                )\n            helpstr = \"%s\\n%s\" % (\n                usage,\n                \"Use '--help' to get more comprehensive information.\")\n        else:\n            helpstr = parser.format_help()\n        # better for help2man\n        # for main command -- should be different sections. And since we are in\n        # heavy output massaging mode...\n        if \"commands for dataset operations\" in helpstr.lower():\n            opt_args_str = '*Global options*'\n            pos_args_str = '*Commands*'\n            # tune up usage -- default one is way too heavy\n            helpstr = re.sub(r'^[uU]sage: .*?\\n\\s*\\n',\n                             'Usage: datalad [global-opts] command [command-opts]\\n\\n',\n                             helpstr,\n                             flags=re.MULTILINE | re.DOTALL)\n            # and altogether remove sections with long list of commands\n            helpstr = re.sub(r'positional arguments:\\s*\\n\\s*{.*}\\n', '', helpstr)\n        else:\n            opt_args_str = \"*Options*\"\n            pos_args_str = \"*Arguments*\"\n        helpstr = re.sub(r'optional arguments:', opt_args_str, helpstr)\n        helpstr = re.sub(r'positional arguments:', pos_args_str, helpstr)\n        # usage is on the same line\n        helpstr = re.sub(r'^usage:', 'Usage:', helpstr)\n\n        if interactive and option_string == '--help':\n            import pydoc\n            pydoc.pager(helpstr)\n        else:\n            print(helpstr)\n        sys.exit(0)\n\n\nclass LogLevelAction(argparse.Action):\n    def __call__(self, parser, namespace, values, option_string=None):\n        from ..log import LoggerHelper\n        LoggerHelper().set_level(level=values)\n\n\n# MIH: Disabled. Non-functional, untested.\n#class PBSAction(argparse.Action):\n#    \"\"\"Action to schedule actual command execution via PBS (e.g. Condor)\"\"\"\n#    def __call__(self, parser, namespace, values, option_string=None):\n#        pbs = values[0]\n#        import pdb; pdb.set_trace()\n#        i = 1\n\n\ndef parser_add_version_opt(parser, mod_name, include_name=False, delay=False):\n    \"\"\"Setup --version option\n\n    Parameters\n    ----------\n    parser:\n    mod_name: str, optional\n    include_name: bool, optional\n    delay: bool, optional\n      If set to True, no action is taken immediately, and rather\n      we assign the function which would print the version. Necessary for\n      early pre-parsing of the cmdline\n    \"\"\"\n\n    def print_version():\n        mod = sys.modules.get(mod_name, None)\n        version = getattr(mod, '__version__', None)\n        if version is None:\n            # Let's use the standard Python mechanism if underlying module\n            # did not provide __version__\n            try:\n                import pkg_resources\n                version = pkg_resources.get_distribution(mod_name).version\n            except:\n                version = \"unknown\"\n        if include_name:\n            print(\"%s %s\" % (mod_name, version))\n        else:\n            print(version)\n        sys.exit(0)\n\n    class versionAction(argparse.Action):\n        def __call__(self, parser, args, values, option_string=None):\n            if delay:\n                setattr(args, self.dest, print_version)\n            else:\n                print_version()\n\n    parser.add_argument(\n        \"--version\",\n        nargs=0,\n        action=versionAction,\n        help=(\n            \"show the program's version\"\n            if not mod_name\n            else \"show the module and its version which provides the command\")\n    )\n\n\ndef parser_add_common_opt(parser, opt, names=None, **kwargs):\n    from . import common_args\n    opt_tmpl = getattr(common_args, opt)\n    opt_kwargs = opt_tmpl[2].copy()\n    opt_kwargs.update(kwargs)\n    if names is None:\n        parser.add_argument(*opt_tmpl[1], **opt_kwargs)\n    else:\n        parser.add_argument(*names, **opt_kwargs)\n\n\ndef parser_add_common_options(parser, version=None):\n    parser_add_common_opt(parser, 'log_level')\n    parser_add_common_opt(parser, 'pbs_runner')\n    parser_add_common_opt(parser, 'change_path')\n    if version is not None:\n        warnings.warn(\"Passing 'version' to parser_add_common_options \"\n                      \"no longer has an effect \"\n                      \"and will be removed in a future release.\",\n                      DeprecationWarning)\n    parser_add_version_opt(parser, 'datalad', include_name=False, delay=True)\n    if __debug__:\n        parser.add_argument(\n            '--dbg', action='store_true', dest='common_debug',\n            help=\"enter Python debugger when uncaught exception happens\")\n        parser.add_argument(\n            '--idbg', action='store_true', dest='common_idebug',\n            help=\"enter IPython debugger when uncaught exception happens\")\n    parser.add_argument(\n        '-c', action='append', dest='cfg_overrides', metavar='KEY=VALUE',\n        help=\"\"\"configuration variable setting. Overrides any configuration\n        read from a file, but is potentially overridden itself by configuration\n        variables in the process environment.\"\"\")\n    parser.add_argument(\n        '-f', '--output-format', dest='common_output_format',\n        default='tailored',\n        type=ensure_unicode,\n        metavar=\"{default,json,json_pp,tailored,'<template>'}\",\n        help=\"\"\"select format for returned command results. 'tailored'\n        enables a command-specific rendering style that is typically\n        tailored to human consumption, if there is one for a specific\n        command, or otherwise falls back on the the 'default' output\n        format (this is the standard behavior); 'default' give one line\n        per result reporting action, status, path and an optional message;\n        'json' renders a JSON object with all properties for each result (one per\n        line); 'json_pp' pretty-prints JSON spanning multiple lines;\n        '<template>' reports any value(s) of any result properties in any format\n        indicated by the template (e.g. '{path}'; compare with JSON\n        output for all key-value choices). The template syntax follows the Python\n        \"format() language\". It is possible to report individual\n        dictionary values, e.g. '{metadata[name]}'. If a 2nd-level key contains\n        a colon, e.g. 'music:Genre', ':' must be substituted by '#' in the template,\n        like so: '{metadata[music#Genre]}'.\"\"\")\n    parser.add_argument(\n        '--report-status', dest='common_report_status',\n        choices=['success', 'failure', 'ok', 'notneeded', 'impossible', 'error'],\n        help=\"\"\"constrain command result report to records matching the given\n        status. 'success' is a synonym for 'ok' OR 'notneeded', 'failure' stands\n        for 'impossible' OR 'error'.\"\"\")\n    parser.add_argument(\n        '--report-type', dest='common_report_type',\n        choices=['dataset', 'file'],\n        action='append',\n        help=\"\"\"constrain command result report to records matching the given\n        type. Can be given more than once to match multiple types.\"\"\")\n    parser.add_argument(\n        '--on-failure', dest='common_on_failure',\n        choices=['ignore', 'continue', 'stop'],\n        # no default: better be configure per-command\n        help=\"\"\"when an operation fails: 'ignore' and continue with remaining\n        operations, the error is logged but does not lead to a non-zero exit code\n        of the command; 'continue' works like 'ignore', but an error causes a\n        non-zero exit code; 'stop' halts on first failure and yields non-zero exit\n        code. A failure is any result with status 'impossible' or 'error'.\"\"\")\n    parser.add_argument(\n        '--cmd', dest='_', action='store_true',\n        help=\"\"\"syntactical helper that can be used to end the list of global\n        command line options before the subcommand label. Options taking\n        an arbitrary number of arguments may require to be followed by a single\n        --cmd in order to enable identification of the subcommand.\"\"\")\n\n\ndef strip_arg_from_argv(args, value, opt_names):\n    \"\"\"Strip an originally listed option (with its value) from the list cmdline args\n    \"\"\"\n    # Yarik doesn't know better\n    if args is None:\n        args = sys.argv\n    # remove present pbs-runner option\n    args_clean = []\n    skip = 0\n    for i, arg in enumerate(args):\n        if skip:\n            # we skip only one as instructed\n            skip -= 1\n            continue\n        if not (arg in opt_names and i < len(args) - 1 and args[i + 1] == value):\n            args_clean.append(arg)\n        else:\n            # we need to skip this one and next one\n            skip = 1\n    return args_clean\n\n\ndef run_via_pbs(args, pbs):\n    assert(pbs in ('condor',))  # for now\n\n    # TODO: RF to support multiple backends, parameters, etc, for now -- just condor, no options\n    f = NamedTemporaryFile('w', prefix='datalad-%s-' % pbs, suffix='.submit', delete=False)\n    try:\n        pwd = getpwd()\n        logs = f.name.replace('.submit', '.log')\n        exe = args[0]\n        # TODO: we might need better way to join them, escaping spaces etc.  There must be a stock helper\n        #exe_args = ' '.join(map(repr, args[1:])) if len(args) > 1 else ''\n        exe_args = ' '.join(args[1:]) if len(args) > 1 else ''\n        f.write(\"\"\"\\\nExecutable = %(exe)s\nInitialdir = %(pwd)s\nOutput = %(logs)s\nError = %(logs)s\ngetenv = True\n\narguments = %(exe_args)s\nqueue\n\"\"\" % locals())\n        f.close()\n        Runner().run(['condor_submit', f.name])\n        lgr.info(\"Scheduled execution via %s.  Logs will be stored under %s\", pbs, logs)\n    finally:\n        unlink(f.name)\n\n\n# TODO: useful also outside of cmdline, move to support/\nfrom os import curdir\n\n\ndef get_repo_instance(path=curdir, class_=None):\n    \"\"\"Returns an instance of appropriate datalad repository for path.\n    Check whether a certain path is inside a known type of repository and\n    returns an instance representing it. May also check for a certain type\n    instead of detecting the type of repository.\n\n    Parameters\n    ----------\n    path: str\n      path to check; default: current working directory\n    class_: class\n      if given, check whether path is inside a repository, that can be\n      represented as an instance of the passed class.\n\n    Raises\n    ------\n    RuntimeError, in case cwd is not inside a known repository.\n    \"\"\"\n\n    from os.path import ismount, exists, normpath, isabs\n    from datalad.support.exceptions import InvalidGitRepositoryError\n    from ..utils import expandpath\n    from ..support.gitrepo import GitRepo\n    from ..support.annexrepo import AnnexRepo\n\n    dir_ = expandpath(path)\n    abspath_ = path if isabs(path) else dir_\n    if class_ is not None:\n        if class_ == AnnexRepo:\n            type_ = \"annex\"\n        elif class_ == GitRepo:\n            type_ = \"git\"\n        else:\n            raise RuntimeError(\"Unknown class %s.\" % str(class_))\n\n    while not ismount(dir_):  # TODO: always correct termination?\n        if exists(opj(dir_, '.git')):\n            # found git dir\n            if class_ is None:\n                # detect repo type:\n                try:\n                    return AnnexRepo(dir_, create=False)\n                except RuntimeError as e:\n                    pass\n                try:\n                    return GitRepo(dir_, create=False)\n                except InvalidGitRepositoryError as e:\n                    raise RuntimeError(\"No datalad repository found in %s\" %\n                                       abspath_)\n            else:\n                try:\n                    return class_(dir_, create=False)\n                except (RuntimeError, InvalidGitRepositoryError) as e:\n                    raise RuntimeError(\"No %s repository found in %s.\" %\n                                       (type_, abspath_))\n        else:\n            dir_ = normpath(opj(dir_, \"..\"))\n\n    if class_ is not None:\n        raise RuntimeError(\"No %s repository found in %s\" % (type_, abspath_))\n    else:\n        raise RuntimeError(\"No datalad repository found in %s\" % abspath_)\n\n\nfrom appdirs import AppDirs\nfrom os.path import join as opj\n\ndirs = AppDirs(\"datalad\", \"datalad.org\")\n",
            "new_file_content": "# emacs: -*- mode: python; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-\n# ex: set sts=4 ts=4 sw=4 noet:\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n#\n#   See COPYING file distributed along with the datalad package for the\n#   copyright and license terms.\n#\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n\"\"\"\n\"\"\"\n\n__docformat__ = 'restructuredtext'\n\nimport argparse\nimport os\nimport re\nimport sys\nimport gzip\nimport warnings\nfrom tempfile import NamedTemporaryFile\nfrom textwrap import wrap\n\nfrom ..cmd import WitlessRunner as Runner\nfrom ..log import is_interactive\nfrom ..utils import (\n    ensure_unicode,\n    getpwd,\n    unlink,\n)\nfrom ..version import __version__\nfrom ..dochelpers import exc_str\n\nfrom logging import getLogger\nlgr = getLogger('datalad.cmdline')\n\n\nclass HelpAction(argparse.Action):\n    def __call__(self, parser, namespace, values, option_string=None):\n        # Lets use the manpage on mature systems but only for subcommands --\n        # --help should behave similar to how git does it:\n        # regular --help for \"git\" but man pages for specific commands.\n        # It is important since we do discover all subcommands from entry\n        # points at run time and thus any static manpage would like be out of\n        # date\n        interactive = is_interactive()\n        if interactive \\\n                and option_string == '--help' \\\n                and ' ' in parser.prog:  # subcommand\n            try:\n                import subprocess\n                # get the datalad manpage to use\n                manfile = os.environ.get('MANPATH', '/usr/share/man') \\\n                    + '/man1/{0}.1.gz'.format(parser.prog.replace(' ', '-'))\n                # extract version field from the manpage\n                if not os.path.exists(manfile):\n                    raise IOError(\"manfile is not found\")\n                with gzip.open(manfile) as f:\n                    man_th = [line for line in f if line.startswith(b\".TH\")][0]\n                man_version = man_th.split(b' ')[-1].strip(b\" '\\\"\\t\\n\").decode('utf-8')\n\n                # don't show manpage if man_version not equal to current datalad_version\n                if __version__ != man_version:\n                    raise ValueError\n                subprocess.check_call(\n                    'man %s 2> /dev/null' % manfile,\n                    shell=True)\n                sys.exit(0)\n            except (subprocess.CalledProcessError, IOError, OSError, IndexError, ValueError) as e:\n                lgr.debug(\"Did not use manpage since %s\", exc_str(e))\n        if option_string == '-h':\n            usage = parser.format_usage()\n            ucomps = re.match(\n                r'(?P<pre>.*){(?P<cmds>.*)}(?P<post>....*)',\n                usage,\n                re.DOTALL)\n            if ucomps:\n                ucomps = ucomps.groupdict()\n                indent_level = len(ucomps['post']) - len(ucomps['post'].lstrip())\n                usage = '{pre}{{{cmds}}}{post}'.format(\n                    pre=ucomps['pre'],\n                    cmds='\\n'.join(wrap(\n                        ', '.join(sorted(c.strip() for c in ucomps['cmds'].split(','))),\n                        break_on_hyphens=False,\n                        subsequent_indent=' ' * indent_level)),\n                    post=ucomps['post'],\n                )\n            helpstr = \"%s\\n%s\" % (\n                usage,\n                \"Use '--help' to get more comprehensive information.\")\n        else:\n            helpstr = parser.format_help()\n        # better for help2man\n        # for main command -- should be different sections. And since we are in\n        # heavy output massaging mode...\n        if \"commands for dataset operations\" in helpstr.lower():\n            opt_args_str = '*Global options*'\n            pos_args_str = '*Commands*'\n            # tune up usage -- default one is way too heavy\n            helpstr = re.sub(r'^[uU]sage: .*?\\n\\s*\\n',\n                             'Usage: datalad [global-opts] command [command-opts]\\n\\n',\n                             helpstr,\n                             flags=re.MULTILINE | re.DOTALL)\n            # and altogether remove sections with long list of commands\n            helpstr = re.sub(r'positional arguments:\\s*\\n\\s*{.*}\\n', '', helpstr)\n        else:\n            opt_args_str = \"*Options*\"\n            pos_args_str = \"*Arguments*\"\n        helpstr = re.sub(r'optional arguments:', opt_args_str, helpstr)\n        helpstr = re.sub(r'positional arguments:', pos_args_str, helpstr)\n        # usage is on the same line\n        helpstr = re.sub(r'^usage:', 'Usage:', helpstr)\n\n        if interactive and option_string == '--help':\n            import pydoc\n            pydoc.pager(helpstr)\n        else:\n            print(helpstr)\n        sys.exit(0)\n\n\nclass LogLevelAction(argparse.Action):\n    def __call__(self, parser, namespace, values, option_string=None):\n        from ..log import LoggerHelper\n        LoggerHelper().set_level(level=values)\n\n\n# MIH: Disabled. Non-functional, untested.\n#class PBSAction(argparse.Action):\n#    \"\"\"Action to schedule actual command execution via PBS (e.g. Condor)\"\"\"\n#    def __call__(self, parser, namespace, values, option_string=None):\n#        pbs = values[0]\n#        import pdb; pdb.set_trace()\n#        i = 1\n\n\ndef parser_add_version_opt(parser, mod_name, include_name=False, delay=False):\n    \"\"\"Setup --version option\n\n    Parameters\n    ----------\n    parser:\n    mod_name: str, optional\n    include_name: bool, optional\n    delay: bool, optional\n      If set to True, no action is taken immediately, and rather\n      we assign the function which would print the version. Necessary for\n      early pre-parsing of the cmdline\n    \"\"\"\n\n    def print_version():\n        mod = sys.modules.get(mod_name, None)\n        version = getattr(mod, '__version__', None)\n        if version is None:\n            # Let's use the standard Python mechanism if underlying module\n            # did not provide __version__\n            try:\n                import pkg_resources\n                version = pkg_resources.get_distribution(mod_name).version\n            except:\n                version = \"unknown\"\n        if include_name:\n            print(\"%s %s\" % (mod_name, version))\n        else:\n            print(version)\n        sys.exit(0)\n\n    class versionAction(argparse.Action):\n        def __call__(self, parser, args, values, option_string=None):\n            if delay:\n                setattr(args, self.dest, print_version)\n            else:\n                print_version()\n\n    parser.add_argument(\n        \"--version\",\n        nargs=0,\n        action=versionAction,\n        help=(\n            \"show the program's version\"\n            if not mod_name\n            else \"show the module and its version which provides the command\")\n    )\n\n\ndef parser_add_common_opt(parser, opt, names=None, **kwargs):\n    from . import common_args\n    opt_tmpl = getattr(common_args, opt)\n    opt_kwargs = opt_tmpl[2].copy()\n    opt_kwargs.update(kwargs)\n    if names is None:\n        parser.add_argument(*opt_tmpl[1], **opt_kwargs)\n    else:\n        parser.add_argument(*names, **opt_kwargs)\n\n\ndef parser_add_common_options(parser, version=None):\n    parser_add_common_opt(parser, 'log_level')\n    parser_add_common_opt(parser, 'pbs_runner')\n    parser_add_common_opt(parser, 'change_path')\n    if version is not None:\n        warnings.warn(\"Passing 'version' to parser_add_common_options \"\n                      \"no longer has an effect \"\n                      \"and will be removed in a future release.\",\n                      DeprecationWarning)\n    parser_add_version_opt(parser, 'datalad', include_name=True, delay=True)\n    if __debug__:\n        parser.add_argument(\n            '--dbg', action='store_true', dest='common_debug',\n            help=\"enter Python debugger when uncaught exception happens\")\n        parser.add_argument(\n            '--idbg', action='store_true', dest='common_idebug',\n            help=\"enter IPython debugger when uncaught exception happens\")\n    parser.add_argument(\n        '-c', action='append', dest='cfg_overrides', metavar='KEY=VALUE',\n        help=\"\"\"configuration variable setting. Overrides any configuration\n        read from a file, but is potentially overridden itself by configuration\n        variables in the process environment.\"\"\")\n    parser.add_argument(\n        '-f', '--output-format', dest='common_output_format',\n        default='tailored',\n        type=ensure_unicode,\n        metavar=\"{default,json,json_pp,tailored,'<template>'}\",\n        help=\"\"\"select format for returned command results. 'tailored'\n        enables a command-specific rendering style that is typically\n        tailored to human consumption, if there is one for a specific\n        command, or otherwise falls back on the the 'default' output\n        format (this is the standard behavior); 'default' give one line\n        per result reporting action, status, path and an optional message;\n        'json' renders a JSON object with all properties for each result (one per\n        line); 'json_pp' pretty-prints JSON spanning multiple lines;\n        '<template>' reports any value(s) of any result properties in any format\n        indicated by the template (e.g. '{path}'; compare with JSON\n        output for all key-value choices). The template syntax follows the Python\n        \"format() language\". It is possible to report individual\n        dictionary values, e.g. '{metadata[name]}'. If a 2nd-level key contains\n        a colon, e.g. 'music:Genre', ':' must be substituted by '#' in the template,\n        like so: '{metadata[music#Genre]}'.\"\"\")\n    parser.add_argument(\n        '--report-status', dest='common_report_status',\n        choices=['success', 'failure', 'ok', 'notneeded', 'impossible', 'error'],\n        help=\"\"\"constrain command result report to records matching the given\n        status. 'success' is a synonym for 'ok' OR 'notneeded', 'failure' stands\n        for 'impossible' OR 'error'.\"\"\")\n    parser.add_argument(\n        '--report-type', dest='common_report_type',\n        choices=['dataset', 'file'],\n        action='append',\n        help=\"\"\"constrain command result report to records matching the given\n        type. Can be given more than once to match multiple types.