Weekly literature reading list (Jev), tests for the Jev tools, maintenance tools documented

tests/unit/test_jev_tools.py

@@ -76,3 +76,29 @@ def test_known_findings_and_evidence(tmp_path: Path) -> None:
     assert ev["first_rows"][1] == "1\tGT" and "log" not in ev  # another step's log line must not leak in
     ev2 = tri.evidence(tmp_path, "t", {"verdict": "ERROR", "error": "exit 137"})
     assert ev2["log"] == ["pi_run: MemAvailable 500 MiB < 800 MiB -- stopping the job"]
+
+
+issue = _load("issue_triage")
+lit = _load("literature_watch")
+
+
+def test_issue_missing_info_and_comment() -> None:
+    body = "### SimurgArray version\n\n_No response_\n\n### Command\n\n```shell\nsimurg genotype\n```\n"
+    assert issue.missing_info(body, "bug") == ["the SimurgArray version"]
+    assert issue.missing_info(body.replace("_No response_", "2.0.0"), "bug") == []
+    assert issue.missing_info("no template at all", "feature") == []
+    d = {"kind": "security", "labels": ["kind/security"], "privacy": ["credentials"], "clinical": True,
+         "missing": []}  # fmt: skip
+    text = issue.comment_text(d)
+    assert "[email protected]" in text and "credentials" in text and "research tool" in text
+
+
+def test_literature_prefilter() -> None:
+    p = lit.Paper
+    papers = [
+        p("bioRxiv", "Fast genotype calling for Infinium arrays", "We call genotypes from IDAT files.", "u1", "d"),
+        p("PubMed", "Fast genotype calling for Infinium arrays!", "Duplicate title.", "u2", "d"),
+        p("bioRxiv", "Protein folding at scale", "Nothing about arrays here.", "u3", "d"),
+        p("bioRxiv", "No abstract", "", "u4", "d"),
+    ]
+    assert [x.url for x in lit.prefilter(papers)] == ["u1"]