runner: Slightly better prose list formatting in the description of -…

…-env

Lists formatted as if they're for computers not humans are a pet peeve
of mine, so address it here.  This copy of prose_list() will also make
it quick to improve other lists in this codebase in the future.

LICENSE.id3c

@@ -0,0 +1,26 @@
+This license applies to the original copy of "prose_list" from the ID3C project
+into this project, incorporated as part of "nextstrain/cli/util.py".  Any
+subsequent modifications this project's copy of "prose_list" are licensed under
+the MIT license of this project, not of ID3C.
+
+MIT License
+
+Copyright (c) 2018 Brotman Baty Institute
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

nextstrain/cli/runner/__init__.py

@@ -13,7 +13,7 @@
 from ..argparse import DirectoryPath, SKIP_AUTO_DEFAULT_IN_HELP
 from ..errors import UserError
 from ..types import Env, Options, RunnerModule
-from ..util import runner_name, runner_module, runner_help, warn
+from ..util import prose_list, runner_name, runner_module, runner_help, warn
 from ..volume import NamedVolume
 
 
@@ -157,7 +157,7 @@ def register_arguments(parser: ArgumentParser, runners: List[RunnerModule], exec
                   "May be specified more than once. "
                   "Overrides any variables of the same name set via --envdir. "
                   "When this option or --envdir is given, the default behaviour of automatically passing thru several \"well-known\" variables is disabled. "
-                  f"The \"well-known\" variables are: {' '.join(hostenv.forwarded_names)}. "
+                  f"The \"well-known\" variables are {prose_list(hostenv.forwarded_names, 'and')}. "
                   "Pass those variables explicitly via --env or --envdir if you need them in combination with other variables. "
                   f"{SKIP_AUTO_DEFAULT_IN_HELP}",
         action  = "append",

nextstrain/cli/util.py

@@ -11,7 +11,7 @@
 import subprocess
 import sys
 from functools import partial
-from typing import Any, Callable, Mapping, List, Optional, Sequence, Tuple, Union, overload
+from typing import Any, Callable, Iterable, Mapping, List, Optional, Sequence, Tuple, Union, overload
 from typing_extensions import Literal
 from packaging.version import parse as parse_version
 from pathlib import Path
@@ -610,3 +610,21 @@ def print_runner_tests(tests: RunnerTestResults):
             remove_prefix("  ", indent(description, "  "))
 
         print(status.get(result, str(result)) + ":", formatted_description)
+
+
+# Copied without modification from lib/id3c/api/utils/__init__.py in the ID3C
+# project¹, which is licensed under the MIT license.  See the LICENSE.id3c file
+# distributed alongside this project's own LICENSE file.
+#
+# ¹ <https://github.com/seattleflu/id3c/blob/fdc3a17a6dd711caa760a6d533aae2be166127fd/lib/id3c/api/utils/__init__.py#L8-L18>
+def prose_list(iterable: Iterable[str], conjunction: str = "or") -> str:
+    """
+    Construct a nice natural language list of items from the *iterable*.  The
+    default *conjunction* is "or".
+    """
+    values = list(iterable)
+
+    if len(values) > 2:
+        return ", ".join([*values[:-1], f"{conjunction} " + values[-1]])
+    else:
+        return f" {conjunction} ".join(values)