modify base container to fix singularity issue

formats/file-renaming-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.4
+current_version = 0.2.4-dev2
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
@@ -22,6 +22,10 @@ replace = version = "{new_version}"
 
 [bumpversion:file:plugin.json]
 
+[bumpversion:file:filerenaming.cwl]
+
+[bumpversion:file:ict.yaml]
+
 [bumpversion:file:VERSION]
 
 [bumpversion:file:src/polus/images/formats/file_renaming/__init__.py]

formats/file-renaming-tool/Dockerfile

@@ -1,4 +1,4 @@
-FROM polusai/bfio:2.3.6
+FROM polusai/bfio:2.3.3
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"

formats/file-renaming-tool/README.md

@@ -1,4 +1,4 @@
-# File Renaming(0.2.4-dev0)
+# File Renaming(0.2.4-dev2)
 This WIPP plugin uses supplied file naming patterns to dynamically
 rename and save files in an image collection to a new image collection.
 

formats/file-renaming-tool/VERSION

@@ -1 +1 @@
-0.2.4
+0.2.4-dev2

formats/file-renaming-tool/filerenaming.cwl

@@ -28,7 +28,7 @@ outputs:
     type: Directory
 requirements:
   DockerRequirement:
-    dockerPull: polusai/file-renaming-tool:0.2.4-dev0
+    dockerPull: polusai/file-renaming-tool:0.2.4-dev2
   InitialWorkDirRequirement:
     listing:
     - entry: $(inputs.outDir)

formats/file-renaming-tool/ict.yaml

@@ -1,65 +1,65 @@
 author:
-- Melanie Parham
-- Hamdah Shafqat
+  - Melanie Parham
+  - Hamdah Shafqat
 contact: melanie.parham@axleinfo.com
-container: polusai/file-renaming-tool:0.2.4-dev0
+container: polusai/file-renaming-tool:0.2.4-dev2
 description: Rename and store image collection files in a new image collection
 entrypoint: python3 -m polus.images.formats.file_renaming
 inputs:
-- description: Filename pattern used to separate data
-  format:
-  - string
-  name: filePattern
-  required: true
-  type: string
-- description: Input image collection to be processed by this plugin
-  format:
-  - collection
-  name: inpDir
-  required: true
-  type: path
-- description: Desired filename pattern used to rename and separate data
-  format:
-  - string
-  name: outFilePattern
-  required: true
-  type: string
-- description: Get directory name incorporated in renamed files
-  format:
-  - enum
-  name: mapDirectory
-  required: false
-  type: string
+  - description: Filename pattern used to separate data
+    format:
+      - string
+    name: filePattern
+    required: true
+    type: string
+  - description: Input image collection to be processed by this plugin
+    format:
+      - collection
+    name: inpDir
+    required: true
+    type: path
+  - description: Desired filename pattern used to rename and separate data
+    format:
+      - string
+    name: outFilePattern
+    required: true
+    type: string
+  - description: Get directory name incorporated in renamed files
+    format:
+      - enum
+    name: mapDirectory
+    required: false
+    type: string
 name: polusai/FileRenaming
 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: File Renaming
 ui:
-- description: Filename pattern used to separate data
-  key: inputs.filePattern
-  title: Filename pattern
-  type: text
-- description: Input image collection to be processed by this plugin
-  key: inputs.inpDir
-  title: Input collection
-  type: path
-- description: Desired filename pattern used to rename and separate data
-  key: inputs.outFilePattern
-  title: Output filename pattern
-  type: text
-- description: Get directory name incorporated in renamed files
-  fields:
-  - raw
-  - map
-  - default
-  key: inputs.mapDirectory
-  title: mapDirectory
-  type: select
-version: 0.2.4-dev0
+  - description: Filename pattern used to separate data
+    key: inputs.filePattern
+    title: Filename pattern
+    type: text
+  - description: Input image collection to be processed by this plugin
+    key: inputs.inpDir
+    title: Input collection
+    type: path
+  - description: Desired filename pattern used to rename and separate data
+    key: inputs.outFilePattern
+    title: Output filename pattern
+    type: text
+  - description: Get directory name incorporated in renamed files
+    fields:
+      - raw
+      - map
+      - default
+    key: inputs.mapDirectory
+    title: mapDirectory
+    type: select
+version: 0.2.4-dev2

formats/file-renaming-tool/plugin.json

@@ -1,14 +1,14 @@
 {
   "name": "File Renaming",
-  "version": "0.2.4",
+  "version": "0.2.4-dev2",
   "title": "File Renaming",
   "description": "Rename and store image collection files in a new image collection",
   "author": "Melanie Parham (melanie.parham@axleinfo.com), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/file-renaming-tool:0.2.4",
+  "containerId": "polusai/file-renaming-tool:0.2.4-dev2",
   "baseCommand": [
     "python3",
     "-m",

formats/file-renaming-tool/pyproject.toml

@@ -1,10 +1,10 @@
 [tool.poetry]
 name = "polus-images-formats-file-renaming"
-version = "0.2.4"
-description = "Rename and store image collection files in a new image collection"
+version = "0.2.4-dev2"
+description = "Convert BioFormats datatypes to ome.tif or ome.zarr file format"
 authors = [
-"Melanie Parham <melanie.parham@axleinfo.com>",
-"Hamdah Shafqat abbasi <hamdahshafqat.abbasi@nih.gov>"
+    "Hamdah Shafqat abbasi <hamdahshafqat.abbasi@nih.gov>",
+    "Melanie Parham <melanie.parham@axleinfo.com>",
 ]
 readme = "README.md"
 packages = [{include = "polus", from = "src"}]
@@ -26,3 +26,8 @@ pytest = "^7.2.1"
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]

formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py

@@ -1,4 +1,4 @@
 """File Renaming."""
-__version__ = "0.2.4"
+__version__ = "0.2.4-dev2"
 
 from . import file_renaming