\"\"\")\n    parser.add_argument(\n        '--on-failure', dest='common_on_failure',\n        choices=['ignore', 'continue', 'stop'],\n        # no default: better be configure per-command\n        help=\"\"\"when an operation fails: 'ignore' and continue with remaining\n        operations, the error is logged but does not lead to a non-zero exit code\n        of the command; 'continue' works like 'ignore', but an error causes a\n        non-zero exit code; 'stop' halts on first failure and yields non-zero exit\n        code. A failure is any result with status 'impossible' or 'error'.\"\"\")\n    parser.add_argument(\n        '--cmd', dest='_', action='store_true',\n        help=\"\"\"syntactical helper that can be used to end the list of global\n        command line options before the subcommand label. Options taking\n        an arbitrary number of arguments may require to be followed by a single\n        --cmd in order to enable identification of the subcommand.\"\"\")\n\n\ndef strip_arg_from_argv(args, value, opt_names):\n    \"\"\"Strip an originally listed option (with its value) from the list cmdline args\n    \"\"\"\n    # Yarik doesn't know better\n    if args is None:\n        args = sys.argv\n    # remove present pbs-runner option\n    args_clean = []\n    skip = 0\n    for i, arg in enumerate(args):\n        if skip:\n            # we skip only one as instructed\n            skip -= 1\n            continue\n        if not (arg in opt_names and i < len(args) - 1 and args[i + 1] == value):\n            args_clean.append(arg)\n        else:\n            # we need to skip this one and next one\n            skip = 1\n    return args_clean\n\n\ndef run_via_pbs(args, pbs):\n    assert(pbs in ('condor',))  # for now\n\n    # TODO: RF to support multiple backends, parameters, etc, for now -- just condor, no options\n    f = NamedTemporaryFile('w', prefix='datalad-%s-' % pbs, suffix='.submit', delete=False)\n    try:\n        pwd = getpwd()\n        logs = f.name.replace('.submit', '.log')\n        exe = args[0]\n        # TODO: we might need better way to join them, escaping spaces etc.  There must be a stock helper\n        #exe_args = ' '.join(map(repr, args[1:])) if len(args) > 1 else ''\n        exe_args = ' '.join(args[1:]) if len(args) > 1 else ''\n        f.write(\"\"\"\\\nExecutable = %(exe)s\nInitialdir = %(pwd)s\nOutput = %(logs)s\nError = %(logs)s\ngetenv = True\n\narguments = %(exe_args)s\nqueue\n\"\"\" % locals())\n        f.close()\n        Runner().run(['condor_submit', f.name])\n        lgr.info(\"Scheduled execution via %s.  Logs will be stored under %s\", pbs, logs)\n    finally:\n        unlink(f.name)\n\n\n# TODO: useful also outside of cmdline, move to support/\nfrom os import curdir\n\n\ndef get_repo_instance(path=curdir, class_=None):\n    \"\"\"Returns an instance of appropriate datalad repository for path.\n    Check whether a certain path is inside a known type of repository and\n    returns an instance representing it. May also check for a certain type\n    instead of detecting the type of repository.\n\n    Parameters\n    ----------\n    path: str\n      path to check; default: current working directory\n    class_: class\n      if given, check whether path is inside a repository, that can be\n      represented as an instance of the passed class.\n\n    Raises\n    ------\n    RuntimeError, in case cwd is not inside a known repository.\n    \"\"\"\n\n    from os.path import ismount, exists, normpath, isabs\n    from datalad.support.exceptions import InvalidGitRepositoryError\n    from ..utils import expandpath\n    from ..support.gitrepo import GitRepo\n    from ..support.annexrepo import AnnexRepo\n\n    dir_ = expandpath(path)\n    abspath_ = path if isabs(path) else dir_\n    if class_ is not None:\n        if class_ == AnnexRepo:\n            type_ = \"annex\"\n        elif class_ == GitRepo:\n            type_ = \"git\"\n        else:\n            raise RuntimeError(\"Unknown class %s.\" % str(class_))\n\n    while not ismount(dir_):  # TODO: always correct termination?\n        if exists(opj(dir_, '.git')):\n            # found git dir\n            if class_ is None:\n                # detect repo type:\n                try:\n                    return AnnexRepo(dir_, create=False)\n                except RuntimeError as e:\n                    pass\n                try:\n                    return GitRepo(dir_, create=False)\n                except InvalidGitRepositoryError as e:\n                    raise RuntimeError(\"No datalad repository found in %s\" %\n                                       abspath_)\n            else:\n                try:\n                    return class_(dir_, create=False)\n                except (RuntimeError, InvalidGitRepositoryError) as e:\n                    raise RuntimeError(\"No %s repository found in %s.\" %\n                                       (type_, abspath_))\n        else:\n            dir_ = normpath(opj(dir_, \"..\"))\n\n    if class_ is not None:\n        raise RuntimeError(\"No %s repository found in %s\" % (type_, abspath_))\n    else:\n        raise RuntimeError(\"No datalad repository found in %s\" % abspath_)\n\n\nfrom appdirs import AppDirs\nfrom os.path import join as opj\n\ndirs = AppDirs(\"datalad\", \"datalad.org\")\n",
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                                "content": "    parser_add_version_opt(parser, 'datalad', include_name=False, delay=True)",
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                                "content": "    parser_add_version_opt(parser, 'datalad', include_name=True, delay=True)",
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                            "name": "parser_add_common_options",
                            "content": "def parser_add_common_options(parser, version=None):\n    parser_add_common_opt(parser, 'log_level')\n    parser_add_common_opt(parser, 'pbs_runner')\n    parser_add_common_opt(parser, 'change_path')\n    if version is not None:\n        warnings.warn(\"Passing 'version' to parser_add_common_options \"\n                      \"no longer has an effect \"\n                      \"and will be removed in a future release.\",\n                      DeprecationWarning)\n    parser_add_version_opt(parser, 'datalad', include_name=False, delay=True)\n    if __debug__:\n        parser.add_argument(\n            '--dbg', action='store_true', dest='common_debug',\n            help=\"enter Python debugger when uncaught exception happens\")\n        parser.add_argument(\n            '--idbg', action='store_true', dest='common_idebug',\n            help=\"enter IPython debugger when uncaught exception happens\")\n    parser.add_argument(\n        '-c', action='append', dest='cfg_overrides', metavar='KEY=VALUE',\n        help=\"\"\"configuration variable setting. Overrides any configuration\n        read from a file, but is potentially overridden itself by configuration\n        variables in the process environment.\"\"\")\n    parser.add_argument(\n        '-f', '--output-format', dest='common_output_format',\n        default='tailored',\n        type=ensure_unicode,\n        metavar=\"{default,json,json_pp,tailored,'<template>'}\",\n        help=\"\"\"select format for returned command results. 'tailored'\n        enables a command-specific rendering style that is typically\n        tailored to human consumption, if there is one for a specific\n        command, or otherwise falls back on the the 'default' output\n        format (this is the standard behavior); 'default' give one line\n        per result reporting action, status, path and an optional message;\n        'json' renders a JSON object with all properties for each result (one per\n        line); 'json_pp' pretty-prints JSON spanning multiple lines;\n        '<template>' reports any value(s) of any result properties in any format\n        indicated by the template (e.g. '{path}'; compare with JSON\n        output for all key-value choices). The template syntax follows the Python\n        \"format() language\". It is possible to report individual\n        dictionary values, e.g. '{metadata[name]}'. If a 2nd-level key contains\n        a colon, e.g. 'music:Genre', ':' must be substituted by '#' in the template,\n        like so: '{metadata[music#Genre]}'.\"\"\")\n    parser.add_argument(\n        '--report-status', dest='common_report_status',\n        choices=['success', 'failure', 'ok', 'notneeded', 'impossible', 'error'],\n        help=\"\"\"constrain command result report to records matching the given\n        status. 'success' is a synonym for 'ok' OR 'notneeded', 'failure' stands\n        for 'impossible' OR 'error'.\"\"\")\n    parser.add_argument(\n        '--report-type', dest='common_report_type',\n        choices=['dataset', 'file'],\n        action='append',\n        help=\"\"\"constrain command result report to records matching the given\n        type. Can be given more than once to match multiple types.\"\"\")\n    parser.add_argument(\n        '--on-failure', dest='common_on_failure',\n        choices=['ignore', 'continue', 'stop'],\n        # no default: better be configure per-command\n        help=\"\"\"when an operation fails: 'ignore' and continue with remaining\n        operations, the error is logged but does not lead to a non-zero exit code\n        of the command; 'continue' works like 'ignore', but an error causes a\n        non-zero exit code; 'stop' halts on first failure and yields non-zero exit\n        code. A failure is any result with status 'impossible' or 'error'.\"\"\")\n    parser.add_argument(\n        '--cmd', dest='_', action='store_true',\n        help=\"\"\"syntactical helper that can be used to end the list of global\n        command line options before the subcommand label. Options taking\n        an arbitrary number of arguments may require to be followed by a single\n        --cmd in order to enable identification of the subcommand.\"\"\")",
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            "old_file_content": "# emacs: -*- mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-\n# ex: set sts=4 ts=4 sw=4 noet:\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n#\n#   See COPYING file distributed along with the datalad package for the\n#   copyright and license terms.\n#\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n\"\"\"Test functioning of the datalad main cmdline utility \"\"\"\n\nimport os\nimport re\nimport sys\nfrom io import StringIO\nfrom unittest.mock import patch\n\nimport datalad\nfrom ..main import (\n    main,\n    fail_with_short_help,\n    _fix_datalad_ri,\n)\nfrom datalad import __version__\nfrom datalad.cmd import (\n    WitlessRunner as Runner,\n    StdOutErrCapture,\n)\nfrom datalad.ui.utils import (\n    get_console_width,\n    get_terminal_size,\n)\nfrom datalad.api import create\nfrom datalad.utils import (\n    chpwd,\n    Path,\n)\nfrom datalad.tests.utils import (\n    SkipTest,\n    assert_equal,\n    assert_in,\n    assert_not_in,\n    assert_raises,\n    assert_re_in,\n    eq_,\n    in_,\n    ok_startswith,\n    on_windows,\n    slow,\n    with_tempfile,\n)\n\n\ndef run_main(args, exit_code=0, expect_stderr=False):\n    \"\"\"Run main() of the datalad, do basic checks and provide outputs\n\n    Parameters\n    ----------\n    args : list\n        List of string cmdline arguments to pass\n    exit_code : int\n        Expected exit code. Would raise AssertionError if differs\n    expect_stderr : bool or string\n        Whether to expect stderr output. If string -- match\n\n    Returns\n    -------\n    stdout, stderr  strings\n       Output produced\n    \"\"\"\n    with patch('sys.stderr', new_callable=StringIO) as cmerr:\n        with patch('sys.stdout', new_callable=StringIO) as cmout:\n            with assert_raises(SystemExit) as cm:\n                main([\"datalad\"] + list(args))\n            assert_equal(cm.exception.code, exit_code)\n            stdout = cmout.getvalue()\n            stderr = cmerr.getvalue()\n            if expect_stderr is False:\n                assert_equal(stderr, \"\")\n            elif expect_stderr is True:\n                # do nothing -- just return\n                pass\n            else:\n                # must be a string\n                assert_equal(stderr, expect_stderr)\n    return stdout, stderr\n\n\n# TODO: switch to stdout for --version output\ndef test_version():\n    # we just get a version if not asking for a version of some command\n    stdout, stderr = run_main(['--version'], expect_stderr=True)\n    eq_(stdout.rstrip(), datalad.__version__)\n\n    stdout, stderr = run_main(['clone', '--version'], expect_stderr=True)\n    ok_startswith(stdout, 'datalad %s\\n' % datalad.__version__)\n    # since https://github.com/datalad/datalad/pull/2733 no license in --version\n    assert_not_in(\"Copyright\", stdout)\n    assert_not_in(\"Permission is hereby granted\", stdout)\n\n    try:\n        import datalad_container\n    except ImportError:\n        pass  # not installed, cannot test with extension\n    else:\n        stdout, stderr = run_main(['containers-list', '--version'], expect_stderr=True)\n        eq_(stdout, 'datalad_container %s\\n' % datalad_container.__version__)\n\n\ndef test_help_np():\n    stdout, stderr = run_main(['--help-np'])\n\n    # Let's extract section titles:\n    # enough of bin/datalad and .tox/py27/bin/datalad -- guarantee consistency! ;)\n    ok_startswith(stdout, 'Usage: datalad')\n    # Sections start/end with * if ran under DATALAD_HELP2MAN mode\n    sections = [l[1:-1] for l in filter(re.compile('^\\*.*\\*$').match, stdout.split('\\n'))]\n    # but order is still not guaranteed (dict somewhere)! TODO\n    # see https://travis-ci.org/datalad/datalad/jobs/80519004\n    # thus testing sets\n    for s in {'Commands for dataset operations',\n              'Commands for metadata handling',\n              'Miscellaneous commands',\n              'General information',\n              'Global options',\n              'Plumbing commands',\n              'Plugins'}:\n        assert_in(s, sections)\n\n    if not get_terminal_size()[0] or 0:\n        raise SkipTest(\n            \"Could not determine terminal size, skipping the rest of the test\")\n\n    # none of the lines must be longer than 80 chars\n    # TODO: decide on   create-sibling and possibly\n    # rewrite-urls\n    accepted_width = get_console_width()\n\n    long_lines = [\"%d %s\" % (len(l), l) for l in stdout.split('\\n')\n                  if len(l) > accepted_width and\n                  '{' not in l  # on nd70 summary line is unsplit\n                  ]\n    if long_lines:\n        raise AssertionError(\n            \"Following lines in --help output were longer than %s chars:\\n%s\"\n            % (accepted_width, '\\n'.join(long_lines))\n        )\n\n\ndef test_usage_on_insufficient_args():\n    stdout, stderr = run_main(['install'], exit_code=2, expect_stderr=True)\n    ok_startswith(stderr, 'usage:')\n\n\ndef test_subcmd_usage_on_unknown_args():\n    stdout, stderr = run_main(['get', '--murks'], exit_code=1, expect_stderr=True)\n    in_('get', stdout)\n\n\ndef test_combined_short_option():\n    stdout, stderr = run_main(['-fjson'], exit_code=2, expect_stderr=True)\n    assert_not_in(\"unrecognized argument\", stderr)\n    assert_in(\"too few arguments\", stderr)\n\n\ndef check_incorrect_option(opts, err_str):\n    # The first line used to be:\n    # stdout, stderr = run_main((sys.argv[0],) + opts, expect_stderr=True, exit_code=2)\n    # But: what do we expect to be in sys.argv[0] here?\n    # It depends on how we invoke the test.\n    # - nosetests -s -v datalad/cmdline/tests/test_main.py would result in:\n    #   sys.argv[0}=='nosetests'\n    # - python -m nose -s -v datalad/cmdline/tests/test_main.py would result in:\n    #   sys.argv[0}=='python -m nose'\n    # - python -c \"import nose; nose.main()\" -s -v datalad/cmdline/tests/test_main.py would result in:\n    #   sys.argv[0]=='-c'\n    # This led to failure in case sys.argv[0] contained an option, that was\n    # defined to be a datalad option too, therefore was a 'known_arg' and was\n    # checked to meet its constraints.\n    # But sys.argv[0] actually isn't used by main at all. It simply doesn't\n    # matter what's in there. The only thing important to pass here is `opts`.\n    stdout, stderr = run_main(opts, expect_stderr=True, exit_code=2)\n    out = stdout + stderr\n    assert_in(\"usage: \", out)\n    assert_re_in(err_str, out, match=False)\n\n\ndef test_incorrect_options():\n    # apparently a bit different if following a good one so let's do both\n    err_invalid = \"error: (invalid|too few arguments|unrecognized argument)\"\n    yield check_incorrect_option, ('--buga',), err_invalid\n    yield check_incorrect_option, ('--dbg', '--buga'), err_invalid\n\n    err_insufficient = err_invalid  # \"specify\"\n    yield check_incorrect_option, ('--dbg',), err_insufficient\n    yield check_incorrect_option, tuple(), err_insufficient\n\n\ndef test_script_shims():\n    runner = Runner()\n    # The EASY-INSTALL checks below aren't valid for editable installs. Use the\n    # existence of setup.py as an indication that install is _probably_\n    # editable. The file should always exist for editable installs, but it can\n    # also exist for non-editable installs when the tests are being executed\n    # from the top of the source tree.\n    setup_exists = (Path(datalad.__file__).parent.parent / \"setup.py\").exists()\n    for script in [\n        'datalad',\n        'git-annex-remote-datalad-archives',\n        'git-annex-remote-datalad']:\n        if not on_windows:\n            # those must be available for execution, and should not contain\n            which = runner.run(['which', script], protocol=StdOutErrCapture)['stdout']\n            # test if there is no easy install shim in there\n            with open(which.rstrip()) as f:\n                content = f.read()\n        else:\n            from distutils.spawn import find_executable\n            content = find_executable(script)\n\n        if not setup_exists:\n            assert_not_in('EASY', content) # NOTHING easy should be there\n            assert_not_in('pkg_resources', content)\n\n        # and let's check that it is our script\n        out = runner.run([script, '--version'], protocol=StdOutErrCapture)\n        version = out['stdout'].rstrip()\n        if script != 'datalad':\n            # datalad --version  would return only version now, but all the `datalad CMD` and\n            # other entry points will still announce their origin, so we would need to strip\n            # it away\n            mod, version = version.split(' ', 1)\n            assert_equal(mod, 'datalad')\n        # we can get git and non git .dev version... so for now\n        # relax\n        get_numeric_portion = lambda v: [x for x in v.split('.') if x.isdigit()]\n        # extract numeric portion\n        assert get_numeric_portion(version) # that my lambda is correctish\n        assert_equal(get_numeric_portion(__version__),\n                     get_numeric_portion(version))\n\n\n@slow  # 11.2591s\n@with_tempfile(mkdir=True)\ndef test_cfg_override(path):\n    with chpwd(path):\n        cmd = ['datalad', 'wtf', '-s', 'some']\n        # control\n        out = Runner().run(cmd, protocol=StdOutErrCapture)['stdout']\n        assert_not_in('datalad.dummy: this', out)\n        # ensure that this is not a dataset's cfg manager\n        assert_not_in('datalad.dataset.id', out)\n        # env var\n        out = Runner(env=dict(os.environ, DATALAD_DUMMY='this')).run(\n            cmd, protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n        # cmdline arg\n        out = Runner().run([cmd[0], '-c', 'datalad.dummy=this'] + cmd[1:],\n                           protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n\n        # now create a dataset in the path. the wtf plugin will switch to\n        # using the dataset's config manager, which must inherit the overrides\n        create(dataset=path)\n        # control\n        out = Runner().run(cmd, protocol=StdOutErrCapture)['stdout']\n        assert_not_in('datalad.dummy: this', out)\n        # ensure that this is a dataset's cfg manager\n        assert_in('datalad.dataset.id', out)\n        # env var\n        out = Runner(env=dict(os.environ, DATALAD_DUMMY='this')).run(\n            cmd, protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n        # cmdline arg\n        out = Runner().run([cmd[0], '-c', 'datalad.dummy=this'] + cmd[1:],\n                           protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n\n\ndef test_incorrect_cfg_override():\n    run_main(['-c', 'some', 'wtf'], exit_code=3)\n    run_main(['-c', 'some=', 'wtf'], exit_code=3)\n    run_main(['-c', 'some.var', 'wtf'], exit_code=3)\n    run_main(['-c', 'some.var=', 'wtf'], exit_code=3)\n\n\ndef test_fail_with_short_help():\n    out = StringIO()\n    with assert_raises(SystemExit) as cme:\n        fail_with_short_help(exit_code=3, out=out)\n    assert_equal(cme.exception.code, 3)\n    assert_equal(out.getvalue(), \"\")\n\n    out = StringIO()\n    with assert_raises(SystemExit) as cme:\n        fail_with_short_help(msg=\"Failed badly\", out=out)\n    assert_equal(cme.exception.code, 1)\n    assert_equal(out.getvalue(), \"error: Failed badly\\n\")\n\n    # Suggestions, hint, etc\n    out = StringIO()\n    with assert_raises(SystemExit) as cme:\n        fail_with_short_help(\n            msg=\"Failed badly\",\n            known=[\"mother\", \"mutter\", \"father\", \"son\"],\n            provided=\"muther\",\n            hint=\"You can become one\",\n            exit_code=0,  # noone forbids\n            what=\"parent\",\n            out=out)\n    assert_equal(cme.exception.code, 0)\n    assert_equal(out.getvalue(),\n                 \"error: Failed badly\\n\"\n                 \"datalad: Unknown parent 'muther'.  See 'datalad --help'.\\n\\n\"\n                 \"Did you mean any of these?\\n\"\n                 \"        mutter\\n\"\n                 \"        mother\\n\"\n                 \"        father\\n\"\n                 \"Hint: You can become one\\n\")\n\ndef test_fix_datalad_ri():\n    assert_equal(_fix_datalad_ri('/'), '/')\n    assert_equal(_fix_datalad_ri('/a/b'), '/a/b')\n    assert_equal(_fix_datalad_ri('//'), '///')\n    assert_equal(_fix_datalad_ri('///'), '///')\n    assert_equal(_fix_datalad_ri('//a'), '///a')\n    assert_equal(_fix_datalad_ri('///a'), '///a')\n    assert_equal(_fix_datalad_ri('//a/b'), '///a/b')\n    assert_equal(_fix_datalad_ri('///a/b'), '///a/b')\n",
