developer_guide.md

Guide for developers

If you need to modify the algorithms/models in PaddleHelix, you have to switch to the developer mode. The core algorithms of PaddleHelix are mostly implemented in Python, but some also in C++, so you cannot develop PaddleHelix simply with pip install --editable {pahelix_path}. To develop on your machine, please do the following:

1. Please follow the installation guide to install all dependencies of PaddleHelix (paddlepaddle >= 2.0.0rc0, pgl >= 1.2.0).

2. If you have already installed distributed PaddleHelix with pip install paddlehelix, please uninstall it with:

   pip uninstall paddlehelix

3. Clone this repository to your local machine, supposed path at "/path_to_your_repo/":

   git clone https://github.com/PaddlePaddle/PaddleHelix.git /path_to_your_repo/
   cd /path_to_your_repo/

4. Depends on which model you'd like to modify, go to 4.1 or 4.2:

   4.1. LinearRNA

   The source code of LinearRNA is at "./c/pahelix/toolkit/linear_rna/linear_rna". You could modify it for your needs. Then remember to return to the root directory of the repository, run scripts below to re-compile (please ensure there are cmake >= 3.6 and g++ >= 4.8 on your machine):

   sh scripts/prepare.sh
   sh scripts/build.sh

   After a successful compilation, import LinearRNA as follows:

   cd build
   python
   >>> import c.pahelix.toolkit.linear_rna.linear_rna as linear_rna

   4.2. Other algorithms

   Except LinearRNA, other algorithms in PaddleHelix are all implemented in Python. If you want to change these algorithms, just find and modify corresponding .py files under the path "./pahelix", then add "/path_to_your_repo/" to your Python environment path:

   import sys
   sys.path.append('/path_to_your_repo/')
   import pahelix

If you have any question or suggestion, feel free to create an issue. We will response as soon as possible.