{
    "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\"\"\"Rerun commands recorded with `datalad run`\"\"\"\n\n__docformat__ = 'restructuredtext'\n\n\nimport logging\nfrom itertools import dropwhile\nimport json\nimport re\n\nfrom datalad.dochelpers import exc_str\nfrom datalad.interface.base import Interface\nfrom datalad.interface.utils import eval_results\nfrom datalad.interface.base import build_doc\nfrom datalad.interface.diff import Diff\nfrom datalad.interface.unlock import Unlock\nfrom datalad.interface.results import get_status_dict\nfrom datalad.interface.run import run_command\n\nfrom datalad.support.constraints import EnsureNone, EnsureStr\nfrom datalad.support.gitrepo import GitCommandError\nfrom datalad.support.param import Parameter\n\nfrom datalad.distribution.dataset import require_dataset\nfrom datalad.distribution.dataset import EnsureDataset\nfrom datalad.distribution.dataset import datasetmethod\n\nlgr = logging.getLogger('datalad.interface.rerun')\n\n\n@build_doc\nclass Rerun(Interface):\n    \"\"\"Re-execute previous `datalad run` commands.\n\n    This will unlock any dataset content that is on record to have\n    been modified by the command in the specified revision.  It will\n    then re-execute the command in the recorded path (if it was inside\n    the dataset). Afterwards, all modifications will be saved.\n\n    Examples:\n\n      Re-execute the command from the previous commit::\n\n        % datalad rerun\n\n      Re-execute any commands in the last five commits::\n\n        % datalad rerun --since=HEAD~5\n\n      Do the same as above, but re-execute the commands on top of\n      HEAD~5 in a detached state::\n\n        % datalad rerun --onto= --since=HEAD~5\n\n      Re-execute all previous commands and compare the old and new\n      results::\n\n        % # on master branch\n        % datalad rerun --branch=verify --since=\n        % # now on verify branch\n        % datalad diff --revision=master..\n        % git log --oneline --left-right --cherry-pick master...\n    \"\"\"\n    _params_ = dict(\n        revision=Parameter(\n            args=(\"revision\",),\n            metavar=\"REVISION\",\n            nargs=\"?\",\n            doc=\"\"\"rerun command(s) in `revision`. By default, the command from\n            this commit will be executed, but [CMD: --since CMD][PY: `since`\n            PY] can be used to construct a revision range.\"\"\",\n            default=\"HEAD\",\n            constraints=EnsureStr()),\n        since=Parameter(\n            args=(\"--since\",),\n            doc=\"\"\"If `since` is a commit-ish, the commands from all commits\n            that are reachable from `revision` but not `since` will be\n            re-executed (in other words, the commands in :command:`git log\n            SINCE..REVISION`). If SINCE is an empty string, it is set to the\n            parent of the first commit that contains a recorded command (i.e.,\n            all commands in :command:`git log REVISION` will be\n            re-executed).\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        branch=Parameter(\n            metavar=\"NAME\",\n            args=(\"-b\", \"--branch\",),\n            doc=\"create and checkout this branch before rerunning the commands.\",\n            constraints=EnsureStr() | EnsureNone()),\n        onto=Parameter(\n            metavar=\"base\",\n            args=(\"--onto\",),\n            doc=\"\"\"start point for rerunning the commands. If not specified,\n            commands are executed at HEAD. This option can be used to specify\n            an alternative start point, which will be checked out with the\n            branch name specified by [CMD: --branch CMD][PY: `branch` PY] or in\n            a detached state otherwise. As a special case, an empty value for\n            this option means to use the commit specified by [CMD: --since\n            CMD][PY: `since` PY].\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        message=Parameter(\n            args=(\"-m\", \"--message\",),\n            metavar=\"MESSAGE\",\n            doc=\"\"\"use MESSAGE for the reran commit rather than the\n            recorded commit message.  In the case of a multi-commit\n            rerun, all the reran commits will have this message.\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        script=Parameter(\n            args=(\"--script\",),\n            metavar=\"FILE\",\n            doc=\"\"\"extract the commands into [CMD: FILE CMD][PY: this file PY]\n            rather than rerunning.\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        dataset=Parameter(\n            args=(\"-d\", \"--dataset\"),\n            doc=\"\"\"specify the dataset from which to rerun a recorded\n            command. If no dataset is given, an attempt is made to\n            identify the dataset based on the current working\n            directory. If a dataset is given, the command will be\n            executed in the root directory of this dataset.\"\"\",\n            constraints=EnsureDataset() | EnsureNone()),\n        # TODO\n        # --list-commands\n        #   go through the history and report any recorded command. this info\n        #   could be used to unlock the associated output files for a rerun\n    )\n\n    @staticmethod\n    @datasetmethod(name='rerun')\n    @eval_results\n    def __call__(\n            revision=\"HEAD\",\n            since=None,\n            dataset=None,\n            branch=None,\n            message=None,\n            onto=None,\n            script=None):\n\n        ds = require_dataset(\n            dataset, check_installed=True,\n            purpose='rerunning a command')\n\n        lgr.debug('rerunning command output underneath %s', ds)\n\n        if script is None and ds.repo.dirty:\n            yield get_status_dict(\n                'run',\n                ds=ds,\n                status='impossible',\n                message=('unsaved modifications present, '\n                         'cannot detect changes by command'))\n            return\n\n        err_info = get_status_dict('run', ds=ds)\n        if not ds.repo.get_hexsha():\n            yield dict(\n                err_info, status='impossible',\n                message='cannot rerun command, nothing recorded')\n            return\n\n        if branch and branch in ds.repo.get_branches():\n            yield get_status_dict(\n                \"run\", ds=ds, status=\"error\",\n                message=\"branch '{}' already exists\".format(branch))\n            return\n\n        if not commit_exists(ds, revision + \"^\"):\n            # Only a single commit is reachable from `revision`.  In\n            # this case, --since has no effect on the range construction.\n            revrange = revision\n        elif since is None:\n            revrange = \"{rev}^..{rev}\".format(rev=revision)\n        elif since.strip() == \"\":\n            revrange = revision\n        else:\n            revrange = \"{}..{}\".format(since, revision)\n\n        if ds.repo.repo.git.rev_list(\"--merges\", revrange, \"--\"):\n            yield get_status_dict(\n                \"run\", ds=ds, status=\"error\",\n                message=\"cannot rerun history with merge commits\")\n            return\n\n        revs = [{\"hexsha\": hexsha,\n                 \"message\": ds.repo.repo.git.show(\n                     hexsha, \"--format=%B\", \"--no-patch\")}\n                for hexsha in ds.repo.repo.git.rev_list(\n                        \"--reverse\", revrange, \"--\").split()]\n\n        for rev in revs:\n            try:\n                subj, info = get_run_info(rev[\"message\"])\n            except ValueError as exc:\n                yield dict(err_info, status='error',\n                           message=\"Error on {}'s message: {}\".format(\n                               rev[\"hexsha\"], exc_str(exc)))\n                return\n            if info is not None:\n                rev[\"run_info\"] = info\n                rev[\"run_subject\"] = subj\n\n        if since is not None and since.strip() == \"\":\n            # For --since='', drop any leading commits that don't have\n            # a run command.\n            revs = list(dropwhile(lambda r: \"run_info\" not in r, revs))\n\n        if script:\n            commands = (r[\"run_info\"][\"cmd\"] for r in revs if \"run_info\" in r)\n            with open(script, 'w') as ofh:\n                header = \"\"\"\\\n#!/bin/sh\n#\n# This file was generated by running (the equivalent of)\n#\n#   datalad rerun --script={script}{since} {revision}\n#\n# in {path}\\n\\n\"\"\"\n                ofh.write(header.format(\n                    script=script,\n                    since=\"\" if since is None else \" --since=\" + since,\n                    revision=ds.repo.repo.git.rev_parse(revision),\n                    path=ds.path))\n\n                for cmd in commands:\n                    if isinstance(cmd, list):\n                        cmd = \" \".join(cmd)\n                    ofh.write(cmd + \"\\n\")\n        else:\n            if onto is not None and onto.strip() == \"\":\n                # Special case: --onto='' is the value of --since.\n                # Because we're currently aborting if the revision list\n                # contains merges, we know that, regardless of if and how\n                # --since is specified, the effective value for --since is\n                # the parent of the first revision.\n                onto = revs[0][\"hexsha\"] + \"^\"\n                if not commit_exists(ds, onto):\n                    # This is unlikely to happen in the wild because it\n                    # means that the first commit is a datalad run commit.\n                    # Just abort rather than trying to checkout on orphan\n                    # branch or something like that.\n                    yield get_status_dict(\n                        \"run\", ds=ds, status=\"error\",\n                        message=\"Commit for --onto does not exist.\")\n                    return\n\n            if branch or onto:\n                start_point = onto or \"HEAD\"\n                if branch:\n                    checkout_options = [\"-b\", branch]\n                else:\n                    checkout_options = [\"--detach\"]\n                ds.repo.checkout(start_point, options=checkout_options)\n\n            for rev in revs:\n                hexsha = rev[\"hexsha\"]\n                if \"run_info\" not in rev:\n                    pick = False\n                    try:\n                        ds.repo.repo.git.merge_base(\"--is-ancestor\",\n                                                    hexsha, \"HEAD\")\n                    except GitCommandError:\n                        # Revision is NOT an ancestor of HEAD.\n                        pick = True\n\n                    shortrev = ds.repo.repo.git.rev_parse(\"--short\", hexsha)\n                    err_msg = \"no command for {} found; {}\".format(\n                        shortrev,\n                        \"cherry picking\" if pick else \"skipping\")\n                    yield dict(err_info, status='ok', message=err_msg)\n\n                    if pick:\n                        ds.repo.repo.git.cherry_pick(hexsha)\n                    continue\n\n                run_info = rev[\"run_info\"]\n                # Keep a \"rerun\" trail.\n                if \"chain\" in run_info:\n                    run_info[\"chain\"].append(hexsha)\n                else:\n                    run_info[\"chain\"] = [hexsha]\n\n                # now we have to find out what was modified during the\n                # last run, and enable re-modification ideally, we would\n                # bring back the entire state of the tree with #1424, but\n                # we limit ourself to file addition/not-in-place-modification\n                # for now\n                for r in ds.unlock(new_or_modified(ds, hexsha),\n                                   return_type='generator', result_xfm=None):\n                    yield r\n\n                for r in run_command(run_info['cmd'],\n                                     ds, message or rev[\"run_subject\"],\n                                     rerun_info=run_info):\n                    yield r\n\n\ndef get_run_info(message):\n    \"\"\"Extract run information from `message`\n\n    Parameters\n    ----------\n    message : str\n        A commit message.\n\n    Returns\n    -------\n    A tuple with the command's subject line and a dict with run information.\n    Both these values are None if `message` doesn't have a run command.\n\n    Raises\n    ------\n    A ValueError if the information in `message` is invalid.\n    \"\"\"\n    cmdrun_regex = r'\\[DATALAD RUNCMD\\] (.*)=== Do not change lines below ' \\\n                   r'===\\n(.*)\\n\\^\\^\\^ Do not change lines above \\^\\^\\^'\n    runinfo = re.match(cmdrun_regex, message, re.MULTILINE | re.DOTALL)\n    if not runinfo:\n        return None, None\n\n    rec_subj, runinfo = runinfo.groups()\n\n    try:\n        runinfo = json.loads(runinfo)\n    except Exception as e:\n        raise ValueError(\n            'cannot rerun command, command specification is not valid JSON: '\n            '%s' % exc_str(e)\n        )\n    if 'cmd' not in runinfo:\n        raise ValueError(\"Looks like a run commit but does not have a command\")\n    return rec_subj, runinfo\n\n\ndef new_or_modified(dataset, revision=\"HEAD\"):\n    \"\"\"Yield files that have been added or modified in `revision`.\n\n    Parameters\n    ----------\n    dataset : Dataset\n    revision : string, optional\n        Commit-ish of interest.\n\n    Returns\n    -------\n    Generator that yields AnnotatePaths instances\n    \"\"\"\n    if commit_exists(dataset, revision + \"^\"):\n        revrange = \"{rev}^..{rev}\".format(rev=revision)\n    else:\n        # No other commits are reachable from this revision.  Diff\n        # with an empty tree instead.\n        #             git hash-object -t tree /dev/null\n        empty_tree = \"4b825dc642cb6eb9a060e54bf8d69288fbee4904\"\n        revrange = \"{}..{}\".format(empty_tree, revision)\n    diff = dataset.diff(recursive=True,\n                        revision=revrange,\n                        return_type='generator', result_renderer=None)\n    for r in diff:\n        if r.get('type') == 'file' and r.get('state') in ['added', 'modified']:\n            r.pop('status', None)\n            yield r\n\n\ndef commit_exists(dataset, commit):\n    try:\n        dataset.repo.repo.git.rev_parse(\"--verify\", commit + \"^{commit}\")\n    except:\n        return False\n    return True\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\"\"\"Rerun commands recorded with `datalad run`\"\"\"\n\n__docformat__ = 'restructuredtext'\n\n\nimport logging\nfrom itertools import dropwhile\nimport json\nimport re\n\nfrom datalad.dochelpers import exc_str\nfrom datalad.interface.base import Interface\nfrom datalad.interface.utils import eval_results\nfrom datalad.interface.base import build_doc\nfrom datalad.interface.diff import Diff\nfrom datalad.interface.unlock import Unlock\nfrom datalad.interface.results import get_status_dict\nfrom datalad.interface.run import run_command\n\nfrom datalad.support.constraints import EnsureNone, EnsureStr\nfrom datalad.support.gitrepo import GitCommandError\nfrom datalad.support.param import Parameter\n\nfrom datalad.distribution.dataset import require_dataset\nfrom datalad.distribution.dataset import EnsureDataset\nfrom datalad.distribution.dataset import datasetmethod\n\nlgr = logging.getLogger('datalad.interface.rerun')\n\n\n@build_doc\nclass Rerun(Interface):\n    \"\"\"Re-execute previous `datalad run` commands.\n\n    This will unlock any dataset content that is on record to have\n    been modified by the command in the specified revision.  It will\n    then re-execute the command in the recorded path (if it was inside\n    the dataset). Afterwards, all modifications will be saved.\n\n    Examples:\n\n      Re-execute the command from the previous commit::\n\n        % datalad rerun\n\n      Re-execute any commands in the last five commits::\n\n        % datalad rerun --since=HEAD~5\n\n      Do the same as above, but re-execute the commands on top of\n      HEAD~5 in a detached state::\n\n        % datalad rerun --onto= --since=HEAD~5\n\n      Re-execute all previous commands and compare the old and new\n      results::\n\n        % # on master branch\n        % datalad rerun --branch=verify --since=\n        % # now on verify branch\n        % datalad diff --revision=master..\n        % git log --oneline --left-right --cherry-pick master...\n    \"\"\"\n    _params_ = dict(\n        revision=Parameter(\n            args=(\"revision\",),\n            metavar=\"REVISION\",\n            nargs=\"?\",\n            doc=\"\"\"rerun command(s) in `revision`. By default, the command from\n            this commit will be executed, but [CMD: --since CMD][PY: `since`\n            PY] can be used to construct a revision range.\"\"\",\n            default=\"HEAD\",\n            constraints=EnsureStr()),\n        since=Parameter(\n            args=(\"--since\",),\n            doc=\"\"\"If `since` is a commit-ish, the commands from all commits\n            that are reachable from `revision` but not `since` will be\n            re-executed (in other words, the commands in :command:`git log\n            SINCE..REVISION`). If SINCE is an empty string, it is set to the\n            parent of the first commit that contains a recorded command (i.e.,\n            all commands in :command:`git log REVISION` will be\n            re-executed).\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        branch=Parameter(\n            metavar=\"NAME\",\n            args=(\"-b\", \"--branch\",),\n            doc=\"create and checkout this branch before rerunning the commands.\",\n            constraints=EnsureStr() | EnsureNone()),\n        onto=Parameter(\n            metavar=\"base\",\n            args=(\"--onto\",),\n            doc=\"\"\"start point for rerunning the commands. If not specified,\n            commands are executed at HEAD. This option can be used to specify\n            an alternative start point, which will be checked out with the\n            branch name specified by [CMD: --branch CMD][PY: `branch` PY] or in\n            a detached state otherwise. As a special case, an empty value for\n            this option means to use the commit specified by [CMD: --since\n            CMD][PY: `since` PY].\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        message=Parameter(\n            args=(\"-m\", \"--message\",),\n            metavar=\"MESSAGE\",\n            doc=\"\"\"use MESSAGE for the reran commit rather than the\n            recorded commit message.  In the case of a multi-commit\n            rerun, all the reran commits will have this message.\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        script=Parameter(\n            args=(\"--script\",),\n            metavar=\"FILE\",\n            doc=\"\"\"extract the commands into [CMD: FILE CMD][PY: this file PY]\n            rather than rerunning.\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        dataset=Parameter(\n            args=(\"-d\", \"--dataset\"),\n            doc=\"\"\"specify the dataset from which to rerun a recorded\n            command. If no dataset is given, an attempt is made to\n            identify the dataset based on the current working\n            directory. If a dataset is given, the command will be\n            executed in the root directory of this dataset.