Merge pull request #20 from agerardin/feat/v0.5

Feat/v0.5

regression/rt-cetsa-analysis-tool/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.5.0-dev0
+commit = True
+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:VERSION]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:src/polus/tabular/regression/rt_cetsa_analysis/__init__.py]
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:ict.yml]
+
+[bumpversion:file:rt_cetsa_analysis.cwl]

regression/rt-cetsa-analysis-tool/.gitignore

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+tests/out

regression/rt-cetsa-analysis-tool/Dockerfile

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+FROM polusai/bfio:2.1.9
+
+# environment variables defined in polusai/bfio
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_LOG="INFO"
+
+COPY env-linux.yml ${EXEC_DIR}/env-linux.yml
+# Work directory defined in the base container
+WORKDIR ${EXEC_DIR}
+
+RUN apt-get update && apt-get install -y wget
+RUN mkdir -p miniconda3 && wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda3/miniconda.sh && \
+bash miniconda3/miniconda.sh -b -u -p miniconda3 && rm miniconda3/miniconda.sh
+RUN /opt/executables/miniconda3/bin/conda env update -f env-linux.yml

regression/rt-cetsa-analysis-tool/Dockerfile-original

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+FROM r-base:4.4.0
+
+
+ARG EXEC_DIR="/opt/executables"
+
+RUN apt-get update && apt-get install -y python3
+
+#Create folders
+RUN mkdir -p ${EXEC_DIR}
+
+# Install R packages external dependencies
+RUN apt-get install -y libssl-dev \
+    && apt-get install -y libcurl4-openssl-dev libfontconfig1-dev \
+    && apt-get install -y libharfbuzz-dev libfribidi-dev \
+    && apt-get install -y libxml2-dev \
+    && apt-get install -y libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
+    && apt-get install -y cmake
+
+# Install required R packages
+ADD requirements/Requirements_1.R ${EXEC_DIR}/Requirements_1.R
+RUN Rscript ${EXEC_DIR}/Requirements_1.R
+
+ADD requirements/Requirements_2.R ${EXEC_DIR}/Requirements_2.R
+RUN Rscript ${EXEC_DIR}/Requirements_2.R
+
+ADD requirements/Requirements_3.R ${EXEC_DIR}/Requirements_3.R
+RUN Rscript ${EXEC_DIR}/Requirements_3.R
+
+RUN apt-get install -y --allow-downgrades libxcb-render0=1.15-1 libxcb-shm0=1.15-1 libxcb1=1.15-1
+RUN apt-get install -y  libcairo2-dev
+
+ADD requirements/Requirements_4.R ${EXEC_DIR}/Requirements_4.R
+RUN Rscript ${EXEC_DIR}/Requirements_4.R
+
+RUN apt-get install -y libgit2-dev
+
+ADD requirements/Requirements_6.R ${EXEC_DIR}/Requirements_6.R
+RUN Rscript ${EXEC_DIR}/Requirements_6.R
+
+ADD requirements/Requirements_5.R ${EXEC_DIR}/Requirements_5.R
+RUN Rscript ${EXEC_DIR}/Requirements_5.R
+
+COPY pyproject.toml ${EXEC_DIR}
+COPY README.md ${EXEC_DIR}
+RUN apt-get update && apt-get install -y python3
+RUN apt-get -y install python3-pip python3-venv
+COPY src/ ${EXEC_DIR}/src
+RUN pip3 install ${EXEC_DIR} --no-cache-dir  --break-system-packages
+
+WORKDIR ${EXEC_DIR}
+
+# CMD ["Rscript", "main.R"]
+CMD ["python3", "-m", "polus.tabular.regression.rt_cetsa_analysis"]
+# CMD ["--help"]
+# CMD ["bash"]

regression/rt-cetsa-analysis-tool/README.md

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+# RT_CETSA Analysis Tool (v0.5.0-dev0)
+
+This WIPP plugin runs statistical analysis for the RT-CETSA pipeline.
+
+## 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 eight input argument and one output argument:
+
+| Name            | Description                                        | I/O    | Type        |
+|-----------------|----------------------------------------------------|--------|-------------|
+| `--inpDir` | Input directory containing the all data files | Input  | genericData |
+| `--params` | name of the moltenprot fit params csv file in the input directory | Input  | string      |
+| `--values` | name of the moltenprot baseline corrected values csv file in the input directory
+| `--platemap` | Path to the platemap file | Input | genericData |
+| `--outDir`      | Output file                                        | Output | genericData |
+| `--preview`     | Generate JSON file with outputs                    | Output | JSON        |
+
+## Build options
+
+By default `./build-docker` will build the image using `Dockerfile`, which install R with conda.
+In regression are noticed, this file can be swapped with `Dockerfile-original` which is the original version
+of the dockerfile that is using apt to install all dependencies and is known to work correctly.

