From 82b382fe627ddec70e2dc994af2d8b910139ca6b Mon Sep 17 00:00:00 2001 From: Hamdah Shafqat Abbasi Date: Tue, 5 Nov 2024 07:43:46 -0500 Subject: [PATCH] modify base container to fix singularity issue --- formats/file-renaming-tool/.bumpversion.cfg | 6 +- formats/file-renaming-tool/Dockerfile | 2 +- formats/file-renaming-tool/README.md | 2 +- formats/file-renaming-tool/VERSION | 2 +- formats/file-renaming-tool/filerenaming.cwl | 2 +- formats/file-renaming-tool/ict.yaml | 110 +++++++++--------- formats/file-renaming-tool/plugin.json | 4 +- formats/file-renaming-tool/pyproject.toml | 13 ++- .../images/formats/file_renaming/__init__.py | 2 +- 9 files changed, 76 insertions(+), 67 deletions(-) diff --git a/formats/file-renaming-tool/.bumpversion.cfg b/formats/file-renaming-tool/.bumpversion.cfg index 9f1772079..4894cd358 100644 --- a/formats/file-renaming-tool/.bumpversion.cfg +++ b/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\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\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] diff --git a/formats/file-renaming-tool/Dockerfile b/formats/file-renaming-tool/Dockerfile index 52c8c942e..5a194d252 100644 --- a/formats/file-renaming-tool/Dockerfile +++ b/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" diff --git a/formats/file-renaming-tool/README.md b/formats/file-renaming-tool/README.md index 37e01d17d..cbdd4d0cb 100644 --- a/formats/file-renaming-tool/README.md +++ b/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. diff --git a/formats/file-renaming-tool/VERSION b/formats/file-renaming-tool/VERSION index abd410582..0184eef11 100644 --- a/formats/file-renaming-tool/VERSION +++ b/formats/file-renaming-tool/VERSION @@ -1 +1 @@ -0.2.4 +0.2.4-dev2 diff --git a/formats/file-renaming-tool/filerenaming.cwl b/formats/file-renaming-tool/filerenaming.cwl index 454a1dae8..2eafae2a4 100644 --- a/formats/file-renaming-tool/filerenaming.cwl +++ b/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) diff --git a/formats/file-renaming-tool/ict.yaml b/formats/file-renaming-tool/ict.yaml index 56e75a25e..05b4908e0 100644 --- a/formats/file-renaming-tool/ict.yaml +++ b/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 diff --git a/formats/file-renaming-tool/plugin.json b/formats/file-renaming-tool/plugin.json index 082e9600c..db3792d99 100644 --- a/formats/file-renaming-tool/plugin.json +++ b/formats/file-renaming-tool/plugin.json @@ -1,6 +1,6 @@ { "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)", @@ -8,7 +8,7 @@ "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", diff --git a/formats/file-renaming-tool/pyproject.toml b/formats/file-renaming-tool/pyproject.toml index 3f1d2dafb..b3f924812 100644 --- a/formats/file-renaming-tool/pyproject.toml +++ b/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 ", -"Hamdah Shafqat abbasi " + "Hamdah Shafqat abbasi ", + "Melanie Parham ", ] 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 = [ + "." +] diff --git a/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py b/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py index 53b82f8f8..e0a3361b7 100644 --- a/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py +++ b/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