@iowarp/clio-coder 0.4.5 → 0.4.7

package/library/plugins/materio/tests/test_verify_citations.py

@@ -0,0 +1,337 @@
+#!/usr/bin/env python3
+"""
+Unit tests for the citation verifier. No network — Crossref lookups are
+monkeypatched — so these run deterministically in CI and lock in the
+extraction/classification precision the tool was tuned for.
+
+Run:  python3 tests/test_verify_citations.py     (or: python3 -m unittest)
+"""
+import importlib.util
+import os
+import unittest
+
+_HERE = os.path.dirname(os.path.abspath(__file__))
+_MOD = os.path.join(_HERE, "..", "assets", "scripts",
+                    "verify_citations.py")
+_spec = importlib.util.spec_from_file_location("verify_citations", _MOD)
+vc = importlib.util.module_from_spec(_spec)
+_spec.loader.exec_module(vc)
+
+
+def item(title, year=None, doi="10.0/x", families=()):
+    d = {"title": [title], "DOI": doi,
+         "author": [{"family": f} for f in families]}
+    if year:
+        d["issued"] = {"date-parts": [[year]]}
+    return d
+
+
+KEY_PAPERS_HDR = "## Key Papers\n| Paper | Year | Why Important |\n|---|---|---|\n"
+
+
+class TestExtraction(unittest.TestCase):
+    def test_table_row_title_extracted(self):
+        md = ('## Key Papers\n'
+              '| Tang M., Pistorius P.C., *Additive Manufacturing* 14 — '
+              '"Prediction of lack-of-fusion porosity for powder bed fusion" '
+              '| 2017 | key |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(len(cites), 1)
+        self.assertIn("lack-of-fusion", cites[0].title)
+        self.assertEqual(cites[0].year, "2017")
+
+    def test_prose_emphasis_not_extracted(self):
+        # Quoted emphasis + a citation year + a markdown italic, but no table:
+        # must NOT be treated as a paper title.
+        md = ('VED as a *single* design parameter was shown to "fail to '
+              'capture melt-pool physics" by several groups in 2017.\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(cites, [])
+
+    def test_placeholder_inline_key_detected(self):
+        md = "Recent work [ML domain-discovery 2024] confirms interest.\n"
+        _, placeholders = vc.extract_markdown(md, "x.md")
+        self.assertEqual(len(placeholders), 1)
+
+    def test_bibtex_extraction(self):
+        bib = ('@article{k, title={A Real Title Here}, author={Doe, Jane}, '
+               'year={2020}, doi={10.1/abc}\n}\n')
+        cites = vc.extract_bibtex(bib, "r.bib")
+        self.assertEqual(len(cites), 1)
+        self.assertEqual(cites[0].doi, "10.1/abc")
+
+    # -- (a) truncated / prefix duplicates -----------------------------------
+
+    def test_ellipsis_truncated_title_dropped(self):
+        md = (KEY_PAPERS_HDR +
+              '| "On the limitations of Volumetric Energy Density as a design '
+              'parameter for Selective Laser Melting" | 2017 | x |\n'
+              '\n## References\n| Ref | Year |\n|---|---|\n'
+              '| "On the limitations of Volumetric Energy Density..." | 2017 |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(len(cites), 1)
+        self.assertTrue(cites[0].title.endswith("Selective Laser Melting"))
+
+    def test_ellipsis_title_dropped_even_without_fuller_candidate(self):
+        md = ('## References\n| Ref | Year |\n|---|---|\n'
+              '| "Keyhole fluctuation and pore formation mechanisms…" | 2022 |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(cites, [])
+
+    def test_distinct_complete_prefix_title_preserved(self):
+        md = (KEY_PAPERS_HDR +
+              '| "Keyhole fluctuation and pore formation mechanisms during '
+              'laser powder bed fusion" | 2022 | x |\n'
+              '\n## References\n| Ref | Year |\n|---|---|\n'
+              '| "Keyhole fluctuation and pore formation mechanisms" | 2022 |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual([c.title for c in cites],
+                         ["Keyhole fluctuation and pore formation mechanisms "
+                          "during laser powder bed fusion",
+                          "Keyhole fluctuation and pore formation mechanisms"])
+
+    def test_complete_prefix_titles_preserved_across_files(self):
+        full = vc.Cite(title="A long paper title about keyhole porosity")
+        short = vc.Cite(title="A long paper title about keyhole")
+        other = vc.Cite(title="A different paper about lack of fusion")
+        kept = vc.dedup_truncated([short, full, other])
+        self.assertEqual([c.title for c in kept], [short.title, full.title, other.title])
+
+    # -- (b) authors only from a real author list -----------------------------
+
+    def test_authors_from_et_al_prefix(self):
+        md = (KEY_PAPERS_HDR +
+              '| King W.E. et al. "Observation of keyhole-mode laser melting '
+              'in LPBF" | 2014 | x |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(cites[0].authors, "King W.E. et al.")
