try to build docs locally on gh-pages

pydna-group · Apr 18, 2024 · da3e7e9 · da3e7e9
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diff --git a/.github/workflows/publish-docs.yml b/.github/workflows/publish-docs.yml
@@ -0,0 +1,49 @@
+on: [push, pull_request]
+
+name: "Documentation Status"
+
+permissions:
+  contents: write
+
+jobs:
+  build-and-publish:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+
+    timeout-minutes: 10
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install sphinx numpydoc sphinx-autobuild sphinx-rtd-theme
+
+    - name: Install this Python package
+      run: |
+        pip install .[pydivsufsort]
+
+    - name: Session information
+      run: |
+        python --version
+
+    - name: Build documentation
+      run: |
+        cd docs
+        make html
+
+    - name: Deploy to GitHub pages 🚀
+      if: github.event_name != 'pull_request'
+      uses: JamesIves/[email protected]
+      with:
+        clean: false
+        branch: gh-pages
+        folder: docs/_build/html
diff --git a/docs/BUILD_HTML.sh b/docs/BUILD_HTML.sh
diff --git a/docs/BUILD_RST_FILES.sh b/docs/BUILD_RST_FILES.sh
diff --git a/docs/pics/BMC.png → docs/_static/BMC.png b/docs/pics/BMC.png → docs/_static/BMC.png
diff --git a/docs/pics/BMC_resized.png → docs/_static/BMC_resized.png b/docs/pics/BMC_resized.png → docs/_static/BMC_resized.png
diff --git a/docs/pics/BMC_resized_old.png → docs/_static/BMC_resized_old.png b/docs/pics/BMC_resized_old.png → docs/_static/BMC_resized_old.png
diff --git a/docs/pics/gel.png → docs/_static/gel.png b/docs/pics/gel.png → docs/_static/gel.png
diff --git a/docs/pics/pydna-web.png → docs/_static/pydna-web.png b/docs/pics/pydna-web.png → docs/_static/pydna-web.png
diff --git a/docs/pics/pydna.png → docs/_static/pydna.png b/docs/pics/pydna.png → docs/_static/pydna.png
diff --git a/docs/pics/pydna.resized.png → docs/_static/pydna.resized.png b/docs/pics/pydna.resized.png → docs/_static/pydna.resized.png
diff --git a/docs/pics/pydna240x240.png → docs/_static/pydna240x240.png b/docs/pics/pydna240x240.png → docs/_static/pydna240x240.png
diff --git a/docs/pics/pydna_512x512.png → docs/_static/pydna_512x512.png b/docs/pics/pydna_512x512.png → docs/_static/pydna_512x512.png
diff --git a/docs/pics/pydna_512x512_trsp.png → docs/_static/pydna_512x512_trsp.png b/docs/pics/pydna_512x512_trsp.png → docs/_static/pydna_512x512_trsp.png
diff --git a/docs/pics/pydna_transparent.png → docs/_static/pydna_transparent.png b/docs/pics/pydna_transparent.png → docs/_static/pydna_transparent.png
diff --git a/docs/pics/snake.png → docs/_static/snake.png b/docs/pics/snake.png → docs/_static/snake.png
diff --git a/docs/conf___.py b/docs/conf___.py
diff --git a/docs/cookbook/cookbook.ipynb b/docs/cookbook/cookbook.ipynb
@@ -35,7 +35,7 @@
     "\n",
     "The advantage of documenting with pydna is that the pydna code unambiguously describe the experiment and can be executed to yield the sequence of the of the resulting DNA molecule(s) and all intermediary steps. Pydna code describing a sub cloning is reasonably compact and also meant to be easily readable.\n",
     "\n",
-    "Look [here](https://github.com/BjornFJohansson/pydna-examples) for examples."
+    "Look [here](https://github.com/MetabolicEngineeringGroupCBMA/pydna-examples?tab=readme-ov-file#pydna-examples) for examples."
    ]
   },
   {
-Original file line number
+Diff line change
@@ Expand Up / @@ -35,7 +35,7 @@ @@
         "\n",
         "The advantage of documenting with pydna is that the pydna code unambiguously describe the experiment and can be executed to yield the sequence of the of the resulting DNA molecule(s) and all intermediary steps. Pydna code describing a sub cloning is reasonably compact and also meant to be easily readable.\n",
         "\n",
-        "Look [here](https://github.com/BjornFJohansson/pydna-examples) for examples."
+        "Look [here](https://github.com/MetabolicEngineeringGroupCBMA/pydna-examples?tab=readme-ov-file#pydna-examples) for examples."
        ]
       },
       {
@@ Expand Down @@