Support cryoET data portal API v2

pyproject.toml

@@ -3,16 +3,16 @@ requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
 
 [project]
 name = "ChimeraX-copick"
-version = "0.3.6"
+version = "0.5.0"
 dynamic = ["classifiers", "requires-python"]
 dependencies = [
     "ChimeraX-Core>=1.7",
-    "ChimeraX-ArtiaX>=0.4.9",
+    "ChimeraX-ArtiaX>=0.5.0",
     "ChimeraX-OME-Zarr>=0.5.4",
     "pydantic",
     "hatchling",
     "s3fs>=2024.3.1",
-    "copick[all]>=0.5.2",
+    "copick[all]>=0.6.0",
 ]
 authors = [
   {name = "Utz H. Ermel", email = "utz@ermel.me"},

src/cmd/core.py

@@ -28,9 +28,28 @@ def copick_start(session, config_file: str):
     copick.from_config_file(config_file)
 
 
+def cks(session, shortcut=None):
+    """
+    Enable copick keyboard shortcuts.  Keys typed in the graphics window will be interpreted as shortcuts.
+
+    Parameters
+    ----------
+    shortcut : string
+      Keyboard shortcut to execute.  If no shortcut is specified switch to shortcut input mode.
+    """
+
+    from ..shortcuts.shortcuts import copick_keyboard_shortcuts
+
+    ks = copick_keyboard_shortcuts(session)
+    if shortcut is None:
+        ks.enable_shortcuts()
+    else:
+        ks.try_shortcut(shortcut)
+
+
 def register_copick(logger):
     """Register all commands with ChimeraX, and specify expected arguments."""
-    from chimerax.core.commands import CmdDesc, FileNameArg, register
+    from chimerax.core.commands import CmdDesc, FileNameArg, StringArg, register
 
     def register_copick_start():
         desc = CmdDesc(
@@ -40,4 +59,13 @@ def register_copick_start():
         )
         register("copick start", desc, copick_start)
 
+    def register_copick_keyboard_shortcuts():
+        desc = CmdDesc(
+            optional=[("shortcut", StringArg)],
+            synopsis="Start using Copick keyboard shortcuts.",
+            # url='help:user/commands/copick_start.html'
+        )
+        register("cks", desc, cks)
+
     register_copick_start()
+    register_copick_keyboard_shortcuts()

src/shortcuts/shortcuts.py

@@ -6,7 +6,11 @@
 from chimerax.artiax.particle.ParticleList import delete_selected_particles
 from chimerax.core.session import Session
 from chimerax.log.tool import Log
-from chimerax.shortcuts.shortcuts import Shortcut, keyboard_shortcuts, list_keyboard_shortcuts
+from chimerax.shortcuts.shortcuts import (
+    Keyboard_Shortcuts,
+    Shortcut,
+    shortcut_descriptions,
+)
 
 from ..misc.volops import switch_to_ortho, switch_to_slab
 
@@ -75,8 +79,15 @@ def copick_shortcuts() -> Tuple[List[Tuple[Any, ...]], Tuple[Any, ...]]:
     return csc, catcols
 
 
+def copick_keyboard_shortcuts(session: Session) -> Keyboard_Shortcuts:
+    ks = getattr(session, "copick_shortcuts", None)
+    if ks is None:
+        session.copick_shortcuts = ks = Keyboard_Shortcuts(session)
+    return ks
+
+
 def register_shortcuts(session: Session):
-    ksc = keyboard_shortcuts(session)
+    ksc = copick_keyboard_shortcuts(session)
     ksc.shortcuts.clear()
 
     scs, catcols = copick_shortcuts()
@@ -145,6 +156,11 @@ def toggle_info_label(session: Session):
     session.copick.show_info = not session.copick.show_info
 
 
+def list_copick_shortcuts(session: Session):
+    t = shortcut_descriptions(session.copick_shortcuts, html=True)
+    session.logger.info(t, is_html=True)
+
+
 def show_help(session: Session):
-    list_keyboard_shortcuts(session)
+    list_copick_shortcuts(session)
     session.tools.find_by_class(Log)[0].tool_window.shown = True

src/tool.py

@@ -48,7 +48,7 @@ class CopickTool(ToolInstance):
     # Does this instance persist when session closes
     SESSION_ENDURING = False
     # We do save/restore in sessions
-    SESSION_SAVE = True
+    SESSION_SAVE = False
 
     # Let ChimeraX know about our help page
     def __init__(self, session, tool_name):
@@ -105,7 +105,7 @@ def __init__(self, session, tool_name):
         from .shortcuts.shortcuts import register_shortcuts
 
         register_shortcuts(self.session)
-        run(session, "ks")
+        run(session, "cks")
 
         # Stepper
         self.stepper_list = []

src/ui/QCoPickTreeModel.py

@@ -93,12 +93,3 @@ def flags(self, index: QModelIndex) -> Union[Qt.ItemFlag, None]:
 
         index.internalPointer()
         return Qt.ItemFlag.ItemIsEnabled | Qt.ItemFlag.ItemIsSelectable
-
-        # if item.is_dir:
-        #     return Qt.ItemFlag.ItemIsEnabled | Qt.ItemFlag.ItemIsSelectable
-        #
-        # if item.is_file:
-        #     if item.extension in self._openable_types:
-        #         return Qt.ItemFlag.ItemIsEnabled | Qt.ItemFlag.ItemIsSelectable
-        #     else:
-        #         return Qt.ItemFlag.ItemIsSelectable