test: Tier 0-2 scaffolding (shell syntax, imports, entrypoints, runner metadata)

.github/workflows/ci-dev.yml

@@ -0,0 +1,35 @@
+name: CI (develop)
+
+# Lightweight PR-time test suite that actually gates merges into develop.
+# Runs the unit tests under tests/ inside the published shapepipe container
+# — no conda bootstrap, no multi-OS matrix. Complements ci-release.yml
+# (which is a heavier conda-based suite gating main/master).
+
+on:
+  pull_request:
+    branches:
+      - develop
+  push:
+    branches:
+      - develop
+
+jobs:
+  unit:
+    name: Unit tests
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/cosmostat/shapepipe:develop
+      options: --user root
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Reinstall shapepipe from the checkout
+        # The container ships a snapshot of the repo under /app. Replace it
+        # with the PR's checkout so tests run against the proposed code.
+        run: |
+          pip install --no-deps --force-reinstall -e .
+
+      - name: Run unit tests
+        run: |
+          pytest tests/unit/ -v --no-cov -p no:warnings

.gitignore

@@ -134,3 +134,4 @@ dmypy.json
 *shapepipe_run_*
 *shapepipe_runs*
 code
+CLAUDE.md

pyproject.toml

@@ -55,4 +55,4 @@ canfar_monitor_log = "shapepipe.canfar_run:run_monitor_log"
 
 [tool.pytest.ini_options]
 addopts = "--verbose --cov=shapepipe"
-testpaths = ["shapepipe"]
+testpaths = ["tests", "src/shapepipe/tests"]

tests/conftest.py

@@ -0,0 +1,15 @@
+"""Shared pytest fixtures for the repository-level test suite."""
+
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture(scope="session")
+def repo_root() -> Path:
+    """Absolute path to the repository root.
+
+    Tests live at ``<root>/tests/``, so the root is two parents up
+    from this conftest file.
+    """
+    return Path(__file__).resolve().parent.parent

tests/unit/test_config_parse.py

@@ -0,0 +1,34 @@
+"""Every example INI config must parse as a valid configparser file.
+
+Uses ``RawConfigParser`` so ``$SP_RUN``-style variable references don't
+trigger interpolation errors. This catches malformed section headers,
+duplicate keys within a section, and missing ``=``/``:`` separators.
+"""
+
+import configparser
+from pathlib import Path
+
+import pytest
+
+
+def _config_files(root: Path) -> list[Path]:
+    return sorted((root / "example").rglob("*.ini"))
+
+
+def pytest_generate_tests(metafunc):
+    if "config_path" in metafunc.fixturenames:
+        root = Path(__file__).resolve().parents[2]
+        configs = _config_files(root)
+        metafunc.parametrize(
+            "config_path",
+            configs,
+            ids=[str(p.relative_to(root)) for p in configs],
+        )
+
+
+def test_config_parses(config_path: Path) -> None:
+    parser = configparser.RawConfigParser(strict=True)
+    parser.read(config_path, encoding="utf-8")
+    assert parser.sections(), (
+        f"{config_path} parsed but has no sections — likely malformed"
+    )

