Pinning pyarrow under 17.0 for tools using vaex (#553)

* build: pinning pyarrow under 17.0 * fix: numba and llvmlite versions in region-segmentation-eval-tool
PolusAI · Jul 19, 2024 · 31746f5 · 31746f5
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diff --git a/features/nyxus-tool/.bumpversion.cfg b/features/nyxus-tool/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.7
+current_version = 0.1.8-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

diff --git a/features/nyxus-tool/README.md b/features/nyxus-tool/README.md
@@ -1,4 +1,4 @@
-# Nyxus-Plugin(v0.1.7)
+# Nyxus-Plugin(v0.1.8-dev0)
 
 
 Nyxus plugin uses parallel processing of [Nyxus python package](https://pypi.org/project/nyxus/) to extract nyxus features from intensity-label image data. Especially useful when processing high throughput screens.

diff --git a/features/nyxus-tool/VERSION b/features/nyxus-tool/VERSION
@@ -1 +1 @@
-0.1.7
+0.1.8-dev0
diff --git a/features/nyxus-tool/plugin.json b/features/nyxus-tool/plugin.json
@@ -1,7 +1,7 @@
 {
   "name": "Nyxus plugin",
-  "version": "0.1.7",
-  "containerId": "polusai/nyxus-tool:0.1.7",
+  "version": "0.1.8-dev0",
+  "containerId": "polusai/nyxus-tool:0.1.8-dev0",
   "title": "Nyxus plugin",
   "description": "Nyxus plugin allows to make use of parallel pocessing for extracting nyxus features",
   "author": "Nick Schaub (nick.schaub@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)",

diff --git a/features/nyxus-tool/pyproject.toml b/features/nyxus-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-features-nyxus-plugin"
-version = "0.1.7"
+version = "0.1.8-dev0"
 description = ""
 authors = [
            "Nick Schaub <nick.schaub@nih.gov>",
@@ -21,6 +21,7 @@ vaex = "^4.17.0"
 preadator = "0.4.0.dev2"
 pytest-sugar = "^0.9.7"
 pytest-xdist = "^3.5.0"
+pyarrow = ">=16.0,<17.0"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

diff --git a/features/nyxus-tool/src/polus/images/features/nyxus_plugin/__init__.py b/features/nyxus-tool/src/polus/images/features/nyxus_plugin/__init__.py
@@ -1,2 +1,2 @@
 """Nyxus Plugin."""
-__version__ = "0.1.7"
+__version__ = "0.1.8-dev0"
diff --git a/features/pixel-segmentation-eval-tool/.bumpversion.cfg b/features/pixel-segmentation-eval-tool/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.12
+current_version = 0.1.13-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

diff --git a/features/pixel-segmentation-eval-tool/CHANGELOG.md b/features/pixel-segmentation-eval-tool/CHANGELOG.md
@@ -1,4 +1,4 @@
-# pixel-segmentation-eval(v0.1.12)
+# pixel-segmentation-eval(v0.1.13-dev0)
 
 1. This plugin is updated only to the new plugin standards
 2. `csv` python packages is replaced with vaex for adding support for additional tabular file formats `.arrow`, `.feather`.

diff --git a/features/pixel-segmentation-eval-tool/README.md b/features/pixel-segmentation-eval-tool/README.md
@@ -1,4 +1,4 @@
-# Pixel segmentation eval (v0.1.12)
+# Pixel segmentation eval (v0.1.13-dev0)
 
 Plugin to generate evaluation metrics for pixel-wise comparison of ground truth and predicted images. Contact [Vishakha Goyal](mailto:vishakha.goyal@nih.gov) , [Hamdah Shafqat Abbasi](mailto:hamdahshafqat.abbasi@nih.gov) for more information.
 

