tsibley

@contextmanager
def modified_environ(**overlay):
    """
    XXX FIXME

    >>> ...
    """
    def _update_environ(d):
        for k, v in d.items():
            yield k, os.environ.pop(k, None)

tsibley

from itertools import chain, starmap
from shlex import quote as shquote
from typing import Dict, Union

flatten = chain.from_iterable


def augur_options(opts: Dict[str, Union[str, list, None]]) -> str:
    """
    Converts a dictionary of command-line config options to a string suitable

tsibley

from typing import Dict, Union
from shlex import quote as shquote, split as shsplitwords


def shquotewords(s: str) -> str:
    """
    Split string *s* into (POSIX) shell words, quote each word, and join them
    back into a string.

    This is suitable for properly quoting multi-word, user-defined values which

tsibley

from typing import Dict, Union
from shlex import quote as shquote, split as shsplitwords

def shquotewords(s: str) -> str:
    """
    Split string *s* into (POSIX) shell words, quote each word, and join them
    back into a string.

    This is suitable for properly quoting multi-word, user-defined values which
    should follow shell quoting and escaping semantics (e.g. to allow spaces in

tsibley

~/nextstrain/all/mers-beast-tutorial ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/documentation ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/phyloTree ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/react-sidebar ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/auctor ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/sphinx-theme ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/forecasts-ncov ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/sacra ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/mumps ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/project-board ~/nextstrain/all ~/nextstrain/all

tsibley

336   23:16:13.793490 execve("/usr/local/bin/keep-header", ["keep-header", "/nextstrain/augur/tests/data/cla"..., "--", "cat"], 0xffffe2014b50 /* 15 vars */) = 0
336   23:16:13.796029 mmap(NULL, 344, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xffff9e21a000
336   23:16:13.796925 set_tid_address(0x4ed240) = 336
336   23:16:13.797856 brk(NULL)               = 0x291e3000
336   23:16:13.798676 brk(0x291e5000)         = 0x291e5000
336   23:16:13.799447 mmap(0x291e3000, 4096, PROT_NONE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x291e3000
336   23:16:13.800253 mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xffff9e219000
336   23:16:13.801241 rt_sigprocmask(SIG_SETMASK, ~[ILL FPE SEGV RTMIN RT_1 RT_2], [], 8) = 0
336   23:16:13.802083 rt_sigprocmask(SIG_UNBLOCK, [RT_1 RT_2], NULL, 8) = 0
336   23:16:13.802898 mmap(NULL, 143360, PROT_NONE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xffff9e1f6000

tsibley

#!/bin/bash
set -euo pipefail

group="${1:?usage: $(basename "$0") <group-name>}"

echo "# $group group"
echo
for role in owners editors viewers; do
    echo "# $role"
    aws cognito-idp list-users-in-group \

tsibley

title	authors	authorLinks	affiliations	date	dataset
Test narrative which renders markdown as the main panel	James Hadfield	https://twitter.com/hamesjadfield	Fred Hutch, Seattle, USA	2020-04-23	https://nextstrain.org/mumps/na?d=tree

tsibley

tsibley

{"filename": "guides/communicate/create-pdf.md", "lineno": 61, "status": "unchecked", "code": 0, "uri": "", "info": ""}
{"filename": "install.rst", "lineno": 24, "status": "unchecked", "code": 0, "uri": "#choosing-a-runtime", "info": ""}
{"filename": "guides/share/groups/migrate-from-s3.rst", "lineno": 98, "status": "unchecked", "code": 0, "uri": "#group-customization", "info": ""}
{"filename": "guides/share/groups/customize.rst", "lineno": 12, "status": "unchecked", "code": 0, "uri": "#groups-roles", "info": ""}
{"filename": "learn/parts.rst", "lineno": 5, "status": "unchecked", "code": 0, "uri": "#term-Augur", "info": ""}
{"filename": "learn/parts.rst", "lineno": 5, "status": "unchecked", "code": 0, "uri": "#term-Auspice", "info": ""}
{"filename": "learn/parts.rst", "lineno": 82, "status": "unchecked", "code": 0, "uri": "#term-JSONs", "info": ""}
{"filename": "learn/parts.rst", "lineno": 234, "status": "unchecked", "code": 0, "uri": "#term-Nextstrain-CLI", "info": ""}
{"filename": "guides/share/groups/custo