infra: Improve testing usability

.github/workflows/ci.yaml

@@ -38,7 +38,7 @@ jobs:
       env:
         PYTEST_ADDOPTS: "--durations=0"
       run: |
-        hatch test --cover
+        hatch test -m "" --parallel --cover # override default exclusion of slow tests with -m ""
 
   docs:
     runs-on: ubuntu-latest

pyproject.toml

@@ -48,6 +48,16 @@ Changelog = "https://github.com/C2SM/Sirocco/blob/main/CHANGELOG.md"
 # Configuration for [pytest](https://docs.pytest.org)
 addopts = "--pdbcls=IPython.terminal.debugger:TerminalPdb"
 norecursedirs = "tests/cases"
+markers = [
+  "slow: slow integration tests which are not recommended to run locally for normal development"
+]
+filterwarnings = [
+  "error",
+  "ignore::UserWarning",
+  'ignore:datetime.datetime.utcfromtimestamp\(\) is deprecated:DeprecationWarning',  # from aio_pika via duration
+  "ignore:There is no current event loop:DeprecationWarning",  # from plumpy via aiida testing tools
+  "ignore:Object of type <DbNode> not in session:sqlalchemy.exc.SAWarning",  # sqlalchemy via aiida testing tools
+]
 
 [tool.coverage.run]
 # Configuration of [coverage.py](https://coverage.readthedocs.io)
@@ -82,8 +92,7 @@ installer = "uv"
 extra-dependencies = [
     "ipdb"
 ]
-default-args = []
-extra-args = ["--doctest-modules"]
+extra-args = ["--doctest-modules", '-m not slow']
 
 [[tool.hatch.envs.hatch-test.matrix]]
 python = ["3.12"]

src/sirocco/core/workflow.py

@@ -116,7 +116,7 @@ def from_config_file(cls: type[Self], config_path: str) -> Self:
         return cls.from_config_workflow(ConfigWorkflow.from_config_file(config_path))
 
     @classmethod
-    def from_config_workflow(cls: type[Self], config_workflow: ConfigWorkflow) -> Workflow:
+    def from_config_workflow(cls: type[Self], config_workflow: ConfigWorkflow) -> Self:
         return cls(
             name=config_workflow.name,
             config_rootdir=config_workflow.rootdir,

tests/conftest.py

@@ -1,7 +1,11 @@
 import pathlib
+import typing
 
 import pytest
 
+from sirocco import pretty_print
+from sirocco.core import _tasks as core_tasks
+from sirocco.core import workflow
 from sirocco.parsing import _yaml_data_models as models
 
 pytest_plugins = ["aiida.tools.pytest_fixtures"]
@@ -20,3 +24,55 @@ def minimal_config() -> models.ConfigWorkflow:
         ),
         parameters={},
     )
+
+
+# configs that are tested for parsing
+ALL_CONFIG_CASES = ["small", "parameters", "large"]
+
+
+@pytest.fixture(params=ALL_CONFIG_CASES)
+def config_case(request) -> typing.Iterator[str]:
+    return request.param
+
+
+@pytest.fixture
+def pprinter() -> typing.Iterator[pretty_print.PrettyPrinter]:
+    return pretty_print.PrettyPrinter()
+
+
+def generate_config_paths(test_case: str):
+    return {
+        "yml": pathlib.Path(f"tests/cases/{test_case}/config/config.yml"),
+        "txt": pathlib.Path(f"tests/cases/{test_case}/data/config.txt"),
+        "svg": pathlib.Path(f"tests/cases/{test_case}/svg/config.svg"),
+    }
+
+
+@pytest.fixture
+def config_paths(config_case) -> typing.Iterator[dict[str, pathlib.Path]]:
+    return generate_config_paths(config_case)
+
+
+def pytest_addoption(parser):
+    parser.addoption("--reserialize", action="store_true", default=False)
+
+
+def serialize_worklfow(config_paths: dict[str, pathlib.Path], workflow: workflow.Workflow) -> None:
+    config_paths["txt"].write_text(pretty_print.PrettyPrinter().format(workflow))
+
+
+def serialize_nml(config_paths: dict[str, pathlib.Path], workflow: workflow.Workflow) -> None:
+    nml_refdir = config_paths["txt"].parent / "ICON_namelists"
+    for task in workflow.tasks:
+        if isinstance(task, core_tasks.icon_task.IconTask):
+            task.create_workflow_namelists(folder=nml_refdir)
+
+
+def pytest_configure(config):
+    if config.getoption("reserialize"):
+        print("Regenerating serialized references")  # noqa: T201 # this is actual UX, not a debug print
+        for config_case in ALL_CONFIG_CASES:
+            config_paths = generate_config_paths(config_case)
+            wf = workflow.Workflow.from_config_file(str(config_paths["yml"]))
+            serialize_worklfow(config_paths=config_paths, workflow=wf)
+            serialize_nml(config_paths=config_paths, workflow=wf)

tests/test_wc_workflow.py

@@ -5,7 +5,6 @@
 from sirocco.core import Workflow
 from sirocco.core._tasks.icon_task import IconTask
 from sirocco.parsing._yaml_data_models import ConfigShellTask, ShellCliArgument
-from sirocco.pretty_print import PrettyPrinter
 from sirocco.vizgraph import VizGraph
 from sirocco.workgraph import AiidaWorkGraph
 
