Cleanup for version release.

.github/workflows/pr-tag.yml

@@ -0,0 +1,26 @@
+name: Bump version
+on:
+  pull_request:
+    types:
+      - closed
+    branches:
+      - master
+
+jobs:
+  build:
+    if: github.event.pull_request.merged == true
+    runs-on: ubuntu-22.04
+    permissions:
+      contents: write
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        ref: ${{ github.event.pull_request.merge_commit_sha }}
+        fetch-depth: '0'
+
+    - name: Bump version and push tag
+      uses: anothrNick/github-tag-action@v1 # Don't use @master or @v1 unless you're happy to test the latest version
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # if you don't want to set write permissions use a PAT token
+        TAG_PREFIX: v
+        DEFAULT_BUMP: patch

python/ouroboros/helpers/memory_usage.py

@@ -40,7 +40,7 @@ def calculate_gigabytes_from_dimensions(shape: tuple[int], dtype: np.dtype) -> f
     num_elements = np.prod(shape)
 
     # Calculate the total number of bytes
-    num_bytes = np.multiply(num_elements, dtype_size, dtype=np.float64)
+    num_bytes = np.multiply(num_elements, dtype_size, dtype=np.uint64)
 
     return num_bytes / GIGABYTE
 

python/ouroboros/helpers/volume_cache.py

@@ -16,6 +16,7 @@ def __init__(
         flush_cache=FLUSH_CACHE,
     ) -> None:
         self.bounding_boxes = bounding_boxes
+
         self.link_rects = link_rects
         self.cv = cloud_volume_interface
         self.mip = mip

python/ouroboros/pipeline/slice_parallel_pipeline.py

@@ -85,8 +85,6 @@ def _process(self, input_data: tuple[any]) -> None | str:
                     "unit": "um"
                 }
 
-                print(f"Resolution: {volume_cache.get_resolution_um()} | {resolution}")
-
                 # Determine the dimensions of the image
                 has_color_channels = volume_cache.has_color_channels()
                 num_color_channels = (
@@ -105,7 +103,7 @@ def _process(self, input_data: tuple[any]) -> None | str:
                     output_file_path,
                     temp_data,
                     software="ouroboros",
-                    resolution=resolution[:2], 	# XY Resolution
+                    resolution=resolution[:2],     # XY Resolution
                     resolutionunit=resolutionunit,
                     photometric=(
                         "rgb"
@@ -227,8 +225,9 @@ def thread_worker_iterative(
     volume_cache, volumes_range, data_queue, single_thread=False
 ):
     for i in volumes_range:
-        # Create a packet of data to process
+        # Create a packet of data to process - Make the threading check make more sense.
         data = volume_cache.create_processing_data(i, parallel=single_thread)
+
         data_queue.put(data)
 
         # Remove the volume from the cache after the packet is created

python/ouroboros/pipeline/slices_geom_pipeline.py

@@ -1,4 +1,3 @@
-from pydantic import BaseModel
 from ouroboros.helpers.coordinates import convert_points_between_volumes
 from ouroboros.helpers.slice import calculate_slice_rects
 from ouroboros.helpers.spline import Spline

python/pyproject.toml

@@ -24,15 +24,16 @@ tifffile = "^2024.6.18"
 pydantic = "^2.7.4"
 tqdm = "^4.66.4"
 imagecodecs = "^2024.6.1"
-fastapi = "^0.111.0"
+fastapi = "^0.115.0"
 asyncio = "^3.4.3"
 uuid = "^1.30"
-sse-starlette = "^2.1.2"
+sse-starlette = "^2.3.2"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.2.2"
 pytest-cov = "^6.1.1"
-pyinstaller = "^6.8.0"
+pyinstaller = "^6.13.0"
+setuptools = "^78.1.1"
 coverage = "^7.6.0"
 
 [build-system]