fix: Testisolation - kb_dir repointet config.ROOT, lint loest Kollektionen gegen den uebergebenen Baum auf (4.1.1, #44)

Files changed:
- CHANGES.md
- VERSION
- instructions/dev/testing-conventions.md
- tools/chemenu/lint_core.py
- tools/chemenu/tests/conftest.py
- tools/chemenu/tests/test_hermetic_env.py
- tools/chemenu/tests/test_lint.py

tools/chemenu/lint_core.py

@@ -165,9 +165,15 @@ def run_lint(kb_dir: Path) -> dict:
     # propagated, a deleted page, or a URL pasted where a title belongs - used
     # to pass every check. Which fields hold page titles is declared by each
     # type-spec's `page_ref_fields:`, not hardcoded here.
+    # Resolved against the directory `run_lint()` was handed, not against
+    # `config.KB_DIR`. A page under a tree that is not the configured corpus -
+    # every fixture tree, and any `lint <path>` aimed elsewhere - raised
+    # `ValueError` here and read as "no collection", which made the label
+    # authorisation below skip the edge in silence rather than judge it
+    # (Gitea #44).
     def _collection_of(page):
         try:
-            return page.path.relative_to(config.KB_DIR).parts[0]
+            return page.path.relative_to(kb_dir).parts[0]
         except (ValueError, IndexError):
             return None
 
@@ -211,7 +217,9 @@ def run_lint(kb_dir: Path) -> dict:
                 destination = _collection_of(target_page)
                 if destination is None:
                     continue
-                allowed = kb_collections.authorised_labels(source_collection, destination)
+                allowed = kb_collections.authorised_labels(
+                    source_collection, destination, kb_dir
+                )
                 if edge.label not in allowed:
                     unauthorised_labels.append(
                         {

tools/chemenu/tests/conftest.py

@@ -1,4 +1,5 @@
 import os
+import subprocess
 from pathlib import Path
 
 import pytest
@@ -37,6 +38,78 @@ _GIT_ENV = (
 )
 
 
+def _working_tree_state() -> str | None:
+    """`git status --porcelain` for the checkout the tests live in, or None if
+    there is no git available to ask."""
+    try:
+        result = subprocess.run(
+            ["git", "-C", str(config._PACKAGE_ROOT), "status", "--porcelain"],
+            capture_output=True,
+            text=True,
+            timeout=60,
+        )
+    except (OSError, subprocess.SubprocessError):
+        return None
+    return result.stdout if result.returncode == 0 else None
+
+
+_TREE_GUARD_MESSAGE = (
+    "A test wrote into the repository checkout instead of into its tmp_path.\n"
+    "`git status --porcelain` moved while the suite ran:\n\n"
+    "  before:\n{before}\n"
+    "  after:\n{after}\n\n"
+    "This is the class of bug Gitea #44 describes: code under test resolves a "
+    "path through `config.ROOT`/`config.KB_DIR` rather than through the "
+    "directory the fixture handed it, so the write lands in the real tree. Fix "
+    "the fixture (repoint `config.ROOT`, as `raw_dir` and `kb_dir` do) or the "
+    "code path, never the symptom.\n"
+    "To find the test that did it, re-run with CHEMENU_TREE_GUARD=each - the "
+    "guard then checks after every test and fails on the first one that moves "
+    "the tree."
+)
+
+
+@pytest.fixture(scope="session", autouse=True)
+def repository_tree_guard():
+    """Fail the run if the suite moved a file in the real checkout.
+
+    Two `git status` calls for the whole session, which is why this is on by
+    default: it catches the whole class rather than the one case that was
+    noticed. It compares before against after rather than demanding a clean
+    tree, so it says nothing about a developer's own uncommitted work.
+
+    It cannot name the culprit - set `CHEMENU_TREE_GUARD=each` for that, which
+    trades a `git status` per test for a failure on the test that did it.
+    """
+    before = _working_tree_state()
+    yield
+    after = _working_tree_state()
+    if before is None or after is None or before == after:
+        return
+    raise AssertionError(
+        _TREE_GUARD_MESSAGE.format(before=before or "(clean)", after=after or "(clean)")
+    )
+
+
+@pytest.fixture(autouse=True)
+def per_test_tree_guard(repository_tree_guard):
+    """The bisect half of `repository_tree_guard`, off unless asked for.
+
+    `CHEMENU_TREE_GUARD=each` turns the session-wide "something moved the tree"
+    into "this test moved the tree", at the cost of a `git status` per test.
+    """
+    if os.environ.get("CHEMENU_TREE_GUARD") != "each":
+        yield
+        return
+    before = _working_tree_state()
+    yield
+    after = _working_tree_state()
+    if before is not None and after is not None and before != after:
+        raise AssertionError(
+            _TREE_GUARD_MESSAGE.format(before=before or "(clean)", after=after or "(clean)")
+        )
+
+
 @pytest.fixture(autouse=True)
 def hermetic_environment(tmp_path: Path, monkeypatch: pytest.MonkeyPatch):
     """Cut every test off from the machine it runs on.
@@ -159,13 +232,25 @@ def raw_dir(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> Path:
 
 
 @pytest.fixture
-def kb_dir(tmp_path: Path) -> Path:
+def kb_dir(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> Path:
     """A minimal fixture kb/ with the standard collection layout, populated
     with a handful of pages covering entities/concepts/sources/comparisons.
 
