Merge branch 'develop' of ssh://localhost:14147/Users/pett/src/chimer…

…ax into develop

.gitignore

@@ -102,6 +102,7 @@ src/bundles/chem_group/src/__init__.py
 src/bundles/chem_group/bundle_info.xml
 src/bundles/looking_glass/holoplaycore-*.tar.gz
 src/bundles/md_crds/gromacs/xdrfile-1.1b/
+src/bundles/md_crds/gromacs/xdrfile-1.1.4/
 src/bundles/meeting/src/server.pem
 src/bundles/mmcif/mmcif_cpp/include/
 src/bundles/mmcif/src/mmcif.cpp

src/bundles/basic_actions/bundle_info.xml

@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-BasicActions" version="1.1.2"
+<BundleInfo name="ChimeraX-BasicActions" version="1.1.3"
             package="chimerax.basic_actions" customInit="true"
             minSessionVersion="1" maxSessionVersion="1">
 

src/bundles/basic_actions/src/cmd.py

@@ -50,7 +50,10 @@ def name_frozen(session, name, objects):
     if _is_reserved(name):
         raise UserError("\"%s\" is reserved and cannot be redefined" % name)
     if objects.empty():
-        raise UserError("nothing is selected by specifier")
+        if session.in_script:
+            session.logger.warning("Nothing is selected by specifier")
+        else:
+            raise UserError("Nothing is selected by specifier")
     from chimerax.core.commands import register_selector
     register_selector(name, objects, session.logger, user=True)
     session.basic_actions.define(name, objects)

src/bundles/core/src/__main__.py

@@ -684,6 +684,10 @@ def init(argv, event_loop=True):
 
     # initialize qt
     if opts.gui:
+        if os.environ.get("WAYLAND_DISPLAY", ""):
+            # ChimeraX needs to use XWayland for now
+            os.environ["QT_QPA_PLATFORM"] = "xcb"
+            os.environ["PYOPENGL_PLATFORM"] = "x11"
         from chimerax.ui import initialize_qt
 
         initialize_qt()

src/bundles/dicom/src/dicom_hierarchy.py

@@ -520,7 +520,7 @@ def __init__(
             rsi = int(rsi)
         self.rescale_intercept = rsi
         self.rescale_slope = int(self.dicom_series.rescale_slope)
-        if not self.contour_series:
+        if self.image_series and not self.contour_series:
             bits = self.sample_file.get("BitsAllocated")
             rep = self.sample_file.get("PixelRepresentation")
             self.value_type = self.numpy_value_type(
@@ -663,6 +663,18 @@ def to_models(self, open_models, derived, sgrids):
                 "be available." % (self.number, self.patient_id)
             )
 
+    @property
+    def number(self):
+        if self.sample_file.get("SeriesNumber", None) is None:
+            self.session.logger.warning("SeriesNumber not specified; setting to 0")
+            return 0
+        else:
+            return int(self.sample_file.get("SeriesNumber", 0))
+
+    @property
+    def patient_id(self):
+        return self.sample_file.get("PatientID", "")
+
     @property
     def columns(self):
         return self.sample_file.get("Columns")

src/bundles/graphics/src/vertexShader.txt

@@ -47,7 +47,7 @@ uniform mat4 view_matrix; // Map scene coordinates to camera coordinates
 #endif
 
 #if defined(USE_VOLUME_RAYCASTING)
-uniform vec3 step_size;
+uniform float step_size;
 uniform vec3 camera_pos;
 uniform float camera_fov;
 uniform vec2 window_size;

src/bundles/open_command/bundle_info.xml

@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-OpenCommand" version="1.14" package="chimerax.open_command"
+<BundleInfo name="ChimeraX-OpenCommand" version="1.14.1" package="chimerax.open_command"
             minSessionVersion="1" maxSessionVersion="1">
 
   <!-- Additional information about bundle source -->

src/bundles/open_command/src/dialog.py

@@ -273,12 +273,14 @@ def set_use_native_open_file_dialog(use):
     global _use_native_open_file_dialog
     _use_native_open_file_dialog = use
 
-def make_qt_name_filters(session, *, no_filter="All files (*)"):
+def make_qt_name_filters(session, *, no_filter="All files (*)", format_names=None):
     openable_formats = [fmt for fmt in session.open_command.open_data_formats if fmt.suffixes]
+    if format_names is not None:
+        openable_formats = [fmt for fmt in openable_formats if fmt.name in format_names]
     openable_formats.sort(key=lambda fmt: fmt.synopsis.casefold())
     file_filters = ["%s (%s)" % (fmt.synopsis, "*" + " *".join(fmt.suffixes))
         for fmt in openable_formats]
-    if no_filter is not None:
+    if no_filter is not None and format_names is None:
         file_filters = [no_filter] + file_filters
     return file_filters, openable_formats, no_filter
 
@@ -293,13 +295,16 @@ def show_fetch_by_id_dialog(session, database_name=None, *, debug=False):
     _fetch_by_id_dialog.show()
     _fetch_by_id_dialog.raise_()
 
-def show_open_file_dialog(session, initial_directory=None, format_name=None):
+def show_open_file_dialog(session, initial_directory=None, format_names=None):
     if initial_directory is None:
         initial_directory = ''
-    file_filters, openable_formats, no_filter = make_qt_name_filters(session)
+    file_filters, openable_formats, no_filter = make_qt_name_filters(session, format_names=format_names)
     fmt_name2filter = dict(zip([fmt.name for fmt in openable_formats], file_filters[1:]))
-    filter2fmt = dict(zip(file_filters[1:], openable_formats))
-    filter2fmt[no_filter] = None
+    if format_names is None:
+        filter2fmt = dict(zip(file_filters[1:], openable_formats))
+        filter2fmt[no_filter] = None
+    else:
+        filter2fmt = dict(zip(file_filters, openable_formats))
     from Qt.QtWidgets import QFileDialog
     qt_filter = ";;".join(file_filters)
     if _use_native_open_file_dialog: