specs+regimes(training): update base encoder, deprecate old regimes

.dockerignore

@@ -137,3 +137,5 @@ venv.bak/
 
 # Pyre type checker
 .pyre/
+
+src/

.gitignore

@@ -148,3 +148,5 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+src/

docker/Dockerfile.all.p39

@@ -1,10 +1,10 @@
-FROM pytorch/pytorch:2.0.0-cuda11.7-cudnn8-runtime
+FROM pytorch/pytorch:2.0.1-cuda11.7-cudnn8-runtime
 
 ENV DEBIAN_FRONTEND="noninteractive"
 
 RUN apt-get update \
   && apt-get install -y git build-essential wget curl vim ffmpeg libsm6 libxext6 software-properties-common unixodbc-dev \
-  && pip install posix-ipc \
+  && pip install --no-cache-dir posix-ipc gevent \
   && apt-get --purge autoremove -y build-essential \
   && apt-get clean \
   && rm -rf /var/lib/apt/lists/* \
@@ -22,6 +22,6 @@ RUN apt-get update \
 ENV PYTHONPATH /opt/zetta_utils
 WORKDIR /opt/zetta_utils
 ADD pyproject.toml /opt/zetta_utils/
-RUN pip install '.[modules]'
+RUN pip install --no-cache-dir '.[modules]'
 COPY . /opt/zetta_utils/
 RUN zetta --help

pyproject.toml

@@ -17,7 +17,7 @@ classifiers = [
 keywords = ["neuroscience connectomics EM"]
 license = { text = "MIT" }
 urls = { Homepage = "https://github.com/zettaai/zetta_utils" }
-requires-python = ">3.8,<3.11"
+requires-python = ">3.8,<3.12"
 dependencies = [
     "attrs >= 21.3",
     "typeguard == 4.1.5",

specs/examples/training/ddp.cue

@@ -40,7 +40,7 @@ regime: {
 }
 trainer: {
 	"@type":            "ZettaDefaultTrainer"
-	accelerator:        "cuda"
+	accelerator:        "gpu"
 	devices:            1
 	num_nodes:          32
 	max_epochs:         100

zetta_utils/api/v0.py

@@ -411,26 +411,12 @@
 from zetta_utils.training.datasets.sample_indexers.volumetric_strided_indexer import (
     VolumetricStridedIndexer,
 )
+from zetta_utils.training.lightning.regimes.alignment.base_coarsener import (
+    BaseCoarsenerRegime,
+)
 from zetta_utils.training.lightning.regimes.alignment.base_encoder import (
     BaseEncoderRegime,
 )
-from zetta_utils.training.lightning.regimes.alignment.encoding_coarsener import (
-    EncodingCoarsenerRegime,
-)
-from zetta_utils.training.lightning.regimes.alignment.encoding_coarsener_gen_x1 import (
-    EncodingCoarsenerGenX1Regime,
-)
-from zetta_utils.training.lightning.regimes.alignment.encoding_coarsener_highres import (
-    EncodingCoarsenerHighRes,
-    center_crop_norm,
-    warp_by_px,
-)
-from zetta_utils.training.lightning.regimes.alignment.minima_encoder import (
-    MinimaEncoderRegime,
-)
-from zetta_utils.training.lightning.regimes.alignment.misalignment_detector import (
-    MisalignmentDetectorRegime,
-)
 from zetta_utils.training.lightning.regimes.alignment.misalignment_detector_aced import (
     MisalignmentDetectorAcedRegime,
 )

zetta_utils/training/lightning/regimes/alignment/__init__.py

@@ -1,6 +1,2 @@
-from . import encoding_coarsener
-from . import encoding_coarsener_highres
-from . import encoding_coarsener_gen_x1
-from . import base_encoder
-from . import misalignment_detector
-from . import misalignment_detector_aced
+from . import base_encoder, misalignment_detector_aced
+from .deprecated import encoding_coarsener