Merge pull request #5 from domonik/new-dev

removes old readme link

.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

.github/test-package.yml → .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

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/
 

environment.yml

@@ -9,6 +9,7 @@ dependencies:
   - viennarna
   - biopython
   - pandas
+  - networkx
   - plotly
   - dash >=2.5
   - dash-bootstrap-components