\"\"\",\n            constraints=EnsureDataset() | EnsureNone()),\n        # TODO\n        # --list-commands\n        #   go through the history and report any recorded command. this info\n        #   could be used to unlock the associated output files for a rerun\n    )\n\n    @staticmethod\n    @datasetmethod(name='rerun')\n    @eval_results\n    def __call__(\n            revision=\"HEAD\",\n            since=None,\n            dataset=None,\n            branch=None,\n            message=None,\n            onto=None,\n            script=None):\n\n        ds = require_dataset(\n            dataset, check_installed=True,\n            purpose='rerunning a command')\n\n        lgr.debug('rerunning command output underneath %s', ds)\n\n        if script is None and ds.repo.dirty:\n            yield get_status_dict(\n                'run',\n                ds=ds,\n                status='impossible',\n                message=('unsaved modifications present, '\n                         'cannot detect changes by command'))\n            return\n\n        err_info = get_status_dict('run', ds=ds)\n        if not ds.repo.get_hexsha():\n            yield dict(\n                err_info, status='impossible',\n                message='cannot rerun command, nothing recorded')\n            return\n\n        if branch and branch in ds.repo.get_branches():\n            yield get_status_dict(\n                \"run\", ds=ds, status=\"error\",\n                message=\"branch '{}' already exists\".format(branch))\n            return\n\n        if not commit_exists(ds, revision + \"^\"):\n            # Only a single commit is reachable from `revision`.  In\n            # this case, --since has no effect on the range construction.\n            revrange = revision\n        elif since is None:\n            revrange = \"{rev}^..{rev}\".format(rev=revision)\n        elif since.strip() == \"\":\n            revrange = revision\n        else:\n            revrange = \"{}..{}\".format(since, revision)\n\n        if ds.repo.repo.git.rev_list(\"--merges\", revrange, \"--\"):\n            yield get_status_dict(\n                \"run\", ds=ds, status=\"error\",\n                message=\"cannot rerun history with merge commits\")\n            return\n\n        revs = [{\"hexsha\": hexsha,\n                 \"message\": ds.repo.repo.git.show(\n                     hexsha, \"--format=%B\", \"--no-patch\")}\n                for hexsha in ds.repo.repo.git.rev_list(\n                        \"--reverse\", revrange, \"--\").split()]\n\n        for rev in revs:\n            try:\n                subj, info = get_run_info(rev[\"message\"])\n            except ValueError as exc:\n                yield dict(err_info, status='error',\n                           message=\"Error on {}'s message: {}\".format(\n                               rev[\"hexsha\"], exc_str(exc)))\n                return\n            if info is not None:\n                rev[\"run_info\"] = info\n                rev[\"run_subject\"] = subj\n\n        if since is not None and since.strip() == \"\":\n            # For --since='', drop any leading commits that don't have\n            # a run command.\n            revs = list(dropwhile(lambda r: \"run_info\" not in r, revs))\n\n        if script:\n            commands = (r[\"run_info\"][\"cmd\"] for r in revs if \"run_info\" in r)\n            with open(script, 'w') as ofh:\n                header = \"\"\"\\\n#!/bin/sh\n#\n# This file was generated by running (the equivalent of)\n#\n#   datalad rerun --script={script}{since} {revision}\n#\n# in {path}\\n\\n\"\"\"\n                ofh.write(header.format(\n                    script=script,\n                    since=\"\" if since is None else \" --since=\" + since,\n                    revision=ds.repo.repo.git.rev_parse(revision),\n                    path=ds.path))\n\n                for cmd in commands:\n                    if isinstance(cmd, list):\n                        cmd = \" \".join(cmd)\n                    ofh.write(cmd + \"\\n\")\n        else:\n            if onto is not None and onto.strip() == \"\":\n                # Special case: --onto='' is the value of --since.\n                # Because we're currently aborting if the revision list\n                # contains merges, we know that, regardless of if and how\n                # --since is specified, the effective value for --since is\n                # the parent of the first revision.\n                onto = revs[0][\"hexsha\"] + \"^\"\n                if not commit_exists(ds, onto):\n                    # This is unlikely to happen in the wild because it\n                    # means that the first commit is a datalad run commit.\n                    # Just abort rather than trying to checkout on orphan\n                    # branch or something like that.\n                    yield get_status_dict(\n                        \"run\", ds=ds, status=\"error\",\n                        message=\"Commit for --onto does not exist.\")\n                    return\n\n            if branch or onto:\n                start_point = onto or \"HEAD\"\n                if branch:\n                    checkout_options = [\"-b\", branch]\n                else:\n                    checkout_options = [\"--detach\"]\n                ds.repo.checkout(start_point, options=checkout_options)\n\n            for rev in revs:\n                hexsha = rev[\"hexsha\"]\n                if \"run_info\" not in rev:\n                    pick = False\n                    try:\n                        ds.repo.repo.git.merge_base(\"--is-ancestor\",\n                                                    hexsha, \"HEAD\")\n                    except GitCommandError:\n                        # Revision is NOT an ancestor of HEAD.\n                        pick = True\n\n                    shortrev = ds.repo.repo.git.rev_parse(\"--short\", hexsha)\n                    err_msg = \"no command for {} found; {}\".format(\n                        shortrev,\n                        \"cherry picking\" if pick else \"skipping\")\n                    yield dict(err_info, status='ok', message=err_msg)\n\n                    if pick:\n                        ds.repo.repo.git.cherry_pick(hexsha)\n                    continue\n\n                run_info = rev[\"run_info\"]\n                # Keep a \"rerun\" trail.\n                if \"chain\" in run_info:\n                    run_info[\"chain\"].append(hexsha)\n                else:\n                    run_info[\"chain\"] = [hexsha]\n\n                # now we have to find out what was modified during the\n                # last run, and enable re-modification ideally, we would\n                # bring back the entire state of the tree with #1424, but\n                # we limit ourself to file addition/not-in-place-modification\n                # for now\n                for r in ds.unlock(new_or_modified(ds, hexsha),\n                                   return_type='generator', result_xfm=None):\n                    yield r\n\n                for r in run_command(run_info['cmd'],\n                                     ds, message or rev[\"run_subject\"],\n                                     rerun_info=run_info):\n                    yield r\n\n\ndef get_run_info(message):\n    \"\"\"Extract run information from `message`\n\n    Parameters\n    ----------\n    message : str\n        A commit message.\n\n    Returns\n    -------\n    A tuple with the command's subject line and a dict with run information.\n    Both these values are None if `message` doesn't have a run command.\n\n    Raises\n    ------\n    A ValueError if the information in `message` is invalid.\n    \"\"\"\n    cmdrun_regex = r'\\[DATALAD RUNCMD\\] (.*)=== Do not change lines below ' \\\n                   r'===\\n(.*)\\n\\^\\^\\^ Do not change lines above \\^\\^\\^'\n    runinfo = re.match(cmdrun_regex, message, re.MULTILINE | re.DOTALL)\n    if not runinfo:\n        return None, None\n\n    rec_subj, runinfo = runinfo.groups()\n\n    try:\n        runinfo = json.loads(runinfo)\n    except Exception as e:\n        raise ValueError(\n            'cannot rerun command, command specification is not valid JSON: '\n            '%s' % exc_str(e)\n        )\n    if 'cmd' not in runinfo:\n        raise ValueError(\"Looks like a run commit but does not have a command\")\n    return rec_subj.rstrip(), runinfo\n\n\ndef new_or_modified(dataset, revision=\"HEAD\"):\n    \"\"\"Yield files that have been added or modified in `revision`.\n\n    Parameters\n    ----------\n    dataset : Dataset\n    revision : string, optional\n        Commit-ish of interest.\n\n    Returns\n    -------\n    Generator that yields AnnotatePaths instances\n    \"\"\"\n    if commit_exists(dataset, revision + \"^\"):\n        revrange = \"{rev}^..{rev}\".format(rev=revision)\n    else:\n        # No other commits are reachable from this revision.  Diff\n        # with an empty tree instead.\n        #             git hash-object -t tree /dev/null\n        empty_tree = \"4b825dc642cb6eb9a060e54bf8d69288fbee4904\"\n        revrange = \"{}..{}\".format(empty_tree, revision)\n    diff = dataset.diff(recursive=True,\n                        revision=revrange,\n                        return_type='generator', result_renderer=None)\n    for r in diff:\n        if r.get('type') == 'file' and r.get('state') in ['added', 'modified']:\n            r.pop('status', None)\n            yield r\n\n\ndef commit_exists(dataset, commit):\n    try:\n        dataset.repo.repo.git.rev_parse(\"--verify\", commit + \"^{commit}\")\n    except:\n        return False\n    return True\n",
            "header": {
                "file": {
                    "path": "datalad/interface/rerun.py"
                },
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                "old_commit_hash": "03a14b646",
                "new_commit_hash": "5cb2bb89d",
                "mode": "100644"
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            "binary_line": null,
            "minus_file": {
                "path": "a/datalad/interface/rerun.py"
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                        "section": "def get_run_info(message):"
                    },
                    "line_group": {
                        "all_lines": [
                            {
                                "content": "        )",
                                "type": "context"
                            },
                            {
                                "content": "    if 'cmd' not in runinfo:",
                                "type": "context"
                            },
                            {
                                "content": "        raise ValueError(\"Looks like a run commit but does not have a command\")",
                                "type": "context"
                            },
                            {
                                "content": "    return rec_subj, runinfo",
                                "type": "deleted"
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                                "content": "    return rec_subj.rstrip(), runinfo",
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                                "type": "context"
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                        {
                            "file_name": "datalad/interface/rerun.py",
                            "type": "function",
                            "name": "get_run_info",
                            "content": "def get_run_info(message):\n    \"\"\"Extract run information from `message`\n\n    Parameters\n    ----------\n    message : str\n        A commit message.\n\n    Returns\n    -------\n    A tuple with the command's subject line and a dict with run information.\n    Both these values are None if `message` doesn't have a run command.\n\n    Raises\n    ------\n    A ValueError if the information in `message` is invalid.\n    \"\"\"\n    cmdrun_regex = r'\\[DATALAD RUNCMD\\] (.*)=== Do not change lines below ' \\\n                   r'===\\n(.*)\\n\\^\\^\\^ Do not change lines above \\^\\^\\^'\n    runinfo = re.match(cmdrun_regex, message, re.MULTILINE | re.DOTALL)\n    if not runinfo:\n        return None, None\n\n    rec_subj, runinfo = runinfo.groups()\n\n    try:\n        runinfo = json.loads(runinfo)\n    except Exception as e:\n        raise ValueError(\n            'cannot rerun command, command specification is not valid JSON: '\n            '%s' % exc_str(e)\n        )\n    if 'cmd' not in runinfo:\n        raise ValueError(\"Looks like a run commit but does not have a command\")\n    return rec_subj, runinfo",
                            "ast_type_str": "FunctionDef",
                            "start_lineno": 305,
                            "end_lineno": 339,
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            "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\"\"\"test command datalad {re,}run\n\n\"\"\"\n\n__docformat__ = 'restructuredtext'\n\nimport logging\n\nfrom datalad.tests.utils import (\n    known_failure_direct_mode,\n    known_failure_v6,\n)\n\nfrom os.path import join as opj\nfrom os.path import relpath\nfrom os import mkdir\nfrom datalad.utils import chpwd\n\nfrom datalad.distribution.dataset import Dataset\nfrom datalad.support.exceptions import NoDatasetArgumentFound\nfrom datalad.support.exceptions import CommandError\nfrom datalad.support.exceptions import IncompleteResultsError\nfrom datalad.support.gitrepo import GitCommandError\nfrom datalad.tests.utils import ok_, assert_false, neq_\nfrom datalad.api import run\nfrom datalad.interface.rerun import get_run_info, new_or_modified\nfrom datalad.tests.utils import assert_raises\nfrom datalad.tests.utils import assert_dict_equal\nfrom datalad.tests.utils import with_tempfile\nfrom datalad.tests.utils import with_tree\nfrom datalad.tests.utils import ok_clean_git\nfrom datalad.tests.utils import ok_exists\nfrom datalad.tests.utils import ok_file_under_git\nfrom datalad.tests.utils import create_tree\nfrom datalad.tests.utils import eq_\nfrom datalad.tests.utils import assert_status\nfrom datalad.tests.utils import assert_result_count\nfrom datalad.tests.utils import assert_in\nfrom datalad.tests.utils import assert_not_in\nfrom datalad.tests.utils import swallow_logs\nfrom datalad.tests.utils import swallow_outputs\nfrom datalad.tests.utils import assert_in_results\nfrom datalad.tests.utils import skip_if_on_windows\nfrom datalad.tests.utils import ignore_nose_capturing_stdout\nfrom datalad.tests.utils import slow\n\n\n@with_tempfile(mkdir=True)\ndef test_invalid_call(path):\n    with chpwd(path):\n        # no dataset, no luck\n        assert_raises(NoDatasetArgumentFound, run, 'doesntmatter')\n        # dirty dataset\n        ds = Dataset(path).create()\n        create_tree(ds.path, {'this': 'dirty'})\n        assert_status('impossible', run('doesntmatter', on_failure='ignore'))\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@with_tempfile(mkdir=True)\ndef test_basics(path, nodspath):\n    ds = Dataset(path).create()\n    last_state = ds.repo.get_hexsha()\n    # run inside the dataset\n    with chpwd(path), \\\n            swallow_outputs():\n        # provoke command failure\n        with assert_raises(CommandError) as cme:\n            ds.run('7i3amhmuch9invalid')\n            # let's not speculate that the exit code is always 127\n            ok_(cme.code > 0)\n        eq_(last_state, ds.repo.get_hexsha())\n        # now one that must work\n        res = ds.run('touch empty', message='TEST')\n        ok_clean_git(ds.path)\n        assert_result_count(res, 2)\n        # TODO 'state' is still untracked!!!\n        assert_result_count(res, 1, action='add', path=opj(ds.path, 'empty'), type='file')\n        assert_result_count(res, 1, action='save', path=ds.path)\n        commit_msg = ds.repo.repo.head.commit.message\n        ok_(commit_msg.startswith('[DATALAD RUNCMD] TEST'))\n        # crude test that we have a record for the PWD\n        assert_in('\"pwd\": \".\"', commit_msg)\n        last_state = ds.repo.get_hexsha()\n        # now run a command that will not alter the dataset\n        res = ds.run('touch empty', message='NOOP_TEST')\n        assert_status('notneeded', res)\n        eq_(last_state, ds.repo.get_hexsha())\n\n    # run outside the dataset, should still work but with limitations\n    with chpwd(nodspath), \\\n            swallow_outputs():\n        res = ds.run(['touch', 'empty2'], message='TEST')\n        assert_status('ok', res)\n        assert_result_count(res, 1, action='add', path=opj(ds.path, 'empty2'), type='file')\n\n    # running without a command is a noop\n    with chpwd(path):\n        with swallow_logs(new_level=logging.WARN) as cml:\n            ds.run()\n            assert_in(\"No command given\", cml.out)\n\n\n@slow  # 17.1880s\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\ndef test_rerun(path, nodspath):\n    ds = Dataset(path).create()\n    sub = ds.create('sub')\n    probe_path = opj(sub.path, 'sequence')\n    # run inside the dataset\n    with chpwd(path), \\\n            swallow_outputs():\n        ds.run('echo x$(cat sub/sequence) > sub/sequence')\n    # command ran once, all clean\n    ok_clean_git(ds.path)\n    eq_('x\\n', open(probe_path).read())\n    # now, for a rerun we can be anywhere, PWD and all are recorded\n    # moreover, rerun must figure out which bits to unlock, even in\n    # subdatasets\n    with chpwd(nodspath), \\\n            swallow_outputs():\n        ds.rerun()\n    ok_clean_git(ds.path)\n    # ran twice now\n    eq_('xx\\n', open(probe_path).read())\n    # Make a non-run commit.\n    with open(opj(path, \"nonrun-file\"), \"w\") as f:\n        f.write(\"foo\")\n    ds.add(\"nonrun-file\")\n    # Now rerun the buried command.\n    ds.rerun(revision=\"HEAD~\", message=\"rerun buried\")\n    eq_('xxx\\n', open(probe_path).read())\n    # Also check that the messasge override worked.\n    eq_(ds.repo.repo.head.commit.message.splitlines()[0],\n        \"[DATALAD RUNCMD] rerun buried\")\n    # Or a range of commits, skipping non-run commits.\n    ds.rerun(since=\"HEAD~3\")\n    eq_('xxxxx\\n', open(probe_path).read())\n    # Or --since= to run all reachable commits.\n    ds.rerun(since=\"\")\n    eq_('xxxxxxxxxx\\n', open(probe_path).read())\n    # If the history to rerun has a merge commit, we abort.\n    ds.repo.checkout(\"HEAD~3\", options=[\"-b\", \"topic\"])\n    with open(opj(path, \"topic-file\"), \"w\") as f:\n        f.write(\"topic\")\n    ds.add(\"topic-file\")\n    ds.repo.checkout(\"master\")\n    ds.repo.merge(\"topic\")\n    ok_clean_git(ds.path)\n    assert_raises(IncompleteResultsError, ds.rerun)\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_onto(path):\n    ds = Dataset(path).create()\n\n    grow_file = opj(path, \"grows\")\n\n    ds.run('echo static-content > static')\n    ds.repo.repo.git.tag(\"static\")\n    ds.run('echo x$(cat grows) > grows')\n    ds.rerun()\n    eq_('xx\\n', open(grow_file).read())\n\n    # If we run the \"static\" change on top of itself, we end up in the\n    # same (but detached) place.\n    ds.rerun(revision=\"static\", onto=\"static\")\n    ok_(ds.repo.get_active_branch() is None)\n    eq_(ds.repo.repo.git.rev_parse(\"HEAD\"),\n        ds.repo.repo.git.rev_parse(\"static\"))\n\n    # If we run the \"static\" change from the same \"base\", we end up\n    # with a new commit.\n    ds.repo.checkout(\"master\")\n    ds.rerun(revision=\"static\", onto=\"static^\")\n    ok_(ds.repo.get_active_branch() is None)\n    neq_(ds.repo.repo.git.rev_parse(\"HEAD\"),\n         ds.repo.repo.git.rev_parse(\"static\"))\n    assert_result_count(ds.diff(revision=\"HEAD..static\"), 0)\n    for revrange in [\"..static\", \"static..\"]:\n        assert_result_count(\n            ds.repo.repo.git.rev_list(revrange).split(), 1)\n\n    # Unlike the static change, if we run the ever-growing change on\n    # top of itself, we end up with a new commit.\n    ds.repo.checkout(\"master\")\n    ds.rerun(onto=\"HEAD\")\n    ok_(ds.repo.get_active_branch() is None)\n    neq_(ds.repo.repo.git.rev_parse(\"HEAD\"),\n         ds.repo.repo.git.rev_parse(\"master\"))\n\n    # An empty `onto` means use the parent of the first revision.\n    ds.repo.checkout(\"master\")\n    ds.rerun(since=\"static^\", onto=\"\")\n    ok_(ds.repo.get_active_branch() is None)\n    for revrange in [\"..master\", \"master..\"]:\n        assert_result_count(\n            ds.repo.repo.git.rev_list(revrange).split(), 3)\n\n    # An empty `onto` means use the parent of the first revision that\n    # has a run command.