Codex/paper progress and preview fixes

agents/workspace_layout.py

@@ -93,6 +93,26 @@ def _migrate_legacy_idea_workspace(workspace_root: Path) -> None:
         shutil.move(str(legacy_exp), str(suite_main))
 
 
+def _ensure_dir_or_current_link(path: Path) -> None:
+    """Create a directory unless the path is already a symlink/current pointer.
+
+    ``current`` paths are allowed to be:
+    - a real directory
+    - a symlink to the canonical run / paper dir
+    - a placeholder directory later populated with ``CURRENT_RUN.txt``
+
+    ``Path.mkdir(exist_ok=True)`` still raises ``FileExistsError`` on symlinks
+    on some runtimes, so we special-case them here.
+    """
+    if path.is_symlink():
+        return
+    if path.exists():
+        if path.is_dir():
+            return
+        raise FileExistsError(f"Workspace path exists and is not a directory: {path}")
+    path.mkdir(parents=True, exist_ok=True)
+
+
 def _resolve_suite_for_run(run_id: int) -> str:
     row = db.fetchone("SELECT experiment_suite FROM experiment_runs WHERE id=?", (int(run_id),))
     if row:
@@ -137,14 +157,14 @@ def get_idea_workspace(insight_id: int, insight: dict | None = None, *, create:
         "canonical_run_id": insight.get("canonical_run_id"),
     }
     if create:
-        workspace_root.mkdir(parents=True, exist_ok=True)
-        plan_root.mkdir(parents=True, exist_ok=True)
+        _ensure_dir_or_current_link(workspace_root)
+        _ensure_dir_or_current_link(plan_root)
         for key in ("paper_root", "paper_current_root", "paper_bundles_root", "paper_manifests_root"):
-            Path(layout[key]).mkdir(parents=True, exist_ok=True)
-        experiments_root.mkdir(parents=True, exist_ok=True)
+            _ensure_dir_or_current_link(Path(layout[key]))
+        _ensure_dir_or_current_link(experiments_root)
         for suite in KNOWN_EXPERIMENT_SUITES:
-            (experiments_root / suite / "runs").mkdir(parents=True, exist_ok=True)
-            (experiments_root / suite / "current").mkdir(parents=True, exist_ok=True)
+            _ensure_dir_or_current_link(experiments_root / suite / "runs")
+            _ensure_dir_or_current_link(experiments_root / suite / "current")
 
     if sync_db and insight.get("id") is not None:
         desired = {
@@ -197,10 +217,10 @@ def ensure_run_workspace(
         "spec_root": run_root / "spec",
         "codex_root": run_root / "codex",
     }
-    suite_runs_root.mkdir(parents=True, exist_ok=True)
-    suite_current_root.mkdir(parents=True, exist_ok=True)
+    _ensure_dir_or_current_link(suite_runs_root)
+    _ensure_dir_or_current_link(suite_current_root)
     for key in ("run_root", "code_root", "results_root", "spec_root", "codex_root"):
-        Path(info[key]).mkdir(parents=True, exist_ok=True)
+        _ensure_dir_or_current_link(Path(info[key]))
     return info
 
 

pyproject.toml

@@ -18,6 +18,7 @@ dependencies = [
   "numpy>=1.26",
   "pydantic>=2.0",
   "pymupdf>=1.24",
+  "PyYAML>=6.0",
   "waitress>=3.0",
 ]
 keywords = ["knowledge-graph", "science", "literature-mining", "arxiv", "research-ideas", "open-science"]

requirements.txt

@@ -5,4 +5,5 @@ pymupdf>=1.24
 psycopg[binary]>=3.1
 matplotlib>=3.8
 numpy>=1.26
+PyYAML>=6.0
 waitress>=3.0

tests/test_workspace_layout.py

@@ -79,6 +79,22 @@ def test_promote_canonical_run_falls_back_to_marker_when_current_dir_locked(self
         self.assertTrue(marker.exists())
         self.assertEqual(marker.read_text(encoding="utf-8"), str(layout["run_root"]))
 
+    def test_get_idea_workspace_tolerates_existing_current_symlink(self):
+        database.execute("INSERT INTO deep_insights (id, tier, title) VALUES (1, 2, 'Idea Workspace')")
+        database.commit()
+
+        root = self.workspace_root / "idea_1"
+        target = root / "legacy_target"
+        target.mkdir(parents=True, exist_ok=True)
+        current_link = root / "experiments" / "main" / "current"
+        current_link.parent.mkdir(parents=True, exist_ok=True)
+        current_link.symlink_to(target, target_is_directory=True)
+
+        layout = workspace_layout.get_idea_workspace(1)
+
+        self.assertTrue(Path(layout["experiment_current_root"]).is_symlink())
+        self.assertEqual(Path(layout["experiment_current_root"]).resolve(), target.resolve())
+
     def test_backfill_script_maps_legacy_run_and_manuscript_dirs(self):
         legacy_run = Path(self.tmpdir.name) / "legacy_run"
         (legacy_run / "code").mkdir(parents=True, exist_ok=True)

web/static/css/style.css

@@ -900,6 +900,76 @@ header#topBar {
     overflow-y: auto;
 }
 
+.paper-mini-stats {
+    margin-bottom: 14px;
+}
+
+.stat-card-mini {
+    min-height: 86px;
+}
+
+.paper-flow-list {
+    display: flex;
+    flex-direction: column;
+    gap: 10px;
+}
+
+.paper-flow-item {
+    border: 1px solid var(--border);
+    background: var(--bg-card);
+    border-radius: var(--radius);
+    padding: 14px 16px;
+    transition: border-color var(--transition), background var(--transition), transform var(--transition);
+}
+
+.paper-flow-item:hover {
+    border-color: var(--border-hover);
+    background: var(--bg-card-hover);
+    transform: translateY(-1px);
+}
+
+.paper-flow-head {
+    display: flex;
+    justify-content: space-between;
+    align-items: flex-start;
+    gap: 12px;
+    margin-bottom: 8px;
+}
+
+.paper-flow-title {
+    font-size: 0.9rem;
+    font-weight: 600;
+    color: var(--text-primary);
+    line-height: 1.45;
+}
+
+.paper-flow-meta {
+    display: flex;
+    flex-wrap: wrap;
+    gap: 12px;
+    color: var(--text-dim);
+    font-size: 0.72rem;
+    margin-bottom: 8px;
+}
+
+.paper-flow-note {
+    color: var(--text-secondary);
+    font-size: 0.78rem;
+    line-height: 1.6;
+    margin-top: 6px;
+}
+
+.paper-flow-error {
+    color: var(--red);
+}
+
+.paper-flow-actions {
+    display: flex;
+    flex-wrap: wrap;
+    gap: 8px;
+    margin-top: 12px;
+}
+
 .paper-row {
     padding: 12px 14px;
     border-radius: 8px;