FandanGO - core plugin

This is the core plugin of the FandanGO application.

How to deploy it

1. FandanGO uses conda package manager for installation. If you do not have conda already installed (run which conda in your console), install Miniconda as in example below (replace /path/for/miniconda/ with the proper path):

   wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
   bash Miniconda3-latest-Linux-x86_64.sh -b -p /path/for/miniconda
   

   On a Mac you can use the command brew install miniconda

2. Make sure you are running bash shell (run echo $SHELL in your console), then initialize conda (replace /path/for/miniconda/ with the proper path):

   source /path/for/miniconda/etc/profile.d/conda.sh
   

3. Create the conda environment:

   conda create --name fandanGO python=3.12
   

4. Activate environment and install the core (replace /path/for/fandanGO-core with the proper path):

   conda activate fandanGO
   git clone https://github.com/FragmentScreen/fandanGO-core.git
   pip install -e /path/for/fandanGO-core
   

   You will need to run conda init SHELLNAME prior to this, on Mac this is likely to be conda init zsh

5. Create a launcher file, let's call it "fandanGO", with the following content (replace /path/for/miniconda/ with the proper path):

   #!/usr/bin/env python3
   import os
   import sys
   
   cmd = 'eval "$(/path/for/miniconda/bin/conda shell.bash hook)" && conda activate fandanGO && '
   cmd += "python -m core %s" % " ".join(sys.argv[1:])
   
   exit(os.WEXITSTATUS(os.system(cmd)))
   

6. Give execution permissions to it:

   chmod +x fandanGO
   

7. Create an alias for the FandanGO launcher in your .bashrc file (replace /path/for/fandanGO with the proper path):

   alias fandanGO='/path/for/fandanGO'
   

8. Play with FandangGO!💃:

   fandanGO --help
   

Plugins

How to install/uninstall a plugin

• Install:

  fandanGO install-plugin --plugin /path/to/fandanGO-plugin
  

• Uninstall:

  fandanGO uninstall-plugin --plugin fandanGO-plugin
  

How to develop a new plugin

A FandanGO plugin should have:

1. The structure of a Python module installable by pip.

2. In the setup.py file, an entry point for fandango.plugin with the following structure:

   entry_points={
        'fandango.plugin': 'fandanGOPluginName = pythonModuleName'
    }
   

3. A __init__.py file with a Plugin class extending the core.Plugin class with the functions:

   • define_args (optional): for each action implemented in the plugin defines the parameters needed (furthermore the fandanGO project name)
   • define_methods (mandatory): for each action implemented in the plugin defines the method that will take care of it.

4. For integrity reasons, your plugin database should store the FandanGO project name as one of the table fields.

You can take as example the fandanGO-cryoem-cnb plugin placed at https://github.com/FragmentScreen/fandanGO-cryoem-cnb

Security Scanning

This repo uses OSV Scanner for vulnerability detection.

When it runs:

• Daily at 03:00 UTC (full scan)
• On PRs targeting main (changed deps only)
• On push to main (full scan)

If vulnerabilities are found:

1. Check the Security tab for alerts
2. To ignore false positives, add entries to osv-scanner.toml:

   [[IgnoredVulns]]
   id = "GHSA-xxxx-xxxx-xxxx"
   reason = "Justification"

References:

• OSV Scanner docs
• GitHub Action
• OSV Database