ci: drop unread steps, fold partial failures, Nextflow runtime tests into Lint And Test

.github/workflows/benchmarks_weekly.yml

@@ -104,10 +104,6 @@ jobs:
         id: setup
         run: 'true'
 
-      - name: Generate Sophios Validation Jsonschema
-        if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
-        run: cd sophios/ && sophios --generate_schemas
-
       - name: Generate Sophios Python API Workflows (*.py -> *.wic)
         if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
         # Corpus preparation: the corpus cases compile the *.wic files it writes.

.github/workflows/lint_and_test.yml

@@ -223,17 +223,6 @@ jobs:
         if: ${{ runner.os == 'Linux' && !cancelled() && steps.setup.outcome == 'success' }}
         run: cd sophios/ && autopep8 --exit-code --recursive --diff --max-line-length 120 examples/ src/ tests/
 
-      - name: Generate Sophios Validation Jsonschema
-        if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
-        run: cd sophios/ && sophios --generate_schemas
-
-        # Please read docs/validation.md#Property-Based-Testing
-        # This is essentially an integration test for all of the
-        # Sophios Python API workflows as well as the Sophios Python API itself.
-      - name: Validate sophios Python API Workflows (*.py -> *.wic)
-        if: ${{ !cancelled() && steps.setup.outcome == 'success' && steps.corpus.outcome == 'success' }}
-        run: cd sophios/ && pytest tests/core/test_python_api_workflow.py -k test_validate_generated_python_workflows
-
       - name: Build Documentation
         if: ${{ runner.os == 'Linux' && !cancelled() && steps.setup.outcome == 'success' }}
         run: cd sophios/docs && make html
@@ -352,6 +341,34 @@ jobs:
         # Also, cannot run on Windows (natively) yet
         run: cd sophios/ && pytest -k test_scattering_scaling
 
+      # Pipelines run under the pinned Nextflow: tests/core/nextflow, marked `nextflow`. The corpus
+      # under Nextflow is Run Workflows'. Nextflow does not run on Windows.
+      - name: Setup Java for Nextflow
+        if: ${{ runner.os == 'Linux' && !cancelled() && steps.setup.outcome == 'success' }}
+        uses: actions/setup-java@v5
+        with:
+          distribution: temurin
+          java-version: "17"
+
+      - name: Install pinned Nextflow
+        if: ${{ runner.os == 'Linux' && !cancelled() && steps.setup.outcome == 'success' }}
+        env:
+          NXF_VER: "26.04.2"
+        run: |
+          curl --fail --silent --show-error https://get.nextflow.io | bash
+          install -m 0755 nextflow "${RUNNER_TEMP}/nextflow"
+          echo "${RUNNER_TEMP}" >> "${GITHUB_PATH}"
+          NXF_ANSI_LOG=false "${RUNNER_TEMP}/nextflow" -version | grep 'version 26.04.2'
+
+      - name: PyTest Nextflow Runtime
+        if: ${{ runner.os == 'Linux' && !cancelled() && steps.setup.outcome == 'success' }}
+        timeout-minutes: 20
+        env:
+          NXF_ANSI_LOG: "false"
+          NXF_OFFLINE: "true"
+          NXF_VER: "26.04.2"
+        run: cd sophios/ && pytest tests/core/nextflow -m "nextflow and not nextflow_corpus"
+
       # NOTE: The steps below are for repository_dispatch only. For all other steps, please insert above
       # this comment.
 

.github/workflows/lint_and_test_macos.yml

@@ -117,17 +117,6 @@ jobs:
         # "SC1017 (error): Literal carriage return. Run script through tr -d '\r' ."
         run: shellcheck -e SC1017 $(find sophios/ -name "*.sh" -and -not -path "./3/*")
 
-      - name: Generate Sophios Validation Jsonschema
-        if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
-        run: cd sophios/ && sophios --generate_schemas
-
-        # Please read docs/validation.md#Property-Based-Testing
-        # This is essentially an integration test for all of the
-        # Sophios Python API workflows as well as the Sophios Python API itself.
-      - name: Validate Sophios Python API Workflows (*.py -> *.wic)
-        if: ${{ !cancelled() && steps.setup.outcome == 'success' && steps.corpus.outcome == 'success' }}
-        run: cd sophios/ && pytest tests/core/test_python_api_workflow.py -k test_validate_generated_python_workflows
-
       - name: Build Documentation
         if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
         run: cd sophios/docs && make html

