refactor(dynacell): replace microssim dep with cubic.metrics.MicroMS3IM

cubic 0.7.0a4 ships a native MicroSSIM / MicroMS3IM implementation,
making the upstream juglab/microssim git pin redundant. Swap dynacell's
calculate_microssim to lazy-import `cubic.metrics.MicroMS3IM` so the
existing test stubs in `test_evaluation_metrics.py` (which fake
`cubic.metrics` at module load) keep working unchanged.

Notes on the wiring:
- Top-of-file `from microssim import MicroMS3IM` (try/except shim) and
  the `_require_microssim` helper are removed; metrics.py no longer
  references upstream microssim.
- `_require_cubic()` is NOT called from `calculate_microssim`. That
  helper requires the GPU stack (cupy, cucim) and would regress
  CPU-only eval runs that only need MicroMS3IM; the lazy import alone
  is the gate.
- The cubic.metrics stub gains `MicroMS3IM = object` so future tests
  exercising calculate_microssim won't need to re-extend it.

Lock + workspace:
- `applications/dynacell/pyproject.toml` bumps `cubic==0.7.0a2` →
  `cubic==0.7.0a4` and drops the microssim git pin from
  `optional-dependencies.eval`.
- Workspace `[tool.uv.sources]` carries a temporary git override
  pointing cubic at the 0.7.0a4 release commit until PyPI catches up.
  Remove the override after the cubic release lands on PyPI.
- `uv.lock` regenerated; no more `juglab/microssim` references.

README sweep: drop microssim from the optional-deps shortlist.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: alxndrkalinin

applications/dynacell/pyproject.toml

@@ -43,13 +43,12 @@ optional-dependencies.eval = [
   "aicsmlsegment",
   "aicssegmentation",
   "cellpose",
-  "cubic==0.7.0a2",
+  "cubic==0.7.0a4",
   "dynaclr",
   "hydra-core>=1.2",
   "iohub",
   "itk",
   "matplotlib",
-  "microssim @ git+https://github.com/juglab/microssim.git@8bccb17d",
   "pandas",
   "scikit-image",
   "scikit-learn>=1.4",

applications/dynacell/src/dynacell/evaluation/README.md

@@ -250,7 +250,7 @@ eval_timing.csv                 # region timer log (always on)
 
 ## Installation
 
-Heavy optional deps (`aicssegmentation`, `segmenter-model-zoo`, `cubic`, `microssim`, `transformers`, `dynaclr`):
+Heavy optional deps (`aicssegmentation`, `segmenter-model-zoo`, `cubic`, `transformers`, `dynaclr`):
 
 ```bash
 uv pip install -e "applications/dynacell[eval]"

applications/dynacell/src/dynacell/evaluation/metrics.py

@@ -3,11 +3,6 @@
 import numpy as np
 import torch
 
-try:
-    from microssim import MicroMS3IM
-except ImportError:
-    MicroMS3IM = None  # type: ignore[assignment, misc]
-
 try:
     from cubic.cuda import ascupy, asnumpy
     from cubic.feature.voxel import regionprops_table
@@ -24,11 +19,6 @@
 from dynacell.evaluation.utils import _minmax_norm
 
 
-def _require_microssim():
-    if MicroMS3IM is None:
-        raise ImportError("microssim is required for MicroMS3IM computation. Install it with: pip install microssim")
-
-
 def _require_cubic():
     if ascupy is None:
         raise ImportError(
@@ -259,8 +249,8 @@ def compute_pixel_metrics(prediction, target, spacing, fsc_kwargs=None, spectral
 
 def calculate_microssim(microssim_data):
     """Calculate MicroMS3IM scores across a collection of images."""
-    _require_microssim()
-    _require_cubic()
+    from cubic.metrics import MicroMS3IM
+
     targets = np.concatenate([img["target"] for img in microssim_data], axis=0)
     predictions = np.concatenate([img["predict"] for img in microssim_data], axis=0)
 

applications/dynacell/tests/test_evaluation_metrics.py

@@ -13,16 +13,14 @@
 
 def _import_metrics_with_stubs(monkeypatch):
     """Import the metrics module with lightweight optional-dependency stubs."""
-    microssim_module = types.ModuleType("microssim")
-    microssim_module.MicroMS3IM = object
-
     cubic_module = types.ModuleType("cubic")
     cubic_cuda_module = types.ModuleType("cubic.cuda")
     cubic_cuda_module.ascupy = lambda x: x
     cubic_cuda_module.asnumpy = lambda x: x
 
     cubic_metrics_module = types.ModuleType("cubic.metrics")
     cubic_metrics_module.fsc_resolution = lambda *args, **kwargs: {}
+    cubic_metrics_module.MicroMS3IM = object
 
     cubic_bandlimited_module = types.ModuleType("cubic.metrics.bandlimited")
     cubic_bandlimited_module.spectral_pcc = lambda *args, **kwargs: 0.0
@@ -31,7 +29,6 @@ def _import_metrics_with_stubs(monkeypatch):
     cubic_feature_voxel_module = types.ModuleType("cubic.feature.voxel")
     cubic_feature_voxel_module.regionprops_table = lambda *args, **kwargs: {}
 
-    monkeypatch.setitem(sys.modules, "microssim", microssim_module)
     monkeypatch.setitem(sys.modules, "cubic", cubic_module)
     monkeypatch.setitem(sys.modules, "cubic.cuda", cubic_cuda_module)
     monkeypatch.setitem(sys.modules, "cubic.metrics", cubic_metrics_module)

pyproject.toml

@@ -58,6 +58,11 @@ cytoland = { workspace = true }
 airtable-utils = { workspace = true }
 qc = { workspace = true }
 dynacell = { workspace = true }
+# Temporary: cubic 0.7.0a4 is not yet on PyPI. Remove this entry once the
+# release is published; the workspace falls back to PyPI for `cubic==0.7.0a4`
+# pinned in `applications/dynacell/pyproject.toml`. The URL is the canonical
+# cubic Repository (per PyPI metadata).
+cubic = { git = "https://github.com/alxndrkalinin/cubic.git", rev = "424343f5e1c9f34921936b037863479c91072b28" }
 waveorder = { git = "https://github.com/mehta-lab/waveorder.git", branch = "main" }
 aicssegmentation = { git = "https://github.com/alxndrkalinin/aics-segmentation.git", branch = "main" }
 segmenter-model-zoo = { git = "https://github.com/alxndrkalinin/segmenter_model_zoo.git", branch = "main" }