\n    ds.repo.checkout(\"master\")\n    ds.rerun(since=\"\", onto=\"\", branch=\"from-base\")\n    eq_(ds.repo.get_active_branch(), \"from-base\")\n    assert_result_count(ds.diff(revision=\"master..from-base\"), 0)\n    eq_(ds.repo.get_merge_base([\"static\", \"from-base\"]),\n        ds.repo.repo.git.rev_parse(\"static^\"))\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_chain(path):\n    ds = Dataset(path).create()\n    commits = []\n\n    grow_file = opj(path, \"grows\")\n    ds.run('echo x$(cat grows) > grows')\n    ds.repo.repo.git.tag(\"first-run\")\n\n    for _ in range(3):\n        commits.append(ds.repo.get_hexsha())\n        ds.rerun()\n        _, info = get_run_info(ds.repo.repo.head.commit.message)\n        assert info[\"chain\"] == commits\n\n    ds.rerun(revision=\"first-run\")\n    _, info = get_run_info(ds.repo.repo.head.commit.message)\n    assert info[\"chain\"] == commits[:1]\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\ndef test_rerun_old_flag_compatibility(path):\n    ds = Dataset(path).create()\n    ds.run(\"echo x$(cat grows) > grows\")\n    # Deprecated `datalad --rerun` still runs the last commit's\n    # command.\n    ds.run(rerun=True)\n    eq_(\"xx\\n\", open(opj(path, \"grows\")).read())\n    # Running with --rerun and a command ignores the command.\n    with swallow_logs(new_level=logging.WARN) as cml:\n        ds.run(rerun=True, cmd=\"ignored\")\n        assert_in(\"Ignoring provided command in --rerun mode\", cml.out)\n        eq_(\"xxx\\n\", open(opj(path, \"grows\")).read())\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_just_one_commit(path):\n    ds = Dataset(path).create()\n\n    # Check out an orphan branch so that we can test the \"one commit\n    # in a repo\" case.\n    ds.repo.checkout(\"orph\", options=[\"--orphan\"])\n    ds.repo.repo.git.reset(\"--hard\")\n\n    ds.run('echo static-content > static')\n    assert_result_count(ds.repo.repo.git.rev_list(\"HEAD\").split(), 1)\n\n    # Rerunning with just one commit doesn't raise an error ...\n    ds.rerun()\n    # ... but we're still at one commit because the content didn't\n    # change.\n    assert_result_count(ds.repo.repo.git.rev_list(\"HEAD\").split(), 1)\n\n    # We abort rather than trying to do anything when --onto='' and\n    # --since='' are given together and the first commit contains a\n    # run command.\n    ds.repo.commit(msg=\"empty\", options=[\"--allow-empty\"])\n    assert_raises(IncompleteResultsError, ds.rerun, since=\"\", onto=\"\")\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_run_failure(path):\n    ds = Dataset(path).create()\n\n    hexsha_initial = ds.repo.get_hexsha()\n\n    with assert_raises(CommandError):\n        ds.run(\"echo x$(cat grows) > grows && false\")\n    eq_(hexsha_initial, ds.repo.get_hexsha())\n    ok_(ds.repo.dirty)\n\n    msgfile = opj(ds.repo.repo.git_dir, \"COMMIT_EDITMSG\")\n    ok_exists(msgfile)\n\n    ds.add(\".\", save=False)\n    ds.save(message_file=msgfile)\n    ok_clean_git(ds.path)\n    neq_(hexsha_initial, ds.repo.get_hexsha())\n\n    outfile = opj(ds.path, \"grows\")\n    eq_('x\\n', open(outfile).read())\n\n    # There is no CommandError on rerun if the non-zero error matches the\n    # original code.\n    ds.rerun()\n    eq_('xx\\n', open(outfile).read())\n\n    # On the other hand, we fail if we rerun a command and there is a non-zero\n    # error that doesn't match.\n    ds.run(\"[ ! -e bar ] && echo c >bar\")\n    ok_clean_git(ds.path)\n    with assert_raises(CommandError):\n        ds.rerun()\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\ndef test_rerun_branch(path):\n    ds = Dataset(path).create()\n\n    ds.repo.repo.git.tag(\"prerun\")\n\n    outfile = opj(path, \"run-file\")\n\n    ds.run('echo x$(cat run-file) > run-file')\n    ds.rerun()\n    eq_('xx\\n', open(outfile).read())\n\n    with open(opj(path, \"nonrun-file\"), \"w\") as f:\n        f.write(\"foo\")\n    ds.add(\"nonrun-file\")\n\n    # Rerun the commands on a new branch that starts at the parent\n    # commit of the first run.\n    ds.rerun(since=\"prerun\", onto=\"prerun\", branch=\"rerun\")\n\n    eq_(ds.repo.get_active_branch(), \"rerun\")\n    eq_('xx\\n', open(outfile).read())\n\n    # NOTE: This test depends on the non-run commit above following a run\n    # commit.  Otherwise, all the metadata (e.g., author date) aside from the\n    # parent commit that is used to generate the commit ID may be set when\n    # running the tests, which would result in two commits rather than three.\n    for revrange in [\"rerun..master\", \"master..rerun\"]:\n        assert_result_count(\n            ds.repo.repo.git.rev_list(revrange).split(), 3)\n    eq_(ds.repo.get_merge_base([\"master\", \"rerun\"]),\n        ds.repo.repo.git.rev_parse(\"prerun\"))\n\n    # Start rerun branch at tip of current branch.\n    ds.repo.checkout(\"master\")\n    ds.rerun(since=\"prerun\", branch=\"rerun2\")\n    eq_(ds.repo.get_active_branch(), \"rerun2\")\n    eq_('xxxx\\n', open(outfile).read())\n\n    assert_result_count(\n        ds.repo.repo.git.rev_list(\"master..rerun2\").split(), 2)\n    assert_result_count(\n        ds.repo.repo.git.rev_list(\"rerun2..master\").split(), 0)\n\n    # Using an existing branch name fails.\n    ds.repo.checkout(\"master\")\n    assert_raises(IncompleteResultsError,\n                  ds.rerun, since=\"prerun\", branch=\"rerun2\")\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_cherry_pick(path):\n    ds = Dataset(path).create()\n\n    ds.repo.repo.git.tag(\"prerun\")\n    ds.run('echo abc > runfile')\n    with open(opj(path, \"nonrun-file\"), \"w\") as f:\n        f.write(\"foo\")\n    ds.add(\"nonrun-file\")\n\n    for onto, text in [(\"HEAD\", \"skipping\"), (\"prerun\", \"cherry picking\")]:\n        results = ds.rerun(since=\"prerun\", onto=onto)\n        assert_in_results(results, status='ok', path=ds.path)\n        assert any(r.get(\"message\", \"\").endswith(text) for r in results)\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_outofdate_tree(path):\n    ds = Dataset(path).create()\n    input_file = opj(path, \"foo\")\n    output_file = opj(path, \"out\")\n    with open(input_file, \"w\") as f:\n        f.write(\"abc\\ndef\")\n    ds.add(\"foo\", to_git=True)\n    # Create inital run.\n    ds.run('grep def foo > out')\n    eq_('def\\n', open(output_file).read())\n    # Change tree so that it is no longer compatible.\n    ds.remove(\"foo\")\n    # Now rerunning should fail because foo no longer exists.\n    assert_raises(CommandError, ds.rerun, revision=\"HEAD~\")\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_ambiguous_revision_file(path):\n    ds = Dataset(path).create()\n    ds.run('echo ambig > ambig')\n    ds.repo.repo.git.tag(\"ambig\")\n    # Don't fail when \"ambig\" refers to both a file and revision.\n    ds.rerun(since=\"\", revision=\"ambig\", branch=\"rerun\")\n    eq_(len(ds.repo.repo.git.rev_list(\"rerun\").split()),\n        len(ds.repo.repo.git.rev_list(\"ambig\", \"--\").split()))\n\n\n@ignore_nose_capturing_stdout\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_subdir(path):\n    ds = Dataset(path).create()\n    subdir = opj(path, 'subdir')\n    mkdir(subdir)\n    with chpwd(subdir):\n        run(\"touch test.dat\")\n    ok_clean_git(ds.path)\n    ok_file_under_git(opj(subdir, \"test.dat\"), annexed=True)\n    rec_msg, runinfo = get_run_info(ds.repo.repo.head.commit.message)\n    eq_(runinfo['pwd'], 'subdir')\n    # now, rerun within root of the dataset\n    with chpwd(ds.path):\n        ds.rerun()\n    ok_clean_git(ds.path)\n    ok_file_under_git(opj(subdir, \"test.dat\"), annexed=True)\n    # and not on top\n    assert_raises(AssertionError, ok_file_under_git, opj(ds.path, \"test.dat\"), annexed=True)\n\n    # but if we run ds.run -- runs within top of the dataset\n    with chpwd(subdir):\n        ds.run(\"touch test2.dat\")\n    ok_clean_git(ds.path)\n    ok_file_under_git(opj(ds.path, \"test2.dat\"), annexed=True)\n    rec_msg, runinfo = get_run_info(ds.repo.repo.head.commit.message)\n    eq_(runinfo['pwd'], '.')\n    # now, rerun within subdir -- smoke for now\n    with chpwd(subdir):\n        ds.rerun()\n\n\n@with_tree(tree={\"d\": {\"to_modify\": \"content1\"},\n                 \"to_remove\": \"content2\",\n                 \"to_modify\": \"content3\",\n                 \"unchanged\": \"content4\"})\ndef test_new_or_modified(path):\n    def apfiles(aps):\n        for ap in aps:\n            yield relpath(ap[\"path\"], path)\n\n    ds = Dataset(path).create(force=True, no_annex=True)\n\n    # Check out an orphan branch so that we can test the \"one commit\n    # in a repo\" case.\n    ds.repo.checkout(\"orph\", options=[\"--orphan\"])\n    ds.repo.add(\".\", commit=True)\n    assert_false(ds.repo.dirty)\n    assert_result_count(ds.repo.repo.git.rev_list(\"HEAD\").split(), 1)\n    # Diffing doesn't fail when the branch contains a single commit.\n    assert_in(\"to_modify\", apfiles(new_or_modified(ds, \"HEAD\")))\n\n    # New files are detected, deletions are not.\n    ds.repo.remove([\"to_remove\"])\n    ok_(ds.repo.dirty)\n\n    with open(opj(path, \"to_add\"), \"w\") as f:\n        f.write(\"content5\")\n    ds.repo.add([\"to_add\"], commit=True)\n    ds.repo.commit(\"add one, remove another\")\n\n    eq_(list(apfiles(new_or_modified(ds, \"HEAD\"))),\n        [\"to_add\"])\n\n    # Modifications are detected.\n    with open(opj(path, \"to_modify\"), \"w\") as f:\n        f.write(\"updated 1\")\n    with open(opj(path, \"d/to_modify\"), \"w\") as f:\n        f.write(\"updated 2\")\n    ds.repo.add([\"to_modify\", \"d/to_modify\"], commit=True)\n\n    eq_(set(apfiles(new_or_modified(ds, \"HEAD\"))),\n        {\"to_modify\", \"d/to_modify\"})\n\n    # Non-HEAD revisions work.\n    ds.repo.commit(\"empty\", options=[\"--allow-empty\"])\n    assert_false(list(apfiles(new_or_modified(ds, \"HEAD\"))))\n    eq_(set(apfiles(new_or_modified(ds, \"HEAD~\"))),\n        {\"to_modify\", \"d/to_modify\"})\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\ndef test_rerun_script(path):\n    ds = Dataset(path).create()\n    ds.run(\"echo a >foo\")\n    ds.run(\"echo b >bar\")\n\n    script_file = opj(path, \"commands.sh\")\n\n    ds.rerun(script=script_file)\n    ok_exists(script_file)\n    with open(script_file) as sf:\n        lines = sf.readlines()\n        assert_in(\"echo b >bar\\n\", lines)\n        assert_not_in(\"echo a >foo\\n\", lines)\n\n    ds.rerun(since=\"\", script=script_file)\n    with open(script_file) as sf:\n        lines = sf.readlines()\n        assert_in(\"echo b >bar\\n\", lines)\n        assert_in(\"echo a >foo\\n\", lines)\n\n\ndef test_rerun_commit_message_check():\n    assert_raises(ValueError,\n                  get_run_info,\n                  \"\"\"\\\n[DATALAD RUNCMD] no command\n\n=== Do not change lines below ===\n{\n \"pwd\": \".\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n\n    assert_raises(ValueError,\n                  get_run_info,\n                  \"\"\"\\\n[DATALAD RUNCMD] junk json\n\n=== Do not change lines below ===\n{\n \"pwd\": \".,\n \"cmd\": \"echo ok >okfile\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n\n    subject, info = get_run_info(\"\"\"\\\n[DATALAD RUNCMD] fine\n\n=== Do not change lines below ===\n{\n \"pwd\": \".\",\n \"cmd\": \"echo ok >okfile\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n    eq_(subject, \"fine\\n\\n\")\n    assert_dict_equal(info,\n                      {\"pwd\": \".\", \"cmd\": \"echo ok >okfile\", \"exit\": 0})\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\"\"\"test command datalad {re,}run\n\n\"\"\"\n\n__docformat__ = 'restructuredtext'\n\nimport logging\n\nfrom datalad.tests.utils import (\n    known_failure_direct_mode,\n    known_failure_v6,\n)\n\nfrom os.path import join as opj\nfrom os.path import relpath\nfrom os import mkdir\nfrom datalad.utils import chpwd\n\nfrom datalad.distribution.dataset import Dataset\nfrom datalad.support.exceptions import NoDatasetArgumentFound\nfrom datalad.support.exceptions import CommandError\nfrom datalad.support.exceptions import IncompleteResultsError\nfrom datalad.support.gitrepo import GitCommandError\nfrom datalad.tests.utils import ok_, assert_false, neq_\nfrom datalad.api import run\nfrom datalad.interface.rerun import get_run_info, new_or_modified\nfrom datalad.tests.utils import assert_raises\nfrom datalad.tests.utils import assert_dict_equal\nfrom datalad.tests.utils import with_tempfile\nfrom datalad.tests.utils import with_tree\nfrom datalad.tests.utils import ok_clean_git\nfrom datalad.tests.utils import ok_exists\nfrom datalad.tests.utils import ok_file_under_git\nfrom datalad.tests.utils import create_tree\nfrom datalad.tests.utils import eq_\nfrom datalad.tests.utils import assert_status\nfrom datalad.tests.utils import assert_result_count\nfrom datalad.tests.utils import assert_in\nfrom datalad.tests.utils import assert_not_in\nfrom datalad.tests.utils import swallow_logs\nfrom datalad.tests.utils import swallow_outputs\nfrom datalad.tests.utils import assert_in_results\nfrom datalad.tests.utils import skip_if_on_windows\nfrom datalad.tests.utils import ignore_nose_capturing_stdout\nfrom datalad.tests.utils import slow\n\n\n@with_tempfile(mkdir=True)\ndef test_invalid_call(path):\n    with chpwd(path):\n        # no dataset, no luck\n        assert_raises(NoDatasetArgumentFound, run, 'doesntmatter')\n        # dirty dataset\n        ds = Dataset(path).create()\n        create_tree(ds.path, {'this': 'dirty'})\n        assert_status('impossible', run('doesntmatter', on_failure='ignore'))\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@with_tempfile(mkdir=True)\ndef test_basics(path, nodspath):\n    ds = Dataset(path).create()\n    last_state = ds.repo.get_hexsha()\n    # run inside the dataset\n    with chpwd(path), \\\n            swallow_outputs():\n        # provoke command failure\n        with assert_raises(CommandError) as cme:\n            ds.run('7i3amhmuch9invalid')\n            # let's not speculate that the exit code is always 127\n            ok_(cme.code > 0)\n        eq_(last_state, ds.repo.get_hexsha())\n        # now one that must work\n        res = ds.run('touch empty', message='TEST')\n        ok_clean_git(ds.path)\n        assert_result_count(res, 2)\n        # TODO 'state' is still untracked!!!\n        assert_result_count(res, 1, action='add', path=opj(ds.path, 'empty'), type='file')\n        assert_result_count(res, 1, action='save', path=ds.path)\n        commit_msg = ds.repo.repo.head.commit.message\n        ok_(commit_msg.startswith('[DATALAD RUNCMD] TEST'))\n        # crude test that we have a record for the PWD\n        assert_in('\"pwd\": \".\"', commit_msg)\n        last_state = ds.repo.get_hexsha()\n        # now run a command that will not alter the dataset\n        res = ds.run('touch empty', message='NOOP_TEST')\n        assert_status('notneeded', res)\n        eq_(last_state, ds.repo.get_hexsha())\n\n    # run outside the dataset, should still work but with limitations\n    with chpwd(nodspath), \\\n            swallow_outputs():\n        res = ds.run(['touch', 'empty2'], message='TEST')\n        assert_status('ok', res)\n        assert_result_count(res, 1, action='add', path=opj(ds.path, 'empty2'), type='file')\n\n    # running without a command is a noop\n    with chpwd(path):\n        with swallow_logs(new_level=logging.WARN) as cml:\n            ds.run()\n            assert_in(\"No command given\", cml.out)\n\n\n@slow  # 17.1880s\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\ndef test_rerun(path, nodspath):\n    ds = Dataset(path).create()\n    sub = ds.create('sub')\n    probe_path = opj(sub.path, 'sequence')\n    # run inside the dataset\n    with chpwd(path), \\\n            swallow_outputs():\n        ds.run('echo x$(cat sub/sequence) > sub/sequence')\n    # command ran once, all clean\n    ok_clean_git(ds.path)\n    eq_('x\\n', open(probe_path).read())\n    # now, for a rerun we can be anywhere, PWD and all are recorded\n    # moreover, rerun must figure out which bits to unlock, even in\n    # subdatasets\n    with chpwd(nodspath), \\\n            swallow_outputs():\n        ds.rerun()\n    ok_clean_git(ds.path)\n    # ran twice now\n    eq_('xx\\n', open(probe_path).read())\n    # Make a non-run commit.\n    with open(opj(path, \"nonrun-file\"), \"w\") as f:\n        f.write(\"foo\")\n    ds.add(\"nonrun-file\")\n    # Now rerun the buried command.\n    ds.rerun(revision=\"HEAD~\", message=\"rerun buried\")\n    eq_('xxx\\n', open(probe_path).read())\n    # Also check that the messasge override worked.\n    eq_(ds.repo.repo.head.commit.message.splitlines()[0],\n        \"[DATALAD RUNCMD] rerun buried\")\n    # Or a range of commits, skipping non-run commits.\n    ds.rerun(since=\"HEAD~3\")\n    eq_('xxxxx\\n', open(probe_path).read())\n    # Or --since= to run all reachable commits.\n    ds.rerun(since=\"\")\n    eq_('xxxxxxxxxx\\n', open(probe_path).read())\n    # If the history to rerun has a merge commit, we abort.\n    ds.repo.checkout(\"HEAD~3\", options=[\"-b\", \"topic\"])\n    with open(opj(path, \"topic-file\"), \"w\") as f:\n        f.write(\"topic\")\n    ds.add(\"topic-file\")\n    ds.repo.checkout(\"master\")\n    ds.repo.merge(\"topic\")\n    ok_clean_git(ds.path)\n    assert_raises(IncompleteResultsError, ds.rerun)\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_onto(path):\n    ds = Dataset(path).create()\n\n    grow_file = opj(path, \"grows\")\n\n    ds.run('echo static-content > static')\n    ds.repo.repo.git.tag(\"static\")\n    ds.run('echo x$(cat grows) > grows')\n    ds.rerun()\n    eq_('xx\\n', open(grow_file).read())\n\n    # If we run the \"static\" change on top of itself, we end up in the\n    # same (but detached) place.\n    ds.rerun(revision=\"static\", onto=\"static\")\n    ok_(ds.repo.get_active_branch() is None)\n    eq_(ds.repo.repo.git.rev_parse(\"HEAD\"),\n        ds.repo.repo.git.rev_parse(\"static\"))\n\n    # If we run the \"static\" change from the same \"base\", we end up\n    # with a new commit.\n    ds.repo.checkout(\"master\")\n    ds.rerun(revision=\"static\", onto=\"static^\")\n    ok_(ds.repo.get_active_branch() is None)\n    neq_(ds.repo.repo.git.rev_parse(\"HEAD\"),\n         ds.repo.repo.git.rev_parse(\"static\"))\n    assert_result_count(ds.diff(revision=\"HEAD..static\"), 0)\n    for revrange in [\"..static\", \"static..\"]:\n        assert_result_count(\n            ds.repo.repo.git.rev_list(revrange).split(), 1)\n\n    # Unlike the static change, if we run the ever-growing change on\n    # top of itself, we end up with a new commit.\n    ds.repo.checkout(\"master\")\n    ds.rerun(onto=\"HEAD\")\n    ok_(ds.repo.get_active_branch() is None)\n    neq_(ds.repo.repo.git.rev_parse(\"HEAD\"),\n         ds.repo.repo.git.rev_parse(\"master\"))\n\n    # An empty `onto` means use the parent of the first revision.\n    ds.repo.checkout(\"master\")\n    ds.rerun(since=\"static^\", onto=\"\")\n    ok_(ds.repo.get_active_branch() is None)\n    for revrange in [\"..master\", \"master..\"]:\n        assert_result_count(\n            ds.repo.repo.git.rev_list(revrange).split(), 3)\n\n    # An empty `onto` means use the parent of the first revision that\n    # has a run command.\n    ds.repo.checkout(\"master\")\n    ds.rerun(since=\"\", onto=\"\", branch=\"from-base\")\n    eq_(ds.repo.get_active_branch(), \"from-base\")\n    assert_result_count(ds.diff(revision=\"master..from-base\"), 0)\n    eq_(ds.repo.get_merge_base([\"static\", \"from-base\"]),\n        ds.repo.repo.git.rev_parse(\"static^\"))\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_chain(path):\n    ds = Dataset(path).create()\n    commits = []\n\n    grow_file = opj(path, \"grows\")\n    ds.run('echo x$(cat grows) > grows')\n    ds.repo.repo.git.tag(\"first-run\")\n\n    for _ in range(3):\n        commits.append(ds.repo.get_hexsha())\n        ds.rerun()\n        _, info = get_run_info(ds.repo.repo.head.commit.message)\n        assert info[\"chain\"] == commits\n\n    ds.rerun(revision=\"first-run\")\n    _, info = get_run_info(ds.repo.repo.head.commit.message)\n    assert info[\"chain\"] == commits[:1]\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\ndef test_rerun_old_flag_compatibility(path):\n    ds = Dataset(path).create()\n    ds.run(\"echo x$(cat grows) > grows\")\n    # Deprecated `datalad --rerun` still runs the last commit's\n    # command.\n    ds.run(rerun=True)\n    eq_(\"xx\\n\", open(opj(path, \"grows\")).read())\n    # Running with --rerun and a command ignores the command.