diff --git a/features/pixel-segmentation-eval-tool/VERSION b/features/pixel-segmentation-eval-tool/VERSION
@@ -1 +1 @@
-0.1.12
+0.1.13-dev0
diff --git a/features/pixel-segmentation-eval-tool/plugin.json b/features/pixel-segmentation-eval-tool/plugin.json
@@ -1,14 +1,14 @@
 {
   "name": "Pixel Segmentation Eval",
-  "version": "0.1.12",
+  "version": "0.1.13-dev0",
   "title": "Pixel Segmentation Eval",
   "description": "Plugin to generate evaluation metrics for pixel-wise comparison of ground truth and predicted images.",
   "author": "Vishakha Goyal (vishakha.goyal@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/polusai/polus-plugins",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/pixel-segmentation-eval-tool:0.1.12",
+  "containerId": "polusai/pixel-segmentation-eval-tool:0.1.13-dev0",
   "baseCommand": [
     "python3",
     "-m",

diff --git a/features/pixel-segmentation-eval-tool/pyproject.toml b/features/pixel-segmentation-eval-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-features-pixel-segmentation-eval"
-version = "0.1.12"
+version = "0.1.13-dev0"
 description = ""
 authors = [
            "Vishakha Goyal <vishakha.goyal@nih.gov>",
@@ -18,6 +18,7 @@ tqdm = "^4.64.1"
 tifffile="^2020.10.1"
 vaex = "^4.7.0"
 scipy = "1.9.3"
+pyarrow = ">=16.0,<17.0"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

diff --git a/...ixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__init__.py b/...ixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__init__.py
@@ -1,3 +1,3 @@
 """Pixel segmentation eval package."""
 
-__version__ = "0.1.12"
+__version__ = "0.1.13-dev0"
diff --git a/features/region-segmentation-eval-tool/.bumpversion.cfg b/features/region-segmentation-eval-tool/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.5
+current_version = 0.2.6-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

diff --git a/features/region-segmentation-eval-tool/VERSION b/features/region-segmentation-eval-tool/VERSION
@@ -1 +1 @@
-0.2.5
+0.2.6-dev0
diff --git a/features/region-segmentation-eval-tool/plugin.json b/features/region-segmentation-eval-tool/plugin.json
@@ -1,14 +1,14 @@
 {
   "name": "Region Segmentation Eval",
-  "version": "0.2.5",
+  "version": "0.2.6-dev0",
   "title": "Region Segmentation Eval",
   "description": "Plugin to generate evaluation metrics for region-wise comparison of ground truth and predicted images.",
   "author": "Vishakha Goyal (vishakha.goyal@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/polusai/polus-plugins",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/region-segmentation-eval-tool:0.2.5",
+  "containerId": "polusai/region-segmentation-eval-tool:0.2.6-dev0",
   "baseCommand": [
     "python3",
     "-m",

diff --git a/features/region-segmentation-eval-tool/pyproject.toml b/features/region-segmentation-eval-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-features-region-segmentation-eval"
-version = "0.2.5"
+version = "0.2.6-dev0"
 description = ""
 authors = [
            "Vishakha Goyal <vishakha.goyal@nih.gov>",
@@ -16,14 +16,16 @@ filepattern = "^2.0.1"
 typer = "^0.7.0"
 tqdm = "^4.64.1"
 scikit-image = "^0.19.3"
-scikit-learn="^0.24.2"
 opencv_python="^4.5.1.48"
 tifffile="^2020.10.1"
 blake3 = "^0.3.3"
-llvmlite = "^0.39.1"
 fastapi = "^0.92.0"
 vaex = "^4.7.0"
 numpy = "<2.0.0"
+pyarrow = ">=16.0,<17.0"
+scikit-learn = "^1.5.1"
+numba = "^0.60.0"
+llvmlite = "^0.43.0"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

diff --git a/...ion-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__init__.py b/...ion-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__init__.py
@@ -1,2 +1,2 @@
 """Region segmentation eval package."""
-__version__ = "0.2.5"
+__version__ = "0.2.6-dev0"
diff --git a/visualization/ome-to-microjson-tool/.bumpversion.cfg b/visualization/ome-to-microjson-tool/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.5
+current_version = 0.1.6-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

diff --git a/visualization/ome-to-microjson-tool/README.md b/visualization/ome-to-microjson-tool/README.md
@@ -1,4 +1,4 @@
-# Ome-to-microjson-plugin(v0.1.5)
+# Ome-to-microjson-plugin(v0.1.6-dev0)
 
 This plugin generate a microjson of polygon coordinates of binary or label segmentations
 