     Every collection carries a COLLECTION.md, both because that is what makes it
     a collection and because the scanner must prove it skips them at a depth the
-    kb-root meta files never reach."""
+    kb-root meta files never reach.
+
+    `config.ROOT` is repointed for the same reason `raw_dir` does it, one
+    collection over: code under test that resolves a path through
+    `config.ROOT`/`config.KB_DIR` rather than through the directory it was
+    handed otherwise reaches the *real* repository. That was not theoretical
+    either - a test calling `kb_state.write_kb_state()` overwrote this
+    checkout's `.wikitool-kb.json`, and `lint`'s collection lookup answered
+    "no collection" for every fixture page, which left `unauthorised_labels`
+    with no working test at all (Gitea #44).
+    """
+    monkeypatch.setattr(config, "ROOT", tmp_path)
+    use_shipped_type_specs(monkeypatch)
     kb = tmp_path / "kb"
     for sub in ("entities/projects", "entities/systems", "entities/tools",
                 "entities/technologies", "entities/people",

tools/chemenu/tests/test_hermetic_env.py

@@ -74,3 +74,23 @@ def test_wiki_author_overrides_the_git_identity(tmp_path: Path,
     monkeypatch.setattr(config, "ROOT", tmp_path)
     monkeypatch.setenv("WIKI_AUTHOR", "Env Override")
     assert config.default_author() == "Env Override"
+
+
+def test_kb_dir_repoints_the_configured_root_at_its_own_tree(kb_dir: Path, tmp_path: Path):
+    """The other half of the isolation, and the one `kb_dir` was missing until
+    Gitea #44: a fixture that builds a corpus but leaves `config.ROOT` on the
+    real checkout hands every `config.KB_DIR` lookup the developer's own wiki -
+    which is how a test overwrote the repository's `.wikitool-kb.json`."""
+    assert config.ROOT == tmp_path
+    assert config.KB_DIR == kb_dir
+
+
+def test_raw_dir_repoints_the_configured_root_at_its_own_tree(raw_dir: Path, tmp_path: Path):
+    assert config.ROOT == tmp_path
+    assert config.RAW_DIR == raw_dir
+
+
+def test_both_corpus_fixtures_keep_the_shipped_type_specs_reachable(kb_dir: Path):
+    """Repointing `ROOT` moves `TYPES_DIR` with it, so the repoint has to be
+    paired with `use_shipped_type_specs()` or no page type resolves at all."""
+    assert (config.TYPES_DIR / "entity.md").is_file()

tools/chemenu/tests/test_lint.py

@@ -15,7 +15,6 @@ from chemenu.commands.lint import (
 )
 from chemenu.frontmatter_io import write_page
 from chemenu.provenance import cite_id, render_cite_block
-from chemenu.tests.conftest import use_shipped_type_specs
 from chemenu.version import Version
 
 
@@ -482,26 +481,18 @@ def test_lint_does_not_count_a_shell_prompt_as_a_quote(kb_dir):
 
 # --- the migration gate on `unlabelled_edges` / `unauthorised_labels` -------
 #
-# These four repoint `config.ROOT` at the fixture tree, which the `kb_dir`
-# fixture alone does not do. Two things need it: `write_kb_state()` writes
-# `.wikitool-kb.json` relative to `ROOT`, and `lint`'s collection lookup
-# resolves a page against `config.KB_DIR` rather than against the directory it
-# was handed - so without the repoint the gate would be read off the real
-# repository's state file.
+# These read and write `.wikitool-kb.json`, which `kb_state` resolves relative
+# to `config.ROOT`. The `kb_dir` fixture repoints `ROOT` at its own tmp_path
+# (Gitea #44), so the gate is read off the fixture tree; before it did, these
+# four ran against the real repository's state file and one of them overwrote
+# it.
 
 
-@pytest.fixture
-def rooted_kb(kb_dir, tmp_path, monkeypatch):
-    monkeypatch.setattr(config, "ROOT", tmp_path)
-    use_shipped_type_specs(monkeypatch)
-    return kb_dir
-
-
-def _page_with_an_unlabelled_edge(rooted_kb):
+def _page_with_an_unlabelled_edge(kb_dir):
     """A `related:` entry that is a bare title rather than a `label: title`
     mapping - the shape every page was in before the 4.0.0 migration."""
     write_page(
-        rooted_kb / "entities/tools/bare-edge.md",
+        kb_dir / "entities/tools/bare-edge.md",
         {"type": "types/entity.md", "entity_type": "tool", "tags": [], "created": "2026-09-03",
          "modified": "2026-09-03", "related": ["Modbus"], "sources": [], "confidence": 0.8,
          "provenance": "general", "summary": "One edge whose label was never declared."},
@@ -509,14 +500,14 @@ def _page_with_an_unlabelled_edge(rooted_kb):
     )
 
