v1.0.0

First pre release, follow Developer installer instructions. When cloning, set the version tag as branch:

git clone https://github.com/MannLabs/alphadia.git --branch v1.0.0

For simple extraction workflows, use the reference provided by alphadia extract -h:

      _   _      _         ___ ___   _   
     /_\ | |_ __| |_  __ _|   \_ _| /_\  
    / _ \| | '_ \ ' \/ _` | |) | | / _ \ 
   /_/ \_\_| .__/_||_\__,_|___/___/_/ \_\
           |_|              version: 1.0.0

Usage: alphadia extract [OPTIONS] OUTPUT_LOCATION

  Extract DIA precursors from a list of raw files using a spectral library.

Options:
  -f, --file PATH            Raw data input files.
  -l, --library FILE         Spectral library in AlphaBase hdf5 format.
  --fdr FLOAT                False discovery rate for the final output.
                             [default: 0.01]
  --keep-decoys BOOLEAN      Keep decoys in the final output.  [default:
                             False]
  --config-path FILE         DO NOT TOUCH - Default config yaml. If not
                             specified, the default config will be used.
  --config-update-path FILE  Config yaml which will be used to update the
                             default config.
  --config-update TEXT       Dict which will be used to update the default
                             config.
  --neptune-token TEXT       Neptune.ai token for continous logging.
  --neptune-tag TEXT         Neptune.ai tag for continous logging.
  --figure-path DIRECTORY    If specified, directory will be used to store
                             calibration figures.
  -h, --help                 Show this message and exit.