check-linear-fit (#73)

Co-authored-by: Brandon Duane Walker <[email protected]>

utils/fitting/check-linear-fit-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/mm/utils/check_linear_fit/__init__.py]

utils/fitting/check-linear-fit-tool/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/fitting/check-linear-fit-tool/.gitignore

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+poetry.lock

utils/fitting/check-linear-fit-tool/CHANGELOG.md

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

utils/fitting/check-linear-fit-tool/Dockerfile

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+# docker build -f Dockerfile -t mrbrandonwalker/check_linear_fit .
+FROM condaforge/mambaforge
+
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_LOG="INFO"
+RUN mkdir -p ${EXEC_DIR}
+
+# 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}
+
+# Install needed packages here
+
+COPY src ${EXEC_DIR}/src
+
+RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+CMD ["--help"]

utils/fitting/check-linear-fit-tool/README.md

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+# check_linear_fit (0.1.0)
+
+check_linear_fit
+
+## Options
+
+This plugin takes     6     input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| script |  | Input | string | string |
+| xs |  | Input | {'type': 'array', 'items': 'float'} | {'type': 'array', 'items': 'float'} |
+| ys |  | Input | {'type': 'array', 'items': 'float'} | {'type': 'array', 'items': 'float'} |
+| tol_quad |  | Input | float | float |
+| slope_min |  | Input | float | float |
+| slope_max |  | Input | float | float |
+| success |  | Output | boolean | boolean |

utils/fitting/check-linear-fit-tool/VERSION

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+0.1.0

utils/fitting/check-linear-fit-tool/check_linear_fit.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: check_linear_fit
+
+doc: |-
+  check_linear_fit
+
+baseCommand: ["python", "-m", "polus.mm.utils.check_linear_fit"]
+
+requirements:
+  DockerRequirement:
+    dockerPull: mrbrandonwalker/check_linear_fit
+  InlineJavascriptRequirement: {}
+
+inputs:
+
+  xs:
+    type:
+      type: array
+      items: float
+    inputBinding:
+      prefix: --xs
+
+  ys:
+    type:
+      type: array
+      items: float
+    inputBinding:
+      prefix: --ys
+
+  tol_quad:
+    type: float
+    inputBinding:
+      prefix: --tol_quad
+
+  slope_min:
+    type: float
+    inputBinding:
+      prefix: --slope_min
+
+  slope_max:
+    type: float
+    inputBinding:
+      prefix: --slope_max
+
+outputs:
+  success:
+    type: boolean
+    outputBinding:
+      outputEval: $(true)  # If check_linear_fit.py didn't call sys.exit(1), then it called sys.exit(0)
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/fitting/check-linear-fit-tool/ict.yml

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+specVersion: "0.1.0"
+name: check_linear_fit
+version: 0.1.0
+container: check-linear-fit-tool
+entrypoint:
+title: check_linear_fit
+description: check_linear_fit
+author: Data Scientist
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: script
+    required: true
+    description:
+    type: string
+    defaultValue: /check_linear_fit.py
+  - name: xs
+    required: true
+    description:
+    type: {'type': 'array', 'items': 'float'}
+  - name: ys
+    required: true
+    description:
+    type: {'type': 'array', 'items': 'float'}
+  - name: tol_quad
+    required: true
+    description:
+    type: float
+  - name: slope_min
+    required: true
+    description:
+    type: float
+  - name: slope_max
+    required: true
+    description:
+    type: float
+outputs:
+  - name: success
+    required: true
+    description:
+    type: boolean
+ui:
+  - key: inputs.script
+    title: "script: "
+    description: ""
+    type: string
+  - key: inputs.xs
+    title: "xs: "
+    description: ""
+    type: {'type': 'array', 'items': 'float'}
+  - key: inputs.ys
+    title: "ys: "
+    description: ""
+    type: {'type': 'array', 'items': 'float'}
+  - key: inputs.tol_quad
+    title: "tol_quad: "
+    description: ""
+    type: float
+  - key: inputs.slope_min
+    title: "slope_min: "
+    description: ""
+    type: float
+  - key: inputs.slope_max
+    title: "slope_max: "
+    description: ""
+    type: float

utils/fitting/check-linear-fit-tool/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-check-linear-fit"
+version = "0.1.0"
+description = "check_linear_fit"
+authors = ["Data Scientist <[email protected]>"]
+readme = "README.md"
+packages = [{include = "polus", from = "src"}]
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12"
+typer = "^0.7.0"
+cwl-utils = "0.33"
+cwltool = "3.1.20240404144621"
+numpy = "1.26.4"
+scipy = "1.13.0"
+
+[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 = [
+  "."
+]

utils/fitting/check-linear-fit-tool/src/polus/mm/utils/check_linear_fit/__init__.py

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+"""check_linear_fit."""
+
+__version__ = "0.1.0"
+
+from polus.mm.utils.check_linear_fit.check_linear_fit import (  # noqa # pylint: disable=unused-import
+    check_linear_fit,
+)

utils/fitting/check-linear-fit-tool/src/polus/mm/utils/check_linear_fit/__main__.py

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+"""Package entrypoint for the check_linear_fit package."""
+
+# Base packages
+import logging
+import sys
+from os import environ
+
+import typer
+from polus.mm.utils.check_linear_fit.check_linear_fit import check_linear_fit
+
+logging.basicConfig(
+    format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s",
+    datefmt="%d-%b-%y %H:%M:%S",
+)
+POLUS_LOG = getattr(logging, environ.get("POLUS_LOG", "INFO"))
+logger = logging.getLogger("polus.mm.utils.check_linear_fit.")
+logger.setLevel(POLUS_LOG)
+
+app = typer.Typer(help="check_linear_fit.")
+
+
+@app.command()
+def main(
+    xs: list[float] = typer.Option(
+        ...,
+        "--xs",
+        help="",
+    ),
+    ys: list[float] = typer.Option(
+        ...,
+        "--ys",
+        help="",
+    ),
+    tol_quad: float = typer.Option(
+        ...,
+        "--tol_quad",
+        help="",
+    ),
+    slope_min: float = typer.Option(
+        ...,
+        "--slope_min",
+        help="",
+    ),
+    slope_max: float = typer.Option(
+        ...,
+        "--slope_max",
+        help="",
+    ),
+) -> None:
+    """check_linear_fit."""
+    logger.info(f"xs: {xs}")
+    logger.info(f"ys: {ys}")
+    logger.info(f"tol_quad: {tol_quad}")
+    logger.info(f"slope_min: {slope_min}")
+    logger.info(f"slope_max: {slope_max}")
+
+    is_linear_and_within_bounds = check_linear_fit(
+        xs=xs,
+        ys=ys,
+        tol_quad=tol_quad,
+        slope_min=slope_min,
+        slope_max=slope_max,
+    )
+    if is_linear_and_within_bounds:
+        sys.exit(0)
+    else:
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    app()