 
-def test_unlabelled_edge_is_advisory_below_kb_version_4(rooted_kb):
+def test_unlabelled_edge_is_advisory_below_kb_version_4(kb_dir):
     """The window the migration document describes: the machinery has landed,
     the corpus has not been converted yet, and `lint --fail-on-error` must not
     refuse the very tree the migration tells the instance to publish unit by
     unit."""
-    _page_with_an_unlabelled_edge(rooted_kb)
+    _page_with_an_unlabelled_edge(kb_dir)
     kb_state.write_kb_state(Version(3, 0, 0), [])
-    report = run_lint(rooted_kb)
+    report = run_lint(kb_dir)
     assert report["unlabelled_edges"] != []
     assert "unlabelled_edges" not in hard_error_keys()
     # Narrowed to the finding under test: the fixture corpus carries unrelated
@@ -525,34 +516,64 @@ def test_unlabelled_edge_is_advisory_below_kb_version_4(rooted_kb):
     assert has_hard_errors({"unlabelled_edges": report["unlabelled_edges"]}) is False
 
 
-def test_unlabelled_edge_is_hard_at_kb_version_4(rooted_kb):
+def test_unlabelled_edge_is_hard_at_kb_version_4(kb_dir):
     """Once the migration is recorded, a bare title is no longer a page waiting
     its turn - it is an edge whose author did not say what it asserts."""
-    _page_with_an_unlabelled_edge(rooted_kb)
+    _page_with_an_unlabelled_edge(kb_dir)
     kb_state.write_kb_state(Version(4, 0, 0), [])
-    report = run_lint(rooted_kb)
+    report = run_lint(kb_dir)
     assert report["unlabelled_edges"] != []
     assert "unlabelled_edges" in hard_error_keys()
     assert has_hard_errors({"unlabelled_edges": report["unlabelled_edges"]}) is True
 
 
-def test_unauthorised_label_is_hard_at_kb_version_4(rooted_kb):
+def test_unauthorised_label_is_hard_at_kb_version_4(kb_dir):
     """The fixture contracts authorise `depends-on` but not `contradicts`."""
     write_page(
-        rooted_kb / "entities/tools/off-menu.md",
+        kb_dir / "entities/tools/off-menu.md",
         {"type": "types/entity.md", "entity_type": "tool", "tags": [], "created": "2026-09-03",
          "modified": "2026-09-03", "related": [{"contradicts": "Modbus"}], "sources": [],
          "confidence": 0.8, "provenance": "general", "summary": "A label off this menu."},
         "\n# off-menu\n\nA label the source collection never authorised.\n",
     )
     kb_state.write_kb_state(Version(4, 0, 0), [])
-    report = run_lint(rooted_kb)
+    report = run_lint(kb_dir)
     assert report["unauthorised_labels"] != []
     assert "unauthorised_labels" in hard_error_keys()
     assert has_hard_errors({"unauthorised_labels": report["unauthorised_labels"]}) is True
 
 
-def test_a_tree_that_never_declared_a_kb_version_keeps_every_key(rooted_kb):
+def test_unauthorised_label_is_judged_in_a_tree_that_is_not_the_configured_kb(
+    kb_dir, tmp_path, monkeypatch
+):
+    """`run_lint()` judges the tree it was handed, not the configured corpus.
+
+    The collection lookup used to resolve a page against `config.KB_DIR`; a
+    page anywhere else raised `ValueError`, read back as "no collection", and
+    the label check skipped the edge without a word. That is why
+    `unauthorised_labels` was untested in practice before Gitea #44 - every
+    fixture tree was somewhere else. Here `ROOT` deliberately points away from
+    the tree under lint, which is the case the old code got wrong.
+    """
+    write_page(
+        kb_dir / "entities/tools/off-menu.md",
+        {"type": "types/entity.md", "entity_type": "tool", "tags": [], "created": "2026-09-03",
+         "modified": "2026-09-03", "related": [{"contradicts": "Modbus"}], "sources": [],
+         "confidence": 0.8, "provenance": "general", "summary": "A label off this menu."},
+        "\n# off-menu\n\nA label the source collection never authorised.\n",
+    )
+    elsewhere = tmp_path / "elsewhere"
+    elsewhere.mkdir()
+    monkeypatch.setattr(config, "ROOT", elsewhere)
+    assert config.KB_DIR != kb_dir
+
+    report = run_lint(kb_dir)
+    assert {
+        "page": "off-menu", "target": "Modbus", "label": "contradicts", "destination": "concepts"
+    } in report["unauthorised_labels"]
+
+
+def test_a_tree_that_never_declared_a_kb_version_keeps_every_key(kb_dir):
     """No `.wikitool-kb.json` means a fresh instance, which starts at the
     current shape rather than migrating into it - so there is no outstanding
     migration for a gated finding to be the noise of."""