            "new_file_content": "# emacs: -*- mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-\n# ex: set sts=4 ts=4 sw=4 noet:\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n#\n#   See COPYING file distributed along with the datalad package for the\n#   copyright and license terms.\n#\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n\"\"\"Test functioning of the datalad main cmdline utility \"\"\"\n\nimport os\nimport re\nimport sys\nfrom io import StringIO\nfrom unittest.mock import patch\n\nimport datalad\nfrom ..main import (\n    main,\n    fail_with_short_help,\n    _fix_datalad_ri,\n)\nfrom datalad import __version__\nfrom datalad.cmd import (\n    WitlessRunner as Runner,\n    StdOutErrCapture,\n)\nfrom datalad.ui.utils import (\n    get_console_width,\n    get_terminal_size,\n)\nfrom datalad.api import create\nfrom datalad.utils import (\n    chpwd,\n    Path,\n)\nfrom datalad.tests.utils import (\n    SkipTest,\n    assert_equal,\n    assert_in,\n    assert_not_in,\n    assert_raises,\n    assert_re_in,\n    eq_,\n    in_,\n    ok_startswith,\n    on_windows,\n    slow,\n    with_tempfile,\n)\n\n\ndef run_main(args, exit_code=0, expect_stderr=False):\n    \"\"\"Run main() of the datalad, do basic checks and provide outputs\n\n    Parameters\n    ----------\n    args : list\n        List of string cmdline arguments to pass\n    exit_code : int\n        Expected exit code. Would raise AssertionError if differs\n    expect_stderr : bool or string\n        Whether to expect stderr output. If string -- match\n\n    Returns\n    -------\n    stdout, stderr  strings\n       Output produced\n    \"\"\"\n    with patch('sys.stderr', new_callable=StringIO) as cmerr:\n        with patch('sys.stdout', new_callable=StringIO) as cmout:\n            with assert_raises(SystemExit) as cm:\n                main([\"datalad\"] + list(args))\n            assert_equal(cm.exception.code, exit_code)\n            stdout = cmout.getvalue()\n            stderr = cmerr.getvalue()\n            if expect_stderr is False:\n                assert_equal(stderr, \"\")\n            elif expect_stderr is True:\n                # do nothing -- just return\n                pass\n            else:\n                # must be a string\n                assert_equal(stderr, expect_stderr)\n    return stdout, stderr\n\n\n# TODO: switch to stdout for --version output\ndef test_version():\n    # we just get a version if not asking for a version of some command\n    stdout, stderr = run_main(['--version'], expect_stderr=True)\n    eq_(stdout.rstrip(), \"datalad %s\" % datalad.__version__)\n\n    stdout, stderr = run_main(['clone', '--version'], expect_stderr=True)\n    ok_startswith(stdout, 'datalad %s\\n' % datalad.__version__)\n    # since https://github.com/datalad/datalad/pull/2733 no license in --version\n    assert_not_in(\"Copyright\", stdout)\n    assert_not_in(\"Permission is hereby granted\", stdout)\n\n    try:\n        import datalad_container\n    except ImportError:\n        pass  # not installed, cannot test with extension\n    else:\n        stdout, stderr = run_main(['containers-list', '--version'], expect_stderr=True)\n        eq_(stdout, 'datalad_container %s\\n' % datalad_container.__version__)\n\n\ndef test_help_np():\n    stdout, stderr = run_main(['--help-np'])\n\n    # Let's extract section titles:\n    # enough of bin/datalad and .tox/py27/bin/datalad -- guarantee consistency! ;)\n    ok_startswith(stdout, 'Usage: datalad')\n    # Sections start/end with * if ran under DATALAD_HELP2MAN mode\n    sections = [l[1:-1] for l in filter(re.compile('^\\*.*\\*$').match, stdout.split('\\n'))]\n    # but order is still not guaranteed (dict somewhere)! TODO\n    # see https://travis-ci.org/datalad/datalad/jobs/80519004\n    # thus testing sets\n    for s in {'Commands for dataset operations',\n              'Commands for metadata handling',\n              'Miscellaneous commands',\n              'General information',\n              'Global options',\n              'Plumbing commands',\n              'Plugins'}:\n        assert_in(s, sections)\n\n    if not get_terminal_size()[0] or 0:\n        raise SkipTest(\n            \"Could not determine terminal size, skipping the rest of the test\")\n\n    # none of the lines must be longer than 80 chars\n    # TODO: decide on   create-sibling and possibly\n    # rewrite-urls\n    accepted_width = get_console_width()\n\n    long_lines = [\"%d %s\" % (len(l), l) for l in stdout.split('\\n')\n                  if len(l) > accepted_width and\n                  '{' not in l  # on nd70 summary line is unsplit\n                  ]\n    if long_lines:\n        raise AssertionError(\n            \"Following lines in --help output were longer than %s chars:\\n%s\"\n            % (accepted_width, '\\n'.join(long_lines))\n        )\n\n\ndef test_usage_on_insufficient_args():\n    stdout, stderr = run_main(['install'], exit_code=2, expect_stderr=True)\n    ok_startswith(stderr, 'usage:')\n\n\ndef test_subcmd_usage_on_unknown_args():\n    stdout, stderr = run_main(['get', '--murks'], exit_code=1, expect_stderr=True)\n    in_('get', stdout)\n\n\ndef test_combined_short_option():\n    stdout, stderr = run_main(['-fjson'], exit_code=2, expect_stderr=True)\n    assert_not_in(\"unrecognized argument\", stderr)\n    assert_in(\"too few arguments\", stderr)\n\n\ndef check_incorrect_option(opts, err_str):\n    # The first line used to be:\n    # stdout, stderr = run_main((sys.argv[0],) + opts, expect_stderr=True, exit_code=2)\n    # But: what do we expect to be in sys.argv[0] here?\n    # It depends on how we invoke the test.\n    # - nosetests -s -v datalad/cmdline/tests/test_main.py would result in:\n    #   sys.argv[0}=='nosetests'\n    # - python -m nose -s -v datalad/cmdline/tests/test_main.py would result in:\n    #   sys.argv[0}=='python -m nose'\n    # - python -c \"import nose; nose.main()\" -s -v datalad/cmdline/tests/test_main.py would result in:\n    #   sys.argv[0]=='-c'\n    # This led to failure in case sys.argv[0] contained an option, that was\n    # defined to be a datalad option too, therefore was a 'known_arg' and was\n    # checked to meet its constraints.\n    # But sys.argv[0] actually isn't used by main at all. It simply doesn't\n    # matter what's in there. The only thing important to pass here is `opts`.\n    stdout, stderr = run_main(opts, expect_stderr=True, exit_code=2)\n    out = stdout + stderr\n    assert_in(\"usage: \", out)\n    assert_re_in(err_str, out, match=False)\n\n\ndef test_incorrect_options():\n    # apparently a bit different if following a good one so let's do both\n    err_invalid = \"error: (invalid|too few arguments|unrecognized argument)\"\n    yield check_incorrect_option, ('--buga',), err_invalid\n    yield check_incorrect_option, ('--dbg', '--buga'), err_invalid\n\n    err_insufficient = err_invalid  # \"specify\"\n    yield check_incorrect_option, ('--dbg',), err_insufficient\n    yield check_incorrect_option, tuple(), err_insufficient\n\n\ndef test_script_shims():\n    runner = Runner()\n    # The EASY-INSTALL checks below aren't valid for editable installs. Use the\n    # existence of setup.py as an indication that install is _probably_\n    # editable. The file should always exist for editable installs, but it can\n    # also exist for non-editable installs when the tests are being executed\n    # from the top of the source tree.\n    setup_exists = (Path(datalad.__file__).parent.parent / \"setup.py\").exists()\n    for script in [\n        'datalad',\n        'git-annex-remote-datalad-archives',\n        'git-annex-remote-datalad']:\n        if not on_windows:\n            # those must be available for execution, and should not contain\n            which = runner.run(['which', script], protocol=StdOutErrCapture)['stdout']\n            # test if there is no easy install shim in there\n            with open(which.rstrip()) as f:\n                content = f.read()\n        else:\n            from distutils.spawn import find_executable\n            content = find_executable(script)\n\n        if not setup_exists:\n            assert_not_in('EASY', content) # NOTHING easy should be there\n            assert_not_in('pkg_resources', content)\n\n        # and let's check that it is our script\n        out = runner.run([script, '--version'], protocol=StdOutErrCapture)\n        version = out['stdout'].rstrip()\n        mod, version = version.split(' ', 1)\n        assert_equal(mod, 'datalad')\n        # we can get git and non git .dev version... so for now\n        # relax\n        get_numeric_portion = lambda v: [x for x in v.split('.') if x.isdigit()]\n        # extract numeric portion\n        assert get_numeric_portion(version) # that my lambda is correctish\n        assert_equal(get_numeric_portion(__version__),\n                     get_numeric_portion(version))\n\n\n@slow  # 11.2591s\n@with_tempfile(mkdir=True)\ndef test_cfg_override(path):\n    with chpwd(path):\n        cmd = ['datalad', 'wtf', '-s', 'some']\n        # control\n        out = Runner().run(cmd, protocol=StdOutErrCapture)['stdout']\n        assert_not_in('datalad.dummy: this', out)\n        # ensure that this is not a dataset's cfg manager\n        assert_not_in('datalad.dataset.id', out)\n        # env var\n        out = Runner(env=dict(os.environ, DATALAD_DUMMY='this')).run(\n            cmd, protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n        # cmdline arg\n        out = Runner().run([cmd[0], '-c', 'datalad.dummy=this'] + cmd[1:],\n                           protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n\n        # now create a dataset in the path. the wtf plugin will switch to\n        # using the dataset's config manager, which must inherit the overrides\n        create(dataset=path)\n        # control\n        out = Runner().run(cmd, protocol=StdOutErrCapture)['stdout']\n        assert_not_in('datalad.dummy: this', out)\n        # ensure that this is a dataset's cfg manager\n        assert_in('datalad.dataset.id', out)\n        # env var\n        out = Runner(env=dict(os.environ, DATALAD_DUMMY='this')).run(\n            cmd, protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n        # cmdline arg\n        out = Runner().run([cmd[0], '-c', 'datalad.dummy=this'] + cmd[1:],\n                           protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n\n\ndef test_incorrect_cfg_override():\n    run_main(['-c', 'some', 'wtf'], exit_code=3)\n    run_main(['-c', 'some=', 'wtf'], exit_code=3)\n    run_main(['-c', 'some.var', 'wtf'], exit_code=3)\n    run_main(['-c', 'some.var=', 'wtf'], exit_code=3)\n\n\ndef test_fail_with_short_help():\n    out = StringIO()\n    with assert_raises(SystemExit) as cme:\n        fail_with_short_help(exit_code=3, out=out)\n    assert_equal(cme.exception.code, 3)\n    assert_equal(out.getvalue(), \"\")\n\n    out = StringIO()\n    with assert_raises(SystemExit) as cme:\n        fail_with_short_help(msg=\"Failed badly\", out=out)\n    assert_equal(cme.exception.code, 1)\n    assert_equal(out.getvalue(), \"error: Failed badly\\n\")\n\n    # Suggestions, hint, etc\n    out = StringIO()\n    with assert_raises(SystemExit) as cme:\n        fail_with_short_help(\n            msg=\"Failed badly\",\n            known=[\"mother\", \"mutter\", \"father\", \"son\"],\n            provided=\"muther\",\n            hint=\"You can become one\",\n            exit_code=0,  # noone forbids\n            what=\"parent\",\n            out=out)\n    assert_equal(cme.exception.code, 0)\n    assert_equal(out.getvalue(),\n                 \"error: Failed badly\\n\"\n                 \"datalad: Unknown parent 'muther'.  See 'datalad --help'.\\n\\n\"\n                 \"Did you mean any of these?\\n\"\n                 \"        mutter\\n\"\n                 \"        mother\\n\"\n                 \"        father\\n\"\n                 \"Hint: You can become one\\n\")\n\ndef test_fix_datalad_ri():\n    assert_equal(_fix_datalad_ri('/'), '/')\n    assert_equal(_fix_datalad_ri('/a/b'), '/a/b')\n    assert_equal(_fix_datalad_ri('//'), '///')\n    assert_equal(_fix_datalad_ri('///'), '///')\n    assert_equal(_fix_datalad_ri('//a'), '///a')\n    assert_equal(_fix_datalad_ri('///a'), '///a')\n    assert_equal(_fix_datalad_ri('//a/b'), '///a/b')\n    assert_equal(_fix_datalad_ri('///a/b'), '///a/b')\n",
            "header": {
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                "new_commit_hash": "527ed6016",
                "mode": "100644"
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                            {
                                "content": "def test_version():",
                                "type": "context"
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                            {
                                "content": "    # we just get a version if not asking for a version of some command",
                                "type": "context"
                            },
                            {
                                "content": "    stdout, stderr = run_main(['--version'], expect_stderr=True)",
                                "type": "context"
                            },
                            {
                                "content": "    eq_(stdout.rstrip(), datalad.__version__)",
                                "type": "deleted"
                            },
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                                "content": "    eq_(stdout.rstrip(), \"datalad %s\" % datalad.__version__)",
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                                "type": "context"
                            },
                            {
                                "content": "    stdout, stderr = run_main(['clone', '--version'], expect_stderr=True)",
                                "type": "context"
                            },
                            {
                                "content": "    ok_startswith(stdout, 'datalad %s\\n' % datalad.__version__)",
                                "type": "context"
                            }
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                    "modified_entities": [
                        {
                            "file_name": "datalad/cmdline/tests/test_main.py",
                            "type": "function",
                            "name": "test_version",
                            "content": "def test_version():\n    # we just get a version if not asking for a version of some command\n    stdout, stderr = run_main(['--version'], expect_stderr=True)\n    eq_(stdout.rstrip(), datalad.__version__)\n\n    stdout, stderr = run_main(['clone', '--version'], expect_stderr=True)\n    ok_startswith(stdout, 'datalad %s\\n' % datalad.__version__)\n    # since https://github.com/datalad/datalad/pull/2733 no license in --version\n    assert_not_in(\"Copyright\", stdout)\n    assert_not_in(\"Permission is hereby granted\", stdout)\n\n    try:\n        import datalad_container\n    except ImportError:\n        pass  # not installed, cannot test with extension\n    else:\n        stdout, stderr = run_main(['containers-list', '--version'], expect_stderr=True)\n        eq_(stdout, 'datalad_container %s\\n' % datalad_container.__version__)",
                            "ast_type_str": "FunctionDef",
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                            {
                                "content": "        # and let's check that it is our script",
                                "type": "context"
                            },
                            {
                                "content": "        out = runner.run([script, '--version'], protocol=StdOutErrCapture)",
                                "type": "context"
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                                "content": "        version = out['stdout'].rstrip()",
                                "type": "context"
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                                "content": "        if script != 'datalad':",
                                "type": "deleted"
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                                "content": "            # datalad --version  would return only version now, but all the `datalad CMD` and",
                                "type": "deleted"
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                                "content": "            # other entry points will still announce their origin, so we would need to strip",
                                "type": "deleted"
                            },
                            {
                                "content": "            # it away",
                                "type": "deleted"
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                                "content": "            mod, version = version.split(' ', 1)",
                                "type": "deleted"
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                                "type": "added"
                            },
                            {
                                "content": "        # we can get git and non git .dev version... so for now",
                                "type": "context"
                            },
                            {
                                "content": "        # relax",
                                "type": "context"
                            },
                            {
                                "content": "        get_numeric_portion = lambda v: [x for x in v.split('.') if x.isdigit()]",
                                "type": "context"
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                                "content": "",
                                "type": "context"
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                            "file_name": "datalad/cmdline/tests/test_main.py",
                            "type": "function",
                            "name": "test_script_shims",
                            "content": "def test_script_shims():\n    runner = Runner()\n    # The EASY-INSTALL checks below aren't valid for editable installs. Use the\n    # existence of setup.py as an indication that install is _probably_\n    # editable. The file should always exist for editable installs, but it can\n    # also exist for non-editable installs when the tests are being executed\n    # from the top of the source tree.\n    setup_exists = (Path(datalad.__file__).parent.parent / \"setup.py\").exists()\n    for script in [\n        'datalad',\n        'git-annex-remote-datalad-archives',\n        'git-annex-remote-datalad']:\n        if not on_windows:\n            # those must be available for execution, and should not contain\n            which = runner.run(['which', script], protocol=StdOutErrCapture)['stdout']\n            # test if there is no easy install shim in there\n            with open(which.rstrip()) as f:\n                content = f.read()\n        else:\n            from distutils.spawn import find_executable\n            content = find_executable(script)\n\n        if not setup_exists:\n            assert_not_in('EASY', content) # NOTHING easy should be there\n            assert_not_in('pkg_resources', content)\n\n        # and let's check that it is our script\n        out = runner.run([script, '--version'], protocol=StdOutErrCapture)\n        version = out['stdout'].rstrip()\n        if script != 'datalad':\n            # datalad --version  would return only version now, but all the `datalad CMD` and\n            # other entry points will still announce their origin, so we would need to strip\n            # it away\n            mod, version = version.split(' ', 1)\n            assert_equal(mod, 'datalad')\n        # we can get git and non git .dev version... so for now\n        # relax\n        get_numeric_portion = lambda v: [x for x in v.split('.') if x.isdigit()]\n        # extract numeric portion\n        assert get_numeric_portion(version) # that my lambda is correctish\n        assert_equal(get_numeric_portion(__version__),\n                     get_numeric_portion(version))",
                            "ast_type_str": "FunctionDef",
                            "start_lineno": 198,
                            "end_lineno": 239,
                            "parent": null
                        }
                    ],
                    "added_entities": [],
                    "deleted_entities": []
                }
            ]
        }
    ],
    "old_commit_hash": "02635fd641ee3875cc596004a12d4ca2e383fd8f^",
    "new_commit_hash": "02635fd641ee3875cc596004a12d4ca2e383fd8f",
    "commit_message": "RF: revert back to having \"datalad\" prefix in datalad --version",
    "commit_date": "2021-04-07T18:56:04-04:00",
    "metadata": {}
}
{
    "repo_name": "datalad",
    "new_commit_hash": "02635fd641ee3875cc596004a12d4ca2e383fd8f",
    "test_file_codes": [
