Nyxus fix entrypoint

features/nyxus-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.8
+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+))?
@@ -26,4 +26,8 @@ replace = version = "{new_version}"
 
 [bumpversion:file:README.md]
 
-[bumpversion:file:src/polus/images/features/nyxus_plugin/__init__.py]
+[bumpversion:file:ict.yaml]
+
+[bumpversion:file:nyxusplugin.cwl]
+
+[bumpversion:file:src/polus/images/features/nyxus_tool/__init__.py]

features/nyxus-tool/CHANGELOG.md

@@ -1,13 +1,3 @@
-## Nyxus Plugin(v0.1.5-dev1)
-1. This plugin is updated only to the new plugin standards
-2. vaex package is included to handle large pandas dataframe and convert to `csv` ouputs by loading dataframe in chunks.
-3. Implemented latest updated filepattern package
-4. Updated nyxus package
-5. Updated preadator package
-6. This plugin is now installable with pip.
-7. Argparse package is replaced with Typer package for command line arguments.
-8. `baseCommand` added in a plugin manifiest.
-9. `--preview` flag is added which shows outputs to be generated by this plugin.
-10. Use `python -m python -m polus.plugins.features.nyxus_plugin` to run plugin from command line.
-11. Replaced `Unittest` with `pytest` package.
-12. This plugin now support additional ouput format for example `arrowipc` and `parquet`
+## [0.1.8-dev0] - 2024-09-26
+- Renamed nyxus-plugin to nyxus-tool.
+- updated nyxus package and bfio base-container image.

features/nyxus-tool/Dockerfile

@@ -1,4 +1,4 @@
-FROM polusai/bfio:2.3.3
+FROM polusai/bfio:2.4.3
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
@@ -21,5 +21,5 @@ RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
 # Set the entrypoint
 # TODO: Change the entrypoint to the tool entrypoint
-ENTRYPOINT ["python3", "-m", "polus.images.features.nyxus"]
+ENTRYPOINT ["python3", "-m", "polus.images.features.nyxus_tool"]
 CMD ["--help"]

features/nyxus-tool/README.md

@@ -1,4 +1,4 @@
-# Nyxus-Plugin(v0.1.8)
+# 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.

features/nyxus-tool/VERSION

@@ -1 +1 @@
-0.1.8
+0.1.8-dev0

features/nyxus-tool/ict.yaml

@@ -1,120 +1,121 @@
 author:
-- Nick Schaub
-- Hamdah Shafqat
+  - Nick Schaub
+  - Hamdah Shafqat
 contact: [email protected]
-container: polusai/nyxus-tool:0.1.7-dev0
-description: Nyxus plugin allows to make use of parallel pocessing for extracting
+container: polusai/nyxus-tool:0.1.8-dev0
+description:
+  Nyxus plugin allows to make use of parallel pocessing for extracting
   nyxus features
-entrypoint: python3 -m polus.images.features.nyxus_plugin
+entrypoint: python3 -m polus.images.features.nyxus_tool
 inputs:
-- description: Collection containing intensity images
-  format:
-  - collection
-  name: inpDir
-  required: true
-  type: path
-- description: Collection containing label images, i.e. groundtruth images
-  format:
-  - collection
-  name: segDir
-  required: true
-  type: path
-- description: Filepattern to parse intensity images
-  format:
-  - string
-  name: intPattern
-  required: true
-  type: string
-- description: Filepattern to parse label images
-  format:
-  - string
-  name: segPattern
-  required: true
-  type: string
-- description: Features or feature groups to be extracted by nyxus plugin
-  format:
-  - array
-  name: features
-  required: false
-  type: array
-- description: Output file format
-  format:
-  - enum
-  name: fileExtension
-  required: true
-  type: string
-- description: Pixel distance between neighboring cells
-  format:
-  - number
-  name: neighborDist
-  required: false
-  type: number
-- description: Pixel size in micrometer
-  format:
-  - number
-  name: pixelPerMicron
-  required: false
-  type: number
-- description: Consider intensity image as single roi and ignoring segmentation mask
-  format:
-  - boolean
-  name: singleRoi
-  required: false
-  type: boolean
+  - description: Collection containing intensity images
+    format:
+      - collection
+    name: inpDir
+    required: true
+    type: path
+  - description: Collection containing label images, i.e. groundtruth images
+    format:
+      - collection
+    name: segDir
+    required: true
+    type: path
+  - description: Filepattern to parse intensity images
+    format:
+      - string
+    name: intPattern
+    required: true
+    type: string
+  - description: Filepattern to parse label images
+    format:
+      - string
+    name: segPattern
+    required: true
+    type: string
+  - description: Features or feature groups to be extracted by nyxus plugin
+    format:
+      - array
+    name: features
+    required: false
+    type: array
+  - description: Output file format
+    format:
+      - enum
+    name: fileExtension
+    required: true
+    type: string
+  - description: Pixel distance between neighboring cells
+    format:
+      - number
+    name: neighborDist
+    required: false
+    type: number
+  - description: Pixel size in micrometer
+    format:
+      - number
+    name: pixelPerMicron
+    required: false
+    type: number
+  - description: Consider intensity image as single roi and ignoring segmentation mask
+    format:
+      - boolean
+    name: singleRoi
+    required: false
+    type: boolean
 name: polusai/Nyxusplugin
 outputs:
-- description: Output collection
-  format:
-  - collection
-  name: outDir
-  required: true
-  type: path
-repository: https://github.com/PolusAI/polus-plugins
+  - description: Output collection
+    format:
+      - collection
+    name: outDir
+    required: true
+    type: path
+repository: https://github.com/PolusAI/image-tools
 specVersion: 1.0.0
 title: Nyxus plugin
 ui:
-- description: Input image collection
-  key: inputs.inpDir
-  title: inpDir
-  type: path
-- description: Label image collection
-  key: inputs.segDir
-  title: segDir
-  type: path
-- description: Filepattern to parse intensity images
-  key: inputs.intPattern
-  title: intPattern
-  type: text
-- description: Filepattern to parse label images
-  key: inputs.segPattern
-  title: segPattern
-  type: text
-- description: Features or feature groups to be extracted by nyxus plugin
-  key: inputs.features
-  title: features
-  type: text
-- description: Ouput file format
-  fields:
-  - .arrow
-  - .feather
-  - .csv
-  - default
-  key: inputs.fileExtension
-  title: fileExtension
-  type: select
-- default: 5
-  description: Pixel distance between neighboring cells
-  key: inputs.neighborDist
-  title: neighborDist
-  type: number
-- default: 1.0
-  description: Pixel size in micrometer
-  key: inputs.pixelPerMicron
-  title: pixelPerMicron
-  type: number
-- default: false
-  description: Consider intensity image as single roi and ignoring segmentation mask
-  key: inputs.singleRoi
-  title: singleRoi
-  type: checkbox
-version: 0.1.7-dev0
+  - description: Input image collection
+    key: inputs.inpDir
+    title: inpDir
+    type: path
+  - description: Label image collection
+    key: inputs.segDir
+    title: segDir
+    type: path
+  - description: Filepattern to parse intensity images
+    key: inputs.intPattern
+    title: intPattern
+    type: text
+  - description: Filepattern to parse label images
+    key: inputs.segPattern
+    title: segPattern
+    type: text
+  - description: Features or feature groups to be extracted by nyxus plugin
+    key: inputs.features
+    title: features
+    type: text
+  - description: Ouput file format
+    fields:
+      - .arrow
+      - .feather
+      - .csv
+      - default
+    key: inputs.fileExtension
+    title: fileExtension
+    type: select
+  - default: 5
+    description: Pixel distance between neighboring cells
+    key: inputs.neighborDist
+    title: neighborDist
+    type: number
+  - default: 1.0
+    description: Pixel size in micrometer
+    key: inputs.pixelPerMicron
+    title: pixelPerMicron
+    type: number
+  - default: false
+    description: Consider intensity image as single roi and ignoring segmentation mask
+    key: inputs.singleRoi
+    title: singleRoi
+    type: checkbox
+version: 0.1.8-dev0

