Merge branch 'trs/various-and-sundry'

Author: tsibley

devel/generate-command-doc

@@ -46,6 +46,10 @@ os.environ.update({
 
     # Ensure we detect a browser for stable `nextstrain view` output.
     "BROWSER": "/bin/true",
+
+    # Ensure HOST and PORT are stable for `nextstrain view` output.
+    "HOST": "127.0.0.1",
+    "PORT": "4000",
 })
 
 from nextstrain.cli import make_parser

nextstrain/cli/__init__.py

@@ -17,7 +17,7 @@
 from types    import SimpleNamespace
 
 from .argparse    import HelpFormatter, register_commands, register_default_command
-from .command     import build, view, deploy, remote, shell, update, setup, check_setup, login, logout, whoami, version, init_shell, authorization, debugger
+from .command     import all_commands, version
 from .debug       import DEBUGGING
 from .errors      import NextstrainCliError, UsageError
 from .util        import warn
@@ -69,31 +69,8 @@ def make_parser():
         formatter_class = HelpFormatter,
     )
 
-    # Maintain these manually for now while the list is very small.  If we need
-    # to support pluggable commands or command discovery, we can switch to
-    # using the "entry points" system:
-    #    https://setuptools.readthedocs.io/en/latest/setuptools.html#dynamic-discovery-of-services-and-plugins
-    #
-    commands = [
-        build,
-        view,
-        deploy,
-        remote,
-        shell,
-        update,
-        setup,
-        check_setup,
-        login,
-        logout,
-        whoami,
-        version,
-        init_shell,
-        authorization,
-        debugger,
-    ]
-
     register_default_command(parser)
-    register_commands(parser, commands)
+    register_commands(parser, all_commands)
     register_version_alias(parser)
 
     return parser

nextstrain/cli/aws/cognito/__init__.py

@@ -194,7 +194,7 @@ def renew_tokens(self, *, refresh_token):
         self.verify_tokens(
             id_token      = result.get("IdToken"),
             access_token  = result.get("AccessToken"),
-            refresh_token = refresh_token)
+            refresh_token = result.get("RefreshToken", refresh_token))
 
 
     def verify_tokens(self, *, id_token, access_token, refresh_token):

nextstrain/cli/browser.py

@@ -0,0 +1,67 @@
+"""
+Web browser interaction.
+
+.. envvar:: BROWSER
+
+    A ``PATH``-like list of web browsers to try in preference order, before
+    falling back to a set of default browsers.  May be program names, e.g.
+    ``firefox``, or absolute paths to specific executables, e.g.
+    ``/usr/bin/firefox``.
+
+.. envvar:: NOBROWSER
+
+    If set to a truthy value (e.g. 1) then no web browser will be considered
+    available.  This can be useful to prevent opening of a browser when there
+    are not other means of doing so.
+"""
+import webbrowser
+from threading import Thread, ThreadError
+from os import environ
+from .util import warn
+
+
+if environ.get("NOBROWSER"):
+    BROWSER = None
+else:
+    # Avoid text-mode browsers
+    TERM = environ.pop("TERM", None)
+    try:
+        BROWSER = webbrowser.get()
+    except:
+        BROWSER = None
+    finally:
+        if TERM is not None:
+            environ["TERM"] = TERM
+
+
+def open_browser(url: str, new_thread: bool = True):
+    """
+    Opens *url* in a web browser.
+
+    Opens in a new tab, if possible, and raises the window to the top, if
+    possible.
+
+    Launches the browser from a separate thread by default so waiting on the
+    browser child process doesn't block the main (or calling) thread.  Set
+    *new_thread* to False to launch from the same thread as the caller (e.g. if
+    you've already spawned a dedicated thread or process for the browser).
+    Note that some registered browsers launch in the background themselves, but
+    not all do, so this feature makes launch behaviour consistent across
+    browsers.
+
+    Prints a warning to stderr if a browser can't be found or can't be
+    launched, as automatically opening a browser is considered a
+    nice-but-not-necessary feature.
+    """
+    if not BROWSER:
+        warn(f"Couldn't open <{url}> in browser: no browser found")
+        return
+
+    try:
+        if new_thread:
+            Thread(target = open_browser, args = (url, False), daemon = True).start()
+        else:
+            # new = 2 means new tab, if possible
+            BROWSER.open(url, new = 2, autoraise = True)
+    except (ThreadError, webbrowser.Error) as err:
+        warn(f"Couldn't open <{url}> in browser: {err!r}")

