From 8702accf3445a73ffed08c6a46b7486054eb42fa Mon Sep 17 00:00:00 2001
From: domonik <schdruzzi@gmail.com>
Date: Tue, 19 Nov 2024 13:54:07 +0100
Subject: [PATCH 1/5] removes old readme link

---
 README.md | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

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/
 

From 7dc38f8d48e46415f0326175bcd8132932b2779f Mon Sep 17 00:00:00 2001
From: domonik <schdruzzi@gmail.com>
Date: Tue, 19 Nov 2024 13:56:31 +0100
Subject: [PATCH 2/5] fixes action path

---
 .github/{ => workflows}/test-package.yml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/{ => workflows}/test-package.yml (100%)

diff --git a/.github/test-package.yml b/.github/workflows/test-package.yml
similarity index 100%
rename from .github/test-package.yml
rename to .github/workflows/test-package.yml

From 506560ef01d2ea4640a8a8520ef43855f38088a6 Mon Sep 17 00:00:00 2001
From: domonik <schdruzzi@gmail.com>
Date: Tue, 19 Nov 2024 14:01:44 +0100
Subject: [PATCH 3/5] fixes conda not initialized

---
 .github/workflows/test-package.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test-package.yml b/.github/workflows/test-package.yml
index 6843c81..d3a21e1 100644
--- a/.github/workflows/test-package.yml
+++ b/.github/workflows/test-package.yml
@@ -33,6 +33,7 @@ jobs:
 
       - name: Install package
         run: |
+          eval "$(conda shell.bash hook)"
           conda activate RNAdistEnv
           pip install ./ --no-deps --no-build-isolation
           pip install pytest

From a75c1f0880e79a3503ff342fb3aea6d0fcc43a1b Mon Sep 17 00:00:00 2001
From: domonik <schdruzzi@gmail.com>
Date: Tue, 19 Nov 2024 14:11:34 +0100
Subject: [PATCH 4/5] fixes conda activate for testing

---
 .github/workflows/build-documentation.yml | 59 +++++++++++++++++++++++
 .github/workflows/test-package.yml        |  3 ++
 2 files changed, 62 insertions(+)
 create mode 100644 .github/workflows/build-documentation.yml

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/workflows/test-package.yml b/.github/workflows/test-package.yml
index d3a21e1..ca47f13 100644
--- a/.github/workflows/test-package.yml
+++ b/.github/workflows/test-package.yml
@@ -1,3 +1,4 @@
+name: "testPackage"
 
 on:
   pull_request:
@@ -40,4 +41,6 @@ jobs:
 
       - name: test package
         run: |
+          eval "$(conda shell.bash hook)"
+          conda activate RNAdistEnv
           pytest --pyargs RNAdist

From 270e80f431730be62578f7498a47f50392cc2415 Mon Sep 17 00:00:00 2001
From: domonik <schdruzzi@gmail.com>
Date: Tue, 19 Nov 2024 14:31:24 +0100
Subject: [PATCH 5/5] action removes directory after install to run pytest

---
 .github/workflows/test-package.yml | 1 +
 environment.yml                    | 1 +
 2 files changed, 2 insertions(+)

diff --git a/.github/workflows/test-package.yml b/.github/workflows/test-package.yml
index ca47f13..5fea2a2 100644
--- a/.github/workflows/test-package.yml
+++ b/.github/workflows/test-package.yml
@@ -43,4 +43,5 @@ jobs:
         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/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