fix: unbreakable Qt5/Qt6 enum bridge and task-type intro audit

CHANGELOG.md

@@ -341,6 +341,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   `GLIBC_2.38 not found` on dlopen.
 
 ### Fixed
+- **Task-type descriptions audited against the runner repos**: GREMLIN now
+  says sequence conservation (PSSM) plus co-evolutionary couplings (input is
+  a sequence; the MSA is an internal HHblits step, and no contact map is
+  produced). Pro-Prime is now
+  described as optimal growth temperature (OGT) prediction and moved from
+  `function` to `fitness`; ThermoMPNN-D is ΔΔG prediction for single/double
+  mutants (not sequence design); HyperMPNN is thermostable design from
+  hyperthermophile-trained weights; LASErMPNN is all-atom ligand-conditioned
+  design with sidechain packing for protonated structures; PLACER models
+  protein-ligand complexes from
+  an input structure (not structure prediction from sequence); OpenDDE is
+  all-atom prediction with MSA and template guidance.
+- **Standalone manager Qt6 enum bridge**: the package manager's Qt5/Qt6 compat
+  layer no longer allowlists the enum members it happens to use. It now
+  mirrors every scoped-enum member of every QtCore/QtGui/QtWidgets class onto
+  the owning class at import, so any Qt5-style unscoped access
+  (`QMessageBox.Ok`, `QFileDialog.DontResolveSymlinks`, ...) resolves on Qt6
+  without per-API bookkeeping. Previously unmapped members raised
+  AttributeError on Qt6 PyMOL builds (e.g. macOS).
 - **Mol* shell message dispatch**: load the isolated viewer shell script after
   its status and host elements exist. Previously the shell received structure
   messages but rejected before loading Mol* because its cached DOM nodes were

