Update docs (#24)

* fix imports

* add manifest.in

* update docs

* Remove whiscy_protocol.sh script

* linting

* update tests

INSTALLATION.md

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+# Install Whiscy
+
+Below we will go into a step-by-step guide on how to install Whiscy. Instructions are provived for Ubuntu Linux, in other systems the installation process may vary.
+
+## Third-Party
+
+Whiscy depends on the following third-party software:
+
+- Muscle
+- FreeSASA
+- HSSPCONV
+- Protdist
+
+The installation of these dependencies is described in the [THIRDPARTY.md](THIRDPARTY.md) file.
+
+## Whiscy
+
+To install Whiscy, follow these steps:
+
+- Clone the repository:
+
+    ```bash
+    git clone https://github.com/haddocking/whiscy && cd whiscy
+    ```
+
+- Install the scripts
+
+  Make sure you are using an environment with Python3.11+
+
+  ```bash
+  pip install .
+  ```
+
+- Check the installation
+
+    ```text
+    $ whiscy -h
+    usage: whiscy [-h] [-o output_file] [--version]
+                  surface_list conversion_table alignment_file distance_file
+
+    positional arguments:
+      surface_list          Surface list
+      conversion_table      Conversion table
+      alignment_file        Alignment file
+      distance_file         Distance file
+
+    options:
+      -h, --help            show this help message and exit
+      -o output_file, --output output_file
+                            If set, output prediction to this file
+      --version             show program's version number and exit
+    ```
+
+### Troubleshooting
+
+If you get an error such as `ValueError: MUSCLE_BIN not found in system variables`, make sure you have followed the steps in [THIRDPARTY.md](THIRDPARTY.md) to install the third-party dependencies.

MANIFEST.in

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+include src/whiscy/param/parasmooth.par
+include src/whiscy/param/weight_ma.txt
+include src/whiscy/param/ztable.txt