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Google Code In 2013 Tasks
Note: you may notice many of the projects here have the prefix bio-. This refers to Biogems and does not mean they are exclusively biological packages.
Attention: All of these tasks need MORE DETAIL. Remember, these are secondary school students. Tell them what they need to do to succeed, and where/whom they can ask for help.
These primarily contain tasks in the categories Code, Documentation, and Quality Assurance. While any issue is a valid task, mentors have -- as much as possible -- tried to mark issues by difficulty level.
- NMatrix Dense and sparse linear algebra library for the Ruby language, written in Ruby, C, and C++.
- Plotrb (30+ tasks) Visualization tool based on Vega and D3.
- BioInterchange (3 issues) Generates interchangeable RDF from non-RDF data sources.
- biogems.info website (20 tasks) is a generated website that scapes information from rubygems.org, github etc. For one, we want to add functionality for SciRuby (see also http://biogems.info)
- biogem code generator (11 tasks) Biogem builds on jeweler to generate Ruby gems for bioinformatics
- BioRuby (16 tasks) BioRuby project
- bio-table (18 tasks): Swiss army knife of tabulated data; transforming/filtering tab/csv
- bio-logger (2 tasks): Bio-logger uses monkey-patching to add heaps of functionality to log4r
- Bio-Sequenceserver (37 issues Webserver for BLAST
- bio-sambamba (10 tasks): help to create Ruby bindings to the Sambamba library (processing SAM/BAM files that are commonly used to store aligned nucleotide sequences); requires basic C++ knowledge
- Get all YARV-compatible gems in the SciRuby umbrella project (especially Statsample, NMatrix, Distribution, Minimization, Integration, Plotrb, Rubyvis, PubliSci, etc.) working together. Right now, dependency conflicts exist, particularly surrounding NArray and Ruby/GSL. We have versions of both of these gems (gsl-nmatrix and narray-nmatrix) which work with NMatrix, but they need to be listed as dependencies in place of the old versions.
- Cross-list all SciRuby gems as biogems, so they'll be listed on biogems.info. (Don't rename them with the
bio-extension.) - Ensure all of the SciRuby gems meet the proposed standards for inclusion in SciRuby.
- Create a git repository template for an empty Ruby gem to supplement the instructions listed below. It should also follow the SciRuby gem inclusion draft guidelines.
- Clean up the C, C++, and Ruby function comments throughout NMatrix so they render in beautiful HTML when RDoc is run.
- NMatrix non-API method documentation. Many of the methods throughout the C++ extensions for NMatrix lack clear documentation on parameters, what they return, and sometimes even what they do; this makes it harder for new contributors to jump in and start coding. Pick a less than fully documented method, explore what it does, and add documentation clarifying what you've figured out. NMatrix mentors can suggest simpler or more complicated methods, depending on how deep you want to dive into the code.
- Write instructions for creating a simple Ruby gem with no C or Java extensions.
- Write instructions for creating a Ruby gem with a C or C++ extension. Use NMatrix as your model.
- Write instructions for creating a Ruby gem with a Java extension. Use Ruby-Band as your model.
- Find an answer to this StackOverflow question about the
volatilekeyword in C++. - Find an answer to this StackOverflow question about Travis-CI and GCC versions
- As a preliminary task, research Cucumber and other test frameworks. Add to NMatrix issue #150 information on best practices for standardizing our testing framework.
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Development on most Ruby projects is test-driven. That is, people write specs describing how the code should behave; and then go back and write the code. We need someone to rewrite the NMatrix specs as outlined in the NMatrix issue tracker. Currently, they're organized by features (roughly on the basis of when we added features). Instead, they should be organized by
Object#method. Mentors for these tasks are John Woods and Colin Fuller. -
See research task above on researching Cucumber and other test frameworks prior to embarking on one of these tasks.
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Each existing spec file rewritten counts as a single task (13 files/tasks in total).
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Find a bug in any SciRuby project and write a spec which demonstrates the bug. Send a pull request. The spec should be written as outlined in the NMatrix issue tracker.
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Stress tests for NMatrix code. NMatrix has a lot of back-and-forth between ruby and C++ code, and this sometimes leads to subtle bugs (for example, bugs that only happen when garbage collection runs at a particular time) that aren't caught by the unit tests because they only show up on long-running or complex programs. Pick a functionality and write stress tests that perform that function many times, on huge matrices, etc. Try to break things in unusual ways. (Keep these separate from normal unit tests so that the long-running tests don't get run with every commit.)
- Create a new gem called
plotrb-ui, and using the Rubyvis-basedSciRuby::Plottermodule in the old SciRuby gem as a model, try to create a very simple GUI for Plotrb. Basically, when people edit a plotrb file, the plot should update. Believe it or not, this is a pretty simple task — most of the work is already done in Plotter. If you don't want to create the gem structure, talk to John Woods, and he'll do it for you or show you how. - Write a Plotrb function and rake task / generator for quickly creating jsfiddles for plot code. Zuhao can help with this.
- Update our website to include a Like button for our Facebook page. John Woods can help you with this, and you'll need to ask him for instructions on how to edit our website via github pull requests.
- Develop standard 'stylesheets' for people wanting to make pretty plots in Plotrb or Rubyvis. How thick should the lines be? What fonts look good (serif versus sans serif)? What about the rules (the axes and such)? What about stroke versus fill? This topic might also fall under the UI category, as we expect some coding will be required and you might be able to devise some shortcuts for Plotrb as well. It's divided into several individual tasks.
- Preparation: Devise a plotrb API for applying a stylesheet to plots.
- Screen plots: Devise a stylesheet for screen plots which can be applied with the API.
- Print plots: Devise a stylesheet for print plots which can be applied with the API.