Merge branch 'trs/build/error-if-volumes-unsupported'

CHANGES.md

@@ -13,6 +13,17 @@ development source code and as such may not be routinely kept up to date.
 
 # __NEXT__
 
+## Improvements
+
+* `nextstrain build` now errors if a [development overlay option][] such as
+  `--augur` or `--auspice` is given when using a runtime without support for
+  those (anything but Docker or Singularity).  Previously, it would silently
+  ignore those options when unsupported by the runtime.  The new behaviour
+  matches the behaviour of `nextstrain shell` since 5.0.0.
+  ([#354](https://github.com/nextstrain/cli/pull/354))
+
+[development overlay option]: https://docs.nextstrain.org/projects/cli/en/__NEXT__/commands/build/#development-options-for-docker
+
 
 # 8.0.1 (29 January 2024)
 

devel/release

@@ -102,6 +102,10 @@ update-changelog() {
     # preserving the __NEXT__ heading itself.
     perl -pi -e "s/(?<=^# __NEXT__$)/\n\n\n# $new_version ($today)/" "$changes_file"
 
+    # Replace any occurrences of __NEXT__ under the new version heading, e.g.
+    # for use in doc URLs that should point to the released version.
+    perl -pi -e "s/__NEXT__/$new_version/g if /^# \\Q$new_version/ ... /^# /" "$changes_file"
+
     # Remove the __NEXT__ heading and the sentence «The "__NEXT__" heading
     # below…» for the next commit, but leave the working tree untouched.
     perl -0p -e '

nextstrain/cli/command/build.py

@@ -21,7 +21,8 @@
 from .. import runner
 from ..argparse import add_extended_help_flags, AppendOverwriteDefault, SKIP_AUTO_DEFAULT_IN_HELP
 from ..errors import UsageError, UserError
-from ..util import byte_quantity, warn
+from ..runner import docker, singularity
+from ..util import byte_quantity, runner_name, warn
 from ..volume import store_volume
 
 
@@ -146,6 +147,8 @@ def register_parser(subparser):
 
 
 def run(opts):
+    assert_overlay_volumes_support(opts)
+
     # We must check this before the conditions under which opts.build is
     # optional because otherwise we could pass a missing build dir to a runner
     # which ignores opts.attach.
@@ -233,6 +236,19 @@ def run(opts):
     return runner.run(opts, working_volume = opts.build, cpus = opts.cpus, memory = opts.memory)
 
 
+def assert_overlay_volumes_support(opts):
+    """
+    Check that runtime overlays are supported, if given.
+    """
+    overlay_volumes = [v for v in opts.volumes if v is not opts.build]
+
+    if overlay_volumes and opts.__runner__ not in {docker, singularity}:
+        raise UserError(f"""
+            The {runner_name(opts.__runner__)} runtime does not support overlays (e.g. of {overlay_volumes[0].name}).
+            Use the Docker or Singularity runtimes (via --docker or --singularity) if overlays are necessary.
+            """)
+
+
 def parse_snakemake_args(args):
     """
     Inspects a tiny subset of Snakemake's CLI arguments in order to determine

nextstrain/cli/command/shell.py

@@ -7,11 +7,11 @@
 from .. import resources
 from .. import runner
 from ..argparse import add_extended_help_flags
-from ..errors import UserError
 from ..paths import SHELL_HISTORY
 from ..runner import docker, conda, singularity
 from ..util import colored, remove_prefix, runner_name, warn
 from ..volume import store_volume, NamedVolume
+from .build import assert_overlay_volumes_support
 
 
 def register_parser(subparser):
@@ -43,6 +43,8 @@ def register_parser(subparser):
 
 
 def run(opts):
+    assert_overlay_volumes_support(opts)
+
     # Ensure our build dir exists
     if not opts.build.src.is_dir():
         warn("Error: Build path \"%s\" does not exist or is not a directory." % opts.build.src)
@@ -53,14 +55,6 @@ def run(opts):
 
         return 1
 
-    overlay_volumes = [v for v in opts.volumes if v is not opts.build]
-
-    if overlay_volumes and opts.__runner__ not in {docker, singularity}:
-        raise UserError(f"""
-            The {runner_name(opts.__runner__)} runtime does not support overlays (e.g. of {overlay_volumes[0].name}).
-            Use the Docker or Singularity runtimes (via --docker or --singularity) if overlays are necessary.
-            """)
-
     print(colored("bold", f"Entering the Nextstrain runtime ({runner_name(opts.__runner__)})"))
     print()
 

nextstrain/cli/runner/aws_batch/__init__.py

@@ -163,7 +163,7 @@ def register_arguments(parser) -> None:
 
 
 def run(opts, argv, working_volume = None, extra_env: Env = {}, cpus: int = None, memory: int = None) -> int:
-    # Unlike other runners, the AWS Bach runner currently *requires* a working
+    # Unlike other runners, the AWS Batch runner currently *requires* a working
     # dir in most usages.  This is ok as we only provide the AWS Batch runner
     # for commands which also require a working dir (e.g. build), whereas other
     # runners also work with commands that don't.