diff --git a/.github/workflows/build-documentation.yml b/.github/workflows/build-documentation.yml new file mode 100644 index 0000000..b46b5a9 --- /dev/null +++ b/.github/workflows/build-documentation.yml @@ -0,0 +1,59 @@ +name: build-github-pages +env: + GITHUB_ACTOR: domonik + GITHUB_REPOSITORY: domonik/RNAdist + +on: + push: + tags: + - "v*.*.*" + + + +# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages +permissions: + contents: write + pages: write + id-token: write + +jobs: + build_docs: + runs-on: ubuntu-latest + steps: + - name: Checkout code + uses: actions/checkout@v4 + with: + fetch-depth: 0 + ref: ${{ github.event.workflow_run.head_branch }} + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: 3.10 + + + - name: create environment with mamba + uses: conda-incubator/setup-miniconda@v2 + with: + channels: conda-forge,defaults + auto-activate-base: false + activate-environment: rnadist_doc + environment-file: docs/environment.yml + + - name: Render Rmd files + run: | + eval "$(conda shell.bash hook)" + conda activate rnadist_doc + cd docs + make html + cd .. + + - name: Upload artifact + uses: actions/upload-pages-artifact@v2 + with: + # Upload entire repository + path: 'docs/build/html' + + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v2 \ No newline at end of file diff --git a/.github/test-package.yml b/.github/workflows/test-package.yml similarity index 80% rename from .github/test-package.yml rename to .github/workflows/test-package.yml index 6843c81..5fea2a2 100644 --- a/.github/test-package.yml +++ b/.github/workflows/test-package.yml @@ -1,3 +1,4 @@ +name: "testPackage" on: pull_request: @@ -33,10 +34,14 @@ jobs: - name: Install package run: | + eval "$(conda shell.bash hook)" conda activate RNAdistEnv pip install ./ --no-deps --no-build-isolation pip install pytest - name: test package run: | + eval "$(conda shell.bash hook)" + conda activate RNAdistEnv + rm RNAdist/ -r # Needs to be removed since it will try to test uncompiled package instead pytest --pyargs RNAdist diff --git a/README.md b/README.md index 78c70a0..ac7122d 100644 --- a/README.md +++ b/README.md @@ -3,8 +3,9 @@ RNAdist is a package to approximate expected distances on RNA structures. -## [Getting Started](https://rnadist.readthedocs.io/en/stable/index.html) +## [Getting Started](https://domonik.github.io/RAPDOR/) -For installation details, documentation and various tutorials please have a look at our documentation page on -[ReadtheDocs](https://rnadist.readthedocs.io/en/stable/index.html) +For installation details, documentation and various tutorials please have a look at our documentation page here: + +https://domonik.github.io/RAPDOR/ diff --git a/environment.yml b/environment.yml index 076c8ab..026a238 100644 --- a/environment.yml +++ b/environment.yml @@ -9,6 +9,7 @@ dependencies: - viennarna - biopython - pandas + - networkx - plotly - dash >=2.5 - dash-bootstrap-components