added template for tabular tools

tabular-templates/.gitignore

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+poetry.lock

tabular-templates/python-template/.bumpversion.cfg

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+[bumpversion]
+current_version = 1.1.0-dev1
+commit = False
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:README.md]

tabular-templates/python-template/CHANGELOG.md

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+# CHANGELOG
+
+# 1.0.0
+
+* Generate plugins from templates using cookiecutter.
+
+# 1.1.0
+
+* Generate plugins following updated [standard guidelines](https://labshare.atlassian.net/wiki/spaces/WIPP/pages/3275980801/Python+Plugin+Standards)

tabular-templates/python-template/README.md

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+# WIPP Plugin Cookie Cutter (for Python) (1.1.0-dev1)
+
+This repository is a cookie cutter template that creates the basic scaffold structure of a
+polus plugin and add it to the polus plugins directory structure.
+
+## How to use
+1. Clone `tools-templates` and change to the polus-plugins directory
+2. `cd tabular-templates/python-template`
+3. (optional) Install poetry if not available.
+4. (optional) Create a dedicated environment with conda or venv.
+5.  Install the dependencies: `poetry install`
+6. Modify `cookiecutter.json` to include author and plugin information.`plugin_package` should always start with `polus.tabular`. 
+** NOTE: ** Do not edit values in brackets ({}) as they are edited by cookiecutter directly.
+Those are automatically generated from the previous entries. If your plugin is called 
+"Awesome Function", then the plugin folder and docker container will have the name `awesome-function-plugin`.
+7. Create your plugin skeleton: `python -m cookiecutter . --no-input`
+
+
+## Plugin Standard
+The generated plugin will be compatible with polus most up-to-date guidelines :
+see [standard guidelines](https://labshare.atlassian.net/wiki/spaces/WIPP/pages/3275980801/Python+Plugin+Standards)
+
+The code generated provides out-of-box support for :
+    - customizing the plugin code.
+    - implementing tests.
+    - creating and running a container.
+    - managing versioning.
+    - updating documentation (README, CHANGELOG).
+    - maintaining a WIPP manifest (plugin.json).
+
+
+## Executing the plugin
+
+The plugin should be run as a package.
+To install the package :
+
+`pip install .`
+
+The skeleton code can be run this way :
+From the plugin's top directory (with the default values):
+
+`python -m polus.tabular.package1.package2.awesome_function -i /tmp/inp -o /tmp/out`
+
+This should print some logs with the provided inputs and outputs and return.
+
+## Running tests
+Plugin's developer should use `pytest`.
+Some simple tests have been added to the template as examples.
+Before submitting a PR to `tabular-tools`, other unit tests should be created and added to the `tests`
+directory.
+
+To run tests :
+
+From the plugin's top directory, type `python -m pytest`.
+Depending on how you have set up your environment, you may be able to run the pytest cli directly `pytest`. See pytest doc for how the project source directory is scanned to collect tests.
+This should run a test successfully and return.
+
+
+## Creating and running a container
+
+` ./build-docker.sh &&  ./run-plugin.sh`
+
+Build the docker image and run the container.
+
+### DockerFile
+A docker image is build from a base image with common dependencies pre-installed.
+The image entrypoint will run the plugin's package entrypoint.
+
+### build-docker.sh
+Run this script to build the container.
+
+### run-plugin.sh
+Run the container locally.
+
+
+## Customize the plugin
+
+### Project code
+
+A set of common dependencies are added to `pyproject.toml`.
+Update according to your needs.
+
+### Managing versioning
+
+Making sure that the file version is consistent across files in a plugin can be
+challenging, so the Python template now uses
+[bump2version](https://github.com/c4urself/bump2version)
+to help manage versioning. This automatically changes the `VERSION` and
+`plugin.json` files to the next version, preventing you from having to remember
+to change the version everywhere. The `bumpversion.cfg` can be modified to
+change the version in other files as well.
+
+To use this feature:
+`bump2version --config-file bumpversion.cfg`
+
+### Documentation
+
+#### README.md
+
+A basic description of what the plugin does. This should define all the inputs
+and outputs.
+
+#### CHANGELOG.md
+
+Documents updates made to the plugin.
+
+
+### WIPP manifest (plugin.json).
+
+This file defines the input and output variables for WIPP, and defines the UI
+components showed to the user.

tabular-templates/python-template/VERSION

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+1.1.0-dev0

tabular-templates/python-template/awesome-function-tool/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.1.0
+commit = False
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:src/polus/tabular/package1/package2/awesome_function/__init__.py]

tabular-templates/python-template/awesome-function-tool/.dockerignore

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+.venv
+out
+tests
+__pycache__

tabular-templates/python-template/awesome-function-tool/.gitignore

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+poetry.lock

tabular-templates/python-template/awesome-function-tool/CHANGELOG.md

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+# CHANGELOG
+
+## 0.1.0
+
+Initial release.

