diff --git a/README.md b/README.md index 6369882..0957dbf 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ # READII + [![codecov](https://codecov.io/gh/bhklab/readii/graph/badge.svg?token=obsN5dhXPx)](https://codecov.io/gh/bhklab/readii) [![CI-CD](https://github.com/bhklab/readii/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/bhklab/readii/actions/workflows/ci-cd.yml) [![CodeFactor](https://www.codefactor.io/repository/github/bhklab/readii/badge)](https://www.codefactor.io/repository/github/bhklab/readii) @@ -23,6 +24,7 @@ $ pip install readii ``` ### (recommended) Create new `pixi` environment for a project + ```bash mkdir my_project cd my_project @@ -31,13 +33,15 @@ pixi add --pypi readii ``` ### (recommended) Create new conda virtual environment -``` + +```bash conda create -n readii python=3.9 conda activate readii pip install readii ``` ## Usage + `readii` is a tool to perform radiomic feature extraction on DICOM CT images with region of interest (ROI) segmentations as either DICOM SEG or RTSTRUCT. ```bash @@ -51,21 +55,23 @@ $ readii [INPUT DIRECTORY] [OUTPUT DIRECTORY] \ ### Negative control options -Negative controls are applied to one of three masks: +Negative controls are applied to one of three masks: + 1. full = voxels in the entire image 2. roi = just voxels within the specified region of interest (ROI) in the segmentation 3. non_roi = all voxels except the ROI. The three transformations are: + 1. shuffle = shuffle all voxels in the specified mask 2. randomized = randomly generate new values within the original range within the specified mask 3. randomized_sampled = randomly sample original values with replacement to get new values within the specified mask - ## Contributing Please use the following angular commit message format: -``` + +```text (optional scope): short summary in present tense (optional body: explains motivation for the change) @@ -73,6 +79,7 @@ Please use the following angular commit message format: (optional footer: note BREAKING CHANGES here, and issues to be closed) ``` + `` refers to the kind of change made and is usually one of: - `feat`: A new feature. @@ -88,10 +95,14 @@ Please use the following angular commit message format: Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms. +### Serve Documentation Locally + +```bash +pixi run -e docs doc-serve +``` + ## License `readii` was created by Katy Scott. It is licensed under the terms of the MIT license. -## Credits - -`readii` was created with [`cookiecutter`](https://cookiecutter.readthedocs.io/en/latest/) and the `py-pkgs-cookiecutter` [template](https://github.com/py-pkgs/py-pkgs-cookiecutter). + \ No newline at end of file diff --git a/docs/changelog.md b/docs/changelog.md index 8261b35..9b66b83 100755 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -1,2 +1,5 @@ -```{include} ../CHANGELOG.md -``` \ No newline at end of file + +{% + include-markdown "../CHANGELOG.md" + rewrite-relative-urls=false +%} diff --git a/docs/index.md b/docs/index.md index 6fcdc0e..a5c6074 100755 --- a/docs/index.md +++ b/docs/index.md @@ -1,13 +1,8 @@ -```{include} ../README.md -``` +# READII (Radiomic Extraction and Analysis for DICOM Images) -```{toctree} -:maxdepth: 1 -:hidden: - -example.ipynb -changelog.md -contributing.md -conduct.md -autoapi/index -``` \ No newline at end of file +{% + include-markdown "../README.md" + start="" + end="" + rewrite-relative-urls=false +%} diff --git a/mkdocs.yaml b/mkdocs.yaml new file mode 100644 index 0000000..26c18fc --- /dev/null +++ b/mkdocs.yaml @@ -0,0 +1,53 @@ +site_name: READII +repo_url: https://github.com/bhklab/readii +repo_name: readii +site_description: Package documentation for readii +site_author: bhklab + +watch: [docs, src, mkdocs.yaml] +# The directory where the documentation files are located +docs_dir: docs + +# The directory where the documentation is built (add to .gitignore if changed) +site_dir: site + +# Set a list of CSS files (relative to docs_dir) to be included by the theme +# typically as tags. +extra_css: [] + +# This is the branch where the documentation will pushed to using +# 'mkdocs gh-deploy' and from where it will be served by GitHub Pages. +remote_branch: gh-pages + +# Address when using 'mkdocs serve', format is 'address:port' +dev_addr: 127.0.0.1:8001 + +# The layout of the navigation links +nav: + - Home: index.md + - Changelog: changelog.md + +plugins: + - awesome-pages # simplifies configuring page titles and their order + - search # necessary for search functionality to work + - git-authors # adds authors to pages using git history + - include-markdown # allows for including Markdown files into another Markdown file + +theme: + name: material + features: + - announce.dismiss + - content.action.edit + - content.action.view + - content.code.annotate + - content.code.copy + - content.tooltips + - navigation.footer + - navigation.indexes + - navigation.sections + - navigation.tabs + - navigation.tabs.sticky + - navigation.top + - search.highlight + - search.suggest + - toc.follow \ No newline at end of file diff --git a/pixi.lock b/pixi.lock index 0abb6f1..a4ebbb0 100644 --- a/pixi.lock +++ b/pixi.lock @@ -144,19 +144,18 @@ environments: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - 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-# TODO::add tasks to build documentation +mkdocs = ">=1.6" +mike = ">=2.1" +mkdocs-material = ">=9.5.44,<10" +mkdocstrings = ">=0.27.0,<0.28" +mkdocstrings-python = ">=1.12.2,<2" +mkdocs-include-markdown-plugin = ">=7.1.1,<8" +mkdocs-git-authors-plugin = ">=0.9.0,<0.10" +mkdocs-git-revision-date-localized-plugin = ">=1.2.9,<2" + +[tool.pixi.feature.docs.pypi-dependencies] +mkdocs-awesome-pages-plugin = ">=2.9.3, <3" + +[tool.pixi.feature.docs.tasks.doc-build] +cmd = "mkdocs build -f mkdocs.yaml" +inputs = ["docs", "mkdocs.yaml"] +outputs = ["site"] + +[tool.pixi.feature.docs.tasks.doc-serve] +cmd = "mkdocs serve -f mkdocs.yaml" +inputs = ["docs", "mkdocs.yaml"] ############################################## STYLE ############################################### # See config/ruff.toml for the configuration