nextstrain/cli/command/__init__.py

@@ -0,0 +1,43 @@
+from . import (
+    build,
+    view,
+    deploy,
+    remote,
+    shell,
+    update,
+    setup,
+    check_setup,
+    login,
+    logout,
+    whoami,
+    version,
+    init_shell,
+    authorization,
+    debugger,
+)
+
+# Maintain this list manually for now while its relatively static.  If we need
+# to support pluggable commands or command discovery, we can switch to using
+# the "entry points" system:
+#    https://setuptools.readthedocs.io/en/latest/setuptools.html#dynamic-discovery-of-services-and-plugins
+#
+# The order of this list is important and intentional: it determines the order
+# in various user interfaces, e.g. `nextstrain --help`.
+#
+all_commands = [
+    build,
+    view,
+    deploy,
+    remote,
+    shell,
+    update,
+    setup,
+    check_setup,
+    login,
+    logout,
+    whoami,
+    version,
+    init_shell,
+    authorization,
+    debugger,
+]

nextstrain/cli/command/view.py

@@ -48,7 +48,6 @@
 from multiprocessing import Process, ProcessError
 import re
 import requests
-import webbrowser
 from inspect import cleandoc
 from os import environ
 from pathlib import Path
@@ -57,6 +56,7 @@
 from typing import Iterable, NamedTuple, Tuple, Union
 from .. import runner
 from ..argparse import add_extended_help_flags, SUPPRESS, SKIP_AUTO_DEFAULT_IN_HELP
+from ..browser import BROWSER, open_browser as __open_browser
 from ..runner import docker, ambient, conda, singularity
 from ..util import colored, remove_suffix, warn
 from ..volume import NamedVolume
@@ -67,16 +67,6 @@
 PORT = environ.get("PORT") or "4000"
 
 
-# Avoid text-mode browsers
-TERM = environ.pop("TERM", None)
-try:
-    BROWSER = webbrowser.get()
-except:
-    BROWSER = None
-finally:
-    if TERM is not None:
-        environ["TERM"] = TERM
-
 OPEN_DEFAULT = bool(BROWSER)
 
 
@@ -454,8 +444,4 @@ def _open_browser(url: str):
         warn(f"Couldn't open <{url}> in browser: Auspice never started listening")
         return
 
-    try:
-        # new = 2 means new tab, if possible
-        BROWSER.open(url, new = 2, autoraise = True)
-    except webbrowser.Error as err:
-        warn(f"Couldn't open <{url}> in browser: {err!r}")
+    __open_browser(url, new_thread = False)

nextstrain/cli/remote/nextstrain_dot_org.py

@@ -464,12 +464,14 @@ def delete(url: urllib.parse.ParseResult, recursively: bool = False, dry_run: bo
             raise UserError(f"Path {path} does not seem to exist")
 
         for resource in resources:
-            yield "nextstrain.org" + str(resource.path)
+            endpoint = api_endpoint(resource.path)
+
+            yield endpoint
 
             if dry_run:
                 continue
 
-            response = http.delete(api_endpoint(resource.path))
+            response = http.delete(endpoint)
 
             raise_for_status(response)
 
@@ -648,6 +650,10 @@ def __init__(self):
     def __call__(self, request: requests.PreparedRequest) -> requests.PreparedRequest:
         if self.user and origin(request.url) == origin(NEXTSTRAIN_DOT_ORG):
             request.headers["Authorization"] = self.user.http_authorization
+
+            # Used in error handling for more informative error messages
+            request._user = self.user # type: ignore
+
         return request
 
 
@@ -708,7 +714,10 @@ def raise_for_status(response: requests.Response) -> None:
                     """, msg = indent("\n".join(wrap(msg)), "  ")) from err
 
         elif status in {401, 403}:
-            user = current_user()
+            try:
+                user = response.request._user # type: ignore
+            except AttributeError:
+                user = None
 
             if user:
                 challenge = authn_challenge(response) if status == 401 else None

nextstrain/cli/remote/s3.py

@@ -7,10 +7,7 @@
 Nextstrain :term:`datasets <docs:dataset>` and :term:`narratives
 <docs:narrative>` hosted on `Amazon S3 <https://aws.amazon.com/s3/>`_.
 This functionality is primarily intended for use by the Nextstrain team and
-operators of self-hosted :term:`docs:Auspice` instances.  It is also used to
-manage the contents of :doc:`Nextstrain Groups
-<docs:learn/groups/index>` that have not migrated to using the
-:doc:`/remotes/nextstrain.org`.
+operators of self-hosted :term:`docs:Auspice` instances.
 
 
 Remote paths