features/nyxus-tool/nyxusplugin.cwl

@@ -48,7 +48,7 @@ outputs:
     type: Directory
 requirements:
   DockerRequirement:
-    dockerPull: polusai/nyxus-tool:0.1.7-dev0
+    dockerPull: polusai/nyxus-tool:0.1.8-dev0
   InitialWorkDirRequirement:
     listing:
     - entry: $(inputs.outDir)

features/nyxus-tool/package-release.sh

@@ -10,7 +10,7 @@ bump2version --config-file bumpversion.cfg --new-version ${version} --allow-dirt
 ./build-docker.sh
 
 # Push to dockerhub
-docker push polusai/nyxus-plugin:${version}
+docker push polusai/nyxus-tool:${version}
 
 # Run unittests
 python -m unittest

features/nyxus-tool/plugin.json

@@ -1,18 +1,18 @@
 {
   "name": "Nyxus plugin",
-  "version": "0.1.8",
-  "containerId": "polusai/nyxus-tool:0.1.8",
+  "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 ([email protected]), Hamdah Shafqat Abbasi ([email protected])",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
-  "repository": "https://github.com/PolusAI/polus-plugins",
+  "repository": "https://github.com/PolusAI/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
   "baseCommand": [
     "python3",
     "-m",
-    "polus.images.features.nyxus_plugin"
+    "polus.images.features.nyxus_tool"
   ],
   "inputs": [
     {

features/nyxus-tool/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
-name = "polus-images-features-nyxus-plugin"
-version = "0.1.8"
+name = "polus-images-features-nyxus-tool"
+version = "0.1.8-dev0"
 description = ""
 authors = [
            "Nick Schaub <[email protected]>",
@@ -14,14 +14,13 @@ python = ">=3.9,<3.12"
 filepattern = "2.0.4"
 typer = "^0.7.0"
 tqdm = "^4.66.1"
-nyxus = "^0.7.3"
-fastapi = "^0.92.0"
-astropy = "5.2.1"
+nyxus = "^0.8.2"
 vaex = "^4.17.0"
 preadator = "0.4.0.dev2"
 pytest-sugar = "^0.9.7"
 pytest-xdist = "^3.5.0"
 pyarrow = ">=16.0,<17.0"
+numpy = "<2.0.0"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"
@@ -32,7 +31,7 @@ mypy = "^1.0.0"
 pytest = "^7.2.1"
 ipykernel = "^6.21.2"
 requests = "^2.28.2"
-scikit-image = "^0.20.0"
+scikit-image = "0.24.0"
 
 [build-system]
 requires = ["poetry-core"]

features/nyxus-tool/run-plugin.sh

@@ -21,7 +21,7 @@ out_dir=/data/path_to_output
 # docker run polusai/nyxus-plugin:${version}
 
 docker run --mount type=bind,source=${datapath},target=/data/ \
-            polusai/nyxus-plugin:${version} \
+            polusai/nyxus-tool:${version} \
             --inpDir ${inp_dir} \
             --segDir ${seg_dir} \
             --outDir ${out_dir} \

features/nyxus-tool/src/polus/images/features/nyxus_tool/__init__.py

@@ -0,0 +1,2 @@
+"""Nyxus Plugin."""
+__version__ = "0.1.8-dev0"