BioPerl Timeline

This timeline provides a rough guideline of how the project will be done.

Before April 25:

  • Familiarize myself completely with cpanm, working to install CPAN modules in a local::lib
  • Study the BioPerl repository on GitHub, making sure to understand the many interdependencies of the modules
  • Continue working to understand testing and module authoring required for the reorganization
  • Continue project for Sol Genomics to create module to upload to CPAN

Follow up: On track so far. Sol Genomics module can be found at:   github Bio-AGP

April 25 – May 23 (Before the official coding time):

  • Actively communicate with my mentor (via IRC, email and mailing lists) to plan the details of the project and ultimate goals that can be accomplished in the limited time frame
  • Continue to study the interdependencies of the BioPerl modules to continue planning of the reorganization
  • Continue to study dependency management and discovery
  • Completely understand CPAN distribution creation and uploading

Follow up: The handling of the project has changed somewhat. We have decided to make a Dist::Zilla plugin bundle for the Bioperl project. github Dist::Zilla BioPerl PluginBundle

May 24 – June 13 (Official coding period starts):

  • Begin reorganization from the bottom up, by breaking out the Bio::Root distribution
  • Write new build file for Bio::Root distribution
  • Edit the bioperl-live build file to show updated dependency requirements
  • Ensure test file for each feature is up to date as well to ensure configuration, building, testing, bundling and installing the distribution will be successful
  • Write README file
  • Publish on CPAN
  • Communicate with mentor about progress, continue planning of reorganization

June 13 – July 4:

  • Break out Bio::Das and Bio::Event from the BioPerl distribution, as their only dependency within BioPerl is Bio::Root
  • Write new build file for Bio::Das and Bio::Event distributions
  • Edit the bioperl-live build file to show updated dependency requirements
  • Ensure test file for each feature is up to date as well to ensure configuration, building, testing, bundling and installing the distribution will be successful
  • Write README files
  • Publish on CPAN
  • Communicate with mentor about progress, continue planning of reorganization

July 4 – July 25:

  • Extract Bio::Location from the BioPerl distribution
  • Write new build file for Bio::Location distribution
  • Edit the bioperl-live build file to show updated dependency requirements
  • Ensure test file for each feature is up to date as well to ensure configuration, building, testing, bundling and installing the distribution will be successful
  • Write README file
  • Publish on CPAN
  • Communicate with mentor about progress, continue planning of reorganization

JULY 11-15th MID TERM EVALUATION

July 11 – July 15:

  • Communicate with mentor about progress of project so far, re-evaluate the project goals for the summer based on time left

July 25-August 16:

  • Extract Bio::Factory and Bio::Coordinate from the BioPerl distributions, as their only dependencies within BioPerl were Bio::Root and Bio::Location
  • Write new build file for Bio::Factory and Bio::Coordinate distributions
  • Edit the bioperl-live build file to show updated dependency requirements
  • Ensure test file for each feature is up to date as well to ensure configuration, building, testing, bundling and installing the distribution will be successful
  • Write README files
  • Publish on CPAN
  • Communicate with mentor about progress, continue planning of reorganization

August 16- August 22:

  • Finalize all documentation, README files and make roadmap of continued reorganization

 

1 Comment

  1. Cheers, and good luck with the project. It’s going to be great to have an overhaul of BioPerl!!

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