Fix bugs and update CI

_viash.yaml

@@ -0,0 +1 @@
+viash_version: 0.8.2

tests/integration/test_run_component/dummy_config.vsh.yaml

@@ -23,7 +23,9 @@ functionality:
   test_resources:
     - type: python_script
       path: test_script.py
+    - path: /tests/integration/test_run_component/dummy_config.vsh.yaml
 platforms:
+  - type: native
   - type: docker
     image: python:3.10
     test_setup:
@@ -32,5 +34,11 @@ platforms:
       - type: python
         packages:
           - /viashpy
-  - type: native
+          - ruamel.yaml
+      - type: apt
+        packages:
+          - default-jdk
+      - type: docker
+        run: |
+          curl -fsSL dl.viash.io | bash; mv viash /usr/local/bin/
   - type: nextflow

tests/integration/test_run_component/test_script.py

@@ -1,7 +1,10 @@
 import pytest
 import sys
+from pathlib import Path
 from io import StringIO
-from contextlib import redirect_stdout
+from ruamel.yaml import YAML
+from contextlib import redirect_stdout, redirect_stderr
+import uuid
 
 ### VIASH START # noqa: E266
 meta = {
@@ -10,29 +13,83 @@
 ### VIASH END # noqa: E266
 
 
-def test_run_component(run_component):
-    captured_output = run_component(["--output", "bar.txt"])
-    with open("bar.txt", "r") as open_output_file:
-        contents = open_output_file.read()
-        assert contents == "foo!"
-    assert (
-        captured_output is not None
-    ), "Some output from stdout or stderr should have been captured"
-    assert b"This is a logging statement" in captured_output
+@pytest.fixture()
+def random_config_path(tmp_path):
+    def wrapper():
+        unique_filename = f"{str(uuid.uuid4())}.vsh.yaml"
+        temp_file = tmp_path / unique_filename
+        return temp_file
 
+    return wrapper
 
-if __name__ == "__main__":
+
+class TestRunExecutable:
+    meta = meta
+
+    def test_run_component(self, run_component):
+        captured_output = run_component(["--output", "bar.txt"])
+        with open("bar.txt", "r") as open_output_file:
+            contents = open_output_file.read()
+            assert contents == "foo!"
+        assert (
+            captured_output is not None
+        ), "Some output from stdout or stderr should have been captured"
+        assert b"This is a logging statement" in captured_output
+
+
+class TestRunUsingConfig:
+    meta = meta
+
+    @pytest.fixture()
+    def viash_source_config_path(self, random_config_path):
+        yaml_interface = YAML(typ="safe", pure=True)
+        yaml_interface.default_flow_style = False
+        original_config = yaml_interface.load(
+            Path(f"{meta['resources_dir']}/dummy_config.vsh.yaml")
+        )
+        del original_config["functionality"]["test_resources"]
+        del original_config["functionality"]["resources"][1]
+        result_path = random_config_path()
+        yaml_interface.dump(original_config, result_path)
+        return result_path
+
+    def test_run_component_check_correct_memory_syntax(self, run_component):
+        captured_output = run_component(["--output", "bar.txt"])
+        with open("bar.txt", "r") as open_output_file:
+            contents = open_output_file.read()
+            assert contents == "foo!"
+        assert (
+            captured_output is not None
+        ), "Some output from stdout or stderr should have been captured"
+        assert (
+            b"--memory looks like a parameter but is not a defined parameter and will instead be treated as a positional argument"
+            not in captured_output
+        )
+
+
+def run_pytest_and_capture_output():
     temp_stdout = StringIO()
+    temp_stderr = StringIO()
     print(f"meta: {meta}")
+    with redirect_stdout(temp_stdout), redirect_stderr(temp_stderr):
+        exit_code = pytest.main(
+            [__file__, "--log-cli-level", "DEBUG"], plugins=["viashpy"]
+        )
+    stdout_str = temp_stdout.getvalue()
+    stderr_str = temp_stderr.getvalue()
+    print(f"stdout: {stdout_str}\nstderr: {stderr_str}\nexit_code: {exit_code}")
+    return stdout_str, stderr_str, exit_code
+
+
+if __name__ == "__main__":
     assert (
         meta["memory_gb"] is not None
     ), "This test should be executed with some --memory set."
-    with redirect_stdout(temp_stdout):
-        result = pytest.main([__file__], plugins=["viashpy"])
-    stdout_str = temp_stdout.getvalue()
-    print(stdout_str)
+
+    stdout_str, stderr_str, exit_code = run_pytest_and_capture_output()
     assert (
         "Different values were defined in the 'meta' dictionary that limit memory, choosing the one with the smallest unit"
         not in stdout_str
     )
-    sys.exit(result)
+
+    sys.exit(exit_code)

tests/unittests/fixtures/test_run_component.py

@@ -109,7 +109,7 @@ def test_run_component_different_memory_specification_warnings(
     expected_bytes,
     expected_warning,
 ):
-    expected_memory_args = ""
+    expected_memory_args = ", "
     memory_specifiers = [
         memory_pb,
         memory_tb,
@@ -122,9 +122,9 @@ def test_run_component_different_memory_specification_warnings(
         specifier for specifier in memory_specifiers if specifier != "None"
     ]
     if any(memory_specifiers):
-        expected_memory_args = f', "--memory", "{expected_bytes}B"'
+        expected_memory_args = f', "--memory", "{expected_bytes}B", '
     expected = (
-        '["viash", "run", Path(meta["config"]), "--", "bar"%s]' % expected_memory_args
+        '["viash", "run", Path(meta["config"])%s"--", "bar"]' % expected_memory_args
     )
     makepyfile_and_add_meta(
         f"""
@@ -170,7 +170,7 @@ def test_loading_run_component(mocker, run_component):
     [
         (
             "dummy_config",
-            '["viash", "run", Path(meta["config"]), "--", "bar"%s%s]',
+            '["viash", "run", Path(meta["config"])%s%s, "--", "bar"]',
             "--",
         ),
         ("dummy_config_with_info", '[Path("foo"), "bar"%s%s]', "---"),

tox.ini

@@ -1,6 +1,6 @@
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py3.9,py3.10,py3.11,flake8
+envlist = py3.9,py3.10,py3.11,py3.12flake8
 isolated_build = True
 
 [testenv]

viashpy/_run.py

@@ -79,8 +79,9 @@ def viash_run(
     if not config.is_file():
         raise FileNotFoundError(f"{config} does not exist or is not a file.")
     return check_output(
-        [viash_location, "run", config, "--"]
-        + _add_cpu_and_memory(args, cpus, memory, "--"),
+        _add_cpu_and_memory([viash_location, "run", config], cpus, memory, "--")
+        + ["--"]
+        + args,
         stderr=stderr,
         **popen_kwargs,
     )

viashpy/testing.py

@@ -7,7 +7,8 @@
 from subprocess import CalledProcessError
 import warnings
 
-logger = logging.Logger(__name__)
+logger = logging.getLogger(__name__)
+logger.propagate = True
 
 
 @pytest.fixture
@@ -196,7 +197,7 @@ def wrapper(args_as_list):
         return wrapper
 
     logger.info(
-        "Could not find the original viash config source. "
+        f"Could not find the original viash config source at '{viash_source_config_path}'. "
         "Assuming test script is run from 'viash test' or 'viash_test'."
     )