Simplifications and improvements to tomography plans. Add tomography flyscans test suite.

pixi.toml

@@ -22,7 +22,7 @@ bluesky-tiled-plugins = ">=2.0.9,<3"
 hextools = { path = ".", editable = true }
 nslsii = { git = "https://github.com/NSLS2/nslsii", rev = "main" }
 bluesky = { git = "https://github.com/bluesky/bluesky", rev = "main" }
-ophyd-async = { git = "https://github.com/jwlodek/ophyd-async", rev = "add-codec-and-process-plugin-allow-for-filtering" }
+ophyd-async = { git = "https://github.com/bluesky/ophyd-async", rev = "main" }
 
 [feature.profile.dependencies]
 redis-json-dict = ">=0.2.2,<0.3"
@@ -115,6 +115,7 @@ auto-exporter = "python -m hextools.exporters.auto_exporter"
 
 [feature.exporter.dependencies]
 h5py = ">=3.16.0,<4"
+
 [feature.docs.dependencies]
 sphinx = "*"
 sphinx-autobuild = "*"
@@ -156,5 +157,12 @@ solve-group = "profile"
 
 [feature.py313.tasks]
 tests = "pytest --cov=src/hextools --cov-report=term"
+# Run the tests, then serve the html coverage report whether or not they passed.
+# VS Code's terminal opens file:// links in the editor, but http:// in the browser.
+coverage = """
+pytest --cov=src/hextools --cov-report=term --cov-report=html; \
+echo "Coverage report: http://localhost:8765/index.html (Ctrl-C to stop)" \
+&& python -m http.server 8765 --bind 127.0.0.1 --directory $PIXI_PROJECT_ROOT/htmlcov
+"""
 lint = "pre-commit run --all-files"
 type-check = "ty check src tests"

pyproject.toml

@@ -32,9 +32,9 @@ dependencies = [
   "algotom",
   "ipython",
   "numpy",
-  "bluesky",
-  "nslsii",
-  "ophyd-async[ca, pva]",
+  "bluesky @ git+https://github.com/bluesky/bluesky@main",
+  "nslsii @ git+https://github.com/NSLS2/nslsii@main",
+  "ophyd-async[ca, pva] @ git+https://github.com/bluesky/ophyd-async@main",
   "rich>=15.0.0",
   "scikit-image>=0.26.0",
   "scipy>=1.17.1",
@@ -111,7 +111,7 @@ allow-direct-references = true
 artifacts = ["src/hextools/_version.py"]
 
 [tool.hatch.build.targets.wheel]
-sources = ["src"]
+projects = ["src/hextools"]
 
 [tool.hatch.build.hooks.vcs]
 version-file = "src/hextools/_version.py"

src/hextools/specs.py

@@ -141,6 +141,12 @@ def validate_tomo_dark_flat(run: RunLike, version: str | None = "1") -> None:
 #   sample_name: str                 optional
 #   last_dark_flat_uid: str          optional, see the tomography dark/flat convention
 #   last_dark_flat_scan_id: int      optional, see the tomography dark/flat convention
+#   grid_index: int                  optional, from the step scans: 0-based point index
+#   num_grid_points: int             optional, from the step scans: points in the scan
+#   grid_positions: dict[str, float] optional, from the step scans: step motor name to
+#                                    setpoint; empty when the scan has no step axes
+#   previous_grid_point_uid: str     optional, from the step scans: start uid of the
+#                                    previous point's successful run; absent on first
 # Streams:
 #   primary: collected while flying
 #     <det>                     (num_points, height, width) image stack, external

src/hextools/tomography/alignment.py

@@ -725,14 +725,15 @@ def tomo_alignment_scan(
     fe_shutter = ensure_available(Shutter, fe_shutter=fe_shutter)
     photon_shutter = ensure_available(Shutter, photon_shutter=photon_shutter)
     rot_motor = ensure_available(RotationMotor, rot_motor=rot_motor)
+    # Restored in the cleanup, so the stage returns at full speed before slowing.
+    initial_position = yield from bps.rd(rot_motor.user_readback)
+    initial_velocity = yield from bps.rd(rot_motor.velocity)
 
     @bpp.reset_positions_decorator(
         [
             det.driver.num_images,
             det.driver.acquire_period,
             det.driver.acquire_time,
-            rot_motor,
-            rot_motor.velocity,
         ]
     )
     def _body():
@@ -769,5 +770,7 @@ def _cleanup():
         yield from ensure_shutter_closed(photon_shutter)
         if isinstance(det, KinetixDetector):
             yield from enable_preview_mode(det)
+        yield from bps.mv(rot_motor, initial_position)
+        yield from bps.mv(rot_motor.velocity, initial_velocity)
 
-    return bpp.finalize_wrapper(_body(), _cleanup())
+    return (yield from bpp.finalize_wrapper(_body(), _cleanup()))