.github/workflows/property_weekly.yml

@@ -7,7 +7,7 @@ name: Property Weekly
 # Hermetic: every input is generated (workflows over tests/core/synthetic_tools.py),
 # so nothing here needs a plugin checkout, a config, a container or the
 # self-hosted runner. The nextflow-properties job alone installs Java and the
-# pinned Nextflow, as nextflow.yml does, and runs only the runtime properties.
+# pinned Nextflow, as Lint And Test does, and runs only the runtime properties.
 # It replaces the weekly fuzz job, which sampled an
 # environment-dependent schema that no longer exists.
 #
@@ -133,8 +133,8 @@ jobs:
           --hypothesis-seed="$HYPOTHESIS_SEED" --junitxml=property-reports/api-runtime.xml
 
       # The Nextflow target's compile-side properties: lowering, the executable
-      # model, rendering and reading a pipeline back. Runs under Nextflow stay
-      # in nextflow.yml, which installs it.
+      # model, rendering and reading a pipeline back. Runs under Nextflow are
+      # Lint And Test's, which installs it.
       - name: PyTest Nextflow Target Properties
         if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
         timeout-minutes: 30
@@ -148,8 +148,8 @@ jobs:
           path: property-reports/
           retention-days: 30
 
-  # The runtime properties need Java and the pinned Nextflow. nextflow.yml keeps
-  # running them at scale 1 on push and pull request.
+  # The runtime properties need Java and the pinned Nextflow. Lint And Test keeps
+  # running them at scale 1 on every pull request.
   nextflow-properties:
     concurrency:
       group: ${{ github.workflow }}-nextflow-${{ github.ref }}

.github/workflows/run_workflows.yml

@@ -210,17 +210,6 @@ jobs:
       if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
       run: cd sophios/ && pytest tests/core/test_python_api_workflow.py -k test_compile_python_workflows
 
-    - name: Generate Sophios Validation Jsonschema
-      if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
-      run: cd sophios/ && sophios --generate_schemas
-
-      # Please read docs/validation.md#Property-Based-Testing
-      # This is essentially an integration test for all of the
-      # WIC Python API workflows as well as the WIC Python API itself.
-    - name: Validate Sophios Python API Workflows (*.py -> *.wic)
-      if: ${{ !cancelled() && steps.setup.outcome == 'success' && steps.corpus.outcome == 'success' }}
-      run: cd sophios/ && pytest tests/core/test_python_api_workflow.py -k test_validate_generated_python_workflows
-
     - name: cwl-docker-extract (i.e. recursively docker pull)
       if: ${{ !cancelled() && steps.setup.outcome == 'success' && steps.corpus.outcome == 'success' }}
       # One compile and a round of docker pulls per corpus workflow, mostly
@@ -235,7 +224,7 @@ jobs:
 
     - name: PyTest Python API
       if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
-      run: cd sophios/ && pytest tests/core/test_python_api_workflow.py -k "not test_compile_python_workflows and not test_validate_generated_python_workflows"
+      run: cd sophios/ && pytest tests/core/test_python_api_workflow.py -k "not test_compile_python_workflows"
 
     # Workflow.from_wic and write_wic over every .wic root the config reaches.
     # Only here does the config reach the mm-workflows and image-workflows
@@ -245,37 +234,15 @@ jobs:
       if: ${{ !cancelled() && steps.setup.outcome == 'success' && steps.corpus.outcome == 'success' }}
       run: cd sophios/ && pytest tests/core/test_python_api_from_wic.py
 
-    - name: PyTest Run REST Core Tests
-      if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
-      # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
-      run: cd sophios/ && pytest tests/contrib/test_rest_api.py -k test_rest_core --cwl_runner cwltool
-
-    - name: PyTest Run REST WFB Tests
+    - name: PyTest Contrib (REST core and WFB, ICT to CLT, WFB payload)
       if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
       # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
-      run: cd sophios/ && pytest tests/contrib/test_rest_api.py -k test_rest_wfb --cwl_runner cwltool
-
-    - name: PyTest Run ICT to CLT conversion Tests
-      if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
-      # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
-      run: cd sophios/ && pytest tests/contrib/test_ict_to_clt_conversion.py -k test_ict_to_clt
-
-    - name: PyTest Run update wfb payload Tests
-      if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
-      run: cd sophios/ && pytest tests/contrib/test_fix_payload.py -k test_fix
+      run: cd sophios/ && pytest tests/contrib --cwl_runner cwltool
 