        "# emacs: -*- mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-\n# ex: set sts=4 ts=4 sw=4 noet:\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n#\n#   See COPYING file distributed along with the datalad package for the\n#   copyright and license terms.\n#\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n\"\"\"Test functioning of the datalad main cmdline utility \"\"\"\n\nimport os\nimport re\nimport sys\nfrom io import StringIO\nfrom unittest.mock import patch\n\nimport datalad\nfrom datalad.cmdline.main import (\n    main,\n    fail_with_short_help,\n    _fix_datalad_ri,\n)\nfrom datalad import __version__\nfrom datalad.cmd import (\n    WitlessRunner as Runner,\n    StdOutErrCapture,\n)\nfrom datalad.ui.utils import (\n    get_console_width,\n    get_terminal_size,\n)\nfrom datalad.api import create\nfrom datalad.utils import (\n    chpwd,\n    Path,\n)\nfrom datalad.tests.utils import (\n    SkipTest,\n    assert_equal,\n    assert_in,\n    assert_not_in,\n    assert_raises,\n    assert_re_in,\n    eq_,\n    in_,\n    ok_startswith,\n    on_windows,\n    slow,\n    with_tempfile,\n)\n\n\ndef run_main(args, exit_code=0, expect_stderr=False):\n    \"\"\"Run main() of the datalad, do basic checks and provide outputs\n\n    Parameters\n    ----------\n    args : list\n        List of string cmdline arguments to pass\n    exit_code : int\n        Expected exit code. Would raise AssertionError if differs\n    expect_stderr : bool or string\n        Whether to expect stderr output. If string -- match\n\n    Returns\n    -------\n    stdout, stderr  strings\n       Output produced\n    \"\"\"\n    with patch('sys.stderr', new_callable=StringIO) as cmerr:\n        with patch('sys.stdout', new_callable=StringIO) as cmout:\n            with assert_raises(SystemExit) as cm:\n                main([\"datalad\"] + list(args))\n            assert_equal(cm.exception.code, exit_code)\n            stdout = cmout.getvalue()\n            stderr = cmerr.getvalue()\n            if expect_stderr is False:\n                assert_equal(stderr, \"\")\n            elif expect_stderr is True:\n                # do nothing -- just return\n                pass\n            else:\n                # must be a string\n                assert_equal(stderr, expect_stderr)\n    return stdout, stderr\n\n\n# TODO: switch to stdout for --version output\ndef test_version():\n    # we just get a version if not asking for a version of some command\n    stdout, stderr = run_main(['--version'], expect_stderr=True)\n    eq_(stdout.rstrip(), \"datalad %s\" % datalad.__version__)\n\n    stdout, stderr = run_main(['clone', '--version'], expect_stderr=True)\n    ok_startswith(stdout, 'datalad %s\\n' % datalad.__version__)\n    # since https://github.com/datalad/datalad/pull/2733 no license in --version\n    assert_not_in(\"Copyright\", stdout)\n    assert_not_in(\"Permission is hereby granted\", stdout)\n\n    try:\n        import datalad_container\n    except ImportError:\n        pass  # not installed, cannot test with extension\n    else:\n        stdout, stderr = run_main(['containers-list', '--version'], expect_stderr=True)\n        eq_(stdout, 'datalad_container %s\\n' % datalad_container.__version__)\n\n\ndef test_help_np():\n    stdout, stderr = run_main(['--help-np'])\n\n    # Let's extract section titles:\n    # enough of bin/datalad and .tox/py27/bin/datalad -- guarantee consistency! ;)\n    ok_startswith(stdout, 'Usage: datalad')\n    # Sections start/end with * if ran under DATALAD_HELP2MAN mode\n    sections = [l[1:-1] for l in filter(re.compile('^\\*.*\\*$').match, stdout.split('\\n'))]\n    # but order is still not guaranteed (dict somewhere)! TODO\n    # see https://travis-ci.org/datalad/datalad/jobs/80519004\n    # thus testing sets\n    for s in {'Commands for dataset operations',\n              'Commands for metadata handling',\n              'Miscellaneous commands',\n              'General information',\n              'Global options',\n              'Plumbing commands',\n              'Plugins'}:\n        assert_in(s, sections)\n\n    if not get_terminal_size()[0] or 0:\n        raise SkipTest(\n            \"Could not determine terminal size, skipping the rest of the test\")\n\n    # none of the lines must be longer than 80 chars\n    # TODO: decide on   create-sibling and possibly\n    # rewrite-urls\n    accepted_width = get_console_width()\n\n    long_lines = [\"%d %s\" % (len(l), l) for l in stdout.split('\\n')\n                  if len(l) > accepted_width and\n                  '{' not in l  # on nd70 summary line is unsplit\n                  ]\n    if long_lines:\n        raise AssertionError(\n            \"Following lines in --help output were longer than %s chars:\\n%s\"\n            % (accepted_width, '\\n'.join(long_lines))\n        )\n\n\ndef test_usage_on_insufficient_args():\n    stdout, stderr = run_main(['install'], exit_code=2, expect_stderr=True)\n    ok_startswith(stderr, 'usage:')\n\n\ndef test_subcmd_usage_on_unknown_args():\n    stdout, stderr = run_main(['get', '--murks'], exit_code=1, expect_stderr=True)\n    in_('get', stdout)\n\n\ndef test_combined_short_option():\n    stdout, stderr = run_main(['-fjson'], exit_code=2, expect_stderr=True)\n    assert_not_in(\"unrecognized argument\", stderr)\n    assert_in(\"too few arguments\", stderr)\n\n\ndef check_incorrect_option(opts, err_str):\n    # The first line used to be:\n    # stdout, stderr = run_main((sys.argv[0],) + opts, expect_stderr=True, exit_code=2)\n    # But: what do we expect to be in sys.argv[0] here?\n    # It depends on how we invoke the test.\n    # - nosetests -s -v datalad/cmdline/tests/test_main.py would result in:\n    #   sys.argv[0}=='nosetests'\n    # - python -m nose -s -v datalad/cmdline/tests/test_main.py would result in:\n    #   sys.argv[0}=='python -m nose'\n    # - python -c \"import nose; nose.main()\" -s -v datalad/cmdline/tests/test_main.py would result in:\n    #   sys.argv[0]=='-c'\n    # This led to failure in case sys.argv[0] contained an option, that was\n    # defined to be a datalad option too, therefore was a 'known_arg' and was\n    # checked to meet its constraints.\n    # But sys.argv[0] actually isn't used by main at all. It simply doesn't\n    # matter what's in there. The only thing important to pass here is `opts`.\n    stdout, stderr = run_main(opts, expect_stderr=True, exit_code=2)\n    out = stdout + stderr\n    assert_in(\"usage: \", out)\n    assert_re_in(err_str, out, match=False)\n\n\ndef test_incorrect_options():\n    # apparently a bit different if following a good one so let's do both\n    err_invalid = \"error: (invalid|too few arguments|unrecognized argument)\"\n    yield check_incorrect_option, ('--buga',), err_invalid\n    yield check_incorrect_option, ('--dbg', '--buga'), err_invalid\n\n    err_insufficient = err_invalid  # \"specify\"\n    yield check_incorrect_option, ('--dbg',), err_insufficient\n    yield check_incorrect_option, tuple(), err_insufficient\n\n\ndef test_script_shims():\n    runner = Runner()\n    # The EASY-INSTALL checks below aren't valid for editable installs. Use the\n    # existence of setup.py as an indication that install is _probably_\n    # editable. The file should always exist for editable installs, but it can\n    # also exist for non-editable installs when the tests are being executed\n    # from the top of the source tree.\n    setup_exists = (Path(datalad.__file__).parent.parent / \"setup.py\").exists()\n    for script in [\n        'datalad',\n        'git-annex-remote-datalad-archives',\n        'git-annex-remote-datalad']:\n        if not on_windows:\n            # those must be available for execution, and should not contain\n            which = runner.run(['which', script], protocol=StdOutErrCapture)['stdout']\n            # test if there is no easy install shim in there\n            with open(which.rstrip()) as f:\n                content = f.read()\n        else:\n            from distutils.spawn import find_executable\n            content = find_executable(script)\n\n        if not setup_exists:\n            assert_not_in('EASY', content) # NOTHING easy should be there\n            assert_not_in('pkg_resources', content)\n\n        # and let's check that it is our script\n        out = runner.run([script, '--version'], protocol=StdOutErrCapture)\n        version = out['stdout'].rstrip()\n        mod, version = version.split(' ', 1)\n        assert_equal(mod, 'datalad')\n        # we can get git and non git .dev version... so for now\n        # relax\n        get_numeric_portion = lambda v: [x for x in v.split('.') if x.isdigit()]\n        # extract numeric portion\n        assert get_numeric_portion(version) # that my lambda is correctish\n        assert_equal(get_numeric_portion(__version__),\n                     get_numeric_portion(version))\n\n\n@slow  # 11.2591s\n@with_tempfile(mkdir=True)\ndef test_cfg_override(path):\n    with chpwd(path):\n        cmd = ['datalad', 'wtf', '-s', 'some']\n        # control\n        out = Runner().run(cmd, protocol=StdOutErrCapture)['stdout']\n        assert_not_in('datalad.dummy: this', out)\n        # ensure that this is not a dataset's cfg manager\n        assert_not_in('datalad.dataset.id', out)\n        # env var\n        out = Runner(env=dict(os.environ, DATALAD_DUMMY='this')).run(\n            cmd, protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n        # cmdline arg\n        out = Runner().run([cmd[0], '-c', 'datalad.dummy=this'] + cmd[1:],\n                           protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n\n        # now create a dataset in the path. the wtf plugin will switch to\n        # using the dataset's config manager, which must inherit the overrides\n        create(dataset=path)\n        # control\n        out = Runner().run(cmd, protocol=StdOutErrCapture)['stdout']\n        assert_not_in('datalad.dummy: this', out)\n        # ensure that this is a dataset's cfg manager\n        assert_in('datalad.dataset.id', out)\n        # env var\n        out = Runner(env=dict(os.environ, DATALAD_DUMMY='this')).run(\n            cmd, protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n        # cmdline arg\n        out = Runner().run([cmd[0], '-c', 'datalad.dummy=this'] + cmd[1:],\n                           protocol=StdOutErrCapture)['stdout']\n        assert_in('datalad.dummy: this', out)\n\n\ndef test_incorrect_cfg_override():\n    run_main(['-c', 'some', 'wtf'], exit_code=3)\n    run_main(['-c', 'some=', 'wtf'], exit_code=3)\n    run_main(['-c', 'some.var', 'wtf'], exit_code=3)\n    run_main(['-c', 'some.var=', 'wtf'], exit_code=3)\n\n\ndef test_fail_with_short_help():\n    out = StringIO()\n    with assert_raises(SystemExit) as cme:\n        fail_with_short_help(exit_code=3, out=out)\n    assert_equal(cme.exception.code, 3)\n    assert_equal(out.getvalue(), \"\")\n\n    out = StringIO()\n    with assert_raises(SystemExit) as cme:\n        fail_with_short_help(msg=\"Failed badly\", out=out)\n    assert_equal(cme.exception.code, 1)\n    assert_equal(out.getvalue(), \"error: Failed badly\\n\")\n\n    # Suggestions, hint, etc\n    out = StringIO()\n    with assert_raises(SystemExit) as cme:\n        fail_with_short_help(\n            msg=\"Failed badly\",\n            known=[\"mother\", \"mutter\", \"father\", \"son\"],\n            provided=\"muther\",\n            hint=\"You can become one\",\n            exit_code=0,  # noone forbids\n            what=\"parent\",\n            out=out)\n    assert_equal(cme.exception.code, 0)\n    assert_equal(out.getvalue(),\n                 \"error: Failed badly\\n\"\n                 \"datalad: Unknown parent 'muther'.  See 'datalad --help'.\\n\\n\"\n                 \"Did you mean any of these?\\n\"\n                 \"        mutter\\n\"\n                 \"        mother\\n\"\n                 \"        father\\n\"\n                 \"Hint: You can become one\\n\")\n\ndef test_fix_datalad_ri():\n    assert_equal(_fix_datalad_ri('/'), '/')\n    assert_equal(_fix_datalad_ri('/a/b'), '/a/b')\n    assert_equal(_fix_datalad_ri('//'), '///')\n    assert_equal(_fix_datalad_ri('///'), '///')\n    assert_equal(_fix_datalad_ri('//a'), '///a')\n    assert_equal(_fix_datalad_ri('///a'), '///a')\n    assert_equal(_fix_datalad_ri('//a/b'), '///a/b')\n    assert_equal(_fix_datalad_ri('///a/b'), '///a/b')\n",
        "import pytest\nimport tempfile\nimport os\n\n\n@pytest.fixture\ndef path():\n    with tempfile.TemporaryDirectory() as tmpdir:\n        yield tmpdir\n\n\n@pytest.fixture(autouse=True)\ndef setup_git_config():\n    with tempfile.TemporaryDirectory() as home:\n        old_home = os.environ.get(\"HOME\")\n        os.environ[\"HOME\"] = home\n        os.system('git config --global user.name \"DataLad Tester\"')\n        os.system('git config --global user.email \"test@example.com\"')\n        yield\n        if old_home:\n            os.environ[\"HOME\"] = old_home\n"
    ],
    "test_file_names": [
        "test_1.py",
        "conftest.py"
    ],
    "setup_res_code": 0,
    "setup_res_stdout": "Starting Datalad installation attempts...\nVerifying installation...\nDatalad version: 0.14.1.dev132\n✅ Installation successful!\nSuccessfully installed Datalad using Python 3.9\n",
    "setup_res_stderr": "Using CPython 3.9.21\nCreating virtual environment at: .venv\nActivate with: source .venv/bin/activate\nResolved 25 packages in 84ms\nInstalled 25 packages in 4.01s\n + coverage==7.6.10\n + docopt==0.6.2\n + exceptiongroup==1.2.2\n + grabbit==0.2.6\n + importlib-resources==6.4.5\n + iniconfig==2.0.0\n + nibabel==5.3.2\n + num2words==0.5.14\n + numpy==2.0.2\n + packaging==24.2\n + pandas==2.2.3\n + patsy==1.0.1\n + pluggy==1.5.0\n + pybids==0.6.5\n + pytest==8.3.4\n + pytest-cov==6.0.0\n + python-dateutil==2.9.0.post0\n + pytz==2024.2\n + scipy==1.13.1\n + setuptools==75.6.0\n + six==1.17.0\n + tomli==2.2.1\n + typing-extensions==4.12.2\n + tzdata==2024.2\n + zipp==3.21.0\nResolved 63 packages in 3.38s\nPrepared 1 package in 2.64s\nInstalled 57 packages in 584ms\n + annexremote==1.6.6\n + appdirs==1.4.4\n + backports-tarfile==1.2.0\n + beautifulsoup4==4.12.3\n + boto==2.49.0\n + certifi==2024.12.14\n + cffi==1.17.1\n + chardet==5.2.0\n + charset-normalizer==3.4.1\n + citeproc-py==0.6.0\n + cryptography==44.0.0\n + datalad==0.14.1 (from file:///home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_02635fd641ee3875cc596004a12d4ca2e383fd8f)\n + deprecated==1.2.15\n + distro==1.9.0\n + duecredit==0.10.2\n + exifread==3.0.0\n + fasteners==0.19\n + httpretty==1.1.4\n + humanize==4.11.0\n + idna==3.10\n + importlib-metadata==8.5.0\n + iso8601==2.1.0\n + jaraco-classes==3.4.0\n + jaraco-context==6.0.1\n + jaraco-functools==4.1.0\n + jeepney==0.8.0\n + jsmin==3.0.1\n + keyring==25.6.0\n + keyrings-alt==5.0.2\n + looseversion==1.3.0\n + lxml==5.3.0\n + more-itertools==10.5.0\n + msgpack==1.1.0\n + multidict==6.1.0\n + mutagen==1.47.0\n + nose==1.3.7\n + patool==1.15.0\n + pillow==11.0.0\n + propcache==0.2.1\n + pycparser==2.22\n + pygithub==2.5.0\n + pyjwt==2.10.1\n + pynacl==1.5.0\n + pyperclip==1.9.0\n + python-xmp-toolkit==2.0.2\n + pyyaml==6.0.2\n + requests==2.32.3\n + requests-ftp==0.3.1\n + secretstorage==3.3.3\n + simplejson==3.19.3\n + soupsieve==2.6\n + tqdm==4.67.1\n + urllib3==1.26.20\n + vcrpy==7.0.0\n + whoosh==2.7.4\n + wrapt==1.17.0\n + yarl==1.18.3\nResolved 97 packages in 156ms\nInstalled 32 packages in 906ms\n + alabaster==0.7.16\n + asv==0.6.4\n + asv-runner==0.2.1\n + babel==2.16.0\n + build==1.2.2.post1\n + distlib==0.3.9\n + docutils==0.21.2\n + filelock==3.16.1\n + gprof2dot==2024.6.6\n + imagesize==1.4.1\n + jinja2==3.1.5\n + json5==0.10.0\n + markupsafe==3.0.2\n + nose-timer==1.0.1\n + platformdirs==4.3.6\n + psutil==6.1.1\n + pygments==2.18.0\n + pympler==1.1\n + pypandoc==1.14\n + pyproject-hooks==1.2.0\n + snowballstemmer==2.2.0\n + sphinx==7.4.7\n + sphinx-rtd-theme==3.0.2\n + sphinxcontrib-applehelp==2.0.0\n + sphinxcontrib-devhelp==2.0.0\n + sphinxcontrib-htmlhelp==2.1.0\n + sphinxcontrib-jquery==4.1\n + sphinxcontrib-jsmath==1.0.1\n + sphinxcontrib-qthelp==2.0.0\n + sphinxcontrib-serializinghtml==2.0.0\n + tabulate==0.9.0\n + virtualenv==20.28.0\n",
    "new_commit_res_code": 1,
    "new_commit_res_stdout": "============================= test session starts ==============================\nplatform linux -- Python 3.9.21, pytest-8.3.4, pluggy-1.5.0\nrootdir: /home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_02635fd641ee3875cc596004a12d4ca2e383fd8f\nconfigfile: pyproject.toml\nplugins: cov-6.0.0\ncollected 11 items\n\nr2e_tests/test_1.py .s...xFF...                                          [100%]\n\n=================================== FAILURES ===================================\n______________________________ test_script_shims _______________________________\n\n    def test_script_shims():\n        runner = Runner()\n        # The EASY-INSTALL checks below aren't valid for editable installs. Use the\n        # existence of setup.py as an indication that install is _probably_\n        # editable. The file should always exist for editable installs, but it can\n        # also exist for non-editable installs when the tests are being executed\n        # from the top of the source tree.\n        setup_exists = (Path(datalad.__file__).parent.parent / \"setup.py\").exists()\n        for script in [\n            'datalad',\n            'git-annex-remote-datalad-archives',\n            'git-annex-remote-datalad']:\n            if not on_windows:\n                # those must be available for execution, and should not contain\n                which = runner.run(['which', script], protocol=StdOutErrCapture)['stdout']\n                # test if there is no easy install shim in there\n                with open(which.rstrip()) as f:\n                    content = f.read()\n            else:\n                from distutils.spawn import find_executable\n                content = find_executable(script)\n    \n            if not setup_exists:\n                assert_not_in('EASY', content) # NOTHING easy should be there\n                assert_not_in('pkg_resources', content)\n    \n            # and let's check that it is our script\n>           out = runner.run([script, '--version'], protocol=StdOutErrCapture)\n\nr2e_tests/test_1.py:225: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/cmd.py:379: in run\n    results = event_loop.run_until_complete(\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/asyncio/base_events.py:647: in run_until_complete\n    return future.result()\ndatalad/cmd.py:102: in run_async_cmd\n    transport, protocol = await proc\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/asyncio/base_events.py:1676: in subprocess_exec\n    transport = await self._make_subprocess_transport(\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/asyncio/unix_events.py:197: in _make_subprocess_transport\n    transp = _UnixSubprocessTransport(self, protocol, args, shell,\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/asyncio/base_subprocess.py:36: in __init__\n    self._start(args=args, shell=shell, stdin=stdin, stdout=stdout,\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/asyncio/unix_events.py:789: in _start\n    self._proc = subprocess.Popen(\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/subprocess.py:951: in __init__\n    self._execute_child(args, executable, preexec_fn, close_fds,\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\nself = <Popen: returncode: 255 args: ('datalad', '--version')>\nargs = ['datalad', '--version'], executable = b'datalad', preexec_fn = None\nclose_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None\ncreationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 16\nc2pwrite = 18, errread = 19, errwrite = 20, restore_signals = True, gid = None\ngids = None, uid = None, umask = -1, start_new_session = False\n\n    def _execute_child(self, args, executable, preexec_fn, close_fds,\n                       pass_fds, cwd, env,\n                       startupinfo, creationflags, shell,\n                       p2cread, p2cwrite,\n                       c2pread, c2pwrite,\n                       errread, errwrite,\n                       restore_signals,\n                       gid, gids, uid, umask,\n                       start_new_session):\n        \"\"\"Execute program (POSIX version)\"\"\"\n    \n        if isinstance(args, (str, bytes)):\n            args = [args]\n        elif isinstance(args, os.PathLike):\n            if shell:\n                raise TypeError('path-like args is not allowed when '\n                                'shell is true')\n            args = [args]\n        else:\n            args = list(args)\n    \n        if shell:\n            # On Android the default shell is at '/system/bin/sh'.\n            unix_shell = ('/system/bin/sh' if\n                      hasattr(sys, 'getandroidapilevel') else '/bin/sh')\n            args = [unix_shell, \"-c\"] + args\n            if executable:\n                args[0] = executable\n    \n        if executable is None:\n            executable = args[0]\n    \n        sys.audit(\"subprocess.Popen\", executable, args, cwd, env)\n    \n        if (_USE_POSIX_SPAWN\n                and os.path.dirname(executable)\n                and preexec_fn is None\n                and not close_fds\n                and not pass_fds\n                and cwd is None\n                and (p2cread == -1 or p2cread > 2)\n                and (c2pwrite == -1 or c2pwrite > 2)\n                and (errwrite == -1 or errwrite > 2)\n                and not start_new_session\n                and gid is None\n                and gids is None\n                and uid is None\n                and umask < 0):\n            self._posix_spawn(args, executable, env, restore_signals,\n                              p2cread, p2cwrite,\n                              c2pread, c2pwrite,\n                              errread, errwrite)\n            return\n    \n        orig_executable = executable\n    \n        # For transferring possible exec failure from child to parent.\n        # Data format: \"exception name:hex errno:description\"\n        # Pickle is not used; it is complex and involves memory allocation.\n        errpipe_read, errpipe_write = os.pipe()\n        # errpipe_write must not be in the standard io 0, 1, or 2 fd range.\n        low_fds_to_close = []\n        while errpipe_write < 3:\n            low_fds_to_close.append(errpipe_write)\n            errpipe_write = os.dup(errpipe_write)\n        for low_fd in low_fds_to_close:\n            os.close(low_fd)\n        try:\n            try:\n                # We must avoid complex work that could involve\n                # malloc or free in the child process to avoid\n                # potential deadlocks, thus we do all this here.\n                # and pass it to fork_exec()\n    \n                if env is not None:\n                    env_list = []\n                    for k, v in env.items():\n                        k = os.fsencode(k)\n                        if b'=' in k:\n                            raise ValueError(\"illegal environment variable name\")\n                        env_list.append(k + b'=' + os.fsencode(v))\n                else:\n                    env_list = None  # Use execv instead of execve.\n                executable = os.fsencode(executable)\n                if os.path.dirname(executable):\n                    executable_list = (executable,)\n                else:\n                    # This matches the behavior of os._execvpe().