tests/unit/test_entrypoints.py

@@ -0,0 +1,77 @@
+"""Every ``[project.scripts]`` entry must resolve and handle ``-h`` cleanly.
+
+The test skips entries whose command isn't on PATH — that's an install
+concern, not a code concern. When a command *is* installed, ``-h``
+must exit 0 or 2 (argparse's help exit code) with non-empty output.
+This catches entry points whose target function treats ``-h`` as a
+positional argument, or whose argparser is initialised so late the
+help flag never runs.
+"""
+
+import shutil
+import subprocess
+import tomllib
+from pathlib import Path
+
+import pytest
+
+# Entry points known to mishandle ``-h`` — tracked via ``xfail`` so the
+# suite stays green and the issue is discoverable once fixed.
+KNOWN_XFAIL = {
+    "summary_run":
+        "treats '-h' as the 'patch' positional arg, tries to mkdir '-h'",
+    # All three import shapepipe.canfar_run, which fails with
+    # IndentationError in canfar_monitor.py:55.
+    "canfar_submit_job":
+        "IndentationError in canfar_monitor.py:55 (transitive)",
+    "canfar_monitor":
+        "IndentationError in canfar_monitor.py:55 (transitive)",
+    "canfar_monitor_log":
+        "IndentationError in canfar_monitor.py:55 (transitive)",
+}
+
+
+def _scripts_from_pyproject() -> dict[str, str]:
+    root = Path(__file__).resolve().parents[2]
+    pyproject = tomllib.loads((root / "pyproject.toml").read_text())
+    return pyproject.get("project", {}).get("scripts", {})
+
+
+def _params():
+    for name in sorted(_scripts_from_pyproject().keys()):
+        if name in KNOWN_XFAIL:
+            yield pytest.param(
+                name,
+                marks=pytest.mark.xfail(
+                    reason=KNOWN_XFAIL[name], strict=True, raises=Exception
+                ),
+            )
+        else:
+            yield name
+
+
+def pytest_generate_tests(metafunc):
+    if "script_name" in metafunc.fixturenames:
+        metafunc.parametrize("script_name", list(_params()))
+
+
+def test_entrypoint_help(script_name: str) -> None:
+    if shutil.which(script_name) is None:
+        pytest.skip(
+            f"{script_name} not on PATH — not installed in this env"
+        )
+    result = subprocess.run(
+        [script_name, "-h"],
+        capture_output=True,
+        text=True,
+        timeout=30,
+    )
+    # argparse help exits 0; some parsers use 2. Either is fine so
+    # long as *something* was printed, meaning the help path ran.
+    assert result.returncode in (0, 2), (
+        f"{script_name} -h exited {result.returncode}\n"
+        f"stdout: {result.stdout}\nstderr: {result.stderr}"
+    )
+    assert result.stdout or result.stderr, (
+        f"{script_name} -h produced no output"
+    )

tests/unit/test_imports.py

@@ -0,0 +1,88 @@
+"""Every public ``shapepipe.*`` submodule must import cleanly.
+
+Catches module-level syntax errors, typos in import paths, circular
+imports, and (crucially) the pattern where a module unconditionally
+imports an optional dependency — a ``try/except ImportError`` guard
+placed *after* a failing top-level import is unreachable.
+
+Assumes the shapepipe package and its declared dependencies are
+installed (the official container, or ``pip install -e .``).
+"""
+
+import importlib
+import pkgutil
+
+import pytest
+
+import shapepipe
+
+# Modules with known-broken transitive imports — tracked so the suite
+# lands green but the failure is discoverable and auto-notifies (via
+# ``strict=True``) once the upstream fix lands.
+KNOWN_XFAIL = {
+    # IndentationError at canfar_monitor.py:55 (docstring/body mismatch).
+    "shapepipe.canfar.canfar_monitor":
+        "IndentationError in canfar_monitor.py:55",
+    "shapepipe.canfar_run":
+        "IndentationError in canfar_monitor.py:55 (transitive)",
+    # stile v0.1 hard-imports treecorr.corr2, which newer treecorr removed.
+    "shapepipe.modules.mccd_package.mccd_plot_utilities":
+        "stile v0.1 imports removed treecorr.corr2",
+    "shapepipe.modules.mccd_plots_runner":
+        "stile v0.1 imports removed treecorr.corr2",
+    "shapepipe.modules.random_cat_package.random_cat":
+        "stile v0.1 imports removed treecorr.corr2",
+    "shapepipe.modules.random_cat_runner":
+        "stile v0.1 imports removed treecorr.corr2",
+    # Modules added in v1.x Dockerfile rewrites that import deps not in
+    # the develop image (astroquery, numba, fitsio) or removed from
+    # stdlib/setuptools (pkg_resources).
+    "shapepipe.modules.mask_package.mask":
+        "astroquery not in develop Docker image",
+    "shapepipe.modules.mask_runner":
+        "astroquery not in develop Docker image (transitive)",
+    "shapepipe.modules.ngmix_package.ngmix":
+        "numba not in develop Docker image",
+    "shapepipe.modules.ngmix_runner":
+        "numba not in develop Docker image (transitive)",
+    "shapepipe.modules.split_exp_package.split_exp":
+        "uses deprecated pkg_resources (setuptools>=68)",
+    "shapepipe.modules.split_exp_runner":
+        "uses deprecated pkg_resources (transitive)",
+    "shapepipe.modules.uncompress_fits_package.uncompress_fits":
+        "fitsio not installed (declared as optional extra)",
+    "shapepipe.modules.uncompress_fits_runner":
+        "fitsio not installed (transitive)",
+}
+
+
+def _iter_shapepipe_modules() -> list[str]:
+    return sorted(
+        m.name
+        for m in pkgutil.walk_packages(
+            shapepipe.__path__, prefix="shapepipe."
+        )
+        if "tests" not in m.name.split(".")
+    )
+
+
+def _params():
+    for name in _iter_shapepipe_modules():
+        if name in KNOWN_XFAIL:
+            yield pytest.param(
+                name,
+                marks=pytest.mark.xfail(
+                    reason=KNOWN_XFAIL[name], strict=True, raises=Exception
+                ),
+            )
+        else:
+            yield name
+
+
+def pytest_generate_tests(metafunc):
+    if "module_name" in metafunc.fixturenames:
+        metafunc.parametrize("module_name", list(_params()))
+
+
+def test_module_imports(module_name: str) -> None:
+    importlib.import_module(module_name)