     - name: PyTest Run Workflows
       if: ${{ !cancelled() && steps.setup.outcome == 'success' && steps.corpus.outcome == 'success' }}
       run: cd sophios/ && pytest tests/core/test_examples.py -k test_run_workflows_on_push --workers "${PYTEST_WORKERS}" --cwl_runner cwltool --durations=0 # --cov
 
-    # test_run_partial_failures_pass is skip_pypi_ci, so the packaging lane
-    # excludes it, and every other invocation of this file selects a different
-    # -k — it ran nowhere. Its sibling test_run_partial_failures_fail_without_flag
-    # carries no marker and is already covered by default collection.
-    - name: PyTest Run Partial Failures
-      if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
-      run: cd sophios/ && pytest tests/core/test_examples.py -k test_run_partial_failures_pass --cwl_runner cwltool
-
     # The corpus workflows the Nextflow target supports, compiled with it and
     # run under Nextflow with Docker: tests/core/nextflow/test_corpus.py. The
     # steps above run them under cwltool, which never reaches the Nextflow

.github/workflows/run_workflows_weekly.yml

@@ -176,17 +176,6 @@ jobs:
       if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
       run: cd sophios/ && pytest tests/core/test_python_api_workflow.py -k test_compile_python_workflows
 
-    - name: Generate Sophios Validation Jsonschema
-      if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
-      run: cd sophios/ && sophios --generate_schemas
-
-      # Please read docs/validation.md#Property-Based-Testing
-      # This is essentially an integration test for all of the
-      # Sophios Python API workflows as well as the WIC Python API itself.
-    - name: Validate Sophios Python API Workflows (*.py -> *.wic)
-      if: ${{ !cancelled() && steps.setup.outcome == 'success' && steps.corpus.outcome == 'success' }}
-      run: cd sophios/ && pytest tests/core/test_python_api_workflow.py -k test_validate_generated_python_workflows
-
     - name: PyTest Tool Builder
       if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
       run: cd sophios/ && pytest tests/core/test_python_api_tool_builder.py

install/system_deps_ci.yml

@@ -23,7 +23,7 @@ dependencies:
   - cryptography
   - zstandard
 # Run Workflows runs the corpus under Nextflow on a push, with the Nextflow and
-# the Java the Nextflow lane pins (NXF_VER and java-version in nextflow.yml).
+# the Java Lint And Test pins for its Nextflow runtime tests (NXF_VER and java-version).
 # The package runs its own jar, so nothing it needs lives outside this
 # environment.
   - nextflow=26.04.2

tests/core/test_examples.py

@@ -113,13 +113,13 @@ def _artifacts(root: CompilationArtifact) -> list[CompilationArtifact]:
 
 @pytest.mark.skip_pypi_ci
 @pytest.mark.slow
-@pytest.mark.parametrize("yml_path_str, yml_path", yml_paths_tuples_on_push)
+@pytest.mark.parametrize("yml_path_str, yml_path", yml_paths_tuples_on_push + yml_paths_partial_failure)
 def test_run_workflows_on_push(yml_path_str: str, yml_path: Path, cwl_runner: str,
                                corpus_registry: CorpusRegistry) -> None:
     """Runs every workflow auto-discovered from the directories in 'search_paths_wic',
-       except the fragments, intensive workflows and partial failures that the
-       config_ci.json files list."""
-    args = get_args(str(yml_path))
+       except the fragments and intensive workflows that the config_ci.json files list;
+       those listed as partial failures run with --partial_failure_enable."""
+    args = get_args(str(yml_path), ['--partial_failure_enable'] if yml_path_str in run_partial_failures else [])
     run_workflows(yml_path_str, yml_path, cwl_runner, args, corpus_registry)
 
 
@@ -177,15 +177,6 @@ def compiled(flags: list[str]) -> list[tuple[Any, ...]]:
 
 
 # partial failure tests
-@pytest.mark.skip_pypi_ci
-@pytest.mark.parametrize("yml_path_str, yml_path", yml_paths_partial_failure)
-def test_run_partial_failures_pass(yml_path_str: str, yml_path: Path, cwl_runner: str,
-                                   corpus_registry: CorpusRegistry) -> None:
-    """Run workflows allowing partial failures. yml files of workflows which are known to have failure steps"""
-    args = get_args(str(yml_path), ['--partial_failure_enable'])
-    run_workflows(yml_path_str, yml_path, cwl_runner, args, corpus_registry)
-
-
 @pytest.mark.parametrize("yml_path_str, yml_path", yml_paths_partial_failure)
 def test_run_partial_failures_fail_without_flag(yml_path_str: str, yml_path: Path, cwl_runner: str,
                                                 corpus_registry: CorpusRegistry) -> None:

tests/core/test_python_api_workflow.py

@@ -17,7 +17,6 @@
 from unittest.mock import Mock, patch
 
 from hypothesis import example, given, strategies as st
-from jsonschema import Draft202012Validator
 import pytest
 import yaml
 