CLAUDE.md

@@ -53,12 +53,18 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 - **Test-case-driven fixes**: For live/integration issues, first encode the observed behavior as the smallest test case or skip guard, then make the smallest production/test change, run the focused keyword gate (for example `make kw-test PYTEST_KW=openkinetics`), and update `CHANGELOG.md`. Treat environment-dependent live API responses such as expected HTTP `4xx`/`5xx` as explicit skips, while keeping non-HTTP client errors failing.
 - **PR babysitting workflow** — after opening a PR, own it through the squash-merge marker:
   1. Work on a fix branch off `main`; conventional commit messages; never push to `main` directly.
-  2. Babysit CI until green, then read every bot review comment (codex, coderabbit, codacy, deepsource) and decide per comment: fix or debate — reply with evidence (file:line) when the code already handles it.
+  2. Babysit CI until green, then read every bot review comment from codex and
+     coderabbit and decide per comment: fix or debate — reply with evidence
+     (file:line) when the code already handles it. **DeepSource and Codacy are
+     ignored** — their check statuses and comments are noise (stylistic lint
+     profiles configured opposite to project conventions): don't fix, don't
+     debate, don't treat them as blocking. No branch protection gates on them.
+     Their findings get handled periodically in dedicated batch-fix PRs.
   3. **Server PRs** (`server/` — REvoCompute): deploy to the live SLURM server with `REVODESIGN_SERVER_ENV=/repo/REvoDesign/server/.env.production.v7-slurm bash server/run/restart.sh restart --use-proxy` (absolute env path, exactly ONE restart running at a time), then live-verify the affected pages on `https://revocompute.yaoyy.moe` and `https://revocompute-direct.yaoyy.moe` (auth-walled pages via guest login `group_users` through `/compute/api/auth/login`). Disk-full recovery: `docker buildx prune`, apptainer cache clean, remove obsolete SIFs under `/mnt/data/srv/revodesign/server-slurm/images/`. Submit living tests with real data files from `tests/data` when behavior changed. Check the fixed page behaves as designed in incognito (cache-free), not just that the served static files contain the change.
   4. **Main program PRs** (PyMOL plugin): CI and review comments only — no server deploy. Run the relevant gates (`make kw-test PYTEST_KW='<keyword>'`); cross-Qt checks exist in `REvoDesignTestFlight` (PyQt5) and `REvoDesignTestFlightQt6`.
   5. When CI is green and every comment is fixed or debated, push a final empty marker commit `chore: Done fixing — <what was live/CI verified>` as the branch head (the plain `Done fixing` prefix is an intentional exception to the conventional-commit rule, matching the squash-merge habit); the user squash-merges from there.
 - **Standalone bootstrapper encoding**: Keep `src/REvoDesign/tools/package_manager.py` ASCII-only because it is published as `REvoDesign_PyMOL.py` and may be saved through locale-aware Windows tools. A UTF-8-to-GBK transcode turns characters such as `→` into bytes beginning with `0xA1`, which Python 3 rejects while parsing the file as UTF-8. Preserve both the GBK-compilation regression test and the `check-standalone-source-ascii` pre-commit guard; non-ASCII text remains acceptable in normal packaged modules.
-- **Simplified-Chinese Windows living test**: After merging the installer change, republish both `REvoDesign_PyMOL.py` and `manifest.json` before testing so the Gist artifacts match the merged source. Test the documented first-install flow early on a Simplified-Chinese Windows machine with the system UTF-8 option **off** (the default CP936/GBK adverse path); record `chcp`, download the raw Gist through the normal user path, install it in PyMOL, and confirm bootstrap and installation succeed while the deferred UTF-8 guidance dialog appears once without blocking plugin registration. Repeat with **Region → Administrative language settings → Change system locale → “Beta: Use Unicode UTF-8 for worldwide language support”** enabled and the machine rebooted (CP65001); bootstrap and installation must also succeed, and the dialog must not appear. The toggle is a user workaround for non-English CMD/Windows PowerShell streams, not a prerequisite or substitute for CP936 compatibility.
+- **Simplified-Chinese Windows living test**: After merging the installer change, republish both `REvoDesign_PyMOL.py` and `manifest.json` before testing so the Gist artifacts match the merged source. Test the documented first-install flow early on a Simplified-Chinese Windows machine with the system UTF-8 option **off** (the default CP936/GBK adverse path); record `chcp`, download the raw Gist through the normal user path, install it in PyMOL, and confirm bootstrap and installation succeed. Repeat with **Region → Administrative language settings → Change system locale → “Beta: Use Unicode UTF-8 for worldwide language support”** enabled and the machine rebooted (CP65001); bootstrap and installation must also succeed. The UTF-8 guidance lives in the docs only — the package manager no longer probes code pages or shows a dialog. The toggle is a user workaround for non-English CMD/Windows PowerShell streams, not a prerequisite or substitute for CP936 compatibility.
 - **Version bumping**:
   1. Update `__version__` in `src/REvoDesign/__init__.py` (validate format at https://regex101.com/r/6AoOI9/1).
   2. Run `make tag` — it extracts old/new versions from the git diff, inserts a dated `[new_version]` section in `CHANGELOG.md`, commits `CHANGELOG.md` + `__init__.py`, creates an annotated tag with the changelog between versions, and pushes with `--tags`.

docs/user-guide/installation.md

@@ -41,9 +41,6 @@ Supported operating systems:
     REvoDesign continues to test the default Simplified-Chinese Windows
     CP936/GBK path. This setting is a recommended interoperability workaround,
     not a prerequisite or a substitute for reporting encoding problems.
-    When the Package Manager detects CP936 during PyMOL startup, it displays
-    this procedure as a reminder. The reminder appears once per PyMOL session
-    and does not block the plugin from loading.
 
 ## Install PyMOL
 
@@ -60,6 +57,18 @@ pymol
 
 If you already have a working PyMOL installation (2.5+), skip this step.
 