\n                    executable_list = tuple(\n                        os.path.join(os.fsencode(dir), executable)\n                        for dir in os.get_exec_path(env))\n                fds_to_keep = set(pass_fds)\n                fds_to_keep.add(errpipe_write)\n                self.pid = _posixsubprocess.fork_exec(\n                        args, executable_list,\n                        close_fds, tuple(sorted(map(int, fds_to_keep))),\n                        cwd, env_list,\n                        p2cread, p2cwrite, c2pread, c2pwrite,\n                        errread, errwrite,\n                        errpipe_read, errpipe_write,\n                        restore_signals, start_new_session,\n                        gid, gids, uid, umask,\n                        preexec_fn)\n                self._child_created = True\n            finally:\n                # be sure the FD is closed no matter what\n                os.close(errpipe_write)\n    \n            self._close_pipe_fds(p2cread, p2cwrite,\n                                 c2pread, c2pwrite,\n                                 errread, errwrite)\n    \n            # Wait for exec to fail or succeed; possibly raising an\n            # exception (limited in size)\n            errpipe_data = bytearray()\n            while True:\n                part = os.read(errpipe_read, 50000)\n                errpipe_data += part\n                if not part or len(errpipe_data) > 50000:\n                    break\n        finally:\n            # be sure the FD is closed no matter what\n            os.close(errpipe_read)\n    \n        if errpipe_data:\n            try:\n                pid, sts = os.waitpid(self.pid, 0)\n                if pid == self.pid:\n                    self._handle_exitstatus(sts)\n                else:\n                    self.returncode = sys.maxsize\n            except ChildProcessError:\n                pass\n    \n            try:\n                exception_name, hex_errno, err_msg = (\n                        errpipe_data.split(b':', 2))\n                # The encoding here should match the encoding\n                # written in by the subprocess implementations\n                # like _posixsubprocess\n                err_msg = err_msg.decode()\n            except ValueError:\n                exception_name = b'SubprocessError'\n                hex_errno = b'0'\n                err_msg = 'Bad exception data from child: {!r}'.format(\n                              bytes(errpipe_data))\n            child_exception_type = getattr(\n                    builtins, exception_name.decode('ascii'),\n                    SubprocessError)\n            if issubclass(child_exception_type, OSError) and hex_errno:\n                errno_num = int(hex_errno, 16)\n                child_exec_never_called = (err_msg == \"noexec\")\n                if child_exec_never_called:\n                    err_msg = \"\"\n                    # The error must be from chdir(cwd).\n                    err_filename = cwd\n                else:\n                    err_filename = orig_executable\n                if errno_num != 0:\n                    err_msg = os.strerror(errno_num)\n>               raise child_exception_type(errno_num, err_msg, err_filename)\nE               FileNotFoundError: [Errno 2] No such file or directory: 'datalad'\n\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/subprocess.py:1837: FileNotFoundError\n______________________________ test_cfg_override _______________________________\n\narg = (), kw = {'path': '/tmp/tmp-page2annex53spyt6o'}\nfilename = '/tmp/datalad_temp_test_cfg_overrider541dw9p'\n\n    @wraps(t)\n    def  _wrap_with_tempfile(*arg, **kw):\n        if 'dir' not in tkwargs.keys():\n            # if not specified otherwise, respect datalad.tests.temp.dir config\n            # as this is a test helper\n            tkwargs['dir'] = dl_cfg.get(\"datalad.tests.temp.dir\")\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_cfg_override() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:757: TypeError\n==================================== PASSES ====================================\n_______________________ test_usage_on_insufficient_args ________________________\n----------------------------- Captured stderr call -----------------------------\n[ERROR] Please provide at least a source or a path [install.py:__call__:183] (InsufficientArgumentsError) \n------------------------------ Captured log call -------------------------------\nERROR    datalad.cmdline:main.py:448 Please provide at least a source or a path [install.py:__call__:183] (InsufficientArgumentsError)\n______________________ test_subcmd_usage_on_unknown_args _______________________\n----------------------------- Captured stderr call -----------------------------\n[ERROR] unknown argument: --murks \n------------------------------ Captured log call -------------------------------\nERROR    datalad.cmdline:main.py:382 unknown argument: --murks\n_________________________ test_incorrect_cfg_override __________________________\n----------------------------- Captured stderr call -----------------------------\n[ERROR] Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some'] \n[ERROR] Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some='] \n[ERROR] Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some.var'] \n[ERROR] Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some.var='] \n------------------------------ Captured log call -------------------------------\nERROR    datalad.cmdline:main.py:408 Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some']\nERROR    datalad.cmdline:main.py:408 Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some=']\nERROR    datalad.cmdline:main.py:408 Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some.var']\nERROR    datalad.cmdline:main.py:408 Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some.var=']\n_____________________________ test_fix_datalad_ri ______________________________\n----------------------------- Captured stderr call -----------------------------\n[INFO] Changing // back to /// as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion \n[INFO] Changing //a back to ///a as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion \n[INFO] Changing //a/b back to ///a/b as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion \n------------------------------ Captured log call -------------------------------\nINFO     datalad.cmdline:main.py:355 Changing // back to /// as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion\nINFO     datalad.cmdline:main.py:355 Changing //a back to ///a as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion\nINFO     datalad.cmdline:main.py:355 Changing //a/b back to ///a/b as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion\n=========================== short test summary info ============================\nPASSED r2e_tests/test_1.py::test_version\nPASSED r2e_tests/test_1.py::test_usage_on_insufficient_args\nPASSED r2e_tests/test_1.py::test_subcmd_usage_on_unknown_args\nPASSED r2e_tests/test_1.py::test_combined_short_option\nPASSED r2e_tests/test_1.py::test_incorrect_cfg_override\nPASSED r2e_tests/test_1.py::test_fail_with_short_help\nPASSED r2e_tests/test_1.py::test_fix_datalad_ri\nSKIPPED [1] .venv/lib/python3.9/site-packages/_pytest/unittest.py:385: Could not determine terminal size, skipping the rest of the test\nXFAIL r2e_tests/test_1.py::test_incorrect_options - reason: [NOTRUN] yield tests were removed in pytest 4.0 - test_incorrect_options will be ignored\nFAILED r2e_tests/test_1.py::test_script_shims - FileNotFoundError: [Errno 2] ...\nFAILED r2e_tests/test_1.py::test_cfg_override - TypeError: test_cfg_override(...\n============== 2 failed, 7 passed, 1 skipped, 1 xfailed in 3.44s ===============\n",
    "new_commit_res_stderr": "",
    "old_commit_res_code": 1,
    "old_commit_res_stdout": "============================= test session starts ==============================\nplatform linux -- Python 3.9.21, pytest-8.3.4, pluggy-1.5.0\nrootdir: /home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_02635fd641ee3875cc596004a12d4ca2e383fd8f\nconfigfile: pyproject.toml\nplugins: cov-6.0.0\ncollected 11 items\n\nr2e_tests/test_1.py Fs...xFF...                                          [100%]\n\n=================================== FAILURES ===================================\n_________________________________ test_version _________________________________\n\n    def test_version():\n        # we just get a version if not asking for a version of some command\n        stdout, stderr = run_main(['--version'], expect_stderr=True)\n>       eq_(stdout.rstrip(), \"datalad %s\" % datalad.__version__)\n\nr2e_tests/test_1.py:92: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\na = '0.14.1.dev131', b = 'datalad 0.14.1.dev131', msg = None\n\n    def eq_(a, b, msg=None):\n        \"\"\"Shorthand for 'assert a == b, \"%r != %r\" % (a, b)\n        \"\"\"\n        if not a == b:\n>           raise AssertionError(msg or \"%r != %r\" % (a, b))\nE           AssertionError: '0.14.1.dev131' != 'datalad 0.14.1.dev131'\n\n.venv/lib/python3.9/site-packages/nose/tools/trivial.py:29: AssertionError\n______________________________ test_script_shims _______________________________\n\n    def test_script_shims():\n        runner = Runner()\n        # The EASY-INSTALL checks below aren't valid for editable installs. Use the\n        # existence of setup.py as an indication that install is _probably_\n        # editable. The file should always exist for editable installs, but it can\n        # also exist for non-editable installs when the tests are being executed\n        # from the top of the source tree.\n        setup_exists = (Path(datalad.__file__).parent.parent / \"setup.py\").exists()\n        for script in [\n            'datalad',\n            'git-annex-remote-datalad-archives',\n            'git-annex-remote-datalad']:\n            if not on_windows:\n                # those must be available for execution, and should not contain\n                which = runner.run(['which', script], protocol=StdOutErrCapture)['stdout']\n                # test if there is no easy install shim in there\n                with open(which.rstrip()) as f:\n                    content = f.read()\n            else:\n                from distutils.spawn import find_executable\n                content = find_executable(script)\n    \n            if not setup_exists:\n                assert_not_in('EASY', content) # NOTHING easy should be there\n                assert_not_in('pkg_resources', content)\n    \n            # and let's check that it is our script\n>           out = runner.run([script, '--version'], protocol=StdOutErrCapture)\n\nr2e_tests/test_1.py:225: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/cmd.py:379: in run\n    results = event_loop.run_until_complete(\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/asyncio/base_events.py:647: in run_until_complete\n    return future.result()\ndatalad/cmd.py:102: in run_async_cmd\n    transport, protocol = await proc\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/asyncio/base_events.py:1676: in subprocess_exec\n    transport = await self._make_subprocess_transport(\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/asyncio/unix_events.py:197: in _make_subprocess_transport\n    transp = _UnixSubprocessTransport(self, protocol, args, shell,\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/asyncio/base_subprocess.py:36: in __init__\n    self._start(args=args, shell=shell, stdin=stdin, stdout=stdout,\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/asyncio/unix_events.py:789: in _start\n    self._proc = subprocess.Popen(\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/subprocess.py:951: in __init__\n    self._execute_child(args, executable, preexec_fn, close_fds,\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\nself = <Popen: returncode: 255 args: ('datalad', '--version')>\nargs = ['datalad', '--version'], executable = b'datalad', preexec_fn = None\nclose_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None\ncreationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 16\nc2pwrite = 18, errread = 19, errwrite = 20, restore_signals = True, gid = None\ngids = None, uid = None, umask = -1, start_new_session = False\n\n    def _execute_child(self, args, executable, preexec_fn, close_fds,\n                       pass_fds, cwd, env,\n                       startupinfo, creationflags, shell,\n                       p2cread, p2cwrite,\n                       c2pread, c2pwrite,\n                       errread, errwrite,\n                       restore_signals,\n                       gid, gids, uid, umask,\n                       start_new_session):\n        \"\"\"Execute program (POSIX version)\"\"\"\n    \n        if isinstance(args, (str, bytes)):\n            args = [args]\n        elif isinstance(args, os.PathLike):\n            if shell:\n                raise TypeError('path-like args is not allowed when '\n                                'shell is true')\n            args = [args]\n        else:\n            args = list(args)\n    \n        if shell:\n            # On Android the default shell is at '/system/bin/sh'.\n            unix_shell = ('/system/bin/sh' if\n                      hasattr(sys, 'getandroidapilevel') else '/bin/sh')\n            args = [unix_shell, \"-c\"] + args\n            if executable:\n                args[0] = executable\n    \n        if executable is None:\n            executable = args[0]\n    \n        sys.audit(\"subprocess.Popen\", executable, args, cwd, env)\n    \n        if (_USE_POSIX_SPAWN\n                and os.path.dirname(executable)\n                and preexec_fn is None\n                and not close_fds\n                and not pass_fds\n                and cwd is None\n                and (p2cread == -1 or p2cread > 2)\n                and (c2pwrite == -1 or c2pwrite > 2)\n                and (errwrite == -1 or errwrite > 2)\n                and not start_new_session\n                and gid is None\n                and gids is None\n                and uid is None\n                and umask < 0):\n            self._posix_spawn(args, executable, env, restore_signals,\n                              p2cread, p2cwrite,\n                              c2pread, c2pwrite,\n                              errread, errwrite)\n            return\n    \n        orig_executable = executable\n    \n        # For transferring possible exec failure from child to parent.\n        # Data format: \"exception name:hex errno:description\"\n        # Pickle is not used; it is complex and involves memory allocation.\n        errpipe_read, errpipe_write = os.pipe()\n        # errpipe_write must not be in the standard io 0, 1, or 2 fd range.\n        low_fds_to_close = []\n        while errpipe_write < 3:\n            low_fds_to_close.append(errpipe_write)\n            errpipe_write = os.dup(errpipe_write)\n        for low_fd in low_fds_to_close:\n            os.close(low_fd)\n        try:\n            try:\n                # We must avoid complex work that could involve\n                # malloc or free in the child process to avoid\n                # potential deadlocks, thus we do all this here.\n                # and pass it to fork_exec()\n    \n                if env is not None:\n                    env_list = []\n                    for k, v in env.items():\n                        k = os.fsencode(k)\n                        if b'=' in k:\n                            raise ValueError(\"illegal environment variable name\")\n                        env_list.append(k + b'=' + os.fsencode(v))\n                else:\n                    env_list = None  # Use execv instead of execve.\n                executable = os.fsencode(executable)\n                if os.path.dirname(executable):\n                    executable_list = (executable,)\n                else:\n                    # This matches the behavior of os._execvpe().\n                    executable_list = tuple(\n                        os.path.join(os.fsencode(dir), executable)\n                        for dir in os.get_exec_path(env))\n                fds_to_keep = set(pass_fds)\n                fds_to_keep.add(errpipe_write)\n                self.pid = _posixsubprocess.fork_exec(\n                        args, executable_list,\n                        close_fds, tuple(sorted(map(int, fds_to_keep))),\n                        cwd, env_list,\n                        p2cread, p2cwrite, c2pread, c2pwrite,\n                        errread, errwrite,\n                        errpipe_read, errpipe_write,\n                        restore_signals, start_new_session,\n                        gid, gids, uid, umask,\n                        preexec_fn)\n                self._child_created = True\n            finally:\n                # be sure the FD is closed no matter what\n                os.close(errpipe_write)\n    \n            self._close_pipe_fds(p2cread, p2cwrite,\n                                 c2pread, c2pwrite,\n                                 errread, errwrite)\n    \n            # Wait for exec to fail or succeed; possibly raising an\n            # exception (limited in size)\n            errpipe_data = bytearray()\n            while True:\n                part = os.read(errpipe_read, 50000)\n                errpipe_data += part\n                if not part or len(errpipe_data) > 50000:\n                    break\n        finally:\n            # be sure the FD is closed no matter what\n            os.close(errpipe_read)\n    \n        if errpipe_data:\n            try:\n                pid, sts = os.waitpid(self.pid, 0)\n                if pid == self.pid:\n                    self._handle_exitstatus(sts)\n                else:\n                    self.returncode = sys.maxsize\n            except ChildProcessError:\n                pass\n    \n            try:\n                exception_name, hex_errno, err_msg = (\n                        errpipe_data.split(b':', 2))\n                # The encoding here should match the encoding\n                # written in by the subprocess implementations\n                # like _posixsubprocess\n                err_msg = err_msg.decode()\n            except ValueError:\n                exception_name = b'SubprocessError'\n                hex_errno = b'0'\n                err_msg = 'Bad exception data from child: {!r}'.format(\n                              bytes(errpipe_data))\n            child_exception_type = getattr(\n                    builtins, exception_name.decode('ascii'),\n                    SubprocessError)\n            if issubclass(child_exception_type, OSError) and hex_errno:\n                errno_num = int(hex_errno, 16)\n                child_exec_never_called = (err_msg == \"noexec\")\n                if child_exec_never_called:\n                    err_msg = \"\"\n                    # The error must be from chdir(cwd).\n                    err_filename = cwd\n                else:\n                    err_filename = orig_executable\n                if errno_num != 0:\n                    err_msg = os.strerror(errno_num)\n>               raise child_exception_type(errno_num, err_msg, err_filename)\nE               FileNotFoundError: [Errno 2] No such file or directory: 'datalad'\n\n../../../../.local/share/uv/python/cpython-3.9.21-linux-x86_64-gnu/lib/python3.9/subprocess.py:1837: FileNotFoundError\n______________________________ test_cfg_override _______________________________\n\narg = (), kw = {'path': '/tmp/tmp-page2annexi9wtf_hc'}\nfilename = '/tmp/datalad_temp_test_cfg_overridez898c85y'\n\n    @wraps(t)\n    def  _wrap_with_tempfile(*arg, **kw):\n        if 'dir' not in tkwargs.keys():\n            # if not specified otherwise, respect datalad.tests.temp.dir config\n            # as this is a test helper\n            tkwargs['dir'] = dl_cfg.get(\"datalad.tests.temp.dir\")\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_cfg_override() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:757: TypeError\n==================================== PASSES ====================================\n_______________________ test_usage_on_insufficient_args ________________________\n----------------------------- Captured stderr call -----------------------------\n[ERROR] Please provide at least a source or a path [install.py:__call__:183] (InsufficientArgumentsError) \n------------------------------ Captured log call -------------------------------\nERROR    datalad.cmdline:main.py:448 Please provide at least a source or a path [install.py:__call__:183] (InsufficientArgumentsError)\n______________________ test_subcmd_usage_on_unknown_args _______________________\n----------------------------- Captured stderr call -----------------------------\n[ERROR] unknown argument: --murks \n------------------------------ Captured log call -------------------------------\nERROR    datalad.cmdline:main.py:382 unknown argument: --murks\n_________________________ test_incorrect_cfg_override __________________________\n----------------------------- Captured stderr call -----------------------------\n[ERROR] Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some'] \n[ERROR] Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some='] \n[ERROR] Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some.var'] \n[ERROR] Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some.var='] \n------------------------------ Captured log call -------------------------------\nERROR    datalad.cmdline:main.py:408 Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some']\nERROR    datalad.cmdline:main.py:408 Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some=']\nERROR    datalad.cmdline:main.py:408 Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some.var']\nERROR    datalad.cmdline:main.py:408 Configuration override without section/variable or value assignment (must be 'section.variable=value'): ['some.var=']\n_____________________________ test_fix_datalad_ri ______________________________\n----------------------------- Captured stderr call -----------------------------\n[INFO] Changing // back to /// as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion \n[INFO] Changing //a back to ///a as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion \n[INFO] Changing //a/b back to ///a/b as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion \n------------------------------ Captured log call -------------------------------\nINFO     datalad.cmdline:main.py:355 Changing // back to /// as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion\nINFO     datalad.cmdline:main.py:355 Changing //a back to ///a as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion\nINFO     datalad.cmdline:main.py:355 Changing //a/b back to ///a/b as it was probably changed by MINGW/MSYS, see http://www.mingw.org/wiki/Posix_path_conversion\n=========================== short test summary info ============================\nPASSED r2e_tests/test_1.py::test_usage_on_insufficient_args\nPASSED r2e_tests/test_1.py::test_subcmd_usage_on_unknown_args\nPASSED r2e_tests/test_1.py::test_combined_short_option\nPASSED r2e_tests/test_1.py::test_incorrect_cfg_override\nPASSED r2e_tests/test_1.py::test_fail_with_short_help\nPASSED r2e_tests/test_1.py::test_fix_datalad_ri\nSKIPPED [1] .venv/lib/python3.9/site-packages/_pytest/unittest.py:385: Could not determine terminal size, skipping the rest of the test\nXFAIL r2e_tests/test_1.py::test_incorrect_options - reason: [NOTRUN] yield tests were removed in pytest 4.0 - test_incorrect_options will be ignored\nFAILED r2e_tests/test_1.py::test_version - AssertionError: '0.14.1.dev131' !=...\nFAILED r2e_tests/test_1.py::test_script_shims - FileNotFoundError: [Errno 2] ...\nFAILED r2e_tests/test_1.py::test_cfg_override - TypeError: test_cfg_override(...\n============== 3 failed, 6 passed, 1 skipped, 1 xfailed in 1.46s ===============\n",
    "old_commit_res_stderr": ""
}
datalad/cmdline/helpers.py datalad/cmdline/tests/test_main.py
We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
[ISSUE]
**Title:** Missing "datalad" Prefix in `datalad --version` Output Causes Version Checks to Fail

