sidebar & pip install

README.md

@@ -3,7 +3,7 @@
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
 
 The Heat-Geodesic embedding preserves the heat-geodesic dissimilarity
-defined as
+defined as 
 ```math
 d_t(x_i,x_j) = \bigg[ -4t \log (\mathbf{H}_t)_{ij} - \sigma 4 t \log(\mathbf{V})_{ij} \bigg] ^{1/2},
 ```
@@ -26,29 +26,33 @@ Reduction](https://arxiv.org/abs/2305.19043).
 
 ## Install
 
-The package is not yet available with pip or conda. To install it, you
-can clone this repo and install from `setup.py`.
+The package is available on PyPI, you can install it by running
 
 ``` sh
-git clone https://github.com/KrishnaswamyLab/HeatGeo.git
-cd HeatGeo
-pip install -e .
+pip install heatgeo
 ```
 
 To reproduce the results in `experiments/` or try the embeddings with
 different graph constructions, you need additional packages that can be
 installed via the development version. In this case run
 
 ``` sh
-cd HeatGeo
-pip install -e '.[dev]'
+pip install heatgeo['dev']
 ```
 
 We provide an example below.
 
 ## How to use
 
-Google colab example on the swiss roll [![Run in Google
+To create the embedding of a dataset `data`, run
+
+``` python
+from heatgeo.embedding import HeatGeo
+emb_op = HeatGeo(knn=5)
+emb = emb_op.fit_transform(data)
+```
+
+We provide a Google colab example on the swiss roll [![Run in Google
 Colab](https://img.shields.io/static/v1?label=Run%20in&message=Google%20Colab&color=orange&logo=Google%20Cloud.png)](https://colab.research.google.com/drive/1SkxGfWz8KLQpcea9MsdP7QEoe-yh5Iai?usp=sharing)
 
 The directory `experiments` contains code to reproduce our main results.

nbs/index.ipynb

@@ -43,17 +43,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The package is not yet available with pip or conda. To install it, you can clone this repo and install from `setup.py`.\n",
+    "The package is available on PyPI, you can install it by running\n",
     "```sh\n",
-    "git clone https://github.com/KrishnaswamyLab/HeatGeo.git\n",
-    "cd HeatGeo\n",
-    "pip install -e .\n",
+    "pip install heatgeo\n",
     "```\n",
     "To reproduce the results in `experiments/` or try the embeddings with different graph constructions, you need additional packages that can be installed via the development version. In this case run\n",
     "```sh\n",
-    "cd HeatGeo\n",
-    "pip install -e '.[dev]'\n",
+    "pip install heatgeo['dev']\n",
     "```\n",
+    "\n",
     "We provide an example below."
    ]
   },
@@ -63,7 +61,14 @@
    "metadata": {},
    "source": [
     "## How to use\n",
-    "Google colab example on the swiss roll [![Run in Google Colab](https://img.shields.io/static/v1?label=Run%20in&message=Google%20Colab&color=orange&logo=Google%20Cloud)](https://colab.research.google.com/drive/1SkxGfWz8KLQpcea9MsdP7QEoe-yh5Iai?usp=sharing)\n",
+    "To create the embedding of a dataset `data`, run\n",
+    "```python\n",
+    "from heatgeo.embedding import HeatGeo\n",
+    "emb_op = HeatGeo(knn=5)\n",
+    "emb = emb_op.fit_transform(data)\n",
+    "```\n",
+    "\n",
+    "We provide a Google colab example on the swiss roll [![Run in Google Colab](https://img.shields.io/static/v1?label=Run%20in&message=Google%20Colab&color=orange&logo=Google%20Cloud)](https://colab.research.google.com/drive/1SkxGfWz8KLQpcea9MsdP7QEoe-yh5Iai?usp=sharing)\n",
     "\n",
     "The directory `experiments` contains code to reproduce our main results. We used `hydra`, the parameters can be changed in `config` or directly in the CLI. \n",
     "In `notebooks`, we provide examples on toy datasets.\n"

nbs/sidebar.yml

@@ -2,10 +2,10 @@ website:
   sidebar:
     contents:
       - index.ipynb
-      - cheb.ipynb
-      - embedding.ipynb
-      - graph.ipynb
-      - heat_filter.ipynb
-      - mds.ipynb
-      - other_emb.ipynb
-      - utils.ipynb
+      - 00_embedding.ipynb
+      - 01_heat_filter.ipynb
+      - 02_cheb.ipynb
+      - 03_mds.ipynb
+      - 04_graph.ipynb
+      - 06_utils.ipynb
+      - 07_other_emb.ipynb