+### macOS notes
+
+- Use **PyMOL Open-Source on native Apple Silicon**. The conda-forge build
+  above installs the `osx-arm64` binary automatically on Apple Silicon — no
+  Rosetta required. The official **PyMOL bundle runs under Rosetta x86_64
+  emulation and is not recommended**; REvoDesign is tested against the native
+  conda-forge build, not the emulated bundle.
+- **Xcode Command Line Tools** are required to compile dependencies that have
+  no prebuilt wheel. Install them once before the first installation:
+
+    xcode-select --install
+
 ## Install REvoDesign Package Manager
 
 1. Open PyMOL.

server/config/task_types.yaml

@@ -75,7 +75,7 @@ task_types:
   gremlin:
     display_name: "PSSM-GREMLIN"
     category: evolution
-    intro: "Co-evolutionary contact and coupling prediction from a multiple sequence alignment (PSSM + GREMLIN)."
+    intro: "Sequence conservation (PSI-BLAST PSSM) and co-evolutionary couplings (GREMLIN) for a protein sequence."
     runtime_family: "gremlin"
     input_extension: ".fasta"
     input_label: "FASTA file"
@@ -232,7 +232,7 @@ task_types:
   opendde:
     display_name: "OpenDDE"
     category: structure
-    intro: "OpenDDE structure prediction with MSA-based guidance."
+    intro: "All-atom structure prediction with MSA and template guidance (OpenDDE)."
     runtime_family: "opendde"
     gpus: true
     input_extension: ".json"
@@ -277,7 +277,7 @@ task_types:
   hypermpnn:
     display_name: "HyperMPNN"
     category: inverse_folding
-    intro: "ProteinMPNN sequence design for the given backbone."
+    intro: "Thermostable sequence design using hyperthermophile-trained ProteinMPNN weights (HyperMPNN)."
     runtime_family: "mpnn"
     input_extension: ".pdb"
     input_label: "PDB file"
@@ -415,7 +415,7 @@ task_types:
   lasermpnn:
     display_name: "LASErMPNN"
     category: inverse_folding
-    intro: "Structure-conditioned sequence design (LASErMPNN)."
+    intro: "Ligand-conditioned sequence design and sidechain packing for protonated (all-atom) structures (LASErMPNN)."
     runtime_family: "mpnn"
     input_extension: ".pdb"
     input_extensions: [".pdb", ".cif", ".mmcif"]
@@ -457,7 +457,7 @@ task_types:
   thermompnn:
     display_name: "ThermoMPNN-D"
     category: fitness
-    intro: "Thermostability-tuned sequence design (ThermoMPNN-D)."
+    intro: "Stability change (ΔΔG) prediction for single and double mutants (ThermoMPNN-D)."
     runtime_family: "mpnn"
     input_extension: ".pdb"
     input_label: "PDB file"
@@ -480,8 +480,8 @@ task_types:
 
   prime:
     display_name: "Pro-Prime"
-    category: function
-    intro: "Enzyme function (EC number) prediction from a sequence (Pro-Prime)."
+    category: fitness
+    intro: "Optimal growth temperature (OGT) prediction from a protein sequence (Pro-Prime)."
     runtime_family: "prime"
     runner_args: ["ogt"]
     gpus: true
@@ -585,7 +585,7 @@ task_types:
   placer:
     display_name: "PLACER"
     category: structure
-    intro: "Structure prediction with PLACER."
+    intro: "All-atom modeling of protein-ligand complexes from an input structure (PLACER)."
     runtime_family: "placer-rfdiffusion"
     runner_args: ["placer"]
     gpus: true

server/docker/runners/common/task_context.py

@@ -29,5 +29,5 @@
 elif command == "files":
     print(json.dumps(manifest["files"]))
 else:
-    sys.stderr.write("task_context.py: unknown command {!r}\n".format(command))
+    sys.stderr.write(f"task_context.py: unknown command {command!r}\n")
     sys.exit(2)