**Description:**
When running the `datalad --version` command, the output only displays the version number without the expected "datalad" prefix. This discrepancy causes version verification processes to fail, as they are designed to check for the prefix.

**Example Buggy Code:**
```python
stdout, stderr = run_main(['--version'], expect_stderr=True)
print(stdout.rstrip())  # Output: '0.14.1.dev131'
```

**Expected Behavior:**
The `datalad --version` command should include the "datalad" prefix in its output, for example:
```
datalad 0.14.1.dev131
```

**Actual Behavior:**
The command outputs only the version number without the prefix:
```
0.14.1.dev131
```
This lack of prefix leads to assertion failures in tests that expect the output to start with "datalad".

[/ISSUE]
--- END ISSUE ---

Below are some code segments, each from a relevant file. One or more of these files may contain bugs.

--- BEGIN FILE ---
```
### datalad/cmdline/helpers.py
# emacs: -*- mode: python; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-
# ex: set sts=4 ts=4 sw=4 noet:
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
#   See COPYING file distributed along with the datalad package for the
#   copyright and license terms.
#
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""
"""

__docformat__ = 'restructuredtext'

import argparse
import os
import re
import sys
import gzip
import warnings
from tempfile import NamedTemporaryFile
from textwrap import wrap

from ..cmd import WitlessRunner as Runner
from ..log import is_interactive
from ..utils import (
    ensure_unicode,
    getpwd,
    unlink,
)
from ..version import __version__
from ..dochelpers import exc_str

from logging import getLogger
lgr = getLogger('datalad.cmdline')


class HelpAction(argparse.Action):
    def __call__(self, parser, namespace, values, option_string=None):
        # Lets use the manpage on mature systems but only for subcommands --
        # --help should behave similar to how git does it:
        # regular --help for "git" but man pages for specific commands.
        # It is important since we do discover all subcommands from entry
        # points at run time and thus any static manpage would like be out of
        # date
        interactive = is_interactive()
        if interactive \
                and option_string == '--help' \
                and ' ' in parser.prog:  # subcommand
            try:
                import subprocess
                # get the datalad manpage to use
                manfile = os.environ.get('MANPATH', '/usr/share/man') \
                    + '/man1/{0}.1.gz'.format(parser.prog.replace(' ', '-'))
                # extract version field from the manpage
                if not os.path.exists(manfile):
                    raise IOError("manfile is not found")
                with gzip.open(manfile) as f:
                    man_th = [line for line in f if line.startswith(b".TH")][0]
                man_version = man_th.split(b' ')[-1].strip(b" '\"\t\n").decode('utf-8')

                # don't show manpage if man_version not equal to current datalad_version
                if __version__ != man_version:
                    raise ValueError
                subprocess.check_call(
                    'man %s 2> /dev/null' % manfile,
                    shell=True)
                sys.exit(0)
            except (subprocess.CalledProcessError, IOError, OSError, IndexError, ValueError) as e:
                lgr.debug("Did not use manpage since %s", exc_str(e))
        if option_string == '-h':
            usage = parser.format_usage()
            ucomps = re.match(
                r'(?P<pre>.*){(?P<cmds>.*)}(?P<post>....*)',
                usage,
                re.DOTALL)
            if ucomps:
                ucomps = ucomps.groupdict()
                indent_level = len(ucomps['post']) - len(ucomps['post'].lstrip())
                usage = '{pre}{{{cmds}}}{post}'.format(
                    pre=ucomps['pre'],
                    cmds='\n'.join(wrap(
                        ', '.join(sorted(c.strip() for c in ucomps['cmds'].split(','))),
                        break_on_hyphens=False,
                        subsequent_indent=' ' * indent_level)),
                    post=ucomps['post'],
                )
            helpstr = "%s\n%s" % (
                usage,
                "Use '--help' to get more comprehensive information.")
        else:
            helpstr = parser.format_help()
        # better for help2man
        # for main command -- should be different sections. And since we are in
        # heavy output massaging mode...
        if "commands for dataset operations" in helpstr.lower():
            opt_args_str = '*Global options*'
            pos_args_str = '*Commands*'
            # tune up usage -- default one is way too heavy
            helpstr = re.sub(r'^[uU]sage: .*?\n\s*\n',
                             'Usage: datalad [global-opts] command [command-opts]\n\n',
                             helpstr,
                             flags=re.MULTILINE | re.DOTALL)
            # and altogether remove sections with long list of commands
            helpstr = re.sub(r'positional arguments:\s*\n\s*{.*}\n', '', helpstr)
        else:
            opt_args_str = "*Options*"
            pos_args_str = "*Arguments*"
        helpstr = re.sub(r'optional arguments:', opt_args_str, helpstr)
        helpstr = re.sub(r'positional arguments:', pos_args_str, helpstr)
        # usage is on the same line
        helpstr = re.sub(r'^usage:', 'Usage:', helpstr)

        if interactive and option_string == '--help':
            import pydoc
            pydoc.pager(helpstr)
        else:
            print(helpstr)
        sys.exit(0)


class LogLevelAction(argparse.Action):
    def __call__(self, parser, namespace, values, option_string=None):
        from ..log import LoggerHelper
        LoggerHelper().set_level(level=values)


# MIH: Disabled. Non-functional, untested.
#class PBSAction(argparse.Action):
#    """Action to schedule actual command execution via PBS (e.g. Condor)"""
#    def __call__(self, parser, namespace, values, option_string=None):
#        pbs = values[0]
#        import pdb; pdb.set_trace()
#        i = 1


def parser_add_version_opt(parser, mod_name, include_name=False, delay=False):
    """Setup --version option

    Parameters
    ----------
    parser:
    mod_name: str, optional
    include_name: bool, optional
    delay: bool, optional
      If set to True, no action is taken immediately, and rather
      we assign the function which would print the version. Necessary for
      early pre-parsing of the cmdline
    """

    def print_version():
        mod = sys.modules.get(mod_name, None)
        version = getattr(mod, '__version__', None)
        if version is None:
            # Let's use the standard Python mechanism if underlying module
            # did not provide __version__
            try:
                import pkg_resources
                version = pkg_resources.get_distribution(mod_name).version
            except:
                version = "unknown"
        if include_name:
            print("%s %s" % (mod_name, version))
        else:
            print(version)
        sys.exit(0)

    class versionAction(argparse.Action):
        def __call__(self, parser, args, values, option_string=None):
            if delay:
                setattr(args, self.dest, print_version)
            else:
                print_version()

    parser.add_argument(
        "--version",
        nargs=0,
        action=versionAction,
        help=(
            "show the program's version"
            if not mod_name
            else "show the module and its version which provides the command")
    )


def parser_add_common_opt(parser, opt, names=None, **kwargs):
    from . import common_args
    opt_tmpl = getattr(common_args, opt)
    opt_kwargs = opt_tmpl[2].copy()
    opt_kwargs.update(kwargs)
    if names is None:
        parser.add_argument(*opt_tmpl[1], **opt_kwargs)
    else:
        parser.add_argument(*names, **opt_kwargs)


def parser_add_common_options(parser, version=None):
    parser_add_common_opt(parser, 'log_level')
    parser_add_common_opt(parser, 'pbs_runner')
    parser_add_common_opt(parser, 'change_path')
    if version is not None:
        warnings.warn("Passing 'version' to parser_add_common_options "
                      "no longer has an effect "
                      "and will be removed in a future release.",
                      DeprecationWarning)
    parser_add_version_opt(parser, 'datalad', include_name=False, delay=True)
    if __debug__:
        parser.add_argument(
            '--dbg', action='store_true', dest='common_debug',
            help="enter Python debugger when uncaught exception happens")
        parser.add_argument(
            '--idbg', action='store_true', dest='common_idebug',
            help="enter IPython debugger when uncaught exception happens")
    parser.add_argument(
        '-c', action='append', dest='cfg_overrides', metavar='KEY=VALUE',
        help="""configuration variable setting. Overrides any configuration
        read from a file, but is potentially overridden itself by configuration
        variables in the process environment.""")
    parser.add_argument(
        '-f', '--output-format', dest='common_output_format',
        default='tailored',
        type=ensure_unicode,
        metavar="{default,json,json_pp,tailored,'<template>'}",
        help="""select format for returned command results. 'tailored'
        enables a command-specific rendering style that is typically
        tailored to human consumption, if there is one for a specific
        command, or otherwise falls back on the the 'default' output
        format (this is the standard behavior); 'default' give one line
        per result reporting action, status, path and an optional message;
        'json' renders a JSON object with all properties for each result (one per
        line); 'json_pp' pretty-prints JSON spanning multiple lines;
        '<template>' reports any value(s) of any result properties in any format
        indicated by the template (e.g. '{path}'; compare with JSON
        output for all key-value choices). The template syntax follows the Python
        "format() language". It is possible to report individual
        dictionary values, e.g. '{metadata[name]}'. If a 2nd-level key contains
        a colon, e.g. 'music:Genre', ':' must be substituted by '#' in the template,
        like so: '{metadata[music#Genre]}'.""")
    parser.add_argument(
        '--report-status', dest='common_report_status',
        choices=['success', 'failure', 'ok', 'notneeded', 'impossible', 'error'],
        help="""constrain command result report to records matching the given
        status. 'success' is a synonym for 'ok' OR 'notneeded', 'failure' stands
        for 'impossible' OR 'error'.""")
    parser.add_argument(
        '--report-type', dest='common_report_type',
        choices=['dataset', 'file'],
        action='append',
        help="""constrain command result report to records matching the given
        type. Can be given more than once to match multiple types.""")
    parser.add_argument(
        '--on-failure', dest='common_on_failure',
        choices=['ignore', 'continue', 'stop'],
        # no default: better be configure per-command
        help="""when an operation fails: 'ignore' and continue with remaining
        operations, the error is logged but does not lead to a non-zero exit code
        of the command; 'continue' works like 'ignore', but an error causes a
        non-zero exit code; 'stop' halts on first failure and yields non-zero exit
        code. A failure is any result with status 'impossible' or 'error'.""")
    parser.add_argument(
        '--cmd', dest='_', action='store_true',
        help="""syntactical helper that can be used to end the list of global
        command line options before the subcommand label. Options taking
        an arbitrary number of arguments may require to be followed by a single
        --cmd in order to enable identification of the subcommand.""")


def strip_arg_from_argv(args, value, opt_names):
    """Strip an originally listed option (with its value) from the list cmdline args
    """
    # Yarik doesn't know better
    if args is None:
        args = sys.argv
    # remove present pbs-runner option
    args_clean = []
    skip = 0
    for i, arg in enumerate(args):
        if skip:
            # we skip only one as instructed
            skip -= 1
            continue
        if not (arg in opt_names and i < len(args) - 1 and args[i + 1] == value):
            args_clean.append(arg)
        else:
            # we need to skip this one and next one
            skip = 1
    return args_clean


def run_via_pbs(args, pbs):
    assert(pbs in ('condor',))  # for now

    # TODO: RF to support multiple backends, parameters, etc, for now -- just condor, no options
    f = NamedTemporaryFile('w', prefix='datalad-%s-' % pbs, suffix='.submit', delete=False)
    try:
        pwd = getpwd()
        logs = f.name.replace('.submit', '.log')
        exe = args[0]
        # TODO: we might need better way to join them, escaping spaces etc.  There must be a stock helper
        #exe_args = ' '.join(map(repr, args[1:])) if len(args) > 1 else ''
        exe_args = ' '.join(args[1:]) if len(args) > 1 else ''
        f.write("""\
Executable = %(exe)s
Initialdir = %(pwd)s
Output = %(logs)s
Error = %(logs)s
getenv = True

arguments = %(exe_args)s
queue
""" % locals())
        f.close()
        Runner().run(['condor_submit', f.name])
        lgr.info("Scheduled execution via %s.  Logs will be stored under %s", pbs, logs)
    finally:
        unlink(f.name)


# TODO: useful also outside of cmdline, move to support/
from os import curdir


def get_repo_instance(path=curdir, class_=None):
    """Returns an instance of appropriate datalad repository for path.
    Check whether a certain path is inside a known type of repository and
    returns an instance representing it. May also check for a certain type
    instead of detecting the type of repository.

    Parameters
    ----------
    path: str
      path to check; default: current working directory
    class_: class
      if given, check whether path is inside a repository, that can be
      represented as an instance of the passed class.

    Raises
    ------
    RuntimeError, in case cwd is not inside a known repository.
    """

    from os.path import ismount, exists, normpath, isabs
    from datalad.support.exceptions import InvalidGitRepositoryError
    from ..utils import expandpath
    from ..support.gitrepo import GitRepo
    from ..support.annexrepo import AnnexRepo

    dir_ = expandpath(path)
    abspath_ = path if isabs(path) else dir_
    if class_ is not None:
        if class_ == AnnexRepo:
            type_ = "annex"
        elif class_ == GitRepo:
            type_ = "git"
        else:
            raise RuntimeError("Unknown class %s." % str(class_))

    while not ismount(dir_):  # TODO: always correct termination?
        if exists(opj(dir_, '.git')):
            # found git dir
            if class_ is None:
                # detect repo type:
                try:
                    return AnnexRepo(dir_, create=False)
                except RuntimeError as e:
                    pass
                try:
                    return GitRepo(dir_, create=False)
                except InvalidGitRepositoryError as e:
                    raise RuntimeError("No datalad repository found in %s" %
                                       abspath_)
            else:
                try:
                    return class_(dir_, create=False)
                except (RuntimeError, InvalidGitRepositoryError) as e:
                    raise RuntimeError("No %s repository found in %s." %
                                       (type_, abspath_))
        else:
            dir_ = normpath(opj(dir_, ".."))

    if class_ is not None:
        raise RuntimeError("No %s repository found in %s" % (type_, abspath_))
    else:
        raise RuntimeError("No datalad repository found in %s" % abspath_)


from appdirs import AppDirs
from os.path import join as opj

dirs = AppDirs("datalad", "datalad.org")