@@ -33,7 +32,6 @@
 from sophios.api.python.workflow import (_python_api_types_match, InvalidInputValueError, InvalidLinkError,
                                          InvalidStepError, RunResult, RunState, RunStatus, SophiosError,
                                          SophiosErrorCode, Step, StepInput, Workflow, WorkflowRunError)
-from sophios.lang import parse, to_json, wic_schema
 from sophios.python_cwl_adapter import import_python_file
 from sophios.wic_types import Json, Tools
 
@@ -46,10 +44,6 @@
 from .wic_reading import read_wic
 
 
-AUTOGENERATED_DIR = REPO_ROOT / "autogenerated"
-PYTHON_WORKFLOW_MANIFEST = AUTOGENERATED_DIR / "python_workflow_manifest.json"
-
-
 def _written(workflow: Workflow, directory: Path, name: str | None = None) -> dict[str, Any]:
     """The document `write_wic` writes for `workflow` (or its nested workflow `name`), as `parse` reads it."""
     root = workflow.write_wic(directory)
@@ -132,14 +126,6 @@ def step_factory(*args: Any, **kwargs: Any) -> Any:
         yield
 
 
-def _write_manifest(workflow_paths: list[Path]) -> None:
-    """Record the generated `.wic` paths for the validation step that follows."""
-    AUTOGENERATED_DIR.mkdir(parents=True, exist_ok=True)
-    manifest = sorted({str(path) for path in workflow_paths})
-    PYTHON_WORKFLOW_MANIFEST.write_text(
-        json.dumps(manifest, indent=2), encoding="utf-8")
-
-
 PAIRS = Path(__file__).resolve().parent / "data" / "python_api_pairs"
 _PAIRED = import_python_file("python_api_pairs", PAIRS / "pairs.py")
 #: Each pair's notes, written by hand from the inference rule: the nearest step's output, the others that fit counted.
@@ -730,7 +716,6 @@ def test_compile_python_workflows() -> None:
     tools_cwl = sophios.plugins.get_tools_cwl(global_config)
     paths_tuples = _iter_python_workflow_paths(global_config)
     import_errors: list[str] = []
-    generated_workflows: list[Path] = []
     for path_stem, path in paths_tuples:
         try:
             with _step_registry_injected(tools_cwl):
@@ -739,8 +724,6 @@ def test_compile_python_workflows() -> None:
 
             retval.compile()
             retval.write_wic(path.parent)
-            generated_workflows.extend(
-                path.parent / f"{wf.process_name}.wic" for wf in retval._flatten_subworkflows())
 
             config_ci = path.parent / "config_ci.json"
             json_contents = {}
@@ -761,34 +744,6 @@ def test_compile_python_workflows() -> None:
     if import_errors:
         pytest.fail("Python workflow imports failed:\n" +
                     "\n".join(import_errors))
-    _write_manifest(generated_workflows)
-
-
-@pytest.mark.fast
-def test_validate_generated_python_workflows() -> None:
-    """Every `.wic` the discovery step generated parses clean and validates
-    against the exported schema."""
-    if not PYTHON_WORKFLOW_MANIFEST.exists():
-        pytest.fail(
-            f"Missing generated workflow manifest: {PYTHON_WORKFLOW_MANIFEST}")
-
-    validator = Draft202012Validator(wic_schema())
-    workflow_paths = json.loads(
-        PYTHON_WORKFLOW_MANIFEST.read_text(encoding="utf-8"))
-    validation_errors: list[str] = []
-    for workflow_path_str in workflow_paths:
-        workflow_path = Path(workflow_path_str)
-        parsed = parse(workflow_path.read_text(encoding="utf-8"), workflow_path.name)
-        if not parsed.ok or parsed.document is None:
-            validation_errors.extend(str(d) for d in parsed.diagnostics)
-            continue
-        validation_errors.extend(
-            f"{workflow_path}: {error.message}"
-            for error in validator.iter_errors(to_json(parsed.document)))
-
-    if validation_errors:
-        pytest.fail("Generated workflow validation failed:\n" +
-                    "\n".join(validation_errors))
 
 
 def _detach_run_from_the_container_engine(monkeypatch: pytest.MonkeyPatch) -> None: