Merge pull request #4 from ulysseherbach/update-docs

Update docs

.github/workflows/github-pages.yml

@@ -47,13 +47,13 @@ jobs:
           sudo apt-get -y install pandoc
           pip install -r docs/requirements.txt
       - name: Build documentation
-        run: sphinx-build docs docs/_build/html
+        run: sphinx-build -b dirhtml docs docs/_build
       - name: Setup Pages
         uses: actions/configure-pages@v5
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3
         with:
-          path: 'docs/_build/html'
+          path: 'docs/_build'
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v4

README.md

@@ -1,3 +1,4 @@
 # FluffyClone
 
 [![GitHub Release](https://img.shields.io/github/v/release/ulysseherbach/fluffyclone?logo=github)](https://github.com/ulysseherbach/fluffyclone)
+[![GitHub Pages status](https://img.shields.io/github/actions/workflow/status/ulysseherbach/fluffyclone/github-pages.yml?label=docs)](https://ulysseherbach.github.io/fluffyclone/)

docs/README.md

@@ -5,23 +5,21 @@ depends on something that is deprecated and removed in `3.12`.
 
 ## Install dependencies
 
-From the root of the project you can install the dependencies required for the 
+From the `docs` folder of the project, you can install the dependencies required for the 
 documentation generation by typing:
 
 ```bash
-pip install -r docs/requirements.txt
+pip install -r requirements.txt
 ```
 
-## Build
+## Build website pages
 
 To build the website run the command:
 
 ```bash
-sphinx-build docs docs/_build/html
+sphinx-build . _build
 ```
 
-or go the `docs` folder and run `make html`.
-
 ## Visualize the website
 
-You can open the `docs/_build/html/index.html` file in your browser.
+You can open the `_build/index.html` file in your browser.

docs/_static/custom.css

@@ -1,3 +1,4 @@
+/* alabaster theme */
 
 a.reference {
     border: 0;
@@ -15,7 +16,19 @@ h1.logo a:hover {
     border: 0;
 }
 
+div.sphinxsidebar h3 {
+    display: none;
+}
+
+/* pydata_sphinx_theme */
+
 /*.bd-search {
     border: 0;
     border-radius: .5rem;
 }*/
+
+/* sphinx_copybutton */
+
+button.copybtn {
+    font-size: 0.85em;
+}

docs/clonal_trees.md

@@ -0,0 +1,26 @@
+# Clonal trees
+
+:::{warning}
+This documentation is still a draft.
+:::
+
+## Define clonal trees
+
+```python
+from fluffyclone import ClonalTree
+```
+
+### Parent sequence encoding
+
+```python
+# Option 1: pass the parent sequence directly
+tree = ClonalTree(0, 0, 0, 2, 5)
+
+# Option 2: define parent sequence first
+p = (0, 0, 0, 2, 5)
+tree = ClonalTree(p)
+
+# Option 3: add root explicitly (node 0 with no parent)
+p = (None, 0, 0, 0, 2, 5)
+tree = ClonalTree(p)
+```

docs/distributions.md

@@ -0,0 +1,32 @@
+# Distributions
+
+:::{warning}
+This documentation is still a draft.
+:::
+
+## Definition
+
+```python
+from fluffyclone import WeightedUniform, WeightedUniformGibbs
+
+# Number of clones
+n_clones = 5
+
+# General form
+model1 = WeightedUniform(n_clones)
+
+# Gibbs form
+model2 = WeightedUniformGibbs(n_clones)
+
+# Using just-in-time-compilation
+model3 = WeightedUniform(n_clones, jit=True)
+model4 = WeightedUniformGibbs(n_clones, jit=True)
+```
+
+## Usage
+
+```python
+# Sampling trees from the model
+tree = model1.sample()
+tree_list = model1.sample(size=10)
+```

docs/index.md

@@ -9,6 +9,13 @@ This documentation is still a draft.
 :::
 
 
+## Installation
+
+```bash
+pip install fluffyclone --upgrade
+```
+
+
 ## Indexes
 
 * [General Index](genindex)
@@ -17,6 +24,10 @@ This documentation is still a draft.
 
 :::{toctree}
 :hidden:
+:maxdepth: 2
 
-quickstart/index
+quickstart
+clonal_trees
+distributions
+models/index
 :::

docs/models/index.md

@@ -0,0 +1,13 @@
+# Models
+
+:::{warning}
+This documentation is still a draft.
+:::
+
+:::{toctree}
+:hidden:
+:maxdepth: 2
+
+model1
+model2
+:::

docs/models/model1.md

@@ -0,0 +1,5 @@
+# Model 1
+
+:::{warning}
+This documentation is still a draft.
+:::

docs/models/model2.md

@@ -0,0 +1,5 @@
+# Model 2
+
+:::{warning}
+This documentation is still a draft.
+:::

docs/quickstart.md

@@ -0,0 +1,22 @@
+# Quickstart
+
+## Define a clonal tree
+
+```python
+from fluffyclone import ClonalTree
+```
+
+### Parent sequence encoding
+
+```python
+# Option 1: pass the parent sequence directly
+tree = ClonalTree(0, 0, 0, 2, 5)
+
+# Option 2: define parent sequence first
+p = (0, 0, 0, 2, 5)
+tree = ClonalTree(p)
+
+# Option 3: add root explicitly (node 0 with no parent)
+p = (None, 0, 0, 0, 2, 5)
+tree = ClonalTree(p)
+```