server/tests/test_input_validation.py

@@ -17,8 +17,8 @@
 
 import pytest
 from conftest import _load_pssm_module, _test_client_auth
+from revocompute.input_validators import MAX_CIF_ATOMS  # noqa: F401
 from revocompute.input_validators import (
-    MAX_CIF_ATOMS,  # noqa: F401
     MAX_CIF_RECORD_LENGTH,
     MAX_FASTA_SEQUENCES,
     MAX_FASTA_TOTAL_RESIDUES,

src/REvoDesign/Qt/qt_wrapper.py

@@ -106,17 +106,6 @@ def _install_scoped_alias(
         setattr(container, member_name, getattr(owner, legacy_name))
 
 
-def _install_flat_alias(owner: object, container_name: str, member_name: str, alias_name: str | None = None) -> None:
-    """Install a flat Qt5-style alias from a scoped Qt6 enum member when missing."""
-
-    flat_name = alias_name or member_name
-    if hasattr(owner, flat_name):
-        return
-    container = getattr(owner, container_name, None)
-    if container is not None and hasattr(container, member_name):
-        setattr(owner, flat_name, getattr(container, member_name))
-
-
 def _qt_enum(owner: Any, enum_name: str, member_name: str) -> Any:
     """Return a Qt enum member using Qt6 scoped lookup with Qt5 fallback."""
 
@@ -178,60 +167,8 @@ def _install_qtcore_scoped_aliases() -> None:
         for member_name in member_names:
             _install_scoped_alias(qt_namespace, container_name, member_name)
 
-    flat_aliases = (
-        ("WidgetAttribute", "WA_DeleteOnClose"),
-        ("WidgetAttribute", "WA_Hover"),
-        ("WidgetAttribute", "WA_ShowWithoutActivating"),
-        ("WidgetAttribute", "WA_TransparentForMouseEvents"),
-        ("WidgetAttribute", "WA_TranslucentBackground"),
-        ("ContextMenuPolicy", "CustomContextMenu"),
-        ("TextFormat", "RichText"),
-        ("TextFormat", "PlainText"),
-        ("CheckState", "Checked"),
-        ("CheckState", "Unchecked"),
-        ("CheckState", "PartiallyChecked"),
-        ("ItemFlag", "ItemIsUserCheckable"),
-        ("ItemFlag", "ItemIsEnabled"),
-        ("Orientation", "Horizontal"),
-        ("Orientation", "Vertical"),
-        ("ScrollBarPolicy", "ScrollBarAsNeeded"),
-        ("ScrollBarPolicy", "ScrollBarAlwaysOff"),
-        ("ScrollBarPolicy", "ScrollBarAlwaysOn"),
-        ("GlobalColor", "yellow"),
-        ("GlobalColor", "blue"),
-        ("GlobalColor", "red"),
-        ("GlobalColor", "green"),
-        ("GlobalColor", "black"),
-        ("GlobalColor", "white"),
-        ("FocusPolicy", "NoFocus"),
-        ("CursorShape", "PointingHandCursor"),
-        ("WindowType", "Tool"),
-        ("WindowType", "FramelessWindowHint"),
-        ("WindowType", "WindowStaysOnTopHint"),
-        ("WindowType", "WindowDoesNotAcceptFocus"),
-        ("WindowType", "SplashScreen"),
-        ("AlignmentFlag", "AlignLeft"),
-        ("AlignmentFlag", "AlignRight"),
-        ("AlignmentFlag", "AlignHCenter"),
-        ("AlignmentFlag", "AlignJustify"),
-        ("AlignmentFlag", "AlignTop"),
-        ("AlignmentFlag", "AlignBottom"),
-        ("AlignmentFlag", "AlignVCenter"),
-        ("AlignmentFlag", "AlignCenter"),
-        ("AlignmentFlag", "AlignLeading"),
-        ("AlignmentFlag", "AlignTrailing"),
-        ("BrushStyle", "NoBrush"),
-        ("DropAction", "CopyAction"),
-        ("DropAction", "MoveAction"),
-        ("DropAction", "LinkAction"),
-        ("DropAction", "IgnoreAction"),
-    )
-    for container_name, member_name in flat_aliases:
-        _install_flat_alias(qt_namespace, container_name, member_name)
-
     for member_name in ("Linear", "InQuad", "OutQuad", "InOutQuad"):
         _install_scoped_alias(QtCore.QEasingCurve, "Type", member_name)
-        _install_flat_alias(QtCore.QEasingCurve, "Type", member_name)
 