tabular-templates/python-template/awesome-function-tool/Dockerfile

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+FROM polusai/bfio:2.1.9
+
+# environment variables defined in polusai/bfio
+# ENV EXEC_DIR="/opt/executables"
+# ENV DATA_DIR="/data"
+# ENV POLUS_EXT=".ome.tif"
+# Change to WARNING for fewer logs, and DEBUG for debugging
+ENV POLUS_LOG="INFO"
+
+ENV POLUS_IMG_EXT=".ome.tif"
+ENV POLUS_TAB_EXT=".csv"
+
+# Work directory defined in the base container
+# WORKDIR ${EXEC_DIR}
+
+COPY pyproject.toml ${EXEC_DIR}
+COPY VERSION ${EXEC_DIR}
+COPY README.md ${EXEC_DIR}
+COPY CHANGELOG.md ${EXEC_DIR}
+COPY src ${EXEC_DIR}/src
+
+RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+# Default command. Additional arguments are provided through the command line
+ENTRYPOINT ["python3", "-m", "polus.tabular.package1.package2.awesome_function"]
+CMD ["--help"]

tabular-templates/python-template/awesome-function-tool/README.md

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+# Awesome Tool (0.1.0)
+
+An awesome function.
+
+## Building
+
+To build the Docker image for the conversion plugin, run `./build-docker.sh`.
+
+## Install WIPP Plugin
+
+If WIPP is running, navigate to the plugins page and add a new plugin. Paste the
+contents of `plugin.json` into the pop-up window and submit.
+
+## Options
+
+This plugin takes 2 input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default
+|---------------|-------------------------|--------|--------|
+| inpDir        | Input image collection to be processed by this plugin | Input | collection
+| filePattern   | Filename pattern used to separate data | Input | string | .*
+| preview   | Generate an output preview | Input | boolean | False
+| outDir        | Output collection | Output | collection

tabular-templates/python-template/awesome-function-tool/VERSION

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+0.1.0

tabular-templates/python-template/awesome-function-tool/build-docker.sh

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+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/awesome-function-tool:${version}

tabular-templates/python-template/awesome-function-tool/plugin.json

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+{
+  "name": "Awesome Tool",
+  "version": "0.1.0",
+  "title": "Awesome Tool",
+  "description": "An awesome function.",
+  "author": "Data Scientist ([email protected])",
+  "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
+  "repository": "https://github.com/polusAI/tabular-tools",
+  "website": "https://ncats.nih.gov/preclinical/core/informatics",
+  "citation": "",
+  "containerId": "polusai/awesome-function-tool:0.1.0",
+  "baseCommand": [
+    "python3",
+    "-m",
+    "polus.tabular.package1.package2.awesome_function"
+  ],
+  "inputs": {
+    "inpDir": {
+      "type": "collection",
+      "title": "Input collection",
+      "description": "Input image collection to be processed by this plugin.",
+      "required": "True"
+    },
+    "filePattern": {
+      "type": "string",
+      "title": "Filename pattern",
+      "description": "Filename pattern used to separate data.",
+      "required": "False",
+      "default": ".*"
+    },
+    "preview": {
+      "type": "boolean",
+      "title": "Preview",
+      "description": "Generate an output preview.",
+      "required": "False",
+      "default": "False"
+    }
+  },
+  "outputs": {
+    "outDir": {
+      "type": "collection",
+      "description": "Output collection."
+    }
+  },
+  "ui": {
+    "inpDir": {
+      "type": "collection",
+      "title": "Input collection",
+      "description": "Input image collection to be processed by this plugin.",
+      "required": "True"
+    },
+    "filePattern": {
+      "type": "string",
+      "title": "Filename pattern",
+      "description": "Filename pattern used to separate data.",
+      "required": "False",
+      "default": "False"
+    },
+    "preview": {
+      "type": "boolean",
+      "title": "Filename pattern",
+      "description": "Generate an output preview.",
+      "required": "False",
+      "default": "False"
+    }
+  }
+}

tabular-templates/python-template/awesome-function-tool/pyproject.toml

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+[tool.poetry]
+name = "polus-tabular-package1-package2-awesome-function"
+version = "0.1.0"
+description = "An awesome function."
+authors = ["Data Scientist <[email protected]>"]
+readme = "README.md"
+packages = [{include = "polus", from = "src"}]
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12"
+bfio = {version = ">=2.3.3,<3.0", extras = ["all"]}
+filepattern = ">=2.0.4,<3.0"
+preadator = "^0.4.0.dev2"
+typer = "^0.7.0"
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+pytest = "^7.4"
+pytest-sugar = "^0.9.6"
+pre-commit = "^3.2.1"
+black = "^23.3.0"
+mypy = "^1.1.1"
+ruff = "^0.0.270"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]

tabular-templates/python-template/awesome-function-tool/run-plugin.sh

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+#!/bin/bash
+
+version=$(<VERSION)
+
+# Update with your data
+inpDir=/tmp/path/to/input
+outDir=/tmp/path/to/output
+filepattern="pattern"
+
+
+container_input_dir="/inpDir"
+container_output_dir="/outDir"
+
+docker run -v $inpDir:/${container_input_dir} \
+           -v $outDir:/${container_output_dir} \
+            --user $(id -u):$(id -g) \
+            polusai/awesome-function-tool:${version} \
+            --inpDir ${container_input_dir} \
+            --filePattern ${filepattern} \
+            --outDir ${container_output_dir}

tabular-templates/python-template/awesome-function-tool/src/polus/tabular/package1/package2/awesome_function/__init__.py

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+"""awesome_function."""
+
+__version__ = "0.1.0"
+
+from polus.tabular.package1.package2.awesome_function.awesome_function import (  # noqa # pylint: disable=unused-import
+    awesome_function,
+)