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Merge pull request #63 from UCD-BDLab/documentation-update-to-match-readme
Documentation update to match readme
2 parents adce87b + 28891d8 commit 21daee6

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‎.DS_Store‎

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‎.gitattributes‎

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*.ipynb linguist-detectable=false
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*.ipynb linguist-detectable=false

‎.github/workflows/pre-commit.yml‎

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jobs:
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pre-commit:
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runs-on: macos-latest
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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python-version: ["3.10", "3.11", "3.12"]
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout code
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- name: Checkout repository
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uses: actions/checkout@v3
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- name: Set up Python
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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- name: Upgrade pre-commit
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run: pip install --upgrade pre-commit
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- name: Verify pre-commit installation
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run: pre-commit --version
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python-version: ${{ matrix.python-version }}
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check-latest: true
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- name: Cache pip dependencies
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uses: actions/cache@v3
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pip install torch_geometric
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shell: bash
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- name: Install system dependencies
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run: |
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brew update
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brew upgrade
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- name: Install R
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uses: r-lib/actions/setup-r@v2
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with:
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r-version: "latest"
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- name: Install R packages
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run: |
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Rscript -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager', repos='https://cran.r-project.org')"
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Rscript -e "install.packages(c('dplyr', 'jsonlite'), repos='https://cran.r-project.org')"
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Rscript -e "BiocManager::install(c('impute', 'preprocessCore', 'GO.db', 'AnnotationDbi'), update=FALSE, ask=FALSE)"
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Rscript -e "install.packages('SmCCNet', repos='https://cran.r-project.org')"
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Rscript -e "install.packages('WGCNA', repos='https://cran.r-project.org')"
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shell: bash
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# - name: Run Pre-Commit Checks
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# run: pre-commit run --all-files --show-diff-on-failure
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# - name: Install R
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# uses: r-lib/actions/setup-r@v2
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# with:
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# r-version: "latest"
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# - name: Install R packages
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# run: |
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# Rscript -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager', repos='https://cran.r-project.org')"
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# Rscript -e "install.packages(c('dplyr', 'jsonlite'), repos='https://cran.r-project.org')"
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# Rscript -e "BiocManager::install(c('impute', 'preprocessCore', 'GO.db', 'AnnotationDbi'), update=FALSE, ask=FALSE)"
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# Rscript -e "install.packages('SmCCNet', repos='https://cran.r-project.org')"
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# Rscript -e "install.packages('WGCNA', repos='https://cran.r-project.org')"
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# shell: bash
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- name: Run Pre-Commit Checks
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run: pre-commit run --all-files --show-diff-on-failure

‎.github/workflows/python-app.yml‎

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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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python-version: ["3.10", "3.11"]
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python-version: ["3.10", "3.11", "3.12"]
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runs-on: ${{ matrix.os }}
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pip install torch_geometric
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shell: bash
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- name: Install R
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uses: r-lib/actions/setup-r@v2
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with:
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r-version: "latest"
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# - name: Install R
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# uses: r-lib/actions/setup-r@v2
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# with:
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# r-version: "latest"
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- name: Install R packages
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run: |
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Rscript -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager', repos='https://cran.r-project.org')"
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Rscript -e "install.packages(c('dplyr', 'jsonlite'), repos='https://cran.r-project.org')"
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Rscript -e "BiocManager::install(c('impute', 'preprocessCore', 'GO.db', 'AnnotationDbi'), update=FALSE, ask=FALSE)"
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Rscript -e "install.packages('SmCCNet', repos='https://cran.r-project.org')"
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Rscript -e "install.packages('WGCNA', repos='https://cran.r-project.org')"
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shell: bash
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# - name: Install R packages
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# run: |
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# Rscript -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager', repos='https://cran.r-project.org')"
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# Rscript -e "install.packages(c('dplyr', 'jsonlite'), repos='https://cran.r-project.org')"
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# Rscript -e "BiocManager::install(c('impute', 'preprocessCore', 'GO.db', 'AnnotationDbi'), update=FALSE, ask=FALSE)"
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# Rscript -e "install.packages('SmCCNet', repos='https://cran.r-project.org')"
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# Rscript -e "install.packages('WGCNA', repos='https://cran.r-project.org')"
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# shell: bash
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- name: Run tests with pytest
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run: |
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find . -name ".coverage*" -delete
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pytest --cov=bioneuralnet --cov-report=xml tests/
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# - name: Run tests with pytest
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# run: |
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# find . -name ".coverage*" -delete
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# pytest --cov=bioneuralnet --cov-report=xml tests/
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v3
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: ./coverage.xml
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flags: unittests
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name: codecov-umbrella
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# - name: Upload coverage to Codecov
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# uses: codecov/codecov-action@v3
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# with:
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# token: ${{ secrets.CODECOV_TOKEN }}
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# files: ./coverage.xml
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# flags: unittests
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# name: codecov-umbrella

‎.gitignore‎

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.mypy_cache
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Quick Start.ipynb
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TCGA-BRCA_Datatest.ipynb
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DevNotes.md
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TCGA-BRCA_Datatest_copy.ipynb
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split
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# Other example data and tests not needed in the repo.
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Output**

‎.pre-commit-config.yaml‎

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exclude: ^docs/
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.3.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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args: ['--maxkb=92160']
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# - repo: https://github.com/psf/black
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# rev: 24.10.0
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# hooks:
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# - id: black
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# name: Format Python code with Black
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# language_version: python3
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.14.1
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hooks:
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- id: mypy
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name: Static type checking with MyPy
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args: [--ignore-missing-imports]
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- repo: local
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hooks:
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- id: remove-pyc-and-pycache
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name: Remove .pyc files and __pycache__ directories
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entry: bash -c "find . \( -path './.venv' -o -path './docs' -o -path './node_modules' \) -prune -o -type f -name '*.pyc' -exec rm -f {} + -o -type d -name '__pycache__' -exec rm -rf {} +"
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language: system
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stages: [pre-commit]
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- id: clean-coverage-files
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name: Remove stale .coverage files
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entry: bash -c "find . -name '.coverage*' -delete"
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language: system
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stages: [pre-commit]
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- id: check-forbidden-files
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name: Prevent adding forbidden file types except in allowed directory
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entry: |
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bash -c '
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FILES="$(git diff --cached --name-only)"
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if echo "$FILES" | grep -E "\.RData$"; then
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echo "Forbidden file types detected (RData)!"
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exit 1
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fi
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if echo "$FILES" | grep -E "\.csv$" | grep -vE "^bioneuralnet/datasets/(example1|brca|monet)/"; then
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echo "Forbidden CSV files detected (outside allowed folders)!"
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exit 1
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fi
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'
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language: system
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stages: [pre-commit]
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# - id: run-tests
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# name: Run Tests with Pytest
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# entry: pytest --ignore=docs/source/examples --cov=bioneuralnet --cov-report=term-missing || true
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# language: system
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# types: [python]

‎CHANGELOG.md‎

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All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/).
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## [0.2.0b2] - 2025-02-16
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## [1.0.1] to [1.0.7] - 2025-04-24
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- **BUG**: A bug related to rdata files missing
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- **New realease**: A new release will include documentation for the other updates. (1.1.0)
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- **New realease**: A new release will include documentation for the other updates. (1.1.0)

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