```
--- END FILE ---

Please first localize the bug based on the issue statement, and then generate *SEARCH/REPLACE* edits to fix the issue.

Every *SEARCH/REPLACE* edit must use this format:
1. The file path
2. The start of search block: <<<<<<< SEARCH
3. A contiguous chunk of lines to search for in the existing source code
4. The dividing line: =======
5. The lines to replace into the source code
6. The end of the replace block: >>>>>>> REPLACE

Here is an example:

```python
### mathweb/flask/app.py
<<<<<<< SEARCH
from flask import Flask
=======
import math
from flask import Flask
>>>>>>> REPLACE
```
</solution>

Please note that the *SEARCH/REPLACE* edit REQUIRES PROPER INDENTATION. If you would like to add the line '        print(x)', you must fully write that out, with all those spaces before the code!
Wrap each *SEARCH/REPLACE* edit in a code block as shown in the example above. If you have multiple *SEARCH/REPLACE* edits, use a separate code block for each one.
[ISSUE]
**Title:** Missing "datalad" Prefix in `datalad --version` Output Causes Version Checks to Fail

**Description:**
When running the `datalad --version` command, the output only displays the version number without the expected "datalad" prefix. This discrepancy causes version verification processes to fail, as they are designed to check for the prefix.

**Example Buggy Code:**
```python
stdout, stderr = run_main(['--version'], expect_stderr=True)
print(stdout.rstrip())  # Output: '0.14.1.dev131'
```

**Expected Behavior:**
The `datalad --version` command should include the "datalad" prefix in its output, for example:
```
datalad 0.14.1.dev131
```

**Actual Behavior:**
The command outputs only the version number without the prefix:
```
0.14.1.dev131
```
This lack of prefix leads to assertion failures in tests that expect the output to start with "datalad".

[/ISSUE]
{
    "test_version": "PASSED",
    "test_usage_on_insufficient_args": "PASSED",
    "test_subcmd_usage_on_unknown_args": "PASSED",
    "test_combined_short_option": "PASSED",
    "test_script_shims": "PASSED",
    "test_incorrect_cfg_override": "PASSED",
    "test_fail_with_short_help": "PASSED",
    "test_fix_datalad_ri": "PASSED",
    "test_cfg_override": "FAILED"
}
diff --git a/datalad/cmdline/helpers.py b/datalad/cmdline/helpers.py
index f48c159a0..74d27f7de 100644
--- a/datalad/cmdline/helpers.py
+++ b/datalad/cmdline/helpers.py
@@ -202,7 +202,7 @@ def parser_add_common_options(parser, version=None):
                       "no longer has an effect "
                       "and will be removed in a future release.",
                       DeprecationWarning)
-    parser_add_version_opt(parser, 'datalad', include_name=False, delay=True)
+    parser_add_version_opt(parser, 'datalad', include_name=True, delay=True)
     if __debug__:
         parser.add_argument(
             '--dbg', action='store_true', dest='common_debug',

{"datalad/cmdline/helpers.py": "# emacs: -*- mode: python; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-\n# ex: set sts=4 ts=4 sw=4 noet:\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n#\n#   See COPYING file distributed along with the datalad package for the\n#   copyright and license terms.\n#\n# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##\n\"\"\"\n\"\"\"\n\n__docformat__ = 'restructuredtext'\n\nimport argparse\nimport os\nimport re\nimport sys\nimport gzip\nimport warnings\nfrom tempfile import NamedTemporaryFile\nfrom textwrap import wrap\n\nfrom ..cmd import WitlessRunner as Runner\nfrom ..log import is_interactive\nfrom ..utils import (\n    ensure_unicode,\n    getpwd,\n    unlink,\n)\nfrom ..version import __version__\nfrom ..dochelpers import exc_str\n\nfrom logging import getLogger\nlgr = getLogger('datalad.cmdline')\n\n\nclass HelpAction(argparse.Action):\n    def __call__(self, parser, namespace, values, option_string=None):\n        # Lets use the manpage on mature systems but only for subcommands --\n        # --help should behave similar to how git does it:\n        # regular --help for \"git\" but man pages for specific commands.\n        # It is important since we do discover all subcommands from entry\n        # points at run time and thus any static manpage would like be out of\n        # date\n        interactive = is_interactive()\n        if interactive \\\n                and option_string == '--help' \\\n                and ' ' in parser.prog:  # subcommand\n            try:\n                import subprocess\n                # get the datalad manpage to use\n                manfile = os.environ.get('MANPATH', '/usr/share/man') \\\n                    + '/man1/{0}.1.gz'.format(parser.prog.replace(' ', '-'))\n                # extract version field from the manpage\n                if not os.path.exists(manfile):\n                    raise IOError(\"manfile is not found\")\n                with gzip.open(manfile) as f:\n                    man_th = [line for line in f if line.startswith(b\".TH\")][0]\n                man_version = man_th.split(b' ')[-1].strip(b\" '\\\"\\t\\n\").decode('utf-8')\n\n                # don't show manpage if man_version not equal to current datalad_version\n                if __version__ != man_version:\n                    raise ValueError\n                subprocess.check_call(\n                    'man %s 2> /dev/null' % manfile,\n                    shell=True)\n                sys.exit(0)\n            except (subprocess.CalledProcessError, IOError, OSError, IndexError, ValueError) as e:\n                lgr.debug(\"Did not use manpage since %s\", exc_str(e))\n        if option_string == '-h':\n            usage = parser.format_usage()\n            ucomps = re.match(\n                r'(?P<pre>.*){(?P<cmds>.*)}(?P<post>....*)',\n                usage,\n                re.DOTALL)\n            if ucomps:\n                ucomps = ucomps.groupdict()\n                indent_level = len(ucomps['post']) - len(ucomps['post'].lstrip())\n                usage = '{pre}{{{cmds}}}{post}'.format(\n                    pre=ucomps['pre'],\n                    cmds='\\n'.join(wrap(\n                        ', '.join(sorted(c.strip() for c in ucomps['cmds'].split(','))),\n                        break_on_hyphens=False,\n                        subsequent_indent=' ' * indent_level)),\n                    post=ucomps['post'],\n                )\n            helpstr = \"%s\\n%s\" % (\n                usage,\n                \"Use '--help' to get more comprehensive information.\")\n        else:\n            helpstr = parser.format_help()\n        # better for help2man\n        # for main command -- should be different sections. And since we are in\n        # heavy output massaging mode...\n        if \"commands for dataset operations\" in helpstr.lower():\n            opt_args_str = '*Global options*'\n            pos_args_str = '*Commands*'\n            # tune up usage -- default one is way too heavy\n            helpstr = re.sub(r'^[uU]sage: .*?\\n\\s*\\n',\n                             'Usage: datalad [global-opts] command [command-opts]\\n\\n',\n                             helpstr,\n                             flags=re.MULTILINE | re.DOTALL)\n            # and altogether remove sections with long list of commands\n            helpstr = re.sub(r'positional arguments:\\s*\\n\\s*{.*}\\n', '', helpstr)\n        else:\n            opt_args_str = \"*Options*\"\n            pos_args_str = \"*Arguments*\"\n        helpstr = re.sub(r'optional arguments:', opt_args_str, helpstr)\n        helpstr = re.sub(r'positional arguments:', pos_args_str, helpstr)\n        # usage is on the same line\n        helpstr = re.sub(r'^usage:', 'Usage:', helpstr)\n\n        if interactive and option_string == '--help':\n            import pydoc\n            pydoc.pager(helpstr)\n        else:\n            print(helpstr)\n        sys.exit(0)\n\n\nclass LogLevelAction(argparse.Action):\n    def __call__(self, parser, namespace, values, option_string=None):\n        from ..log import LoggerHelper\n        LoggerHelper().set_level(level=values)\n\n\n# MIH: Disabled. Non-functional, untested.\n#class PBSAction(argparse.Action):\n#    \"\"\"Action to schedule actual command execution via PBS (e.g. Condor)\"\"\"\n#    def __call__(self, parser, namespace, values, option_string=None):\n#        pbs = values[0]\n#        import pdb; pdb.set_trace()\n#        i = 1\n\n\ndef parser_add_version_opt(parser, mod_name, include_name=False, delay=False):\n    \"\"\"Setup --version option\n\n    Parameters\n    ----------\n    parser:\n    mod_name: str, optional\n    include_name: bool, optional\n    delay: bool, optional\n      If set to True, no action is taken immediately, and rather\n      we assign the function which would print the version. Necessary for\n      early pre-parsing of the cmdline\n    \"\"\"\n\n    def print_version():\n        mod = sys.modules.get(mod_name, None)\n        version = getattr(mod, '__version__', None)\n        if version is None:\n            # Let's use the standard Python mechanism if underlying module\n            # did not provide __version__\n            try:\n                import pkg_resources\n                version = pkg_resources.get_distribution(mod_name).version\n            except:\n                version = \"unknown\"\n        if include_name:\n            print(\"%s %s\" % (mod_name, version))\n        else:\n            print(version)\n        sys.exit(0)\n\n    class versionAction(argparse.Action):\n        def __call__(self, parser, args, values, option_string=None):\n            if delay:\n                setattr(args, self.dest, print_version)\n            else:\n                print_version()\n\n    parser.add_argument(\n        \"--version\",\n        nargs=0,\n        action=versionAction,\n        help=(\n            \"show the program's version\"\n            if not mod_name\n            else \"show the module and its version which provides the command\")\n    )\n\n\ndef parser_add_common_opt(parser, opt, names=None, **kwargs):\n    from . import common_args\n    opt_tmpl = getattr(common_args, opt)\n    opt_kwargs = opt_tmpl[2].copy()\n    opt_kwargs.update(kwargs)\n    if names is None:\n        parser.add_argument(*opt_tmpl[1], **opt_kwargs)\n    else:\n        parser.add_argument(*names, **opt_kwargs)\n\n\ndef parser_add_common_options(parser, version=None):\n    parser_add_common_opt(parser, 'log_level')\n    parser_add_common_opt(parser, 'pbs_runner')\n    parser_add_common_opt(parser, 'change_path')\n    if version is not None:\n        warnings.warn(\"Passing 'version' to parser_add_common_options \"\n                      \"no longer has an effect \"\n                      \"and will be removed in a future release.\",\n                      DeprecationWarning)\n    parser_add_version_opt(parser, 'datalad', include_name=False, delay=True)\n    if __debug__:\n        parser.add_argument(\n            '--dbg', action='store_true', dest='common_debug',\n            help=\"enter Python debugger when uncaught exception happens\")\n        parser.add_argument(\n            '--idbg', action='store_true', dest='common_idebug',\n            help=\"enter IPython debugger when uncaught exception happens\")\n    parser.add_argument(\n        '-c', action='append', dest='cfg_overrides', metavar='KEY=VALUE',\n        help=\"\"\"configuration variable setting. Overrides any configuration\n        read from a file, but is potentially overridden itself by configuration\n        variables in the process environment.\"\"\")\n    parser.add_argument(\n        '-f', '--output-format', dest='common_output_format',\n        default='tailored',\n        type=ensure_unicode,\n        metavar=\"{default,json,json_pp,tailored,'<template>'}\",\n        help=\"\"\"select format for returned command results. 'tailored'\n        enables a command-specific rendering style that is typically\n        tailored to human consumption, if there is one for a specific\n        command, or otherwise falls back on the the 'default' output\n        format (this is the standard behavior); 'default' give one line\n        per result reporting action, status, path and an optional message;\n        'json' renders a JSON object with all properties for each result (one per\n        line); 'json_pp' pretty-prints JSON spanning multiple lines;\n        '<template>' reports any value(s) of any result properties in any format\n        indicated by the template (e.g. '{path}'; compare with JSON\n        output for all key-value choices). The template syntax follows the Python\n        \"format() language\". It is possible to report individual\n        dictionary values, e.g. '{metadata[name]}'. If a 2nd-level key contains\n        a colon, e.g. 'music:Genre', ':' must be substituted by '#' in the template,\n        like so: '{metadata[music#Genre]}'.\"\"\")\n    parser.add_argument(\n        '--report-status', dest='common_report_status',\n        choices=['success', 'failure', 'ok', 'notneeded', 'impossible', 'error'],\n        help=\"\"\"constrain command result report to records matching the given\n        status. 'success' is a synonym for 'ok' OR 'notneeded', 'failure' stands\n        for 'impossible' OR 'error'.\"\"\")\n    parser.add_argument(\n        '--report-type', dest='common_report_type',\n        choices=['dataset', 'file'],\n        action='append',\n        help=\"\"\"constrain command result report to records matching the given\n        type. Can be given more than once to match multiple types.\"\"\")\n    parser.add_argument(\n        '--on-failure', dest='common_on_failure',\n        choices=['ignore', 'continue', 'stop'],\n        # no default: better be configure per-command\n        help=\"\"\"when an operation fails: 'ignore' and continue with remaining\n        operations, the error is logged but does not lead to a non-zero exit code\n        of the command; 'continue' works like 'ignore', but an error causes a\n        non-zero exit code; 'stop' halts on first failure and yields non-zero exit\n        code. A failure is any result with status 'impossible' or 'error'.\"\"\")\n    parser.add_argument(\n        '--cmd', dest='_', action='store_true',\n        help=\"\"\"syntactical helper that can be used to end the list of global\n        command line options before the subcommand label. Options taking\n        an arbitrary number of arguments may require to be followed by a single\n        --cmd in order to enable identification of the subcommand.\"\"\")\n\n\ndef strip_arg_from_argv(args, value, opt_names):\n    \"\"\"Strip an originally listed option (with its value) from the list cmdline args\n    \"\"\"\n    # Yarik doesn't know better\n    if args is None:\n        args = sys.argv\n    # remove present pbs-runner option\n    args_clean = []\n    skip = 0\n    for i, arg in enumerate(args):\n        if skip:\n            # we skip only one as instructed\n            skip -= 1\n            continue\n        if not (arg in opt_names and i < len(args) - 1 and args[i + 1] == value):\n            args_clean.append(arg)\n        else:\n            # we need to skip this one and next one\n            skip = 1\n    return args_clean\n\n\ndef run_via_pbs(args, pbs):\n    assert(pbs in ('condor',))  # for now\n\n    # TODO: RF to support multiple backends, parameters, etc, for now -- just condor, no options\n    f = NamedTemporaryFile('w', prefix='datalad-%s-' % pbs, suffix='.submit', delete=False)\n    try:\n        pwd = getpwd()\n        logs = f.name.replace('.submit', '.log')\n        exe = args[0]\n        # TODO: we might need better way to join them, escaping spaces etc.  There must be a stock helper\n        #exe_args = ' '.join(map(repr, args[1:])) if len(args) > 1 else ''\n        exe_args = ' '.join(args[1:]) if len(args) > 1 else ''\n        f.write(\"\"\"\\\nExecutable = %(exe)s\nInitialdir = %(pwd)s\nOutput = %(logs)s\nError = %(logs)s\ngetenv = True\n\narguments = %(exe_args)s\nqueue\n\"\"\" % locals())\n        f.close()\n        Runner().run(['condor_submit', f.name])\n        lgr.info(\"Scheduled execution via %s.  Logs will be stored under %s\", pbs, logs)\n    finally:\n        unlink(f.name)\n\n\n# TODO: useful also outside of cmdline, move to support/\nfrom os import curdir\n\n\ndef get_repo_instance(path=curdir, class_=None):\n    \"\"\"Returns an instance of appropriate datalad repository for path.\n    Check whether a certain path is inside a known type of repository and\n    returns an instance representing it. May also check for a certain type\n    instead of detecting the type of repository.\n\n    Parameters\n    ----------\n    path: str\n      path to check; default: current working directory\n    class_: class\n      if given, check whether path is inside a repository, that can be\n      represented as an instance of the passed class.\n\n    Raises\n    ------\n    RuntimeError, in case cwd is not inside a known repository.\n    \"\"\"\n\n    from os.path import ismount, exists, normpath, isabs\n    from datalad.support.exceptions import InvalidGitRepositoryError\n    from ..utils import expandpath\n    from ..support.gitrepo import GitRepo\n    from ..support.annexrepo import AnnexRepo\n\n    dir_ = expandpath(path)\n    abspath_ = path if isabs(path) else dir_\n    if class_ is not None:\n        if class_ == AnnexRepo:\n            type_ = \"annex\"\n        elif class_ == GitRepo:\n            type_ = \"git\"\n        else:\n            raise RuntimeError(\"Unknown class %s.\" % str(class_))\n\n    while not ismount(dir_):  # TODO: always correct termination?\n        if exists(opj(dir_, '.git')):\n            # found git dir\n            if class_ is None:\n                # detect repo type:\n                try:\n                    return AnnexRepo(dir_, create=False)\n                except RuntimeError as e:\n                    pass\n                try:\n                    return GitRepo(dir_, create=False)\n                except InvalidGitRepositoryError as e:\n                    raise RuntimeError(\"No datalad repository found in %s\" %\n                                       abspath_)\n            else:\n                try:\n                    return class_(dir_, create=False)\n                except (RuntimeError, InvalidGitRepositoryError) as e:\n                    raise RuntimeError(\"No %s repository found in %s.\" %\n                                       (type_, abspath_))\n        else:\n            dir_ = normpath(opj(dir_, \"..\"))\n\n    if class_ is not None:\n        raise RuntimeError(\"No %s repository found in %s\" % (type_, abspath_))\n    else:\n        raise RuntimeError(\"No datalad repository found in %s\" % abspath_)\n\n\nfrom appdirs import AppDirs\nfrom os.path import join as opj\n\ndirs = AppDirs(\"datalad\", \"datalad.org\")\n"}
A user will ask you to solve a task. You should first draft your thinking process (inner monologue). Then, generate the solution.

