Make the test suite use this repo's compiled helpers

CHANGELOG.md

@@ -14,6 +14,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   `pathway --method gsea` — the default — now works from a pip/source install.
 - Pathway smoke tests (`pathway --method gsea` and `--method rra`, end to end)
   and a small GMT test fixture.
+- `tests/conftest.py`, which puts this repository's freshly built `RRA` and
+  `mageckGSEA` first on `PATH` when they exist. The suite invokes the helpers by
+  bare name, so under an editable install — which never runs the compile step —
+  it silently tested whichever build came first, including a MAGeCK v1 package's
+  identically named binaries. That reported four `mageckGSEA` failures against
+  fixes present in the checkout, with nothing in the output naming the binary as
+  the cause. The override applies in CI too, since `pip install .` leaves the
+  build outputs in the source tree alongside the copies `data_files` installs;
+  so the two tests that assert the helpers are *installed* now look at the PATH
+  as it stood before the override, keeping a broken installation from passing.
 - `count` writes `<prefix>.pg_unmapped.txt` when `--unmapped-to-file` is given in
   paired-guide mode, recording pairs that were counted but excluded from
   `pg_count.txt` — because the second guide matched no entry in `--list-seq-2`,

tests/conftest.py

@@ -0,0 +1,52 @@
+"""Test configuration for MAGeCK2.
+
+The suite shells out to the bundled C++ helpers by bare name (``RRA``,
+``mageckGSEA``), so it exercises whichever build happens to come first on PATH.
+That is the correct binary after ``pip install .`` -- setup.py compiles the
+helpers and installs them alongside the package -- but not during ordinary local
+development: an editable install never runs that build step, and a MAGeCK v1
+package in the same environment ships commands with the *same names*. The suite
+then silently tests v1's binaries and reports failures against fixes that are
+present in this checkout, which is confusing and points nowhere useful.
+
+Put this repository's own freshly built helpers first on PATH when they exist,
+so the tests always describe this checkout.
+
+Note this override applies in CI too: ``pip install .`` runs ``make`` in the
+source tree, so the build outputs are present there alongside the copies
+``data_files`` installs. The installed copies would then never be exercised, and
+a regression in helper installation could pass CI even though an installed
+MAGeCK2 cannot find its helpers. To keep that coverage, the PATH as it stood
+before this hook ran is published as ``MAGECK2_INSTALLED_PATH``, and the tests
+asserting the helpers are installed look there rather than at the build tree.
+"""
+
+import os
+from pathlib import Path
+
+REPO_ROOT = Path(__file__).resolve().parent.parent
+
+# (binary name, directory the Makefile writes it to)
+HELPER_BIN_DIRS = [
+    ("RRA", REPO_ROOT / "rra" / "bin"),
+    ("mageckGSEA", REPO_ROOT / "gsea" / "bin"),
+]
+
+
+#: The PATH before this hook ran -- i.e. where an *installed* MAGeCK2 finds its
+#: helpers. Published so tests can assert on the installation rather than on the
+#: build tree that gets prepended below.
+INSTALLED_PATH_ENV = "MAGECK2_INSTALLED_PATH"
+
+
+def pytest_configure(config):
+    """Prepend repo-built helper directories to PATH, most specific first."""
+    os.environ.setdefault(INSTALLED_PATH_ENV, os.environ.get("PATH", ""))
+
+    prefix = []
+    for name, bindir in HELPER_BIN_DIRS:
+        if (bindir / name).is_file():
+            prefix.append(str(bindir))
+
+    if prefix:
+        os.environ["PATH"] = os.pathsep.join(prefix + [os.environ.get("PATH", "")])

tests/test_smoke.py

@@ -7,6 +7,7 @@
 push in CI.
 """
 
+import os
 import shutil
 import subprocess
 from pathlib import Path
@@ -24,14 +25,29 @@ def test_package_imports():
     assert __version__
 
 
+def _installed_path():
+    """The PATH as it stood before conftest prepended this repo's build tree.
+
+    The rest of the suite deliberately tests the checkout's own helpers. These
+    two tests are the exception: they check that an *installed* MAGeCK2 can find
+    its helpers, which is what `data_files` is responsible for and what a user
+    running `pip install mageck2` depends on. Looking at the build tree here
+    would let a broken installation pass CI, since `pip install .` leaves the
+    build outputs in the source tree as well.
+    """
+    return os.environ.get("MAGECK2_INSTALLED_PATH", os.environ.get("PATH", ""))
+
+
 def test_rra_binary_on_path():
-    assert shutil.which("RRA") is not None, "compiled RRA binary not found on PATH"
+    assert (
+        shutil.which("RRA", path=_installed_path()) is not None
+    ), "compiled RRA binary not installed onto PATH"
 
 
 def test_mageckgsea_binary_on_path():
     assert (
-        shutil.which("mageckGSEA") is not None
-    ), "compiled mageckGSEA binary not found on PATH"
+        shutil.which("mageckGSEA", path=_installed_path()) is not None
+    ), "compiled mageckGSEA binary not installed onto PATH"
 
 
 def test_mageck2_cli_runs():