+
+    def test_authors_from_surname_and_surname_prefix(self):
+        md = (KEY_PAPERS_HDR +
+              '| W.E. King and R. Smith, "Observation of keyhole-mode laser '
+              'melting in LPBF" | 2014 | x |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(cites[0].authors, "W.E. King and R. Smith")
+
+    def test_authors_from_initials_list_prefix(self):
+        md = (KEY_PAPERS_HDR +
+              '| Tang M., Pistorius P.C., *Additive Manufacturing* 14 — '
+              '"Prediction of lack-of-fusion porosity for powder bed fusion" '
+              '| 2017 | key |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(cites[0].authors, "Tang M., Pistorius P.C.")
+
+    def test_title_first_row_has_no_authors(self):
+        # The literature agent's usual row: the quoted title starts the cell,
+        # followed by a journal. Nothing here is an author string.
+        md = (KEY_PAPERS_HDR +
+              '| "Assessing Volumetric Energy Density as a Predictor of '
+              'Defects" (*JOM*) | 2024 | Recent, rigorous test |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(len(cites), 1)
+        self.assertIsNone(cites[0].authors)
+
+    def test_non_papers_table_never_derives_authors(self):
+        # A year-bearing row outside the Key Papers table: the first cell is
+        # prose with commas, which must not be sent to Crossref as authors.
+        md = ('## Datasets\n| Source | Notes |\n|---|---|\n'
+              '| Zenodo, Ti-6Al-4V | "Processing, microstructure, mechanical '
+              'property dataset for LPBF" (2023) |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(len(cites), 1)
+        self.assertIsNone(cites[0].authors)
+        self.assertEqual(cites[0].year, "2023")
+
+    # -- (c) which parts of the document are scanned --------------------------
+
+    def test_methodological_landscape_table_ignored(self):
+        md = ('## Methodological Landscape\n'
+              '| Approach | Strengths | Limitations | Key Papers |\n'
+              '|---|---|---|---|\n'
+              '| VED maps | Simple | Non-unique | "On the limitations of '
+              'Volumetric Energy Density..."; "Assessing Volumetric Energy '
+              'Density as a Predictor of Defects in LPBF 316L," *JOM* 2024 |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(cites, [])
+
+    def test_landscape_table_ignored_by_heading_when_no_separator(self):
+        md = ('## Methodological Landscape\n'
+              '| In-situ monitoring | "Keyhole fluctuation and pore formation '
+              'mechanisms during LPBF" (2022) |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(cites, [])
+
+    def test_other_table_row_needs_a_year(self):
+        md = ('## Sources\n| Source | Detail |\n|---|---|\n'
+              '| A | "A quoted phrase long enough to look like a title" |\n'
+              '| B | "Another quoted phrase long enough to be a title" 2021 |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual([c.year for c in cites], ["2021"])
+        self.assertIn("Another", cites[0].title)
+
+    def test_key_papers_row_extracted_without_year(self):
+        md = (KEY_PAPERS_HDR +
+              '| "Review of laser powder bed fusion fabricated Ti-6Al-4V" '
+              '| in press | x |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(len(cites), 1)
+        self.assertIsNone(cites[0].year)
+
+    def test_bibtex_block_in_markdown_extracted(self):
+        md = ('## References\n```bibtex\n'
+              '@article{tang2017, title={Prediction of lack-of-fusion porosity '
+              'for powder bed fusion}, author={Tang, Ming}, year={2017}, '
+              'doi={10.1016/j.addma.2016.12.001}\n}\n```\n'
+              'Prose quoting "a phrase long enough to look like a title" in 2017.\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(len(cites), 1)
+        self.assertEqual(cites[0].doi, "10.1016/j.addma.2016.12.001")
+        self.assertEqual(cites[0].year, "2017")
+
+    def test_year_taken_from_year_column_not_title(self):
+        md = (KEY_PAPERS_HDR +
+              '| "AM-Bench 2018 round-robin results for LPBF Ti-6Al-4V" '
+              '| 2020 | x |\n')
+        cites, _ = vc.extract_markdown(md, "x.md")
+        self.assertEqual(cites[0].year, "2020")
+
+
+class TestSurnames(unittest.TestCase):
+    def test_surname_first_format(self):
+        self.assertIn("king", vc._surnames("King W.E. et al."))
+
+    def test_surname_last_format(self):
+        self.assertIn("king", vc._surnames("W.E. King and R. Smith"))
+
+    def test_compound_surname(self):
+        s = vc._surnames("Scipioni Bertoli U. et al.")
+        self.assertIn("scipioni", s)
+        self.assertIn("bertoli", s)
+
+    def test_item_surnames_tokenizes_compound(self):
+        it = item("t", families=["Scipioni Bertoli"])
+        surns = vc._item_surnames(it)
+        self.assertIn("scipioni", surns)
+        self.assertIn("bertoli", surns)
+
+
+class TestClassification(unittest.TestCase):
+    # Tests patch the two Crossref functions; restore them so later test
+    # classes (and any other order) see the real implementations.