@@ -26,28 +25,6 @@ def test_parsing_cli_parameters():
     ]
 
 
-@pytest.fixture
-def pprinter():
-    return PrettyPrinter()
-
-
-def generate_config_paths(test_case: str):
-    return {
-        "yml": Path(f"tests/cases/{test_case}/config/config.yml"),
-        "txt": Path(f"tests/cases/{test_case}/data/config.txt"),
-        "svg": Path(f"tests/cases/{test_case}/svg/config.svg"),
-    }
-
-
-# configs that are tested for parsing
-all_uses_cases = ["small", "parameters", "large"]
-
-
-@pytest.fixture(params=all_uses_cases)
-def config_paths(request):
-    return generate_config_paths(request.param)
-
-
 def test_parse_config_file(config_paths, pprinter):
     reference_str = config_paths["txt"].read_text()
     test_str = pprinter.format(Workflow.from_config_file(config_paths["yml"]))
@@ -59,24 +36,20 @@ def test_parse_config_file(config_paths, pprinter):
         ), f"Workflow graph doesn't match serialized data. New graph string dumped to {new_path}."
 
 
-@pytest.mark.skip(reason="don't run it each time, uncomment to regenerate serilaized data")
-def test_serialize_workflow(config_paths, pprinter):
-    config_paths["txt"].write_text(pprinter.format(Workflow.from_config_file(config_paths["yml"])))
-
-
 def test_vizgraph(config_paths):
     VizGraph.from_config_file(config_paths["yml"]).draw(file_path=config_paths["svg"])
 
 
 # configs that are tested for running workgraph
+@pytest.mark.slow
 @pytest.mark.parametrize(
-    "config_path",
+    "config_case",
     [
-        "tests/cases/small/config/config.yml",
-        "tests/cases/parameters/config/config.yml",
+        "small",
+        "parameters",
     ],
 )
-def test_run_workgraph(config_path, aiida_computer):
+def test_run_workgraph(config_case, config_paths, aiida_computer):  # noqa: ARG001  # config_case is overridden
     """Tests end-to-end the parsing from file up to running the workgraph.
 
     Automatically uses the aiida_profile fixture to create a new profile. Note to debug the test with your profile
@@ -85,18 +58,18 @@ def test_run_workgraph(config_path, aiida_computer):
     # some configs reference computer "localhost" which we need to create beforehand
     aiida_computer("localhost").store()
 
-    core_workflow = Workflow.from_config_file(config_path)
+    core_workflow = Workflow.from_config_file(str(config_paths["yml"]))
     aiida_workflow = AiidaWorkGraph(core_workflow)
     out = aiida_workflow.run()
     assert out.get("execution_count", None).value == 1
 
 
 # configs containing task using icon plugin
 @pytest.mark.parametrize(
-    "config_paths",
-    [generate_config_paths("large")],
+    "config_case",
+    ["large"],
 )
-def test_nml_mod(config_paths, tmp_path):
+def test_nml_mod(config_case, config_paths, tmp_path):  # noqa: ARG001  # config_case is overridden
     nml_refdir = config_paths["txt"].parent / "ICON_namelists"
     wf = Workflow.from_config_file(config_paths["yml"])
     # Create core mamelists
@@ -111,17 +84,3 @@ def test_nml_mod(config_paths, tmp_path):
             new_path = nml.with_suffix(".new")
             new_path.write_text(test_nml)
             assert ref_nml == test_nml, f"Namelist {nml.name} differs between ref and test"
-
-
-@pytest.mark.skip(reason="don't run it each time, uncomment to regenerate serilaized data")
-# configs containing task using icon plugin
-@pytest.mark.parametrize(
-    "config_paths",
-    [generate_config_paths("large")],
-)
-def test_serialize_nml(config_paths):
-    nml_refdir = config_paths["txt"].parent / "ICON_namelists"
-    wf = Workflow.from_config_file(config_paths["yml"])
-    for task in wf.tasks:
-        if isinstance(task, IconTask):
-            task.create_workflow_namelists(folder=nml_refdir)