Unbuffer runner test results

nextstrain/cli/command/check_setup.py

@@ -38,7 +38,7 @@
 from .. import config
 from ..argparse import SKIP_AUTO_DEFAULT_IN_HELP, runner_module_argument
 from ..types import Options
-from ..util import colored, check_for_new_version, runner_name, runner_tests_ok, print_runner_tests
+from ..util import colored, check_for_new_version, runner_name, runner_tests_ok, stream_and_print_results
 from ..runner import all_runners, all_runners_by_name, default_runner # noqa: F401 (it's wrong; we use it in run())
 
 
@@ -84,37 +84,33 @@ def run(opts: Options) -> int:
     # Run and collect our runners' self-tests
     print("Testing your setup…")
 
-    runner_tests = [
+    runner_tests = (
         (runner, runner.test_setup())
             for runner in opts.runners
-    ]
+    )
 
-    runner_status = {
-        runner: runner_tests_ok(tests)
-            for runner, tests in runner_tests
-    }
+    supported_runners = []
 
     # Print test results.  The first print() separates results from the
     # previous header or stderr output, making it easier to read.
     print()
 
     for runner, tests in runner_tests:
-        if runner_status[runner]:
+        print(colored("blue", "#"), "Checking %s…" % (runner_name(runner)))
+
+        tests = stream_and_print_results(tests)
+
+        runner_status = runner_tests_ok(tests)
+        if runner_status:
             supported = success("supported")
+            supported_runners.append(runner)
         else:
             supported = failure("not supported")
 
         print(colored("blue", "#"), "%s is %s" % (runner_name(runner), supported))
-        print_runner_tests(tests)
         print()
 
     # Print overall status.
-    supported_runners = [
-        runner
-            for runner, status_ok in runner_status.items()
-             if status_ok
-    ]
-
     if supported_runners:
         print("Supported Nextstrain runtimes:", ", ".join(success(runner_name(r)) for r in supported_runners))
 

nextstrain/cli/command/setup.py

@@ -13,8 +13,8 @@
 
 from .. import config, console
 from ..argparse import runner_module_argument
-from ..util import colored, runner_name, runner_tests_ok, print_runner_tests
-from ..types import Options
+from ..util import colored, runner_name, runner_tests_ok, stream_and_print_results
+from ..types import Options, RunnerTestResults
 from ..runner import all_runners_by_name, configured_runner, default_runner # noqa: F401 (it's wrong; we use it in run())
 
 
@@ -70,9 +70,9 @@ def run(opts: Options) -> int:
     print(heading(f"Checking setup…"))
 
     if not opts.dry_run:
-        tests = opts.runner.test_setup()
+        tests: RunnerTestResults = opts.runner.test_setup()
 
-        print_runner_tests(tests)
+        tests = stream_and_print_results(tests)
 
         if not runner_tests_ok(tests):
             print()

nextstrain/cli/runner/ambient.py

@@ -75,16 +75,14 @@ def runnable(*argv) -> bool:
             return False
 
 
-    return [
-        ('snakemake is installed and runnable',
-            shutil.which("snakemake") is not None and runnable("snakemake", "--version")),
+    yield ('snakemake is installed and runnable',
+            shutil.which("snakemake") is not None and runnable("snakemake", "--version"))
 
-        ('augur is installed and runnable',
-            shutil.which("augur") is not None and runnable("augur", "--version")),
+    yield ('augur is installed and runnable',
+            shutil.which("augur") is not None and runnable("augur", "--version"))
 
-        ('auspice is installed and runnable',
-            shutil.which("auspice") is not None and runnable("auspice", "--version")),
-    ]
+    yield ('auspice is installed and runnable',
+            shutil.which("auspice") is not None and runnable("auspice", "--version"))
 
 
 def set_default_config() -> None:

nextstrain/cli/runner/aws_batch/__init__.py

@@ -560,16 +560,14 @@ def test_setup() -> RunnerTestResults:
     """
     Check that necessary AWS resources exist.
     """
-    return [
-        ('job description "%s" exists' % DEFAULT_JOB,
-            jobs.definition_exists(DEFAULT_JOB)),
+    yield ('job description "%s" exists' % DEFAULT_JOB,
+            jobs.definition_exists(DEFAULT_JOB))
 
-        ('job queue "%s" exists' % DEFAULT_QUEUE,
-            jobs.queue_exists(DEFAULT_QUEUE)),
+    yield ('job queue "%s" exists' % DEFAULT_QUEUE,
+            jobs.queue_exists(DEFAULT_QUEUE))
 
-        ('S3 bucket "%s" exists' % DEFAULT_S3_BUCKET,
-            s3.bucket_exists(DEFAULT_S3_BUCKET)),
-    ]
+    yield ('S3 bucket "%s" exists' % DEFAULT_S3_BUCKET,
+            s3.bucket_exists(DEFAULT_S3_BUCKET))
 
 
 def set_default_config() -> None:

nextstrain/cli/runner/conda.py

@@ -422,30 +422,27 @@ def runnable(*argv) -> bool:
 
     support = test_support()
 