 
 def _install_qtwidgets_scoped_aliases() -> None:
@@ -319,12 +256,8 @@ def _install_qtwidgets_scoped_aliases() -> None:
         for member_name in member_names:
             _install_scoped_alias(owner, container_name, member_name)
 
-    # QStackedLayout.StackingMode: scoped enum in Qt6 (StackAll, StackOne).
-    # Provide flat aliases (Qt5-style) so that code referencing
-    # QtWidgets.QStackedLayout.StackAll continues to work under Qt6.
     for member_name in ("StackAll", "StackOne"):
         _install_scoped_alias(getattr(QtWidgets, "QStackedLayout", None), "StackingMode", member_name)
-        _install_flat_alias(getattr(QtWidgets, "QStackedLayout", None), "StackingMode", member_name)
 
 
 def _install_qtgui_scoped_aliases() -> None:
@@ -359,7 +292,6 @@ def _install_qtgui_scoped_aliases() -> None:
             _install_scoped_alias(qpalette, "ColorRole", member_name)
     if qpainter is not None:
         _install_scoped_alias(qpainter, "RenderHint", "Antialiasing")
-        _install_flat_alias(qpainter, "RenderHint", "Antialiasing")
 
 
 def _install_qtnetwork_scoped_aliases() -> None:
@@ -388,6 +320,36 @@ def _install_moved_class_aliases() -> None:
             setattr(QtGui, attr_name, fallback)
 
 
+def _install_unscoped_enum_bridge() -> None:
+    """Alias every scoped-enum member onto its owning Qt class.
+
+    On Qt6 bindings enum members live under per-class enum types
+    (``QMessageBox.StandardButton.Ok``), so Qt5-style unscoped access
+    (``QMessageBox.Ok``) raises AttributeError.  Mirror every member of
+    every enum type of every class in the loaded Qt modules onto the
+    class itself, skipping names that already exist, so any flat access
+    resolves on both Qt5 and Qt6 without per-API bookkeeping.  On Qt5
+    and PySide bindings the flat names already resolve, so the bridge
+    aliases nothing and is a no-op.
+    """
+
+    def _is_enum_type(value) -> bool:
+        return isinstance(value, type) and hasattr(value, "__members__")
+
+    for _qt_module in (QtCore, QtGui, QtWidgets, QtNetwork, QtWebSockets, QtSvg, QtUiTools):
+        if _qt_module is None:
+            continue
+        for _cls in list(vars(_qt_module).values()):
+            if not (isinstance(_cls, type) and getattr(_cls, "__module__", "") == _qt_module.__name__):
+                continue
+            for _enum_type in list(vars(_cls).values()):
+                if not _is_enum_type(_enum_type):
+                    continue
+                for _member_name, _member in _enum_type.__members__.items():
+                    if not hasattr(_cls, _member_name):
+                        setattr(_cls, _member_name, _member)
+
+
 _ALIAS_STATE = {"installed": False}
 
 
@@ -403,6 +365,7 @@ def install_qt6_aliases() -> None:
     _install_qtgui_scoped_aliases()
     _install_qtnetwork_scoped_aliases()
     _install_qtwebsockets_scoped_aliases()
+    _install_unscoped_enum_bridge()
     _ALIAS_STATE["installed"] = True