\n    with swallow_logs(new_level=logging.WARN) as cml:\n        ds.run(rerun=True, cmd=\"ignored\")\n        assert_in(\"Ignoring provided command in --rerun mode\", cml.out)\n        eq_(\"xxx\\n\", open(opj(path, \"grows\")).read())\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_just_one_commit(path):\n    ds = Dataset(path).create()\n\n    # Check out an orphan branch so that we can test the \"one commit\n    # in a repo\" case.\n    ds.repo.checkout(\"orph\", options=[\"--orphan\"])\n    ds.repo.repo.git.reset(\"--hard\")\n\n    ds.run('echo static-content > static')\n    assert_result_count(ds.repo.repo.git.rev_list(\"HEAD\").split(), 1)\n\n    # Rerunning with just one commit doesn't raise an error ...\n    ds.rerun()\n    # ... but we're still at one commit because the content didn't\n    # change.\n    assert_result_count(ds.repo.repo.git.rev_list(\"HEAD\").split(), 1)\n\n    # We abort rather than trying to do anything when --onto='' and\n    # --since='' are given together and the first commit contains a\n    # run command.\n    ds.repo.commit(msg=\"empty\", options=[\"--allow-empty\"])\n    assert_raises(IncompleteResultsError, ds.rerun, since=\"\", onto=\"\")\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_run_failure(path):\n    ds = Dataset(path).create()\n\n    hexsha_initial = ds.repo.get_hexsha()\n\n    with assert_raises(CommandError):\n        ds.run(\"echo x$(cat grows) > grows && false\")\n    eq_(hexsha_initial, ds.repo.get_hexsha())\n    ok_(ds.repo.dirty)\n\n    msgfile = opj(ds.repo.repo.git_dir, \"COMMIT_EDITMSG\")\n    ok_exists(msgfile)\n\n    ds.add(\".\", save=False)\n    ds.save(message_file=msgfile)\n    ok_clean_git(ds.path)\n    neq_(hexsha_initial, ds.repo.get_hexsha())\n\n    outfile = opj(ds.path, \"grows\")\n    eq_('x\\n', open(outfile).read())\n\n    # There is no CommandError on rerun if the non-zero error matches the\n    # original code.\n    ds.rerun()\n    eq_('xx\\n', open(outfile).read())\n\n    # On the other hand, we fail if we rerun a command and there is a non-zero\n    # error that doesn't match.\n    ds.run(\"[ ! -e bar ] && echo c >bar\")\n    ok_clean_git(ds.path)\n    with assert_raises(CommandError):\n        ds.rerun()\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\ndef test_rerun_branch(path):\n    ds = Dataset(path).create()\n\n    ds.repo.repo.git.tag(\"prerun\")\n\n    outfile = opj(path, \"run-file\")\n\n    ds.run('echo x$(cat run-file) > run-file')\n    ds.rerun()\n    eq_('xx\\n', open(outfile).read())\n\n    with open(opj(path, \"nonrun-file\"), \"w\") as f:\n        f.write(\"foo\")\n    ds.add(\"nonrun-file\")\n\n    # Rerun the commands on a new branch that starts at the parent\n    # commit of the first run.\n    ds.rerun(since=\"prerun\", onto=\"prerun\", branch=\"rerun\")\n\n    eq_(ds.repo.get_active_branch(), \"rerun\")\n    eq_('xx\\n', open(outfile).read())\n\n    # NOTE: This test depends on the non-run commit above following a run\n    # commit.  Otherwise, all the metadata (e.g., author date) aside from the\n    # parent commit that is used to generate the commit ID may be set when\n    # running the tests, which would result in two commits rather than three.\n    for revrange in [\"rerun..master\", \"master..rerun\"]:\n        assert_result_count(\n            ds.repo.repo.git.rev_list(revrange).split(), 3)\n    eq_(ds.repo.get_merge_base([\"master\", \"rerun\"]),\n        ds.repo.repo.git.rev_parse(\"prerun\"))\n\n    # Start rerun branch at tip of current branch.\n    ds.repo.checkout(\"master\")\n    ds.rerun(since=\"prerun\", branch=\"rerun2\")\n    eq_(ds.repo.get_active_branch(), \"rerun2\")\n    eq_('xxxx\\n', open(outfile).read())\n\n    assert_result_count(\n        ds.repo.repo.git.rev_list(\"master..rerun2\").split(), 2)\n    assert_result_count(\n        ds.repo.repo.git.rev_list(\"rerun2..master\").split(), 0)\n\n    # Using an existing branch name fails.\n    ds.repo.checkout(\"master\")\n    assert_raises(IncompleteResultsError,\n                  ds.rerun, since=\"prerun\", branch=\"rerun2\")\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_cherry_pick(path):\n    ds = Dataset(path).create()\n\n    ds.repo.repo.git.tag(\"prerun\")\n    ds.run('echo abc > runfile')\n    with open(opj(path, \"nonrun-file\"), \"w\") as f:\n        f.write(\"foo\")\n    ds.add(\"nonrun-file\")\n\n    for onto, text in [(\"HEAD\", \"skipping\"), (\"prerun\", \"cherry picking\")]:\n        results = ds.rerun(since=\"prerun\", onto=onto)\n        assert_in_results(results, status='ok', path=ds.path)\n        assert any(r.get(\"message\", \"\").endswith(text) for r in results)\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_outofdate_tree(path):\n    ds = Dataset(path).create()\n    input_file = opj(path, \"foo\")\n    output_file = opj(path, \"out\")\n    with open(input_file, \"w\") as f:\n        f.write(\"abc\\ndef\")\n    ds.add(\"foo\", to_git=True)\n    # Create inital run.\n    ds.run('grep def foo > out')\n    eq_('def\\n', open(output_file).read())\n    # Change tree so that it is no longer compatible.\n    ds.remove(\"foo\")\n    # Now rerunning should fail because foo no longer exists.\n    assert_raises(CommandError, ds.rerun, revision=\"HEAD~\")\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_ambiguous_revision_file(path):\n    ds = Dataset(path).create()\n    ds.run('echo ambig > ambig')\n    ds.repo.repo.git.tag(\"ambig\")\n    # Don't fail when \"ambig\" refers to both a file and revision.\n    ds.rerun(since=\"\", revision=\"ambig\", branch=\"rerun\")\n    eq_(len(ds.repo.repo.git.rev_list(\"rerun\").split()),\n        len(ds.repo.repo.git.rev_list(\"ambig\", \"--\").split()))\n\n\n@ignore_nose_capturing_stdout\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_subdir(path):\n    ds = Dataset(path).create()\n    subdir = opj(path, 'subdir')\n    mkdir(subdir)\n    with chpwd(subdir):\n        run(\"touch test.dat\")\n    ok_clean_git(ds.path)\n    ok_file_under_git(opj(subdir, \"test.dat\"), annexed=True)\n    rec_msg, runinfo = get_run_info(ds.repo.repo.head.commit.message)\n    eq_(runinfo['pwd'], 'subdir')\n    # now, rerun within root of the dataset\n    with chpwd(ds.path):\n        ds.rerun()\n    ok_clean_git(ds.path)\n    ok_file_under_git(opj(subdir, \"test.dat\"), annexed=True)\n    # and not on top\n    assert_raises(AssertionError, ok_file_under_git, opj(ds.path, \"test.dat\"), annexed=True)\n\n    # but if we run ds.run -- runs within top of the dataset\n    with chpwd(subdir):\n        ds.run(\"touch test2.dat\")\n    ok_clean_git(ds.path)\n    ok_file_under_git(opj(ds.path, \"test2.dat\"), annexed=True)\n    rec_msg, runinfo = get_run_info(ds.repo.repo.head.commit.message)\n    eq_(runinfo['pwd'], '.')\n    # now, rerun within subdir -- smoke for now\n    with chpwd(subdir):\n        ds.rerun()\n\n\n@with_tree(tree={\"d\": {\"to_modify\": \"content1\"},\n                 \"to_remove\": \"content2\",\n                 \"to_modify\": \"content3\",\n                 \"unchanged\": \"content4\"})\ndef test_new_or_modified(path):\n    def apfiles(aps):\n        for ap in aps:\n            yield relpath(ap[\"path\"], path)\n\n    ds = Dataset(path).create(force=True, no_annex=True)\n\n    # Check out an orphan branch so that we can test the \"one commit\n    # in a repo\" case.\n    ds.repo.checkout(\"orph\", options=[\"--orphan\"])\n    ds.repo.add(\".\", commit=True)\n    assert_false(ds.repo.dirty)\n    assert_result_count(ds.repo.repo.git.rev_list(\"HEAD\").split(), 1)\n    # Diffing doesn't fail when the branch contains a single commit.\n    assert_in(\"to_modify\", apfiles(new_or_modified(ds, \"HEAD\")))\n\n    # New files are detected, deletions are not.\n    ds.repo.remove([\"to_remove\"])\n    ok_(ds.repo.dirty)\n\n    with open(opj(path, \"to_add\"), \"w\") as f:\n        f.write(\"content5\")\n    ds.repo.add([\"to_add\"], commit=True)\n    ds.repo.commit(\"add one, remove another\")\n\n    eq_(list(apfiles(new_or_modified(ds, \"HEAD\"))),\n        [\"to_add\"])\n\n    # Modifications are detected.\n    with open(opj(path, \"to_modify\"), \"w\") as f:\n        f.write(\"updated 1\")\n    with open(opj(path, \"d/to_modify\"), \"w\") as f:\n        f.write(\"updated 2\")\n    ds.repo.add([\"to_modify\", \"d/to_modify\"], commit=True)\n\n    eq_(set(apfiles(new_or_modified(ds, \"HEAD\"))),\n        {\"to_modify\", \"d/to_modify\"})\n\n    # Non-HEAD revisions work.\n    ds.repo.commit(\"empty\", options=[\"--allow-empty\"])\n    assert_false(list(apfiles(new_or_modified(ds, \"HEAD\"))))\n    eq_(set(apfiles(new_or_modified(ds, \"HEAD~\"))),\n        {\"to_modify\", \"d/to_modify\"})\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\ndef test_rerun_script(path):\n    ds = Dataset(path).create()\n    ds.run(\"echo a >foo\")\n    ds.run(\"echo b >bar\")\n\n    script_file = opj(path, \"commands.sh\")\n\n    ds.rerun(script=script_file)\n    ok_exists(script_file)\n    with open(script_file) as sf:\n        lines = sf.readlines()\n        assert_in(\"echo b >bar\\n\", lines)\n        assert_not_in(\"echo a >foo\\n\", lines)\n\n    ds.rerun(since=\"\", script=script_file)\n    with open(script_file) as sf:\n        lines = sf.readlines()\n        assert_in(\"echo b >bar\\n\", lines)\n        assert_in(\"echo a >foo\\n\", lines)\n\n\ndef test_rerun_commit_message_check():\n    assert_raises(ValueError,\n                  get_run_info,\n                  \"\"\"\\\n[DATALAD RUNCMD] no command\n\n=== Do not change lines below ===\n{\n \"pwd\": \".\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n\n    assert_raises(ValueError,\n                  get_run_info,\n                  \"\"\"\\\n[DATALAD RUNCMD] junk json\n\n=== Do not change lines below ===\n{\n \"pwd\": \".,\n \"cmd\": \"echo ok >okfile\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n\n    subject, info = get_run_info(\"\"\"\\\n[DATALAD RUNCMD] fine\n\n=== Do not change lines below ===\n{\n \"pwd\": \".\",\n \"cmd\": \"echo ok >okfile\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n    eq_(subject, \"fine\")\n    assert_dict_equal(info,\n                      {\"pwd\": \".\", \"cmd\": \"echo ok >okfile\", \"exit\": 0})\n",
            "header": {
                "file": {
                    "path": "datalad/interface/tests/test_run.py"
                },
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            },
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                "old_commit_hash": "42d8a77db",
                "new_commit_hash": "36e3939e7",
                "mode": "100644"
            },
            "is_binary_file": false,
            "binary_line": null,
            "minus_file": {
                "path": "a/datalad/interface/tests/test_run.py"
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            "plus_file": {
                "path": "b/datalad/interface/tests/test_run.py"
            },
            "hunks": [
                {
                    "descriptor": {
                        "old_range": {
                            "start": 587,
                            "length": 6
                        },
                        "new_range": {
                            "start": 587,
                            "length": 6
                        },
                        "section": "def test_rerun_commit_message_check():"
                    },
                    "line_group": {
                        "all_lines": [
                            {
                                "content": " \"exit\": 0",
                                "type": "context"
                            },
                            {
                                "content": "}",
                                "type": "context"
                            },
                            {
                                "content": "^^^ Do not change lines above ^^^\"\"\")",
                                "type": "context"
                            },
                            {
                                "content": "    eq_(subject, \"fine\\n\\n\")",
                                "type": "deleted"
                            },
                            {
                                "content": "    eq_(subject, \"fine\")",
                                "type": "added"
                            },
                            {
                                "content": "    assert_dict_equal(info,",
                                "type": "context"
                            },
                            {
                                "content": "                      {\"pwd\": \".\", \"cmd\": \"echo ok >okfile\", \"exit\": 0})",
                                "type": "context"
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                                "type": "context"
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                    "modified_entities": [
                        {
                            "file_name": "datalad/interface/tests/test_run.py",
                            "type": "function",
                            "name": "test_rerun_commit_message_check",
                            "content": "def test_rerun_commit_message_check():\n    assert_raises(ValueError,\n                  get_run_info,\n                  \"\"\"\\\n[DATALAD RUNCMD] no command\n\n=== Do not change lines below ===\n{\n \"pwd\": \".\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n\n    assert_raises(ValueError,\n                  get_run_info,\n                  \"\"\"\\\n[DATALAD RUNCMD] junk json\n\n=== Do not change lines below ===\n{\n \"pwd\": \".,\n \"cmd\": \"echo ok >okfile\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n\n    subject, info = get_run_info(\"\"\"\\\n[DATALAD RUNCMD] fine\n\n=== Do not change lines below ===\n{\n \"pwd\": \".\",\n \"cmd\": \"echo ok >okfile\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n    eq_(subject, \"fine\\n\\n\")\n    assert_dict_equal(info,\n                      {\"pwd\": \".\", \"cmd\": \"echo ok >okfile\", \"exit\": 0})",
                            "ast_type_str": "FunctionDef",
                            "start_lineno": 554,
                            "end_lineno": 592,
                            "parent": null
                        }
                    ],
                    "added_entities": [],
                    "deleted_entities": []
                }
            ]
        }
    ],
    "old_commit_hash": "9c5ef02a8512d3242997df85016e9c3ce8e3f2b7^",
    "new_commit_hash": "9c5ef02a8512d3242997df85016e9c3ce8e3f2b7",
    "commit_message": "RF: rerun: Strip trailing new lines from the subject\n\nThese shouldn't be here.  They haven't been noticed because they don't\nactually result in a rerun extending the message by \"\\n\\n\" because Git\ncollapses multiple blanks lines into one when storing the commit\nmessage.",
    "commit_date": "2018-04-20T13:10:47-04:00",
    "metadata": {}
}
{
    "repo_name": "datalad",
    "new_commit_hash": "9c5ef02a8512d3242997df85016e9c3ce8e3f2b7",
    "test_file_codes": [
        "# 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\"\"\"test command datalad {re,}run\n\n\"\"\"\n\n__docformat__ = 'restructuredtext'\n\nimport logging\n\nfrom datalad.tests.utils import (\n    known_failure_direct_mode,\n    known_failure_v6,\n)\n\nfrom os.path import join as opj\nfrom os.path import relpath\nfrom os import mkdir\nfrom datalad.utils import chpwd\n\nfrom datalad.distribution.dataset import Dataset\nfrom datalad.support.exceptions import NoDatasetArgumentFound\nfrom datalad.support.exceptions import CommandError\nfrom datalad.support.exceptions import IncompleteResultsError\nfrom datalad.support.gitrepo import GitCommandError\nfrom datalad.tests.utils import ok_, assert_false, neq_\nfrom datalad.api import run\nfrom datalad.interface.rerun import get_run_info, new_or_modified\nfrom datalad.tests.utils import assert_raises\nfrom datalad.tests.utils import assert_dict_equal\nfrom datalad.tests.utils import with_tempfile\nfrom datalad.tests.utils import with_tree\nfrom datalad.tests.utils import ok_clean_git\nfrom datalad.tests.utils import ok_exists\nfrom datalad.tests.utils import ok_file_under_git\nfrom datalad.tests.utils import create_tree\nfrom datalad.tests.utils import eq_\nfrom datalad.tests.utils import assert_status\nfrom datalad.tests.utils import assert_result_count\nfrom datalad.tests.utils import assert_in\nfrom datalad.tests.utils import assert_not_in\nfrom datalad.tests.utils import swallow_logs\nfrom datalad.tests.utils import swallow_outputs\nfrom datalad.tests.utils import assert_in_results\nfrom datalad.tests.utils import skip_if_on_windows\nfrom datalad.tests.utils import ignore_nose_capturing_stdout\nfrom datalad.tests.utils import slow\n\n\n@with_tempfile(mkdir=True)\ndef test_invalid_call(path):\n    with chpwd(path):\n        # no dataset, no luck\n        assert_raises(NoDatasetArgumentFound, run, 'doesntmatter')\n        # dirty dataset\n        ds = Dataset(path).create()\n        create_tree(ds.path, {'this': 'dirty'})\n        assert_status('impossible', run('doesntmatter', on_failure='ignore'))\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@with_tempfile(mkdir=True)\ndef test_basics(path, nodspath):\n    ds = Dataset(path).create()\n    last_state = ds.repo.get_hexsha()\n    # run inside the dataset\n    with chpwd(path), \\\n            swallow_outputs():\n        # provoke command failure\n        with assert_raises(CommandError) as cme:\n            ds.run('7i3amhmuch9invalid')\n            # let's not speculate that the exit code is always 127\n            ok_(cme.code > 0)\n        eq_(last_state, ds.repo.get_hexsha())\n        # now one that must work\n        res = ds.run('touch empty', message='TEST')\n        ok_clean_git(ds.path)\n        assert_result_count(res, 2)\n        # TODO 'state' is still untracked!!!\n        assert_result_count(res, 1, action='add', path=opj(ds.path, 'empty'), type='file')\n        assert_result_count(res, 1, action='save', path=ds.path)\n        commit_msg = ds.repo.repo.head.commit.message\n        ok_(commit_msg.startswith('[DATALAD RUNCMD] TEST'))\n        # crude test that we have a record for the PWD\n        assert_in('\"pwd\": \".\"', commit_msg)\n        last_state = ds.repo.get_hexsha()\n        # now run a command that will not alter the dataset\n        res = ds.run('touch empty', message='NOOP_TEST')\n        assert_status('notneeded', res)\n        eq_(last_state, ds.repo.get_hexsha())\n\n    # run outside the dataset, should still work but with limitations\n    with chpwd(nodspath), \\\n            swallow_outputs():\n        res = ds.run(['touch', 'empty2'], message='TEST')\n        assert_status('ok', res)\n        assert_result_count(res, 1, action='add', path=opj(ds.path, 'empty2'), type='file')\n\n    # running without a command is a noop\n    with chpwd(path):\n        with swallow_logs(new_level=logging.WARN) as cml:\n            ds.run()\n            assert_in(\"No command given\", cml.out)\n\n\n@slow  # 17.1880s\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\ndef test_rerun(path, nodspath):\n    ds = Dataset(path).create()\n    sub = ds.create('sub')\n    probe_path = opj(sub.path, 'sequence')\n    # run inside the dataset\n    with chpwd(path), \\\n            swallow_outputs():\n        ds.run('echo x$(cat sub/sequence) > sub/sequence')\n    # command ran once, all clean\n    ok_clean_git(ds.path)\n    eq_('x\\n', open(probe_path).read())\n    # now, for a rerun we can be anywhere, PWD and all are recorded\n    # moreover, rerun must figure out which bits to unlock, even in\n    # subdatasets\n    with chpwd(nodspath), \\\n            swallow_outputs():\n        ds.rerun()\n    ok_clean_git(ds.path)\n    # ran twice now\n    eq_('xx\\n', open(probe_path).read())\n    # Make a non-run commit.\n    with open(opj(path, \"nonrun-file\"), \"w\") as f:\n        f.write(\"foo\")\n    ds.add(\"nonrun-file\")\n    # Now rerun the buried command.\n    ds.rerun(revision=\"HEAD~\", message=\"rerun buried\")\n    eq_('xxx\\n', open(probe_path).read())\n    # Also check that the messasge override worked.\n    eq_(ds.repo.repo.head.commit.message.splitlines()[0],\n        \"[DATALAD RUNCMD] rerun buried\")\n    # Or a range of commits, skipping non-run commits.\n    ds.rerun(since=\"HEAD~3\")\n    eq_('xxxxx\\n', open(probe_path).read())\n    # Or --since= to run all reachable commits.