tests/unit/test_runner_metadata.py

@@ -0,0 +1,93 @@
+"""Every ``*_runner.py`` module must export a function decorated with
+``@module_runner``.
+
+The decorator attaches introspection metadata the pipeline needs
+(``version``, ``input_module``, ``file_pattern``, ``file_ext``,
+``depends``, ``executes``, ``numbering_scheme``, ``run_method``). A new
+runner that forgets the decorator loads silently but fails at dispatch
+time. This test catches the oversight at import time.
+
+We locate the runner by looking for any top-level function that carries
+the metadata, since the function name doesn't always match the file
+name (e.g. ``pastecat_runner.py`` exports ``paste_cat_runner``).
+"""
+
+import importlib
+import inspect
+import pkgutil
+
+import pytest
+
+import shapepipe.modules
+
+REQUIRED_ATTRS = (
+    "version",
+    "input_module",
+    "file_pattern",
+    "file_ext",
+    "depends",
+    "executes",
+    "numbering_scheme",
+    "run_method",
+)
+
+# Modules imported here but broken upstream — tracked separately.
+# Mapping: module name → xfail reason.
+KNOWN_XFAIL = {
+    # Transitive failures: the runner's own import chain breaks before
+    # we can check metadata. Root causes tracked in test_imports.py.
+    "shapepipe.modules.mccd_plots_runner":
+        "stile v0.1 imports removed treecorr.corr2",
+    "shapepipe.modules.random_cat_runner":
+        "stile v0.1 imports removed treecorr.corr2",
+    "shapepipe.modules.mask_runner":
+        "astroquery not in develop Docker image",
+    "shapepipe.modules.ngmix_runner":
+        "numba not in develop Docker image",
+    "shapepipe.modules.split_exp_runner":
+        "uses deprecated pkg_resources (setuptools>=68)",
+    "shapepipe.modules.uncompress_fits_runner":
+        "fitsio not installed (declared as optional extra)",
+}
+
+
+def _runner_modules() -> list[str]:
+    return sorted(
+        m.name
+        for m in pkgutil.iter_modules(
+            shapepipe.modules.__path__, prefix="shapepipe.modules."
+        )
+        if m.name.endswith("_runner")
+    )
+
+
+def _params():
+    for name in _runner_modules():
+        if name in KNOWN_XFAIL:
+            yield pytest.param(
+                name,
+                marks=pytest.mark.xfail(
+                    reason=KNOWN_XFAIL[name], strict=True, raises=Exception
+                ),
+            )
+        else:
+            yield name
+
+
+def pytest_generate_tests(metafunc):
+    if "runner_module" in metafunc.fixturenames:
+        metafunc.parametrize("runner_module", list(_params()))
+
+
+def test_runner_has_metadata(runner_module: str) -> None:
+    mod = importlib.import_module(runner_module)
+    decorated = [
+        obj
+        for _, obj in inspect.getmembers(mod, inspect.isfunction)
+        if obj.__module__ == runner_module
+        and all(hasattr(obj, a) for a in REQUIRED_ATTRS)
+    ]
+    assert decorated, (
+        f"{runner_module} exports no function decorated with @module_runner "
+        f"(required attrs: {REQUIRED_ATTRS})"
+    )