regression/rt-cetsa-analysis-tool/VERSION

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+0.5.0-dev0

regression/rt-cetsa-analysis-tool/build-docker.sh

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+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/rt-cetsa-analysis-tool:"${version}"

regression/rt-cetsa-analysis-tool/env-linux.yml

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+name: base
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - r-base
+  - r-tidyverse
+  - r-drc
+  - r-stringr
+  - r-readxl
+  - r-stringr
+  - r-ggthemes
+  - r-cowplot
+  - r-hrbrthemes
+  - r-ggpubr
+  - r-MESS
+  - r-devtools

regression/rt-cetsa-analysis-tool/ict.yml

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+author:
+- Nick Schaub
+- Antoine Gerardin
+- Najib Ishaq
+contact: [email protected]
+container: polusai/rt-cetsa-analysis-simple-tool:0.5.0-dev0
+description: Run statisical analysis for the RT-CETSA pipeline.
+entrypoint: python3 -m polus.tabular.regression.rt_cetsa_analysis
+inputs:
+- description: Fit params csv file
+  format:
+  - params
+  name: params
+  required: false
+  type: string
+- description: Baseline corrected csv files
+  format:
+  - values
+  name: values
+  required: false
+  type: string
+- description: platemap excel file
+  format:
+  - platemap
+  name: platemap
+  required: true
+  type: path
+- description: Generate an output preview.
+  format:
+  - preview
+  name: preview
+  required: false
+  type: boolean
+name: polusai/RTCETSAAnalysis
+outputs:
+- description: Output collection
+  format:
+  - outDir
+  name: outDir
+  required: true
+  type: path
+repository: https://github.com/PolusAI/tabular-tools
+specVersion: 1.0.0
+title: RT-CETSA Analysis
+ui:
+- description: Fit params csv file
+  key: inputs.params
+  title: Fit params csv file
+  type: string
+- description: baseline corrected csv file
+  key: inputs.values
+  title: baseline corrected csv file
+  type: string
+- description: platemap excel file
+  key: inputs.platemap
+  title: platemap excel file
+  type: path
+- description: Generate an output preview.
+  key: inputs.preview
+  title: Preview example output of this plugin
+  type: checkbox
+version: 0.5.0-dev0

regression/rt-cetsa-analysis-tool/plugin.json

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+{
+  "name": "RT-CETSA Analysis",
+  "version": "0.5.0-dev0",
+  "title": "RT-CETSA Analysis",
+  "description": "Run statistical analysis for the RT-CETSA pipeline.",
+  "author": "Nicholas Schaub ([email protected]), Antoine Gerardin ([email protected]), Najib Ishaq ([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/rt-cetsa-analysis-simple-tool:0.5.0-dev0",
+  "baseCommand": [
+    "python3",
+    "-m",
+    "polus.tabular.regression.rt_cetsa_analysis"
+  ],
+  "inputs": [
+    {
+      "name": "params",
+      "type": "genericData",
+      "description": "Fit params csv file"
+    },
+    {
+      "name": "values",
+      "type": "genericData",
+      "description": "Baseline corrected csv files"
+    },
+    {
+      "name": "platemap",
+      "type": "genericData",
+      "description": "platemap excel file",
+      "required": true
+    }
+  ],
+  "outputs": [
+    {
+      "name": "outDir",
+      "type": "genericData",
+      "description": "Output data collection"
+    }
+  ],
+  "ui": [
+    {
+      "key": "inputs.inpDir",
+      "title": "Input collection",
+      "description": "Input data collection to be processed by this plugin"
+    },
+    {
+      "key": "inputs.params",
+      "title": "Params",
+      "description": "Params"
+    },
+    {
+      "key": "inputs.values",
+      "title": "Values",
+      "description": "Values"
+    },
+    {
+      "key": "inputs.platemap",
+      "title": "Plate Map",
+      "description": "Plate Map"
+    }
+  ]
+}