\n    ds.rerun(since=\"\")\n    eq_('xxxxxxxxxx\\n', open(probe_path).read())\n    # If the history to rerun has a merge commit, we abort.\n    ds.repo.checkout(\"HEAD~3\", options=[\"-b\", \"topic\"])\n    with open(opj(path, \"topic-file\"), \"w\") as f:\n        f.write(\"topic\")\n    ds.add(\"topic-file\")\n    ds.repo.checkout(\"master\")\n    ds.repo.merge(\"topic\")\n    ok_clean_git(ds.path)\n    assert_raises(IncompleteResultsError, ds.rerun)\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_onto(path):\n    ds = Dataset(path).create()\n\n    grow_file = opj(path, \"grows\")\n\n    ds.run('echo static-content > static')\n    ds.repo.repo.git.tag(\"static\")\n    ds.run('echo x$(cat grows) > grows')\n    ds.rerun()\n    eq_('xx\\n', open(grow_file).read())\n\n    # If we run the \"static\" change on top of itself, we end up in the\n    # same (but detached) place.\n    ds.rerun(revision=\"static\", onto=\"static\")\n    ok_(ds.repo.get_active_branch() is None)\n    eq_(ds.repo.repo.git.rev_parse(\"HEAD\"),\n        ds.repo.repo.git.rev_parse(\"static\"))\n\n    # If we run the \"static\" change from the same \"base\", we end up\n    # with a new commit.\n    ds.repo.checkout(\"master\")\n    ds.rerun(revision=\"static\", onto=\"static^\")\n    ok_(ds.repo.get_active_branch() is None)\n    neq_(ds.repo.repo.git.rev_parse(\"HEAD\"),\n         ds.repo.repo.git.rev_parse(\"static\"))\n    assert_result_count(ds.diff(revision=\"HEAD..static\"), 0)\n    for revrange in [\"..static\", \"static..\"]:\n        assert_result_count(\n            ds.repo.repo.git.rev_list(revrange).split(), 1)\n\n    # Unlike the static change, if we run the ever-growing change on\n    # top of itself, we end up with a new commit.\n    ds.repo.checkout(\"master\")\n    ds.rerun(onto=\"HEAD\")\n    ok_(ds.repo.get_active_branch() is None)\n    neq_(ds.repo.repo.git.rev_parse(\"HEAD\"),\n         ds.repo.repo.git.rev_parse(\"master\"))\n\n    # An empty `onto` means use the parent of the first revision.\n    ds.repo.checkout(\"master\")\n    ds.rerun(since=\"static^\", onto=\"\")\n    ok_(ds.repo.get_active_branch() is None)\n    for revrange in [\"..master\", \"master..\"]:\n        assert_result_count(\n            ds.repo.repo.git.rev_list(revrange).split(), 3)\n\n    # An empty `onto` means use the parent of the first revision that\n    # has a run command.\n    ds.repo.checkout(\"master\")\n    ds.rerun(since=\"\", onto=\"\", branch=\"from-base\")\n    eq_(ds.repo.get_active_branch(), \"from-base\")\n    assert_result_count(ds.diff(revision=\"master..from-base\"), 0)\n    eq_(ds.repo.get_merge_base([\"static\", \"from-base\"]),\n        ds.repo.repo.git.rev_parse(\"static^\"))\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_chain(path):\n    ds = Dataset(path).create()\n    commits = []\n\n    grow_file = opj(path, \"grows\")\n    ds.run('echo x$(cat grows) > grows')\n    ds.repo.repo.git.tag(\"first-run\")\n\n    for _ in range(3):\n        commits.append(ds.repo.get_hexsha())\n        ds.rerun()\n        _, info = get_run_info(ds.repo.repo.head.commit.message)\n        assert info[\"chain\"] == commits\n\n    ds.rerun(revision=\"first-run\")\n    _, info = get_run_info(ds.repo.repo.head.commit.message)\n    assert info[\"chain\"] == commits[:1]\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\ndef test_rerun_old_flag_compatibility(path):\n    ds = Dataset(path).create()\n    ds.run(\"echo x$(cat grows) > grows\")\n    # Deprecated `datalad --rerun` still runs the last commit's\n    # command.\n    ds.run(rerun=True)\n    eq_(\"xx\\n\", open(opj(path, \"grows\")).read())\n    # Running with --rerun and a command ignores the command.\n    with swallow_logs(new_level=logging.WARN) as cml:\n        ds.run(rerun=True, cmd=\"ignored\")\n        assert_in(\"Ignoring provided command in --rerun mode\", cml.out)\n        eq_(\"xxx\\n\", open(opj(path, \"grows\")).read())\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_just_one_commit(path):\n    ds = Dataset(path).create()\n\n    # Check out an orphan branch so that we can test the \"one commit\n    # in a repo\" case.\n    ds.repo.checkout(\"orph\", options=[\"--orphan\"])\n    ds.repo.repo.git.reset(\"--hard\")\n\n    ds.run('echo static-content > static')\n    assert_result_count(ds.repo.repo.git.rev_list(\"HEAD\").split(), 1)\n\n    # Rerunning with just one commit doesn't raise an error ...\n    ds.rerun()\n    # ... but we're still at one commit because the content didn't\n    # change.\n    assert_result_count(ds.repo.repo.git.rev_list(\"HEAD\").split(), 1)\n\n    # We abort rather than trying to do anything when --onto='' and\n    # --since='' are given together and the first commit contains a\n    # run command.\n    ds.repo.commit(msg=\"empty\", options=[\"--allow-empty\"])\n    assert_raises(IncompleteResultsError, ds.rerun, since=\"\", onto=\"\")\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_run_failure(path):\n    ds = Dataset(path).create()\n\n    hexsha_initial = ds.repo.get_hexsha()\n\n    with assert_raises(CommandError):\n        ds.run(\"echo x$(cat grows) > grows && false\")\n    eq_(hexsha_initial, ds.repo.get_hexsha())\n    ok_(ds.repo.dirty)\n\n    msgfile = opj(ds.repo.repo.git_dir, \"COMMIT_EDITMSG\")\n    ok_exists(msgfile)\n\n    ds.add(\".\", save=False)\n    ds.save(message_file=msgfile)\n    ok_clean_git(ds.path)\n    neq_(hexsha_initial, ds.repo.get_hexsha())\n\n    outfile = opj(ds.path, \"grows\")\n    eq_('x\\n', open(outfile).read())\n\n    # There is no CommandError on rerun if the non-zero error matches the\n    # original code.\n    ds.rerun()\n    eq_('xx\\n', open(outfile).read())\n\n    # On the other hand, we fail if we rerun a command and there is a non-zero\n    # error that doesn't match.\n    ds.run(\"[ ! -e bar ] && echo c >bar\")\n    ok_clean_git(ds.path)\n    with assert_raises(CommandError):\n        ds.rerun()\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\ndef test_rerun_branch(path):\n    ds = Dataset(path).create()\n\n    ds.repo.repo.git.tag(\"prerun\")\n\n    outfile = opj(path, \"run-file\")\n\n    ds.run('echo x$(cat run-file) > run-file')\n    ds.rerun()\n    eq_('xx\\n', open(outfile).read())\n\n    with open(opj(path, \"nonrun-file\"), \"w\") as f:\n        f.write(\"foo\")\n    ds.add(\"nonrun-file\")\n\n    # Rerun the commands on a new branch that starts at the parent\n    # commit of the first run.\n    ds.rerun(since=\"prerun\", onto=\"prerun\", branch=\"rerun\")\n\n    eq_(ds.repo.get_active_branch(), \"rerun\")\n    eq_('xx\\n', open(outfile).read())\n\n    # NOTE: This test depends on the non-run commit above following a run\n    # commit.  Otherwise, all the metadata (e.g., author date) aside from the\n    # parent commit that is used to generate the commit ID may be set when\n    # running the tests, which would result in two commits rather than three.\n    for revrange in [\"rerun..master\", \"master..rerun\"]:\n        assert_result_count(\n            ds.repo.repo.git.rev_list(revrange).split(), 3)\n    eq_(ds.repo.get_merge_base([\"master\", \"rerun\"]),\n        ds.repo.repo.git.rev_parse(\"prerun\"))\n\n    # Start rerun branch at tip of current branch.\n    ds.repo.checkout(\"master\")\n    ds.rerun(since=\"prerun\", branch=\"rerun2\")\n    eq_(ds.repo.get_active_branch(), \"rerun2\")\n    eq_('xxxx\\n', open(outfile).read())\n\n    assert_result_count(\n        ds.repo.repo.git.rev_list(\"master..rerun2\").split(), 2)\n    assert_result_count(\n        ds.repo.repo.git.rev_list(\"rerun2..master\").split(), 0)\n\n    # Using an existing branch name fails.\n    ds.repo.checkout(\"master\")\n    assert_raises(IncompleteResultsError,\n                  ds.rerun, since=\"prerun\", branch=\"rerun2\")\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_cherry_pick(path):\n    ds = Dataset(path).create()\n\n    ds.repo.repo.git.tag(\"prerun\")\n    ds.run('echo abc > runfile')\n    with open(opj(path, \"nonrun-file\"), \"w\") as f:\n        f.write(\"foo\")\n    ds.add(\"nonrun-file\")\n\n    for onto, text in [(\"HEAD\", \"skipping\"), (\"prerun\", \"cherry picking\")]:\n        results = ds.rerun(since=\"prerun\", onto=onto)\n        assert_in_results(results, status='ok', path=ds.path)\n        assert any(r.get(\"message\", \"\").endswith(text) for r in results)\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_outofdate_tree(path):\n    ds = Dataset(path).create()\n    input_file = opj(path, \"foo\")\n    output_file = opj(path, \"out\")\n    with open(input_file, \"w\") as f:\n        f.write(\"abc\\ndef\")\n    ds.add(\"foo\", to_git=True)\n    # Create inital run.\n    ds.run('grep def foo > out')\n    eq_('def\\n', open(output_file).read())\n    # Change tree so that it is no longer compatible.\n    ds.remove(\"foo\")\n    # Now rerunning should fail because foo no longer exists.\n    assert_raises(CommandError, ds.rerun, revision=\"HEAD~\")\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_ambiguous_revision_file(path):\n    ds = Dataset(path).create()\n    ds.run('echo ambig > ambig')\n    ds.repo.repo.git.tag(\"ambig\")\n    # Don't fail when \"ambig\" refers to both a file and revision.\n    ds.rerun(since=\"\", revision=\"ambig\", branch=\"rerun\")\n    eq_(len(ds.repo.repo.git.rev_list(\"rerun\").split()),\n        len(ds.repo.repo.git.rev_list(\"ambig\", \"--\").split()))\n\n\n@ignore_nose_capturing_stdout\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\n@known_failure_v6  #FIXME\ndef test_rerun_subdir(path):\n    ds = Dataset(path).create()\n    subdir = opj(path, 'subdir')\n    mkdir(subdir)\n    with chpwd(subdir):\n        run(\"touch test.dat\")\n    ok_clean_git(ds.path)\n    ok_file_under_git(opj(subdir, \"test.dat\"), annexed=True)\n    rec_msg, runinfo = get_run_info(ds.repo.repo.head.commit.message)\n    eq_(runinfo['pwd'], 'subdir')\n    # now, rerun within root of the dataset\n    with chpwd(ds.path):\n        ds.rerun()\n    ok_clean_git(ds.path)\n    ok_file_under_git(opj(subdir, \"test.dat\"), annexed=True)\n    # and not on top\n    assert_raises(AssertionError, ok_file_under_git, opj(ds.path, \"test.dat\"), annexed=True)\n\n    # but if we run ds.run -- runs within top of the dataset\n    with chpwd(subdir):\n        ds.run(\"touch test2.dat\")\n    ok_clean_git(ds.path)\n    ok_file_under_git(opj(ds.path, \"test2.dat\"), annexed=True)\n    rec_msg, runinfo = get_run_info(ds.repo.repo.head.commit.message)\n    eq_(runinfo['pwd'], '.')\n    # now, rerun within subdir -- smoke for now\n    with chpwd(subdir):\n        ds.rerun()\n\n\n@with_tree(tree={\"d\": {\"to_modify\": \"content1\"},\n                 \"to_remove\": \"content2\",\n                 \"to_modify\": \"content3\",\n                 \"unchanged\": \"content4\"})\ndef test_new_or_modified(path):\n    def apfiles(aps):\n        for ap in aps:\n            yield relpath(ap[\"path\"], path)\n\n    ds = Dataset(path).create(force=True, no_annex=True)\n\n    # Check out an orphan branch so that we can test the \"one commit\n    # in a repo\" case.\n    ds.repo.checkout(\"orph\", options=[\"--orphan\"])\n    ds.repo.add(\".\", commit=True)\n    assert_false(ds.repo.dirty)\n    assert_result_count(ds.repo.repo.git.rev_list(\"HEAD\").split(), 1)\n    # Diffing doesn't fail when the branch contains a single commit.\n    assert_in(\"to_modify\", apfiles(new_or_modified(ds, \"HEAD\")))\n\n    # New files are detected, deletions are not.\n    ds.repo.remove([\"to_remove\"])\n    ok_(ds.repo.dirty)\n\n    with open(opj(path, \"to_add\"), \"w\") as f:\n        f.write(\"content5\")\n    ds.repo.add([\"to_add\"], commit=True)\n    ds.repo.commit(\"add one, remove another\")\n\n    eq_(list(apfiles(new_or_modified(ds, \"HEAD\"))),\n        [\"to_add\"])\n\n    # Modifications are detected.\n    with open(opj(path, \"to_modify\"), \"w\") as f:\n        f.write(\"updated 1\")\n    with open(opj(path, \"d/to_modify\"), \"w\") as f:\n        f.write(\"updated 2\")\n    ds.repo.add([\"to_modify\", \"d/to_modify\"], commit=True)\n\n    eq_(set(apfiles(new_or_modified(ds, \"HEAD\"))),\n        {\"to_modify\", \"d/to_modify\"})\n\n    # Non-HEAD revisions work.\n    ds.repo.commit(\"empty\", options=[\"--allow-empty\"])\n    assert_false(list(apfiles(new_or_modified(ds, \"HEAD\"))))\n    eq_(set(apfiles(new_or_modified(ds, \"HEAD~\"))),\n        {\"to_modify\", \"d/to_modify\"})\n\n\n@ignore_nose_capturing_stdout\n@skip_if_on_windows\n@with_tempfile(mkdir=True)\n@known_failure_direct_mode  #FIXME\ndef test_rerun_script(path):\n    ds = Dataset(path).create()\n    ds.run(\"echo a >foo\")\n    ds.run(\"echo b >bar\")\n\n    script_file = opj(path, \"commands.sh\")\n\n    ds.rerun(script=script_file)\n    ok_exists(script_file)\n    with open(script_file) as sf:\n        lines = sf.readlines()\n        assert_in(\"echo b >bar\\n\", lines)\n        assert_not_in(\"echo a >foo\\n\", lines)\n\n    ds.rerun(since=\"\", script=script_file)\n    with open(script_file) as sf:\n        lines = sf.readlines()\n        assert_in(\"echo b >bar\\n\", lines)\n        assert_in(\"echo a >foo\\n\", lines)\n\n\ndef test_rerun_commit_message_check():\n    assert_raises(ValueError,\n                  get_run_info,\n                  \"\"\"\\\n[DATALAD RUNCMD] no command\n\n=== Do not change lines below ===\n{\n \"pwd\": \".\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n\n    assert_raises(ValueError,\n                  get_run_info,\n                  \"\"\"\\\n[DATALAD RUNCMD] junk json\n\n=== Do not change lines below ===\n{\n \"pwd\": \".,\n \"cmd\": \"echo ok >okfile\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n\n    subject, info = get_run_info(\"\"\"\\\n[DATALAD RUNCMD] fine\n\n=== Do not change lines below ===\n{\n \"pwd\": \".\",\n \"cmd\": \"echo ok >okfile\",\n \"exit\": 0\n}\n^^^ Do not change lines above ^^^\"\"\")\n    eq_(subject, \"fine\")\n    assert_dict_equal(info,\n                      {\"pwd\": \".\", \"cmd\": \"echo ok >okfile\", \"exit\": 0})\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...\n❌ Verification failed\nPython 3.9 installation failed, trying Python 3.7...\nVerifying installation...\nDatalad version: 0.9.3.dev1080\n✅ Installation successful!\nSuccessfully installed Datalad using Python 3.7\n",
    "setup_res_stderr": "Using CPython 3.9.21\nCreating virtual environment at: .venv\nActivate with: source .venv/bin/activate\nResolved 25 packages in 38ms\nInstalled 25 packages in 5.62s\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\nerror: The build backend returned an error\n  Caused by: Call to `setuptools.build_meta:__legacy__.build_editable` failed (exit status: 1)\n\n[stderr]\nTraceback (most recent call last):\n  File \"<string>\", line 14, in <module>\n  File \"/home/gcpuser/.cache/uv/builds-v0/.tmp0Q2LQj/lib/python3.9/site-packages/setuptools/build_meta.py\", line 483, in get_requires_for_build_editable\n    return self.get_requires_for_build_wheel(config_settings)\n  File \"/home/gcpuser/.cache/uv/builds-v0/.tmp0Q2LQj/lib/python3.9/site-packages/setuptools/build_meta.py\", line 334, in get_requires_for_build_wheel\n    return self._get_build_requires(config_settings, requirements=[])\n  File \"/home/gcpuser/.cache/uv/builds-v0/.tmp0Q2LQj/lib/python3.9/site-packages/setuptools/build_meta.py\", line 304, in _get_build_requires\n    self.run_setup()\n  File \"/home/gcpuser/.cache/uv/builds-v0/.tmp0Q2LQj/lib/python3.9/site-packages/setuptools/build_meta.py\", line 522, in run_setup\n    super().run_setup(setup_script=setup_script)\n  File \"/home/gcpuser/.cache/uv/builds-v0/.tmp0Q2LQj/lib/python3.9/site-packages/setuptools/build_meta.py\", line 320, in run_setup\n    exec(code, locals())\n  File \"<string>\", line 50, in <module>\nAttributeError: module 'platform' has no attribute 'dist'\n\nhint: This usually indicates a problem with the package or the build environment.\nerror: The build backend returned an error\n  Caused by: Call to `setuptools.build_meta:__legacy__.build_editable` failed (exit status: 1)\n\n[stderr]\nTraceback (most recent call last):\n  File \"<string>\", line 14, in <module>\n  File \"/home/gcpuser/.cache/uv/builds-v0/.tmpTwh4YY/lib/python3.9/site-packages/setuptools/build_meta.py\", line 483, in get_requires_for_build_editable\n    return self.get_requires_for_build_wheel(config_settings)\n  File \"/home/gcpuser/.cache/uv/builds-v0/.tmpTwh4YY/lib/python3.9/site-packages/setuptools/build_meta.py\", line 334, in get_requires_for_build_wheel\n    return self._get_build_requires(config_settings, requirements=[])\n  File \"/home/gcpuser/.cache/uv/builds-v0/.tmpTwh4YY/lib/python3.9/site-packages/setuptools/build_meta.py\", line 304, in _get_build_requires\n    self.run_setup()\n  File \"/home/gcpuser/.cache/uv/builds-v0/.tmpTwh4YY/lib/python3.9/site-packages/setuptools/build_meta.py\", line 522, in run_setup\n    super().run_setup(setup_script=setup_script)\n  File \"/home/gcpuser/.cache/uv/builds-v0/.tmpTwh4YY/lib/python3.9/site-packages/setuptools/build_meta.py\", line 320, in run_setup\n    exec(code, locals())\n  File \"<string>\", line 50, in <module>\nAttributeError: module 'platform' has no attribute 'dist'\n\nhint: This usually indicates a problem with the package or the build environment.\nTraceback (most recent call last):\n  File \"<string>\", line 1, in <module>\n  File \"/home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7/datalad/__init__.py\", line 23, in <module>\n    from datalad.cmd import GitRunner\n  File \"/home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7/datalad/cmd.py\", line 35, in <module>\n    from .utils import on_windows, get_tempfile_kwargs, assure_unicode\n  File \"/home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7/datalad/utils.py\", line 24, in <module>\n    import wrapt\nModuleNotFoundError: No module named 'wrapt'\nUsing CPython 3.7.9\nCreating virtual environment at: .venv\nActivate with: source .venv/bin/activate\nResolved 26 packages in 225ms\nInstalled 26 packages in 5.40s\n + bids==0.0\n + coverage==7.2.7\n + docopt==0.6.2\n + exceptiongroup==1.2.2\n + fasteners==0.19\n + grabbit==0.2.6\n + importlib-metadata==6.7.0\n + iniconfig==2.0.0\n + nibabel==4.0.2\n + num2words==0.5.14\n + numpy==1.21.6\n + packaging==24.0\n + pandas==1.3.5\n + patsy==1.0.1\n + pluggy==1.2.0\n + pybids==0.6.5\n + pytest==7.4.4\n + pytest-cov==4.1.0\n + python-dateutil==2.9.0.post0\n + pytz==2024.2\n + scipy==1.7.3\n + setuptools==68.0.0\n + six==1.17.0\n + tomli==2.0.1\n + typing-extensions==4.7.1\n + zipp==3.15.0\nResolved 85 packages in 3.28s\nPrepared 1 package in 1.20s\nInstalled 77 packages in 58ms\n + appdirs==1.4.4\n + attrs==24.2.0\n + automat==22.10.0\n + beautifulsoup4==4.12.3\n + boto==2.49.0\n + certifi==2024.12.14\n + cffi==1.15.1\n + chardet==5.2.0\n + charset-normalizer==3.4.1\n + citeproc-py==0.6.0\n + constantly==15.1.0\n + cryptography==44.0.0\n + cssselect==1.2.0\n + datalad==0.10.0.dev1 (from file:///home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7)\n + deprecated==1.2.15\n + duecredit==0.9.3\n + exifread==3.0.0\n + filelock==3.12.2\n + gitdb==4.0.12\n + gitpython==3.1.44\n + httpretty==1.1.4\n + humanize==4.6.0\n + hyperlink==21.0.0\n + idna==3.10\n + importlib-resources==5.12.0\n + incremental==22.10.0\n + iso8601==2.1.0\n + itemadapter==0.8.0\n + itemloaders==1.1.0\n + jaraco-classes==3.2.3\n + jeepney==0.8.0\n + jmespath==1.0.1\n + jsmin==3.0.1\n + keyring==24.1.1\n + keyrings-alt==4.2.0\n + lxml==5.3.0\n + mock==5.1.0\n + more-itertools==9.1.0\n + msgpack==1.0.5\n + multidict==6.0.5\n + mutagen==1.47.0\n + nose==1.3.7\n + parsel==1.8.1\n + patool==1.12\n + pillow==9.5.0\n + protego==0.3.0\n + pyasn1==0.5.1\n + pyasn1-modules==0.3.0\n + pycparser==2.21\n + pydispatcher==2.0.7\n + pygithub==2.3.0\n + pyjwt==2.8.0\n + pynacl==1.5.0\n + pyopenssl==24.3.0\n + pyperclip==1.9.0\n + python-xmp-toolkit==2.0.2\n + pyyaml==6.0.1\n + queuelib==1.6.2\n + requests==2.31.0\n + requests-file==2.1.0\n + requests-ftp==0.3.1\n + scrapy==2.9.0\n + secretstorage==3.3.3\n + service-identity==21.1.0\n + simplejson==3.19.3\n + smmap==5.0.2\n + soupsieve==2.4.1\n + tldextract==4.0.0\n + tqdm==4.67.1\n + twisted==23.8.0\n + urllib3==2.0.7\n + vcrpy==4.3.0\n + w3lib==2.1.2\n + whoosh==2.7.4\n + wrapt==1.16.0\n + yarl==1.9.4\n + zope-interface==6.4.post2\nResolved 115 packages in 189ms\nInstalled 29 packages in 106ms\n + alabaster==0.7.13\n + asv==0.6.4\n + asv-runner==0.2.1\n + babel==2.14.0\n + build==1.1.1\n + distlib==0.3.9\n + docutils==0.19\n + imagesize==1.4.1\n + jinja2==3.1.5\n + json5==0.9.16\n + markupsafe==2.1.5\n + nose-timer==1.0.1\n + platformdirs==4.0.0\n + pygments==2.17.2\n + pympler==1.1\n + pypandoc==1.14\n + pyproject-hooks==1.2.0\n + snowballstemmer==2.2.0\n + sphinx==5.3.0\n + sphinx-rtd-theme==2.0.0\n + sphinxcontrib-applehelp==1.0.2\n + sphinxcontrib-devhelp==1.0.2\n + sphinxcontrib-htmlhelp==2.0.0\n + sphinxcontrib-jquery==4.1\n + sphinxcontrib-jsmath==1.0.1\n + sphinxcontrib-qthelp==1.0.3\n + sphinxcontrib-serializinghtml==1.1.5\n + tabulate==0.9.0\n + virtualenv==20.26.6\n",
