updated docs

docs/usecases/usecase1.md

@@ -1 +1,5 @@
-!!! warning "🚧 under construction"
+# Create a sequence network
+
+Download and execute the [Notebook](https://github.com/PyEED/pyeed/blob/main/examples/basics.ipynb) open the notebook either in your Python environment, or follow the [instructions](../installation/jupyterlab.md) to set up the `PyEED-Lab` container as your computing environment including `pyeed`.
+
+When using the `PyEED-Lab` Docker container, navigate in the file browser on the left to the folder that contains the downloaded [notebook](https://github.com/PyEED/pyeed/blob/main/examples/basics.ipynb). Double-click on the notebook to open it in the JupyterLab environment. Then you can execute each cell by pressing ++shift+enter++ or by clicking the `Run` button in the toolbar.

examples/basics.ipynb

@@ -81,8 +81,7 @@
     }
    ],
    "source": [
-    "alignments = Alignment.from_sequences(\n",
-    "    sequences=blast_results, aligner=PairwiseAligner)"
+    "alignments = Alignment.from_sequences(sequences=blast_results, aligner=PairwiseAligner)"
    ]
   },
   {

mkdocs.yml

@@ -14,8 +14,8 @@ nav:
     - Aligning Sequences: quick_start/alignments.md
     - Clustering Sequences: quick_start/clustering.md
     - Creating Sequence Networks: quick_start/networks.md
-  #- 🔎 Use cases:
-  #  - Get an Overview over a Protein Family: usecases/usecase1.md
+  - 🔎 Examples:
+    - Create a sequence network: usecases/usecase1.md
   - ⬇️ Installation:
     - via PIP: installation/via_pip.md
     - Docker: installation/docker.md
@@ -64,6 +64,7 @@ markdown_extensions:
       line_spans: __span
       pygments_lang_class: true
   - admonition
+  - pymdownx.keys
   - pymdownx.details
   - pymdownx.inlinehilite
   - pymdownx.snippets