+    def setUp(self):
+        self._saved = (vc.crossref_by_title, vc.crossref_by_doi)
+
+    def tearDown(self):
+        vc.crossref_by_title, vc.crossref_by_doi = self._saved
+
+    def _title(self, c, patch_items):
+        vc.crossref_by_title = lambda *a, **k: patch_items
+        return vc.verify_one(c, offline=False)
+
+    def test_verified_exact(self):
+        c = vc.Cite(title="Prediction of lack-of-fusion porosity for PBF",
+                    year="2017")
+        status, _ = self._title(c, [item(
+            "Prediction of lack-of-fusion porosity for PBF", 2017)])
+        self.assertEqual(status, "VERIFIED")
+
+    def test_mismatch_by_year(self):
+        c = vc.Cite(title="A study of grain growth in nickel alloys",
+                    year="2010")
+        status, d = self._title(c, [item(
+            "A study of grain growth in nickel alloys", 2024)])
+        self.assertEqual(status, "MISMATCH")
+        self.assertIn("year", d["reason"])
+
+    def test_not_found(self):
+        c = vc.Cite(title="A totally unique fabricated paper title xyzzy")
+        status, _ = self._title(c, [item("Something completely different")])
+        self.assertEqual(status, "NOT_FOUND")
+
+    def test_abbreviated_title_rescued_by_author_year(self):
+        # Weak title similarity, but author surname + year corroborate.
+        c = vc.Cite(
+            title="Observation of keyhole-mode laser melting in LPBF",
+            year="2014", authors="King W.E. et al.")
+        matched = item(
+            "Observation of keyhole-mode laser melting in laser "
+            "powder-bed fusion additive manufacturing systems",
+            2014, families=["King"])
+        status, d = self._title(c, [matched])
+        self.assertEqual(status, "VERIFIED")
+        self.assertIn("author", d["reason"])
+
+    def test_no_results_not_found(self):
+        c = vc.Cite(title="Anything at all here")
+        status, _ = self._title(c, [])
+        self.assertEqual(status, "NOT_FOUND")
+
+    def test_network_error_unverifiable(self):
+        c = vc.Cite(title="Anything at all here")
+        vc.crossref_by_title = lambda *a, **k: None   # None == network failure
+        status, _ = vc.verify_one(c, offline=False)
+        self.assertEqual(status, "UNVERIFIABLE")
+
+    def test_other_agency_doi_is_unverifiable(self):
+        c = vc.Cite(title="Paper registered by another DOI agency", doi="10.9/other")
+        vc.crossref_by_doi = lambda doi: vc.DOI_ABSENT
+        status, d = vc.verify_one(c, offline=False)
+        self.assertEqual(status, "UNVERIFIABLE")
+        self.assertIn("another registration agency", d["reason"])
+
+    def test_offline_is_unverifiable(self):
+        c = vc.Cite(title="Any title", doi="10.1/x")
+        status, _ = vc.verify_one(c, offline=True)
+        self.assertEqual(status, "UNVERIFIABLE")
+
+    def test_no_title_is_unverifiable(self):
+        c = vc.Cite(title=None)
+        status, _ = vc.verify_one(c, offline=False)
+        self.assertEqual(status, "UNVERIFIABLE")
+
+
+class TestRetry(unittest.TestCase):
+    """_get retries once on 429/5xx; urlopen is the only thing patched."""
+
+    def _run(self, codes):
+        import io
+        import urllib.error
+        calls = []
+
+        def fake_urlopen(req, timeout=None):
+            calls.append(req.full_url)
+            code = codes[len(calls) - 1]
+            if code != 200:
+                raise urllib.error.HTTPError(req.full_url, code, "x", {}, None)
+            return io.BytesIO(b'{"message": {"items": []}}')
+
+        saved = (vc.urllib.request.urlopen, vc.RETRY_BACKOFF)
+        vc.urllib.request.urlopen, vc.RETRY_BACKOFF = fake_urlopen, 0
+        try:
+            return vc.crossref_by_title("Some title"), len(calls)
+        finally:
+            vc.urllib.request.urlopen, vc.RETRY_BACKOFF = saved
+
+    def test_503_then_ok_is_retried(self):
+        items, n = self._run([503, 200])
+        self.assertEqual(items, [])
+        self.assertEqual(n, 2)
+
+    def test_429_then_ok_is_retried(self):
+        items, n = self._run([429, 200])
+        self.assertEqual(items, [])
+        self.assertEqual(n, 2)
+
+    def test_second_failure_is_network_error(self):
+        items, n = self._run([503, 503])
+        self.assertIsNone(items)
+        self.assertEqual(n, 2)
+
+    def test_404_is_not_retried(self):
+        items, n = self._run([404, 200])
+        self.assertIsNone(items)
+        self.assertEqual(n, 1)
+
+
+if __name__ == "__main__":
+    unittest.main(verbosity=2)

package/library/prompts/README.md

@@ -0,0 +1,7 @@
+# Prompt Packages
+
+This directory hosts standalone prompt packages. A prompt package distributes reusable task text, parameterized instruction templates, and slash-command expansions.
+
+Internal and system prompt fragments remain built into Clio Coder under `src/domains/prompts/fragments/`.
+
+Community prompt package authoring templates and validator guidelines will be introduced in Slice 2 under `library/_authoring/templates/prompt/`.