    "new_commit_res_code": 1,
    "new_commit_res_stdout": "============================= test session starts ==============================\nplatform linux -- Python 3.7.9, pytest-7.4.4, pluggy-1.2.0\nrootdir: /home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7\nplugins: cov-4.1.0\ncollected 16 items\n\nr2e_tests/test_1.py FEEFFFFFFFFFFFF.                                     [100%]\n\n==================================== ERRORS ====================================\n________________________ ERROR at setup of test_basics _________________________\nfile /home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7/r2e_tests/test_1.py, line 67\n  @ignore_nose_capturing_stdout\n  @skip_if_on_windows\n  @with_tempfile(mkdir=True)\n  @with_tempfile(mkdir=True)\n  def test_basics(path, nodspath):\nE       fixture 'nodspath' not found\n>       available fixtures: cache, capfd, capfdbinary, caplog, capsys, capsysbinary, cov, doctest_namespace, monkeypatch, no_cover, path, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, setup_git_config, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory\n>       use 'pytest --fixtures [testpath]' for help on them.\n\n/home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7/r2e_tests/test_1.py:67\n_________________________ ERROR at setup of test_rerun _________________________\nfile /home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7/r2e_tests/test_1.py, line 114\n  @slow  # 17.1880s\n  @ignore_nose_capturing_stdout\n  @skip_if_on_windows\n  @with_tempfile(mkdir=True)\n  @with_tempfile(mkdir=True)\n  @known_failure_direct_mode  #FIXME\n  def test_rerun(path, nodspath):\nE       fixture 'nodspath' not found\n>       available fixtures: cache, capfd, capfdbinary, caplog, capsys, capsysbinary, cov, doctest_namespace, monkeypatch, no_cover, path, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, setup_git_config, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory\n>       use 'pytest --fixtures [testpath]' for help on them.\n\n/home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7/r2e_tests/test_1.py:114\n=================================== FAILURES ===================================\n______________________________ test_invalid_call _______________________________\n\narg = (), kw = {'path': '/tmp/tmp-page2annexxeb756op'}\nfilename = '/tmp/datalad_temp_test_invalid_callpanh_nmu'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_invalid_call() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n_______________________________ test_rerun_onto ________________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexhd3d467e'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexhd3d467e'}\nfilename = '/tmp/datalad_temp_test_rerun_onto7g5zpi8q'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_onto() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n_______________________________ test_rerun_chain _______________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexz8valkx_'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexz8valkx_'}\nfilename = '/tmp/datalad_temp_test_rerun_chain9rdqfv8g'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_chain() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n______________________ test_rerun_old_flag_compatibility _______________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annex5u7ajml7'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annex5u7ajml7'}\nfilename = '/tmp/datalad_temp_test_rerun_old_flag_compatibilitykq_udqed'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_old_flag_compatibility() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n__________________________ test_rerun_just_one_commit __________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexalm6qjz9'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexalm6qjz9'}\nfilename = '/tmp/datalad_temp_test_rerun_just_one_commitx47s90qj'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_just_one_commit() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n_______________________________ test_run_failure _______________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexci9k9ovm'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexci9k9ovm'}\nfilename = '/tmp/datalad_temp_test_run_failureniztxbji'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_run_failure() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n______________________________ test_rerun_branch _______________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexde7qeiih'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexde7qeiih'}\nfilename = '/tmp/datalad_temp_test_rerun_branch7so_9ciw'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_branch() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n____________________________ test_rerun_cherry_pick ____________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexw2dxu0eq'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexw2dxu0eq'}\nfilename = '/tmp/datalad_temp_test_rerun_cherry_pick826q_bg3'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_cherry_pick() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n__________________________ test_rerun_outofdate_tree ___________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexnkwyniof'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexnkwyniof'}\nfilename = '/tmp/datalad_temp_test_rerun_outofdate_tree1_wdhelh'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_outofdate_tree() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n______________________ test_rerun_ambiguous_revision_file ______________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexu866z_xj'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexu866z_xj'}\nfilename = '/tmp/datalad_temp_test_rerun_ambiguous_revision_filerohj_ftz'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_ambiguous_revision_file() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n______________________________ test_rerun_subdir _______________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexml_exau7'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexml_exau7'}\nfilename = '/tmp/datalad_temp_test_rerun_subdirtjca5ru8'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_subdir() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n_____________________________ test_new_or_modified _____________________________\n\narg = (), kw = {'path': '/tmp/tmp-page2annexi1uhm_ax'}\ntkwargs_ = {'prefix': 'datalad_temp_tree_test_new_or_modified'}\nd = '/tmp/datalad_temp_tree_test_new_or_modifiedqpc16p8j'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        tkwargs_ = get_tempfile_kwargs(tkwargs, prefix=\"tree\", wrapped=t)\n        d = tempfile.mkdtemp(**tkwargs_)\n        create_tree(d, tree, archives_leading_dir=archives_leading_dir)\n        try:\n>           return t(*(arg + (d,)), **kw)\nE           TypeError: test_new_or_modified() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:491: TypeError\n______________________________ test_rerun_script _______________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexpbg9qvlk'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexpbg9qvlk'}\nfilename = '/tmp/datalad_temp_test_rerun_script1ayrayv1'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_script() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n==================================== PASSES ====================================\n=========================== short test summary info ============================\nPASSED r2e_tests/test_1.py::test_rerun_commit_message_check\nERROR r2e_tests/test_1.py::test_basics\nERROR r2e_tests/test_1.py::test_rerun\nFAILED r2e_tests/test_1.py::test_invalid_call - TypeError: test_invalid_call(...\nFAILED r2e_tests/test_1.py::test_rerun_onto - TypeError: test_rerun_onto() go...\nFAILED r2e_tests/test_1.py::test_rerun_chain - TypeError: test_rerun_chain() ...\nFAILED r2e_tests/test_1.py::test_rerun_old_flag_compatibility - TypeError: te...\nFAILED r2e_tests/test_1.py::test_rerun_just_one_commit - TypeError: test_reru...\nFAILED r2e_tests/test_1.py::test_run_failure - TypeError: test_run_failure() ...\nFAILED r2e_tests/test_1.py::test_rerun_branch - TypeError: test_rerun_branch(...\nFAILED r2e_tests/test_1.py::test_rerun_cherry_pick - TypeError: test_rerun_ch...\nFAILED r2e_tests/test_1.py::test_rerun_outofdate_tree - TypeError: test_rerun...\nFAILED r2e_tests/test_1.py::test_rerun_ambiguous_revision_file - TypeError: t...\nFAILED r2e_tests/test_1.py::test_rerun_subdir - TypeError: test_rerun_subdir(...\nFAILED r2e_tests/test_1.py::test_new_or_modified - TypeError: test_new_or_mod...\nFAILED r2e_tests/test_1.py::test_rerun_script - TypeError: test_rerun_script(...\n==================== 13 failed, 1 passed, 2 errors in 2.19s ====================\n",
    "new_commit_res_stderr": "",
    "old_commit_res_code": 1,
    "old_commit_res_stdout": "============================= test session starts ==============================\nplatform linux -- Python 3.7.9, pytest-7.4.4, pluggy-1.2.0\nrootdir: /home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7\nplugins: cov-4.1.0\ncollected 16 items\n\nr2e_tests/test_1.py FEEFFFFFFFFFFFFF                                     [100%]\n\n==================================== ERRORS ====================================\n________________________ ERROR at setup of test_basics _________________________\nfile /home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7/r2e_tests/test_1.py, line 67\n  @ignore_nose_capturing_stdout\n  @skip_if_on_windows\n  @with_tempfile(mkdir=True)\n  @with_tempfile(mkdir=True)\n  def test_basics(path, nodspath):\nE       fixture 'nodspath' not found\n>       available fixtures: cache, capfd, capfdbinary, caplog, capsys, capsysbinary, cov, doctest_namespace, monkeypatch, no_cover, path, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, setup_git_config, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory\n>       use 'pytest --fixtures [testpath]' for help on them.\n\n/home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7/r2e_tests/test_1.py:67\n_________________________ ERROR at setup of test_rerun _________________________\nfile /home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7/r2e_tests/test_1.py, line 114\n  @slow  # 17.1880s\n  @ignore_nose_capturing_stdout\n  @skip_if_on_windows\n  @with_tempfile(mkdir=True)\n  @with_tempfile(mkdir=True)\n  @known_failure_direct_mode  #FIXME\n  def test_rerun(path, nodspath):\nE       fixture 'nodspath' not found\n>       available fixtures: cache, capfd, capfdbinary, caplog, capsys, capsysbinary, cov, doctest_namespace, monkeypatch, no_cover, path, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, setup_git_config, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory\n>       use 'pytest --fixtures [testpath]' for help on them.\n\n/home/gcpuser/buckets/local_repoeval_bucket/repos/datalad_9c5ef02a8512d3242997df85016e9c3ce8e3f2b7/r2e_tests/test_1.py:114\n=================================== FAILURES ===================================\n______________________________ test_invalid_call _______________________________\n\narg = (), kw = {'path': '/tmp/tmp-page2annexmkt2w0p2'}\nfilename = '/tmp/datalad_temp_test_invalid_callzt2tycnx'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_invalid_call() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n_______________________________ test_rerun_onto ________________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexqfo8qpkv'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexqfo8qpkv'}\nfilename = '/tmp/datalad_temp_test_rerun_onto75e15l_i'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_onto() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n_______________________________ test_rerun_chain _______________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexll6muoxn'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexll6muoxn'}\nfilename = '/tmp/datalad_temp_test_rerun_chain8h0tjf7u'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_chain() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n______________________ test_rerun_old_flag_compatibility _______________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexllf6z6dn'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexllf6z6dn'}\nfilename = '/tmp/datalad_temp_test_rerun_old_flag_compatibilityy798ahvn'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_old_flag_compatibility() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n__________________________ test_rerun_just_one_commit __________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexewdenfkv'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexewdenfkv'}\nfilename = '/tmp/datalad_temp_test_rerun_just_one_commit4ujofukj'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_just_one_commit() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n_______________________________ test_run_failure _______________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexmwqf3kay'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexmwqf3kay'}\nfilename = '/tmp/datalad_temp_test_run_failure3jvbzvgb'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_run_failure() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n______________________________ test_rerun_branch _______________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annex0mwzv_rz'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annex0mwzv_rz'}\nfilename = '/tmp/datalad_temp_test_rerun_branch5h61cci9'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_branch() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n____________________________ test_rerun_cherry_pick ____________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexhpi0zh3i'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexhpi0zh3i'}\nfilename = '/tmp/datalad_temp_test_rerun_cherry_pickrvvy3tzv'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_cherry_pick() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n__________________________ test_rerun_outofdate_tree ___________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexpvdicg72'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexpvdicg72'}\nfilename = '/tmp/datalad_temp_test_rerun_outofdate_treeiuavooq5'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_outofdate_tree() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n______________________ test_rerun_ambiguous_revision_file ______________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexz171iyv6'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexz171iyv6'}\nfilename = '/tmp/datalad_temp_test_rerun_ambiguous_revision_fileho45so29'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_ambiguous_revision_file() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n______________________________ test_rerun_subdir _______________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexoc1k2oqc'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexoc1k2oqc'}\nfilename = '/tmp/datalad_temp_test_rerun_subdirbxod2cg3'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_subdir() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n_____________________________ test_new_or_modified _____________________________\n\narg = (), kw = {'path': '/tmp/tmp-page2annexma2ncpsd'}\ntkwargs_ = {'prefix': 'datalad_temp_tree_test_new_or_modified'}\nd = '/tmp/datalad_temp_tree_test_new_or_modifiedwg88pm3n'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        tkwargs_ = get_tempfile_kwargs(tkwargs, prefix=\"tree\", wrapped=t)\n        d = tempfile.mkdtemp(**tkwargs_)\n        create_tree(d, tree, archives_leading_dir=archives_leading_dir)\n        try:\n>           return t(*(arg + (d,)), **kw)\nE           TypeError: test_new_or_modified() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:491: TypeError\n______________________________ test_rerun_script _______________________________\n\nargs = (), kwargs = {'path': '/tmp/tmp-page2annexfym2ayl1'}\nio = <module 'io' from '/home/gcpuser/.local/share/uv/python/cpython-3.7.9-linux-x86_64-gnu/lib/python3.7/io.py'>\n\n    @make_decorator(func)\n    def newfunc(*args, **kwargs):\n        import io\n        try:\n>           func(*args, **kwargs)\n\ndatalad/tests/utils.py:1310: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \ndatalad/tests/utils.py:890: in newfunc\n    return func(*args, **kwargs)\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\narg = (), kw = {'path': '/tmp/tmp-page2annexfym2ayl1'}\nfilename = '/tmp/datalad_temp_test_rerun_scriptphf8xi2n'\n\n    @wraps(t)\n    def newfunc(*arg, **kw):\n        with make_tempfile(wrapped=t, **tkwargs) as filename:\n>           return t(*(arg + (filename,)), **kw)\nE           TypeError: test_rerun_script() got multiple values for argument 'path'\n\ndatalad/tests/utils.py:661: TypeError\n_______________________ test_rerun_commit_message_check ________________________\n\n    def test_rerun_commit_message_check():\n        assert_raises(ValueError,\n                      get_run_info,\n                      \"\"\"\\\n    [DATALAD RUNCMD] no command\n    \n    === Do not change lines below ===\n    {\n     \"pwd\": \".\",\n     \"exit\": 0\n    }\n    ^^^ Do not change lines above ^^^\"\"\")\n    \n        assert_raises(ValueError,\n                      get_run_info,\n                      \"\"\"\\\n    [DATALAD RUNCMD] junk json\n    \n    === Do not change lines below ===\n    {\n     \"pwd\": \".,\n     \"cmd\": \"echo ok >okfile\",\n     \"exit\": 0\n    }\n    ^^^ Do not change lines above ^^^\"\"\")\n    \n        subject, info = get_run_info(\"\"\"\\\n    [DATALAD RUNCMD] fine\n    \n    === Do not change lines below ===\n    {\n     \"pwd\": \".\",\n     \"cmd\": \"echo ok >okfile\",\n     \"exit\": 0\n    }\n    ^^^ Do not change lines above ^^^\"\"\")\n>       eq_(subject, \"fine\")\n\nr2e_tests/test_1.py:590: \n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \n\na = 'fine\\n\\n', b = 'fine', 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: 'fine\\n\\n' != 'fine'\n\n.venv/lib/python3.7/site-packages/nose/tools/trivial.py:29: AssertionError\n=========================== short test summary info ============================\nERROR r2e_tests/test_1.py::test_basics\nERROR r2e_tests/test_1.py::test_rerun\nFAILED r2e_tests/test_1.py::test_invalid_call - TypeError: test_invalid_call(...\nFAILED r2e_tests/test_1.py::test_rerun_onto - TypeError: test_rerun_onto() go...\nFAILED r2e_tests/test_1.py::test_rerun_chain - TypeError: test_rerun_chain() ...\nFAILED r2e_tests/test_1.py::test_rerun_old_flag_compatibility - TypeError: te...\nFAILED r2e_tests/test_1.py::test_rerun_just_one_commit - TypeError: test_reru...\nFAILED r2e_tests/test_1.py::test_run_failure - TypeError: test_run_failure() ...\nFAILED r2e_tests/test_1.py::test_rerun_branch - TypeError: test_rerun_branch(...\nFAILED r2e_tests/test_1.py::test_rerun_cherry_pick - TypeError: test_rerun_ch...\nFAILED r2e_tests/test_1.py::test_rerun_outofdate_tree - TypeError: test_rerun...\nFAILED r2e_tests/test_1.py::test_rerun_ambiguous_revision_file - TypeError: t...\nFAILED r2e_tests/test_1.py::test_rerun_subdir - TypeError: test_rerun_subdir(...\nFAILED r2e_tests/test_1.py::test_new_or_modified - TypeError: test_new_or_mod...\nFAILED r2e_tests/test_1.py::test_rerun_script - TypeError: test_rerun_script(...\nFAILED r2e_tests/test_1.py::test_rerun_commit_message_check - AssertionError:...\n========================= 14 failed, 2 errors in 1.30s =========================\n",
    "old_commit_res_stderr": ""
}
datalad/interface/rerun.py datalad/interface/tests/test_run.py
We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
[ISSUE]