+    yield from support
+
     if not runner_tests_ok(support):
-        return support
+        pass
 
-    if not PREFIX_BIN.exists():
-        return [
-            *support,
-            ("runtime appears set up\n\n"
-             "The Conda runtime appears supported but not yet set up.\n"
-             "Try running `nextstrain setup conda` first.", False),
-        ]
+    elif not PREFIX_BIN.exists():
+        yield ("runtime appears set up\n\n"
+               "The Conda runtime appears supported but not yet set up.\n"
+               "Try running `nextstrain setup conda` first.", False)
 
-    return [
-        *support,
-        ("runtime appears set up", True),
+    else:
+        yield ("runtime appears set up", True)
 
-        ('snakemake is installed and runnable',
-            which_finds_our("snakemake") and runnable("snakemake", "--version")),
+        yield ('snakemake is installed and runnable',
+            which_finds_our("snakemake") and runnable("snakemake", "--version"))
 
-        ('augur is installed and runnable',
-            which_finds_our("augur") and runnable("augur", "--version")),
+        yield ('augur is installed and runnable',
+            which_finds_our("augur") and runnable("augur", "--version"))
 
-        ('auspice is installed and runnable',
-            which_finds_our("auspice") and runnable("auspice", "--version")),
-    ]
+        yield ('auspice is installed and runnable',
+            which_finds_our("auspice") and runnable("auspice", "--version"))
 
 
 def test_support() -> RunnerTestResults:

nextstrain/cli/runner/docker.py

@@ -381,19 +381,20 @@ def test_image_version():
 
         return [(msg, status)]
 
-    return [
-        ('docker is installed',
-            shutil.which("docker") is not None),
-        ('docker run works',
-            test_run()),
-        *test_memory_limit(),
-        *test_image_version(),
-
-        # Rosetta 2 is optional, so convert False (fail) → None (warning)
-        *[(msg, None if status is False else status)
-            for msg, status
-             in test_rosetta_enabled("Rosetta 2 is enabled for faster execution (optional)")],
-    ]
+    yield ('docker is installed',
+        shutil.which("docker") is not None)
+
+    yield ('docker run works',
+        test_run())
+
+    yield from test_memory_limit()
+
+    yield from test_image_version()
+
+    # Rosetta 2 is optional, so convert False (fail) → None (warning)
+    yield from ((msg, None if status is False else status)
+                  for msg, status
+                   in test_rosetta_enabled("Rosetta 2 is enabled for faster execution (optional)"))
 
 
 def set_default_config() -> None:

nextstrain/cli/runner/singularity.py

@@ -334,14 +334,14 @@ def test_run():
         else:
             return True
 
-    return [
-        ("singularity is installed",
-            shutil.which("singularity") is not None),
-        (f"singularity version {singularity_version()} ≥ {SINGULARITY_MINIMUM_VERSION} ({APPTAINER_MINIMUM_VERSION} for Apptainer)",
-            singularity_version_at_least(SINGULARITY_MINIMUM_VERSION, apptainer=APPTAINER_MINIMUM_VERSION)),
-        ("singularity works",
-            test_run()),
-    ]
+    yield ("singularity is installed",
+            shutil.which("singularity") is not None)
+
+    yield (f"singularity version {singularity_version()} ≥ {SINGULARITY_MINIMUM_VERSION} ({APPTAINER_MINIMUM_VERSION} for Apptainer)",
+             singularity_version_at_least(SINGULARITY_MINIMUM_VERSION, apptainer=APPTAINER_MINIMUM_VERSION))
+
+    yield ("singularity works",
+            test_run())
 
 
 def set_default_config() -> None:

nextstrain/cli/types.py

@@ -42,7 +42,7 @@
 
 RunnerSetupStatus = Optional[bool]
 
-RunnerTestResults = List['RunnerTestResult']
+RunnerTestResults = Iterable['RunnerTestResult']
 RunnerTestResult  = Tuple[str, 'RunnerTestResultStatus']
 RunnerTestResultStatus: TypeAlias = Union[bool, None, EllipsisType]
 

nextstrain/cli/util.py

@@ -582,10 +582,12 @@ def runner_tests_ok(tests: RunnerTestResults) -> bool:
     return False not in [result for test, result in tests]
 
 
-def print_runner_tests(tests: RunnerTestResults):
+def stream_and_print_results(tests: RunnerTestResults) -> RunnerTestResults:
     """
-    Prints a formatted version of the return value of a runner's
-    ``test_setup()``.
+    Iterates through and prints runner test results while streaming them
+    forward.
+
+    Messages will only be printed if the generator is consumed downstream.
     """
     success = partial(colored, "green")
     failure = partial(colored, "red")
@@ -612,6 +614,8 @@ def print_runner_tests(tests: RunnerTestResults):
 
         print(status.get(result, str(result)) + ":", formatted_description)
 
+        yield (description, result)
+
 
 def test_rosetta_enabled(msg: str = "Rosetta 2 is enabled") -> RunnerTestResults:
     """