@@ -50,7 +50,7 @@ This plugin can take four input arguments and one output argument:
 ### Run the Docker Container
 
 ```bash
-docker run -v /data:/data polusai/ome-to-microjson-plugin:0.1.5-dev \
+docker run -v /data:/data polusai/ome-to-microjson-plugin:0.1.6-dev0-dev \
   --inpDir /data/input \
   --filePattern ".*.ome.tif" \
   --polygonType "encoding" \

diff --git a/visualization/ome-to-microjson-tool/VERSION b/visualization/ome-to-microjson-tool/VERSION
@@ -1 +1 @@
-0.1.5
+0.1.6-dev0
diff --git a/visualization/ome-to-microjson-tool/plugin.json b/visualization/ome-to-microjson-tool/plugin.json
@@ -1,14 +1,14 @@
 {
   "name": "Ome_to_microjson",
-  "version": "0.1.5",
+  "version": "0.1.6-dev0",
   "title": "Convert binary segmentations to micojson",
   "description": "This plugin create a microjson of polygon coordinates (rectangle, encodings) of binary segmentations.",
   "author": "Hamdah Shafqat abbasi  (hamdahshafqat.abbasi@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/labshare/polus-plugins",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/ome-to-microjson-tool:0.1.5",
+  "containerId": "polusai/ome-to-microjson-tool:0.1.6-dev0",
   "baseCommand": [
     "python3",
     "-m",

diff --git a/visualization/ome-to-microjson-tool/pyproject.toml b/visualization/ome-to-microjson-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-visualization-ome-to-microjson"
-version = "0.1.5"
+version = "0.1.6-dev0"
 description = "This plugin create a microjson of polygon coordinates of binary and label segmentations"
 authors = ["Hamdah Shafqat abbasi  <hamdahshafqat.abbasi@nih.gov>"]
 readme = "README.md"
@@ -19,6 +19,7 @@ llvmlite = "^0.40.1"
 vaex = "^4.17.0"
 scikit-image = "^0.20.0"
 memory-profiler = "^0.61.0"
+pyarrow = ">=16.0,<17.0"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

diff --git a/...ization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__init__.py b/...ization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__init__.py
@@ -1,3 +1,3 @@
 """Ome micojson package."""
 
-__version__ = "0.1.5"
+__version__ = "0.1.6-dev0"
diff --git a/visualization/tabular-to-microjson-tool/.bumpversion.cfg b/visualization/tabular-to-microjson-tool/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.2
+current_version = 0.1.3-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

diff --git a/visualization/tabular-to-microjson-tool/VERSION b/visualization/tabular-to-microjson-tool/VERSION
@@ -1 +1 @@
-0.1.2
+0.1.3-dev0
diff --git a/visualization/tabular-to-microjson-tool/plugin.json b/visualization/tabular-to-microjson-tool/plugin.json
@@ -1,7 +1,7 @@
 {
   "name": "Tabular To Microjson",
-  "version": "0.1.2",
-  "containerId": "polusai/tabular-to-microjson-tool:0.1.2",
+  "version": "0.1.3-dev0",
+  "containerId": "polusai/tabular-to-microjson-tool:0.1.3-dev0",
   "title": "Tabular To Microjson",
   "description": "Generates JSON from tabular data.",
   "author": "Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)",

diff --git a/visualization/tabular-to-microjson-tool/pyproject.toml b/visualization/tabular-to-microjson-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-visualization-tabular-to-microjson"
-version = "0.1.2"
+version = "0.1.3-dev0"
 description = ""
 authors = ["Hamdah Shafqat abbasi <hamdahshafqat.abbasi@nih.gov>"]
 readme = "README.md"
@@ -15,6 +15,7 @@ pandas = "^2.0.3"
 microjson = "^0.1.9"
 vaex = "^4.17.0"
 pydantic = "^2.4.2"
+pyarrow = ">=16.0,<17.0"
 
 
 [tool.poetry.group.dev.dependencies]

diff --git a/...tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py b/...tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py
@@ -1,2 +1,2 @@
 """Tabular to microjson package."""
-__version__ = "0.1.2"
+__version__ = "0.1.3-dev0"