**Title:** Trailing Newlines in Commit Subject Cause Rerun Message Parsing Issues

**Description:**
When a commit message includes trailing newlines in the subject, it leads to unexpected behavior during the rerun process. The presence of these extra newlines causes the subject to be misinterpreted, resulting in failed tests.

**Example Buggy Code:**
```python
subject, info = get_run_info('[DATALAD RUNCMD] fine\n\n=== Do not change lines below ===\n{\n "pwd": ".",\n "cmd": "echo ok >okfile",\n "exit": 0\n}\n^^^ Do not change lines above ^^^')
eq_(subject, "fine\n\n")
```

**Expected Behavior:**
The subject extracted from the commit message should not contain trailing newlines. It should be:
```
fine
```

**Actual Behavior:**
The subject extracted includes trailing newlines, resulting in:
```
fine

```

[/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/interface/rerun.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.
#
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""Rerun commands recorded with `datalad run`"""

__docformat__ = 'restructuredtext'


import logging
from itertools import dropwhile
import json
import re

from datalad.dochelpers import exc_str
from datalad.interface.base import Interface
from datalad.interface.utils import eval_results
from datalad.interface.base import build_doc
from datalad.interface.diff import Diff
from datalad.interface.unlock import Unlock
from datalad.interface.results import get_status_dict
from datalad.interface.run import run_command

from datalad.support.constraints import EnsureNone, EnsureStr
from datalad.support.gitrepo import GitCommandError
from datalad.support.param import Parameter

from datalad.distribution.dataset import require_dataset
from datalad.distribution.dataset import EnsureDataset
from datalad.distribution.dataset import datasetmethod

lgr = logging.getLogger('datalad.interface.rerun')


@build_doc
class Rerun(Interface):
    """Re-execute previous `datalad run` commands.

    This will unlock any dataset content that is on record to have
    been modified by the command in the specified revision.  It will
    then re-execute the command in the recorded path (if it was inside
    the dataset). Afterwards, all modifications will be saved.

    Examples:

      Re-execute the command from the previous commit::

        % datalad rerun

      Re-execute any commands in the last five commits::

        % datalad rerun --since=HEAD~5

      Do the same as above, but re-execute the commands on top of
      HEAD~5 in a detached state::

        % datalad rerun --onto= --since=HEAD~5

      Re-execute all previous commands and compare the old and new
      results::

        % # on master branch
        % datalad rerun --branch=verify --since=
        % # now on verify branch
        % datalad diff --revision=master..
        % git log --oneline --left-right --cherry-pick master...
    """
    _params_ = dict(
        revision=Parameter(
            args=("revision",),
            metavar="REVISION",
            nargs="?",
            doc="""rerun command(s) in `revision`. By default, the command from
            this commit will be executed, but [CMD: --since CMD][PY: `since`
            PY] can be used to construct a revision range.""",
            default="HEAD",
            constraints=EnsureStr()),
        since=Parameter(
            args=("--since",),
            doc="""If `since` is a commit-ish, the commands from all commits
            that are reachable from `revision` but not `since` will be
            re-executed (in other words, the commands in :command:`git log
            SINCE..REVISION`). If SINCE is an empty string, it is set to the
            parent of the first commit that contains a recorded command (i.e.,
            all commands in :command:`git log REVISION` will be
            re-executed).""",
            constraints=EnsureStr() | EnsureNone()),
        branch=Parameter(
            metavar="NAME",
            args=("-b", "--branch",),
            doc="create and checkout this branch before rerunning the commands.",
            constraints=EnsureStr() | EnsureNone()),
        onto=Parameter(
            metavar="base",
            args=("--onto",),
            doc="""start point for rerunning the commands. If not specified,
            commands are executed at HEAD. This option can be used to specify
            an alternative start point, which will be checked out with the
            branch name specified by [CMD: --branch CMD][PY: `branch` PY] or in
            a detached state otherwise. As a special case, an empty value for
            this option means to use the commit specified by [CMD: --since
            CMD][PY: `since` PY].""",
            constraints=EnsureStr() | EnsureNone()),
        message=Parameter(
            args=("-m", "--message",),
            metavar="MESSAGE",
            doc="""use MESSAGE for the reran commit rather than the
            recorded commit message.  In the case of a multi-commit
            rerun, all the reran commits will have this message.""",
            constraints=EnsureStr() | EnsureNone()),
        script=Parameter(
            args=("--script",),
            metavar="FILE",
            doc="""extract the commands into [CMD: FILE CMD][PY: this file PY]
            rather than rerunning.""",
            constraints=EnsureStr() | EnsureNone()),
        dataset=Parameter(
            args=("-d", "--dataset"),
            doc="""specify the dataset from which to rerun a recorded
            command. If no dataset is given, an attempt is made to
            identify the dataset based on the current working
            directory. If a dataset is given, the command will be
            executed in the root directory of this dataset.""",
            constraints=EnsureDataset() | EnsureNone()),
        # TODO
        # --list-commands
        #   go through the history and report any recorded command. this info
        #   could be used to unlock the associated output files for a rerun
    )

    @staticmethod
    @datasetmethod(name='rerun')
    @eval_results
    def __call__(
            revision="HEAD",
            since=None,
            dataset=None,
            branch=None,
            message=None,
            onto=None,
            script=None):

        ds = require_dataset(
            dataset, check_installed=True,
            purpose='rerunning a command')

        lgr.debug('rerunning command output underneath %s', ds)

        if script is None and ds.repo.dirty:
            yield get_status_dict(
                'run',
                ds=ds,
                status='impossible',
                message=('unsaved modifications present, '
                         'cannot detect changes by command'))
            return

        err_info = get_status_dict('run', ds=ds)
        if not ds.repo.get_hexsha():
            yield dict(
                err_info, status='impossible',
                message='cannot rerun command, nothing recorded')
            return

        if branch and branch in ds.repo.get_branches():
            yield get_status_dict(
                "run", ds=ds, status="error",
                message="branch '{}' already exists".format(branch))
            return

        if not commit_exists(ds, revision + "^"):
            # Only a single commit is reachable from `revision`.  In
            # this case, --since has no effect on the range construction.
            revrange = revision
        elif since is None:
            revrange = "{rev}^..{rev}".format(rev=revision)
        elif since.strip() == "":
            revrange = revision
        else:
            revrange = "{}..{}".format(since, revision)

        if ds.repo.repo.git.rev_list("--merges", revrange, "--"):
            yield get_status_dict(
                "run", ds=ds, status="error",
                message="cannot rerun history with merge commits")
            return

        revs = [{"hexsha": hexsha,
                 "message": ds.repo.repo.git.show(
                     hexsha, "--format=%B", "--no-patch")}
                for hexsha in ds.repo.repo.git.rev_list(
                        "--reverse", revrange, "--").split()]

        for rev in revs:
            try:
                subj, info = get_run_info(rev["message"])
            except ValueError as exc:
                yield dict(err_info, status='error',
                           message="Error on {}'s message: {}".format(
                               rev["hexsha"], exc_str(exc)))
                return
            if info is not None:
                rev["run_info"] = info
                rev["run_subject"] = subj

        if since is not None and since.strip() == "":
            # For --since='', drop any leading commits that don't have
            # a run command.
            revs = list(dropwhile(lambda r: "run_info" not in r, revs))

        if script:
            commands = (r["run_info"]["cmd"] for r in revs if "run_info" in r)
            with open(script, 'w') as ofh:
                header = """\
#!/bin/sh
#
# This file was generated by running (the equivalent of)
#
#   datalad rerun --script={script}{since} {revision}
#
# in {path}\n\n"""
                ofh.write(header.format(
                    script=script,
                    since="" if since is None else " --since=" + since,
                    revision=ds.repo.repo.git.rev_parse(revision),
                    path=ds.path))

                for cmd in commands:
                    if isinstance(cmd, list):
                        cmd = " ".join(cmd)
                    ofh.write(cmd + "\n")
        else:
            if onto is not None and onto.strip() == "":
                # Special case: --onto='' is the value of --since.
                # Because we're currently aborting if the revision list
                # contains merges, we know that, regardless of if and how
                # --since is specified, the effective value for --since is
                # the parent of the first revision.
                onto = revs[0]["hexsha"] + "^"
                if not commit_exists(ds, onto):
                    # This is unlikely to happen in the wild because it
                    # means that the first commit is a datalad run commit.
                    # Just abort rather than trying to checkout on orphan
                    # branch or something like that.
                    yield get_status_dict(
                        "run", ds=ds, status="error",
                        message="Commit for --onto does not exist.")
                    return

            if branch or onto:
                start_point = onto or "HEAD"
                if branch:
                    checkout_options = ["-b", branch]
                else:
                    checkout_options = ["--detach"]
                ds.repo.checkout(start_point, options=checkout_options)

            for rev in revs:
                hexsha = rev["hexsha"]
                if "run_info" not in rev:
                    pick = False
                    try:
                        ds.repo.repo.git.merge_base("--is-ancestor",
                                                    hexsha, "HEAD")
                    except GitCommandError:
                        # Revision is NOT an ancestor of HEAD.
                        pick = True

                    shortrev = ds.repo.repo.git.rev_parse("--short", hexsha)
                    err_msg = "no command for {} found; {}".format(
                        shortrev,
                        "cherry picking" if pick else "skipping")
                    yield dict(err_info, status='ok', message=err_msg)

                    if pick:
                        ds.repo.repo.git.cherry_pick(hexsha)
                    continue

                run_info = rev["run_info"]
                # Keep a "rerun" trail.
                if "chain" in run_info:
                    run_info["chain"].append(hexsha)
                else:
                    run_info["chain"] = [hexsha]

                # now we have to find out what was modified during the
                # last run, and enable re-modification ideally, we would
                # bring back the entire state of the tree with #1424, but
                # we limit ourself to file addition/not-in-place-modification
                # for now
                for r in ds.unlock(new_or_modified(ds, hexsha),
                                   return_type='generator', result_xfm=None):
                    yield r

                for r in run_command(run_info['cmd'],
                                     ds, message or rev["run_subject"],
                                     rerun_info=run_info):
                    yield r


def get_run_info(message):
    """Extract run information from `message`

    Parameters
    ----------
    message : str
        A commit message.

    Returns
    -------
    A tuple with the command's subject line and a dict with run information.
    Both these values are None if `message` doesn't have a run command.

    Raises
    ------
    A ValueError if the information in `message` is invalid.
    """
    cmdrun_regex = r'\[DATALAD RUNCMD\] (.*)=== Do not change lines below ' \
                   r'===\n(.*)\n\^\^\^ Do not change lines above \^\^\^'
    runinfo = re.match(cmdrun_regex, message, re.MULTILINE | re.DOTALL)
    if not runinfo:
        return None, None

    rec_subj, runinfo = runinfo.groups()

    try:
        runinfo = json.loads(runinfo)
    except Exception as e:
        raise ValueError(
            'cannot rerun command, command specification is not valid JSON: '
            '%s' % exc_str(e)
        )
    if 'cmd' not in runinfo:
        raise ValueError("Looks like a run commit but does not have a command")
    return rec_subj, runinfo


def new_or_modified(dataset, revision="HEAD"):
    """Yield files that have been added or modified in `revision`.

    Parameters
    ----------
    dataset : Dataset
    revision : string, optional
        Commit-ish of interest.

    Returns
    -------
    Generator that yields AnnotatePaths instances
    """
    if commit_exists(dataset, revision + "^"):
        revrange = "{rev}^..{rev}".format(rev=revision)
    else:
        # No other commits are reachable from this revision.  Diff
        # with an empty tree instead.
        #             git hash-object -t tree /dev/null
        empty_tree = "4b825dc642cb6eb9a060e54bf8d69288fbee4904"
        revrange = "{}..{}".format(empty_tree, revision)
    diff = dataset.diff(recursive=True,
                        revision=revrange,
                        return_type='generator', result_renderer=None)
    for r in diff:
        if r.get('type') == 'file' and r.get('state') in ['added', 'modified']:
            r.pop('status', None)
            yield r