regression/rt-cetsa-analysis-tool/pyproject.toml

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+[tool.poetry]
+name = "polus_tabular_regression_rt_cetsa_analysis"
+version = "0.5.0-dev0"
+description = "Run statiscal analysis for the RT-CETSA pipeline."
+authors = [
+    "Nick Schaub <[email protected]>",
+    "Antoine Gerardin <[email protected]>",
+    "Najib Ishaq <[email protected]>",
+]
+readme = "README.md"
+packages = [{include = "polus", from = "src"}]
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12"
+typer = "^0.7"
+openpyxl = "^3.1.3"
+pandas = "^2.2.2"
+numpy = "^1.26.4"
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+pre-commit = "^3.1.0"
+pytest = "^7.2.1"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.ruff]
+extend = "../../ruff.toml"
+extend-ignore = [
+    "RET505",  # Unnecessary `else` after `return` statement
+    "E501",  # Line too long
+    "ANN001",  # Missing type annotation
+    "D102",  # Missing docstring in public method
+    "ANN201",  # Missing return type annotation
+    "N806",  # Variable in function should be lowercase
+    "D205",  # 1 blank line required between summary line and description
+    "N803",  # Argument name should be lowercase
+    "PLR0913",  # Too many arguments
+    "D415",  # First line should end with a period, question mark, or exclamation point
+    "PLR2004",  # Magic value used in comparison
+    "B006",  # Do not use mutable default arguments
+    "D107",  # Missing docstring
+    "D101",  # Missing docstring
+    "E731",  # Do not assign a lambda expression, use a def
+    "E402",  # Module level import not at top of file
+    "PTH123",  # `open()` should be replaced with `Path.open()`
+    "PTH118",  # `os.path.join()` should be replaced with `/` operator
+    "PTH100",  # `os.path.abspath()` should be replaced with `Path.resolve()`
+    "PLR0915",  # Too many statements
+    "PLR0912",  # Too many branches
+    "C901",  # Function is too complex
+    "T201",  # `print` used
+    "E722",  # Do not use bare 'except'
+    "B904",  # Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
+    "ANN202",  # Missing return type annotation for private function
+    "ARG002",  # Unused method argument
+    "N802",  # Function name should be lowercase
+    "PTH103",  # `os.makedirs()` should be replaced with `Path.mkdir(parents=True)`
+    "ANN003",  # Missing type annotation for `**kwargs`
+    "B007",  # Loop control variable not used within the loop body
+    "ANN204",  # Missing return type annotation for magic method
+    "D417",  # Missing argument descriptions in the docstring
+    "ANN205",  # Missing return type annotation for static method
+    "PLR5501",  # Use `elif` instead of `else` following `if` condition to avoid unnecessary indentation
+    "EM102",  # Exception must not use an f-string literal
+    "D414",  # Section has no content
+    "RUF012",  # Mutable class attributes should be annotated with `typing.ClassVar`
+    "A001",  # Variable `input` is shadowing a Python builtin
+    "A002",  # Argument `input` is shadowing a Python builtin
+    "E741",  # Ambiguous variable name: `l`
+    "PTH120",  # `os.path.dirname()` should be replaced by `Path.parent`
+    "N816",  # Variable `cfFilename` in global scope should not be mixedCase
+    "PTH109",  # `os.getcwd()` should be replaced by `Path.cwd()`
+]

regression/rt-cetsa-analysis-tool/requirements/Requirements_1.R

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+install.packages('argparse')
+install.packages('logging')
+install.packages('tidyverse')

regression/rt-cetsa-analysis-tool/requirements/Requirements_2.R

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+install.packages('drc')

regression/rt-cetsa-analysis-tool/requirements/Requirements_3.R

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+install.packages('readxl')
+install.packages('stringr')
+install.packages('ggthemes')
+install.packages('cowplot')
+install.packages('ggpubr')
+install.packages('MESS')

regression/rt-cetsa-analysis-tool/requirements/Requirements_4.R

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+install.packages('hrbrthemes')

regression/rt-cetsa-analysis-tool/requirements/Requirements_5.R

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+install.packages('devtools')

regression/rt-cetsa-analysis-tool/requirements/Requirements_6.R

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+install.packages('gert')