Your response format must follow the template below:
<think>
Your thoughts or/and draft, like working through an exercise on scratch paper. Be as casual and as long as you want until you are confident to generate a correct solution.
</think>
<solution>
Final solution presented to the user.
</solution>
system
We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
[ISSUE]
**Title:** Missing "datalad" Prefix in `datalad --version` Output Causes Version Checks to Fail

**Description:**
When running the `datalad --version` command, the output only displays the version number without the expected "datalad" prefix. This discrepancy causes version verification processes to fail, as they are designed to check for the prefix.

**Example Buggy Code:**
```python
stdout, stderr = run_main(['--version'], expect_stderr=True)
print(stdout.rstrip())  # Output: '0.14.1.dev131'
```

**Expected Behavior:**
The `datalad --version` command should include the "datalad" prefix in its output, for example:
```
datalad 0.14.1.dev131
```

**Actual Behavior:**
The command outputs only the version number without the prefix:
```
0.14.1.dev131
```
This lack of prefix leads to assertion failures in tests that expect the output to start with "datalad".

[/ISSUE]
--- END ISSUE ---

Below are some code segments, each from a relevant file. One or more of these files may contain bugs.

--- BEGIN FILE ---
```
### datalad/cmdline/helpers.py
# emacs: -*- mode: python; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-
# ex: set sts=4 ts=4 sw=4 noet:
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
#   See COPYING file distributed along with the datalad package for the
#   copyright and license terms.
#
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""
"""

__docformat__ = 'restructuredtext'

import argparse
import os
import re
import sys
import gzip
import warnings
from tempfile import NamedTemporaryFile
from textwrap import wrap

from ..cmd import WitlessRunner as Runner
from ..log import is_interactive
from ..utils import (
    ensure_unicode,
    getpwd,
    unlink,
)
from ..version import __version__
from ..dochelpers import exc_str

from logging import getLogger
lgr = getLogger('datalad.cmdline')


class HelpAction(argparse.Action):
    def __call__(self, parser, namespace, values, option_string=None):
        # Lets use the manpage on mature systems but only for subcommands --
        # --help should behave similar to how git does it:
        # regular --help for "git" but man pages for specific commands.
        # It is important since we do discover all subcommands from entry
        # points at run time and thus any static manpage would like be out of
        # date
        interactive = is_interactive()
        if interactive \
                and option_string == '--help' \
                and ' ' in parser.prog:  # subcommand
            try:
                import subprocess
                # get the datalad manpage to use
                manfile = os.environ.get('MANPATH', '/usr/share/man') \
                    + '/man1/{0}.1.gz'.format(parser.prog.replace(' ', '-'))
                # extract version field from the manpage
                if not os.path.exists(manfile):
                    raise IOError("manfile is not found")
                with gzip.open(manfile) as f:
                    man_th = [line for line in f if line.startswith(b".TH")][0]
                man_version = man_th.split(b' ')[-1].strip(b" '\"\t\n").decode('utf-8')

                # don't show manpage if man_version not equal to current datalad_version
                if __version__ != man_version:
                    raise ValueError
                subprocess.check_call(
                    'man %s 2> /dev/null' % manfile,
                    shell=True)
                sys.exit(0)
            except (subprocess.CalledProcessError, IOError, OSError, IndexError, ValueError) as e:
                lgr.debug("Did not use manpage since %s", exc_str(e))
        if option_string == '-h':
            usage = parser.format_usage()
            ucomps = re.match(
                r'(?P<pre>.*){(?P<cmds>.*)}(?P<post>....*)',
                usage,
                re.DOTALL)
            if ucomps:
                ucomps = ucomps.groupdict()
                indent_level = len(ucomps['post']) - len(ucomps['post'].lstrip())
                usage = '{pre}{{{cmds}}}{post}'.format(
                    pre=ucomps['pre'],
                    cmds='\n'.join(wrap(
                        ', '.join(sorted(c.strip() for c in ucomps['cmds'].split(','))),
                        break_on_hyphens=False,
                        subsequent_indent=' ' * indent_level)),
                    post=ucomps['post'],
                )
            helpstr = "%s\n%s" % (
                usage,
                "Use '--help' to get more comprehensive information.")
        else:
            helpstr = parser.format_help()
        # better for help2man
        # for main command -- should be different sections. And since we are in
        # heavy output massaging mode...
        if "commands for dataset operations" in helpstr.lower():
            opt_args_str = '*Global options*'
            pos_args_str = '*Commands*'
            # tune up usage -- default one is way too heavy
            helpstr = re.sub(r'^[uU]sage: .*?\n\s*\n',
                             'Usage: datalad [global-opts] command [command-opts]\n\n',
                             helpstr,
                             flags=re.MULTILINE | re.DOTALL)
            # and altogether remove sections with long list of commands
            helpstr = re.sub(r'positional arguments:\s*\n\s*{.*}\n', '', helpstr)
        else:
            opt_args_str = "*Options*"
            pos_args_str = "*Arguments*"
        helpstr = re.sub(r'optional arguments:', opt_args_str, helpstr)
        helpstr = re.sub(r'positional arguments:', pos_args_str, helpstr)
        # usage is on the same line
        helpstr = re.sub(r'^usage:', 'Usage:', helpstr)

        if interactive and option_string == '--help':
            import pydoc
            pydoc.pager(helpstr)
        else:
            print(helpstr)
        sys.exit(0)


class LogLevelAction(argparse.Action):
    def __call__(self, parser, namespace, values, option_string=None):
        from ..log import LoggerHelper
        LoggerHelper().set_level(level=values)


# MIH: Disabled. Non-functional, untested.
#class PBSAction(argparse.Action):
#    """Action to schedule actual command execution via PBS (e.g. Condor)"""
#    def __call__(self, parser, namespace, values, option_string=None):
#        pbs = values[0]
#        import pdb; pdb.set_trace()
#        i = 1


def parser_add_version_opt(parser, mod_name, include_name=False, delay=False):
    """Setup --version option

    Parameters
    ----------
    parser:
    mod_name: str, optional
    include_name: bool, optional
    delay: bool, optional
      If set to True, no action is taken immediately, and rather
      we assign the function which would print the version. Necessary for
      early pre-parsing of the cmdline
    """

    def print_version():
        mod = sys.modules.get(mod_name, None)
        version = getattr(mod, '__version__', None)
        if version is None:
            # Let's use the standard Python mechanism if underlying module
            # did not provide __version__
            try:
                import pkg_resources
                version = pkg_resources.get_distribution(mod_name).version
            except:
                version = "unknown"
        if include_name:
            print("%s %s" % (mod_name, version))
        else:
            print(version)
        sys.exit(0)

    class versionAction(argparse.Action):
        def __call__(self, parser, args, values, option_string=None):
            if delay:
                setattr(args, self.dest, print_version)
            else:
                print_version()

    parser.add_argument(
        "--version",
        nargs=0,
        action=versionAction,
        help=(
            "show the program's version"
            if not mod_name
            else "show the module and its version which provides the command")
    )


def parser_add_common_opt(parser, opt, names=None, **kwargs):
    from . import common_args
    opt_tmpl = getattr(common_args, opt)
    opt_kwargs = opt_tmpl[2].copy()
    opt_kwargs.update(kwargs)
    if names is None:
        parser.add_argument(*opt_tmpl[1], **opt_kwargs)
    else:
        parser.add_argument(*names, **opt_kwargs)


def parser_add_common_options(parser, version=None):
    parser_add_common_opt(parser, 'log_level')
    parser_add_common_opt(parser, 'pbs_runner')
    parser_add_common_opt(parser, 'change_path')
    if version is not None:
        warnings.warn("Passing 'version' to parser_add_common_options "
                      "no longer has an effect "
                      "and will be removed in a future release.",
                      DeprecationWarning)
    parser_add_version_opt(parser, 'datalad', include_name=False, delay=True)
    if __debug__:
        parser.add_argument(
            '--dbg', action='store_true', dest='common_debug',
            help="enter Python debugger when uncaught exception happens")
        parser.add_argument(
            '--idbg', action='store_true', dest='common_idebug',
            help="enter IPython debugger when uncaught exception happens")
    parser.add_argument(
        '-c', action='append', dest='cfg_overrides', metavar='KEY=VALUE',
        help="""configuration variable setting. Overrides any configuration
        read from a file, but is potentially overridden itself by configuration
        variables in the process environment.""")
    parser.add_argument(
        '-f', '--output-format', dest='common_output_format',
        default='tailored',
        type=ensure_unicode,
        metavar="{default,json,json_pp,tailored,'<template>'}",
        help="""select format for returned command results. 'tailored'
        enables a command-specific rendering style that is typically
        tailored to human consumption, if there is one for a specific
        command, or otherwise falls back on the the 'default' output
        format (this is the standard behavior); 'default' give one line
        per result reporting action, status, path and an optional message;
        'json' renders a JSON object with all properties for each result (one per
        line); 'json_pp' pretty-prints JSON spanning multiple lines;
        '<template>' reports any value(s) of any result properties in any format
        indicated by the template (e.g. '{path}'; compare with JSON
        output for all key-value choices). The template syntax follows the Python
        "format() language". It is possible to report individual
        dictionary values, e.g. '{metadata[name]}'. If a 2nd-level key contains
        a colon, e.g. 'music:Genre', ':' must be substituted by '#' in the template,
        like so: '{metadata[music#Genre]}'.""")
    parser.add_argument(
        '--report-status', dest='common_report_status',
        choices=['success', 'failure', 'ok', 'notneeded', 'impossible', 'error'],
        help="""constrain command result report to records matching the given
        status. 'success' is a synonym for 'ok' OR 'notneeded', 'failure' stands
        for 'impossible' OR 'error'.""")
    parser.add_argument(
        '--report-type', dest='common_report_type',
        choices=['dataset', 'file'],
        action='append',
        help="""constrain command result report to records matching the given
        type. Can be given more than once to match multiple types.""")
    parser.add_argument(
        '--on-failure', dest='common_on_failure',
        choices=['ignore', 'continue', 'stop'],
        # no default: better be configure per-command
        help="""when an operation fails: 'ignore' and continue with remaining
        operations, the error is logged but does not lead to a non-zero exit code
        of the command; 'continue' works like 'ignore', but an error causes a
        non-zero exit code; 'stop' halts on first failure and yields non-zero exit
        code. A failure is any result with status 'impossible' or 'error'.""")
    parser.add_argument(
        '--cmd', dest='_', action='store_true',
        help="""syntactical helper that can be used to end the list of global
        command line options before the subcommand label. Options taking
        an arbitrary number of arguments may require to be followed by a single
        --cmd in order to enable identification of the subcommand.""")


def strip_arg_from_argv(args, value, opt_names):
    """Strip an originally listed option (with its value) from the list cmdline args
    """
    # Yarik doesn't know better
    if args is None:
        args = sys.argv
    # remove present pbs-runner option
    args_clean = []
    skip = 0
    for i, arg in enumerate(args):
        if skip:
            # we skip only one as instructed
            skip -= 1
            continue
        if not (arg in opt_names and i < len(args) - 1 and args[i + 1] == value):
            args_clean.append(arg)
        else:
            # we need to skip this one and next one
            skip = 1
    return args_clean


def run_via_pbs(args, pbs):
    assert(pbs in ('condor',))  # for now

    # TODO: RF to support multiple backends, parameters, etc, for now -- just condor, no options
    f = NamedTemporaryFile('w', prefix='datalad-%s-' % pbs, suffix='.submit', delete=False)
    try:
        pwd = getpwd()
        logs = f.name.replace('.submit', '.log')
        exe = args[0]
        # TODO: we might need better way to join them, escaping spaces etc.  There must be a stock helper
        #exe_args = ' '.join(map(repr, args[1:])) if len(args) > 1 else ''
        exe_args = ' '.join(args[1:]) if len(args) > 1 else ''
        f.write("""\
Executable = %(exe)s
Initialdir = %(pwd)s
Output = %(logs)s
Error = %(logs)s
getenv = True

arguments = %(exe_args)s
queue
""" % locals())
        f.close()
        Runner().run(['condor_submit', f.name])
        lgr.info("Scheduled execution via %s.  Logs will be stored under %s", pbs, logs)
    finally:
        unlink(f.name)


# TODO: useful also outside of cmdline, move to support/
from os import curdir


def get_repo_instance(path=curdir, class_=None):
    """Returns an instance of appropriate datalad repository for path.
    Check whether a certain path is inside a known type of repository and
    returns an instance representing it. May also check for a certain type
    instead of detecting the type of repository.

    Parameters
    ----------
    path: str
      path to check; default: current working directory
    class_: class
      if given, check whether path is inside a repository, that can be
      represented as an instance of the passed class.

    Raises
    ------
    RuntimeError, in case cwd is not inside a known repository.
    """

    from os.path import ismount, exists, normpath, isabs
    from datalad.support.exceptions import InvalidGitRepositoryError
    from ..utils import expandpath
    from ..support.gitrepo import GitRepo
    from ..support.annexrepo import AnnexRepo

    dir_ = expandpath(path)
    abspath_ = path if isabs(path) else dir_
    if class_ is not None:
        if class_ == AnnexRepo:
            type_ = "annex"
        elif class_ == GitRepo:
            type_ = "git"
        else:
            raise RuntimeError("Unknown class %s." % str(class_))

    while not ismount(dir_):  # TODO: always correct termination?
        if exists(opj(dir_, '.git')):
            # found git dir
            if class_ is None:
                # detect repo type:
                try:
                    return AnnexRepo(dir_, create=False)
                except RuntimeError as e:
                    pass
                try:
                    return GitRepo(dir_, create=False)
                except InvalidGitRepositoryError as e:
                    raise RuntimeError("No datalad repository found in %s" %
                                       abspath_)
            else:
                try:
                    return class_(dir_, create=False)
                except (RuntimeError, InvalidGitRepositoryError) as e:
                    raise RuntimeError("No %s repository found in %s." %
                                       (type_, abspath_))
        else:
            dir_ = normpath(opj(dir_, ".."))

    if class_ is not None:
        raise RuntimeError("No %s repository found in %s" % (type_, abspath_))
    else:
        raise RuntimeError("No datalad repository found in %s" % abspath_)


from appdirs import AppDirs
from os.path import join as opj

dirs = AppDirs("datalad", "datalad.org")

```
--- END FILE ---

Please first localize the bug based on the issue statement, and then generate *SEARCH/REPLACE* edits to fix the issue.

Every *SEARCH/REPLACE* edit must use this format:
1. The file path
2. The start of search block: <<<<<<< SEARCH
3. A contiguous chunk of lines to search for in the existing source code
4. The dividing line: =======
5. The lines to replace into the source code
6. The end of the replace block: >>>>>>> REPLACE

Here is an example:

```python
### mathweb/flask/app.py
<<<<<<< SEARCH
from flask import Flask
=======
import math
from flask import Flask
>>>>>>> REPLACE
```
</solution>

Please note that the *SEARCH/REPLACE* edit REQUIRES PROPER INDENTATION. If you would like to add the line '        print(x)', you must fully write that out, with all those spaces before the code!
Wrap each *SEARCH/REPLACE* edit in a code block as shown in the example above. If you have multiple *SEARCH/REPLACE* edits, use a separate code block for each one.
user