fixed bugs

docs/changelog.md

@@ -1,5 +1,11 @@
 # Kirsche Changelog
 
-## 2021-05-20, 0.1.0
+## 2021-09-21
+
+Added:
+
+- Visualizations!
+
+## 2021-09-16, 0.1.0
 
 First version!

docs/references/visualize.md

@@ -0,0 +1,3 @@
+## visualize
+
+::: kirsche.visualize

docs/tutorials/index.md

@@ -2,17 +2,63 @@
 
 Some tutorials are provided here in this section.
 
+## Install
+
+```
+pip install kirsche
+```
+
+??? warning "Install in an Environment"
+
+    Unless you are using this in a temporary machine like a docker container, it is recommended to install this in an environment.
+
+    For example, using conda, we can create an environment called `kirsche` or any other name you prefer,
+
+    ```
+    conda create -n "kirsche" python=3.7 pip
+    ```
+
+    then activate the environment
+
+    ```
+    conda activate kirsche
+    ```
+
+    Install kirsche in this environment
+
+    ```
+    pip install kirsche
+    ```
+
+### Visualizations
+
+Suppose we have a bib file called `test.bib`, and we would like to generate an html file called `test.html`,
+
+=== "Command"
+
+    ```
+    kirsche visualization -sb "test.bib" -th "test.html"
+    ```
+
+    Open the `test.html` file in your browser.
+
+=== "Results"
+
+
+    ![](assets/visualizations/visualization-demo-1.gif)
+
+
 ### Download metadata only
 
 Using DOIs:
 
-```python
+```
 kirsche metadata -p "10.1016/j.sna.2020.112529" -p "10.1152/jn.00208.2014" -m save/to/file/path
 ```
 
 Using a bib file:
 
-```python
+```
 kirsche metadata -b path/to/your/bib/file -m save/to/file/path
 ```
 
@@ -21,12 +67,12 @@ kirsche metadata -b path/to/your/bib/file -m save/to/file/path
 
 Using DOIs:
 
-```python
+```
 kirsche connections -p "10.1016/j.sna.2020.112529" -p "10.1152/jn.00208.2014" -c save/to/file/path
 ```
 
 Using a bib file:
 
-```python
+```
 kirsche connections -b path/to/your/bib/file -c save/to/file/path
 ```

docs/tutorials/use-in-code.md

@@ -1,4 +1,3 @@
 # Use in Code
 
-## Download Data
-
+The command line tool covers most of the use cases. If more customizations is desired, please refer to [References](../references/index.md) for details about the utilities.

kirsche/command.py

@@ -13,7 +13,7 @@
 from kirsche.dataset import DataViews
 from kirsche.utils.io import load_json
 from kirsche.utils.bib import load_bib
-from kirsche.visalize import make_chart, PaperGraph, visualize
+from kirsche.visualize import make_chart, PaperGraph, visualize
 
 
 logger.remove()

mkdocs.yml

@@ -36,8 +36,8 @@ theme:
   font:
     text: Roboto
     code: Roboto Mono
-  favicon: assets/logo.png
-  logo: assets/logo_badge.svg
+  favicon: assets/logo/logo.png
+  logo: assets/logo/logo_badge.svg
 
 
 
@@ -52,6 +52,7 @@ markdown_extensions:
   - pymdownx.tasklist
   - toc:
       permalink: "¤"
+  - pymdownx.details
 
 plugins:
   - autorefs
@@ -75,6 +76,7 @@ nav:
   - "Home": index.md
   - "Tutorials":
     - "Tutorials": tutorials/index.md
+    - "Use in Python Code": tutorials/use-in-code.md
   - References:
     - "Introduction": references/index.md
     - "Commandline":
@@ -83,6 +85,8 @@ nav:
       - "Download": references/download.md
     - "Connect":
       - "Connect": references/connect.md
+    - "Visualize":
+      - "Visualize": references/visualize.md
     - "Dataset":
       - "Dataset": references/dataset.md
     - "Utils":