def commit_exists(dataset, commit):
    try:
        dataset.repo.repo.git.rev_parse("--verify", commit + "^{commit}")
    except:
        return False
    return True

```
--- 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:** Trailing Newlines in Commit Subject Cause Rerun Message Parsing Issues

**Description:**
When a commit message includes trailing newlines in the subject, it leads to unexpected behavior during the rerun process. The presence of these extra newlines causes the subject to be misinterpreted, resulting in failed tests.

**Example Buggy Code:**
```python
subject, info = get_run_info('[DATALAD RUNCMD] fine\n\n=== Do not change lines below ===\n{\n "pwd": ".",\n "cmd": "echo ok >okfile",\n "exit": 0\n}\n^^^ Do not change lines above ^^^')
eq_(subject, "fine\n\n")
```

**Expected Behavior:**
The subject extracted from the commit message should not contain trailing newlines. It should be:
```
fine
```

**Actual Behavior:**
The subject extracted includes trailing newlines, resulting in:
```
fine

```

[/ISSUE]
{
    "test_rerun_commit_message_check": "PASSED",
    "test_basics": "ERROR",
    "test_rerun": "ERROR",
    "test_invalid_call": "FAILED",
    "test_rerun_onto": "FAILED",
    "test_rerun_chain": "FAILED",
    "test_rerun_old_flag_compatibility": "FAILED",
    "test_rerun_just_one_commit": "FAILED",
    "test_run_failure": "FAILED",
    "test_rerun_branch": "FAILED",
    "test_rerun_cherry_pick": "FAILED",
    "test_rerun_outofdate_tree": "FAILED",
    "test_rerun_ambiguous_revision_file": "FAILED",
    "test_rerun_subdir": "FAILED",
    "test_new_or_modified": "FAILED",
    "test_rerun_script": "FAILED"
}
diff --git a/datalad/interface/rerun.py b/datalad/interface/rerun.py
index 03a14b646..5cb2bb89d 100644
--- a/datalad/interface/rerun.py
+++ b/datalad/interface/rerun.py
@@ -336,7 +336,7 @@ def get_run_info(message):
         )
     if 'cmd' not in runinfo:
         raise ValueError("Looks like a run commit but does not have a command")
-    return rec_subj, runinfo
+    return rec_subj.rstrip(), runinfo
 
 
 def new_or_modified(dataset, revision="HEAD"):

{"datalad/interface/rerun.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\"\"\"Rerun commands recorded with `datalad run`\"\"\"\n\n__docformat__ = 'restructuredtext'\n\n\nimport logging\nfrom itertools import dropwhile\nimport json\nimport re\n\nfrom datalad.dochelpers import exc_str\nfrom datalad.interface.base import Interface\nfrom datalad.interface.utils import eval_results\nfrom datalad.interface.base import build_doc\nfrom datalad.interface.diff import Diff\nfrom datalad.interface.unlock import Unlock\nfrom datalad.interface.results import get_status_dict\nfrom datalad.interface.run import run_command\n\nfrom datalad.support.constraints import EnsureNone, EnsureStr\nfrom datalad.support.gitrepo import GitCommandError\nfrom datalad.support.param import Parameter\n\nfrom datalad.distribution.dataset import require_dataset\nfrom datalad.distribution.dataset import EnsureDataset\nfrom datalad.distribution.dataset import datasetmethod\n\nlgr = logging.getLogger('datalad.interface.rerun')\n\n\n@build_doc\nclass Rerun(Interface):\n    \"\"\"Re-execute previous `datalad run` commands.\n\n    This will unlock any dataset content that is on record to have\n    been modified by the command in the specified revision.  It will\n    then re-execute the command in the recorded path (if it was inside\n    the dataset). Afterwards, all modifications will be saved.\n\n    Examples:\n\n      Re-execute the command from the previous commit::\n\n        % datalad rerun\n\n      Re-execute any commands in the last five commits::\n\n        % datalad rerun --since=HEAD~5\n\n      Do the same as above, but re-execute the commands on top of\n      HEAD~5 in a detached state::\n\n        % datalad rerun --onto= --since=HEAD~5\n\n      Re-execute all previous commands and compare the old and new\n      results::\n\n        % # on master branch\n        % datalad rerun --branch=verify --since=\n        % # now on verify branch\n        % datalad diff --revision=master..\n        % git log --oneline --left-right --cherry-pick master...\n    \"\"\"\n    _params_ = dict(\n        revision=Parameter(\n            args=(\"revision\",),\n            metavar=\"REVISION\",\n            nargs=\"?\",\n            doc=\"\"\"rerun command(s) in `revision`. By default, the command from\n            this commit will be executed, but [CMD: --since CMD][PY: `since`\n            PY] can be used to construct a revision range.\"\"\",\n            default=\"HEAD\",\n            constraints=EnsureStr()),\n        since=Parameter(\n            args=(\"--since\",),\n            doc=\"\"\"If `since` is a commit-ish, the commands from all commits\n            that are reachable from `revision` but not `since` will be\n            re-executed (in other words, the commands in :command:`git log\n            SINCE..REVISION`). If SINCE is an empty string, it is set to the\n            parent of the first commit that contains a recorded command (i.e.,\n            all commands in :command:`git log REVISION` will be\n            re-executed).\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        branch=Parameter(\n            metavar=\"NAME\",\n            args=(\"-b\", \"--branch\",),\n            doc=\"create and checkout this branch before rerunning the commands.\",\n            constraints=EnsureStr() | EnsureNone()),\n        onto=Parameter(\n            metavar=\"base\",\n            args=(\"--onto\",),\n            doc=\"\"\"start point for rerunning the commands. If not specified,\n            commands are executed at HEAD. This option can be used to specify\n            an alternative start point, which will be checked out with the\n            branch name specified by [CMD: --branch CMD][PY: `branch` PY] or in\n            a detached state otherwise. As a special case, an empty value for\n            this option means to use the commit specified by [CMD: --since\n            CMD][PY: `since` PY].\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        message=Parameter(\n            args=(\"-m\", \"--message\",),\n            metavar=\"MESSAGE\",\n            doc=\"\"\"use MESSAGE for the reran commit rather than the\n            recorded commit message.  In the case of a multi-commit\n            rerun, all the reran commits will have this message.\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        script=Parameter(\n            args=(\"--script\",),\n            metavar=\"FILE\",\n            doc=\"\"\"extract the commands into [CMD: FILE CMD][PY: this file PY]\n            rather than rerunning.\"\"\",\n            constraints=EnsureStr() | EnsureNone()),\n        dataset=Parameter(\n            args=(\"-d\", \"--dataset\"),\n            doc=\"\"\"specify the dataset from which to rerun a recorded\n            command. If no dataset is given, an attempt is made to\n            identify the dataset based on the current working\n            directory. If a dataset is given, the command will be\n            executed in the root directory of this dataset.\"\"\",\n            constraints=EnsureDataset() | EnsureNone()),\n        # TODO\n        # --list-commands\n        #   go through the history and report any recorded command. this info\n        #   could be used to unlock the associated output files for a rerun\n    )\n\n    @staticmethod\n    @datasetmethod(name='rerun')\n    @eval_results\n    def __call__(\n            revision=\"HEAD\",\n            since=None,\n            dataset=None,\n            branch=None,\n            message=None,\n            onto=None,\n            script=None):\n\n        ds = require_dataset(\n            dataset, check_installed=True,\n            purpose='rerunning a command')\n\n        lgr.debug('rerunning command output underneath %s', ds)\n\n        if script is None and ds.repo.dirty:\n            yield get_status_dict(\n                'run',\n                ds=ds,\n                status='impossible',\n                message=('unsaved modifications present, '\n                         'cannot detect changes by command'))\n            return\n\n        err_info = get_status_dict('run', ds=ds)\n        if not ds.repo.get_hexsha():\n            yield dict(\n                err_info, status='impossible',\n                message='cannot rerun command, nothing recorded')\n            return\n\n        if branch and branch in ds.repo.get_branches():\n            yield get_status_dict(\n                \"run\", ds=ds, status=\"error\",\n                message=\"branch '{}' already exists\".format(branch))\n            return\n\n        if not commit_exists(ds, revision + \"^\"):\n            # Only a single commit is reachable from `revision`.  In\n            # this case, --since has no effect on the range construction.\n            revrange = revision\n        elif since is None:\n            revrange = \"{rev}^..{rev}\".format(rev=revision)\n        elif since.strip() == \"\":\n            revrange = revision\n        else:\n            revrange = \"{}..{}\".format(since, revision)\n\n        if ds.repo.repo.git.rev_list(\"--merges\", revrange, \"--\"):\n            yield get_status_dict(\n                \"run\", ds=ds, status=\"error\",\n                message=\"cannot rerun history with merge commits\")\n            return\n\n        revs = [{\"hexsha\": hexsha,\n                 \"message\": ds.repo.repo.git.show(\n                     hexsha, \"--format=%B\", \"--no-patch\")}\n                for hexsha in ds.repo.repo.git.rev_list(\n                        \"--reverse\", revrange, \"--\").split()]\n\n        for rev in revs:\n            try:\n                subj, info = get_run_info(rev[\"message\"])\n            except ValueError as exc:\n                yield dict(err_info, status='error',\n                           message=\"Error on {}'s message: {}\".format(\n                               rev[\"hexsha\"], exc_str(exc)))\n                return\n            if info is not None:\n                rev[\"run_info\"] = info\n                rev[\"run_subject\"] = subj\n\n        if since is not None and since.strip() == \"\":\n            # For --since='', drop any leading commits that don't have\n            # a run command.\n            revs = list(dropwhile(lambda r: \"run_info\" not in r, revs))\n\n        if script:\n            commands = (r[\"run_info\"][\"cmd\"] for r in revs if \"run_info\" in r)\n            with open(script, 'w') as ofh:\n                header = \"\"\"\\\n#!/bin/sh\n#\n# This file was generated by running (the equivalent of)\n#\n#   datalad rerun --script={script}{since} {revision}\n#\n# in {path}\\n\\n\"\"\"\n                ofh.write(header.format(\n                    script=script,\n                    since=\"\" if since is None else \" --since=\" + since,\n                    revision=ds.repo.repo.git.rev_parse(revision),\n                    path=ds.path))\n\n                for cmd in commands:\n                    if isinstance(cmd, list):\n                        cmd = \" \".join(cmd)\n                    ofh.write(cmd + \"\\n\")\n        else:\n            if onto is not None and onto.strip() == \"\":\n                # Special case: --onto='' is the value of --since.\n                # Because we're currently aborting if the revision list\n                # contains merges, we know that, regardless of if and how\n                # --since is specified, the effective value for --since is\n                # the parent of the first revision.\n                onto = revs[0][\"hexsha\"] + \"^\"\n                if not commit_exists(ds, onto):\n                    # This is unlikely to happen in the wild because it\n                    # means that the first commit is a datalad run commit.\n                    # Just abort rather than trying to checkout on orphan\n                    # branch or something like that.\n                    yield get_status_dict(\n                        \"run\", ds=ds, status=\"error\",\n                        message=\"Commit for --onto does not exist.\")\n                    return\n\n            if branch or onto:\n                start_point = onto or \"HEAD\"\n                if branch:\n                    checkout_options = [\"-b\", branch]\n                else:\n                    checkout_options = [\"--detach\"]\n                ds.repo.checkout(start_point, options=checkout_options)\n\n            for rev in revs:\n                hexsha = rev[\"hexsha\"]\n                if \"run_info\" not in rev:\n                    pick = False\n                    try:\n                        ds.repo.repo.git.merge_base(\"--is-ancestor\",\n                                                    hexsha, \"HEAD\")\n                    except GitCommandError:\n                        # Revision is NOT an ancestor of HEAD.\n                        pick = True\n\n                    shortrev = ds.repo.repo.git.rev_parse(\"--short\", hexsha)\n                    err_msg = \"no command for {} found; {}\".format(\n                        shortrev,\n                        \"cherry picking\" if pick else \"skipping\")\n                    yield dict(err_info, status='ok', message=err_msg)\n\n                    if pick:\n                        ds.repo.repo.git.cherry_pick(hexsha)\n                    continue\n\n                run_info = rev[\"run_info\"]\n                # Keep a \"rerun\" trail.\n                if \"chain\" in run_info:\n                    run_info[\"chain\"].append(hexsha)\n                else:\n                    run_info[\"chain\"] = [hexsha]\n\n                # now we have to find out what was modified during the\n                # last run, and enable re-modification ideally, we would\n                # bring back the entire state of the tree with #1424, but\n                # we limit ourself to file addition/not-in-place-modification\n                # for now\n                for r in ds.unlock(new_or_modified(ds, hexsha),\n                                   return_type='generator', result_xfm=None):\n                    yield r\n\n                for r in run_command(run_info['cmd'],\n                                     ds, message or rev[\"run_subject\"],\n                                     rerun_info=run_info):\n                    yield r\n\n\ndef get_run_info(message):\n    \"\"\"Extract run information from `message`\n\n    Parameters\n    ----------\n    message : str\n        A commit message.\n\n    Returns\n    -------\n    A tuple with the command's subject line and a dict with run information.\n    Both these values are None if `message` doesn't have a run command.\n\n    Raises\n    ------\n    A ValueError if the information in `message` is invalid.\n    \"\"\"\n    cmdrun_regex = r'\\[DATALAD RUNCMD\\] (.*)=== Do not change lines below ' \\\n                   r'===\\n(.*)\\n\\^\\^\\^ Do not change lines above \\^\\^\\^'\n    runinfo = re.match(cmdrun_regex, message, re.MULTILINE | re.DOTALL)\n    if not runinfo:\n        return None, None\n\n    rec_subj, runinfo = runinfo.groups()\n\n    try:\n        runinfo = json.loads(runinfo)\n    except Exception as e:\n        raise ValueError(\n            'cannot rerun command, command specification is not valid JSON: '\n            '%s' % exc_str(e)\n        )\n    if 'cmd' not in runinfo:\n        raise ValueError(\"Looks like a run commit but does not have a command\")\n    return rec_subj, runinfo\n\n\ndef new_or_modified(dataset, revision=\"HEAD\"):\n    \"\"\"Yield files that have been added or modified in `revision`.\n\n    Parameters\n    ----------\n    dataset : Dataset\n    revision : string, optional\n        Commit-ish of interest.\n\n    Returns\n    -------\n    Generator that yields AnnotatePaths instances\n    \"\"\"\n    if commit_exists(dataset, revision + \"^\"):\n        revrange = \"{rev}^..{rev}\".format(rev=revision)\n    else:\n        # No other commits are reachable from this revision.  Diff\n        # with an empty tree instead.\n        #             git hash-object -t tree /dev/null\n        empty_tree = \"4b825dc642cb6eb9a060e54bf8d69288fbee4904\"\n        revrange = \"{}..{}\".format(empty_tree, revision)\n    diff = dataset.diff(recursive=True,\n                        revision=revrange,\n                        return_type='generator', result_renderer=None)\n    for r in diff:\n        if r.get('type') == 'file' and r.get('state') in ['added', 'modified']:\n            r.pop('status', None)\n            yield r\n\n\ndef commit_exists(dataset, commit):\n    try:\n        dataset.repo.repo.git.rev_parse(\"--verify\", commit + \"^{commit}\")\n    except:\n        return False\n    return True\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:** Trailing Newlines in Commit Subject Cause Rerun Message Parsing Issues

**Description:**
When a commit message includes trailing newlines in the subject, it leads to unexpected behavior during the rerun process. The presence of these extra newlines causes the subject to be misinterpreted, resulting in failed tests.

**Example Buggy Code:**
```python
subject, info = get_run_info('[DATALAD RUNCMD] fine\n\n=== Do not change lines below ===\n{\n "pwd": ".",\n "cmd": "echo ok >okfile",\n "exit": 0\n}\n^^^ Do not change lines above ^^^')
eq_(subject, "fine\n\n")
```

**Expected Behavior:**
The subject extracted from the commit message should not contain trailing newlines. It should be:
```
fine
```

**Actual Behavior:**
The subject extracted includes trailing newlines, resulting in:
```
fine

```

[/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/interface/rerun.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.
#
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""Rerun commands recorded with `datalad run`"""

__docformat__ = 'restructuredtext'


import logging
from itertools import dropwhile
import json
import re

from datalad.dochelpers import exc_str
from datalad.interface.base import Interface
from datalad.interface.utils import eval_results
from datalad.interface.base import build_doc
from datalad.interface.diff import Diff
from datalad.interface.unlock import Unlock
from datalad.interface.results import get_status_dict
from datalad.interface.run import run_command

from datalad.support.constraints import EnsureNone, EnsureStr
from datalad.support.gitrepo import GitCommandError
from datalad.support.param import Parameter

from datalad.distribution.dataset import require_dataset
from datalad.distribution.dataset import EnsureDataset
from datalad.distribution.dataset import datasetmethod

lgr = logging.getLogger('datalad.interface.rerun')


@build_doc
class Rerun(Interface):
    """Re-execute previous `datalad run` commands.

    This will unlock any dataset content that is on record to have
    been modified by the command in the specified revision.  It will
    then re-execute the command in the recorded path (if it was inside
    the dataset). Afterwards, all modifications will be saved.

    Examples:

      Re-execute the command from the previous commit::

        % datalad rerun

      Re-execute any commands in the last five commits::

        % datalad rerun --since=HEAD~5

      Do the same as above, but re-execute the commands on top of
      HEAD~5 in a detached state::

        % datalad rerun --onto= --since=HEAD~5

      Re-execute all previous commands and compare the old and new
      results::

        % # on master branch
        % datalad rerun --branch=verify --since=
        % # now on verify branch
        % datalad diff --revision=master..
        % git log --oneline --left-right --cherry-pick master...
    """
    _params_ = dict(
        revision=Parameter(
            args=("revision",),
            metavar="REVISION",
            nargs="?",
            doc="""rerun command(s) in `revision`. By default, the command from
            this commit will be executed, but [CMD: --since CMD][PY: `since`
            PY] can be used to construct a revision range.""",
            default="HEAD",
            constraints=EnsureStr()),
        since=Parameter(
            args=("--since",),
            doc="""If `since` is a commit-ish, the commands from all commits
            that are reachable from `revision` but not `since` will be
            re-executed (in other words, the commands in :command:`git log
            SINCE..REVISION`). If SINCE is an empty string, it is set to the
            parent of the first commit that contains a recorded command (i.e.,
            all commands in :command:`git log REVISION` will be
            re-executed).""",
            constraints=EnsureStr() | EnsureNone()),
        branch=Parameter(
            metavar="NAME",
            args=("-b", "--branch",),
            doc="create and checkout this branch before rerunning the commands.",
            constraints=EnsureStr() | EnsureNone()),
        onto=Parameter(
            metavar="base",
            args=("--onto",),
            doc="""start point for rerunning the commands. If not specified,
            commands are executed at HEAD. This option can be used to specify
            an alternative start point, which will be checked out with the
            branch name specified by [CMD: --branch CMD][PY: `branch` PY] or in
            a detached state otherwise. As a special case, an empty value for
            this option means to use the commit specified by [CMD: --since
            CMD][PY: `since` PY].""",
            constraints=EnsureStr() | EnsureNone()),
        message=Parameter(
            args=("-m", "--message",),
            metavar="MESSAGE",
            doc="""use MESSAGE for the reran commit rather than the
            recorded commit message.  In the case of a multi-commit
            rerun, all the reran commits will have this message.""",
            constraints=EnsureStr() | EnsureNone()),
        script=Parameter(
            args=("--script",),
            metavar="FILE",
            doc="""extract the commands into [CMD: FILE CMD][PY: this file PY]
            rather than rerunning.""",
            constraints=EnsureStr() | EnsureNone()),
        dataset=Parameter(
            args=("-d", "--dataset"),
            doc="""specify the dataset from which to rerun a recorded
            command. If no dataset is given, an attempt is made to
            identify the dataset based on the current working
            directory. If a dataset is given, the command will be
            executed in the root directory of this dataset.""",
            constraints=EnsureDataset() | EnsureNone()),
        # TODO
        # --list-commands
        #   go through the history and report any recorded command. this info
        #   could be used to unlock the associated output files for a rerun
    )

    @staticmethod
    @datasetmethod(name='rerun')
    @eval_results
    def __call__(
            revision="HEAD",
            since=None,
            dataset=None,
            branch=None,
            message=None,
            onto=None,
            script=None):

        ds = require_dataset(
            dataset, check_installed=True,
            purpose='rerunning a command')

        lgr.debug('rerunning command output underneath %s', ds)

        if script is None and ds.repo.dirty:
            yield get_status_dict(
                'run',
                ds=ds,
                status='impossible',
                message=('unsaved modifications present, '
                         'cannot detect changes by command'))
            return

        err_info = get_status_dict('run', ds=ds)
        if not ds.repo.get_hexsha():
            yield dict(
                err_info, status='impossible',
                message='cannot rerun command, nothing recorded')
            return

        if branch and branch in ds.repo.get_branches():
            yield get_status_dict(
                "run", ds=ds, status="error",
                message="branch '{}' already exists".format(branch))
            return

        if not commit_exists(ds, revision + "^"):
            # Only a single commit is reachable from `revision`.  In
            # this case, --since has no effect on the range construction.
            revrange = revision
        elif since is None:
            revrange = "{rev}^..{rev}".format(rev=revision)
        elif since.strip() == "":
            revrange = revision
        else:
            revrange = "{}..{}".format(since, revision)

        if ds.repo.repo.git.rev_list("--merges", revrange, "--"):
            yield get_status_dict(
                "run", ds=ds, status="error",
                message="cannot rerun history with merge commits")
            return

        revs = [{"hexsha": hexsha,
                 "message": ds.repo.repo.git.show(
                     hexsha, "--format=%B", "--no-patch")}
                for hexsha in ds.repo.repo.git.rev_list(
                        "--reverse", revrange, "--").split()]

        for rev in revs:
            try:
                subj, info = get_run_info(rev["message"])
            except ValueError as exc:
                yield dict(err_info, status='error',
                           message="Error on {}'s message: {}".format(
                               rev["hexsha"], exc_str(exc)))
                return
            if info is not None:
                rev["run_info"] = info
                rev["run_subject"] = subj

        if since is not None and since.strip() == "":
            # For --since='', drop any leading commits that don't have
            # a run command.
            revs = list(dropwhile(lambda r: "run_info" not in r, revs))

        if script:
            commands = (r["run_info"]["cmd"] for r in revs if "run_info" in r)
            with open(script, 'w') as ofh:
                header = """\
#!/bin/sh
#
# This file was generated by running (the equivalent of)
#
#   datalad rerun --script={script}{since} {revision}
#
# in {path}\n\n"""
                ofh.write(header.format(
                    script=script,
                    since="" if since is None else " --since=" + since,
                    revision=ds.repo.repo.git.rev_parse(revision),
                    path=ds.path))

                for cmd in commands:
                    if isinstance(cmd, list):
                        cmd = " ".join(cmd)
                    ofh.write(cmd + "\n")
        else:
            if onto is not None and onto.strip() == "":
                # Special case: --onto='' is the value of --since.
                # Because we're currently aborting if the revision list
                # contains merges, we know that, regardless of if and how
                # --since is specified, the effective value for --since is
                # the parent of the first revision.
                onto = revs[0]["hexsha"] + "^"
                if not commit_exists(ds, onto):
                    # This is unlikely to happen in the wild because it
                    # means that the first commit is a datalad run commit.
                    # Just abort rather than trying to checkout on orphan
                    # branch or something like that.
                    yield get_status_dict(
                        "run", ds=ds, status="error",
                        message="Commit for --onto does not exist.")
                    return

            if branch or onto:
                start_point = onto or "HEAD"
                if branch:
                    checkout_options = ["-b", branch]
                else:
                    checkout_options = ["--detach"]
                ds.repo.checkout(start_point, options=checkout_options)

            for rev in revs:
                hexsha = rev["hexsha"]
                if "run_info" not in rev:
                    pick = False
                    try:
                        ds.repo.repo.git.merge_base("--is-ancestor",
                                                    hexsha, "HEAD")
                    except GitCommandError:
                        # Revision is NOT an ancestor of HEAD.
                        pick = True

                    shortrev = ds.repo.repo.git.rev_parse("--short", hexsha)
                    err_msg = "no command for {} found; {}".format(
                        shortrev,
                        "cherry picking" if pick else "skipping")
                    yield dict(err_info, status='ok', message=err_msg)

                    if pick:
                        ds.repo.repo.git.cherry_pick(hexsha)
                    continue

                run_info = rev["run_info"]
                # Keep a "rerun" trail.
                if "chain" in run_info:
                    run_info["chain"].append(hexsha)
                else:
                    run_info["chain"] = [hexsha]

                # now we have to find out what was modified during the
                # last run, and enable re-modification ideally, we would
                # bring back the entire state of the tree with #1424, but
                # we limit ourself to file addition/not-in-place-modification
                # for now
                for r in ds.unlock(new_or_modified(ds, hexsha),
                                   return_type='generator', result_xfm=None):
                    yield r

                for r in run_command(run_info['cmd'],
                                     ds, message or rev["run_subject"],
                                     rerun_info=run_info):
                    yield r


def get_run_info(message):
    """Extract run information from `message`

    Parameters
    ----------
    message : str
        A commit message.

    Returns
    -------
    A tuple with the command's subject line and a dict with run information.
    Both these values are None if `message` doesn't have a run command.

    Raises
    ------
    A ValueError if the information in `message` is invalid.
    """
    cmdrun_regex = r'\[DATALAD RUNCMD\] (.*)=== Do not change lines below ' \
                   r'===\n(.*)\n\^\^\^ Do not change lines above \^\^\^'
    runinfo = re.match(cmdrun_regex, message, re.MULTILINE | re.DOTALL)
    if not runinfo:
        return None, None

    rec_subj, runinfo = runinfo.groups()

    try:
        runinfo = json.loads(runinfo)
    except Exception as e:
        raise ValueError(
            'cannot rerun command, command specification is not valid JSON: '
            '%s' % exc_str(e)
        )
    if 'cmd' not in runinfo:
        raise ValueError("Looks like a run commit but does not have a command")
    return rec_subj, runinfo


def new_or_modified(dataset, revision="HEAD"):
    """Yield files that have been added or modified in `revision`.

    Parameters
    ----------
    dataset : Dataset
    revision : string, optional
        Commit-ish of interest.

    Returns
    -------
    Generator that yields AnnotatePaths instances
    """
    if commit_exists(dataset, revision + "^"):
        revrange = "{rev}^..{rev}".format(rev=revision)
    else:
        # No other commits are reachable from this revision.  Diff
        # with an empty tree instead.
        #             git hash-object -t tree /dev/null
        empty_tree = "4b825dc642cb6eb9a060e54bf8d69288fbee4904"
        revrange = "{}..{}".format(empty_tree, revision)
    diff = dataset.diff(recursive=True,
                        revision=revrange,
                        return_type='generator', result_renderer=None)
    for r in diff:
        if r.get('type') == 'file' and r.get('state') in ['added', 'modified']:
            r.pop('status', None)
            yield r


def commit_exists(dataset, commit):
    try:
        dataset.repo.repo.git.rev_parse("--verify", commit + "^{commit}")
    except:
        return False
    return True

```
--- 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