The description of createsubdb's subdb-mode leads the user to believe that softlinks to the original database won't be created. A solution would be to improve the argument's description and maybe add another argument to copy files from the original database instead of creating softlinks, as this is not communicated to the user at any moment.

A lot of the Big Data workflow has been baked into the standard operation of the package in recent version updates. It should be updated to reflect the current state of the package, which should simplify the workflow at no cost to performance.

The documentation for column 4 was detailed in #38, but it would be nice to know the precise number of mismatches over the length of the alignment.

Summary:

Quick questions.

There aren't instructions in the README that I can find about how to take advantage of a scheduler. Is that documentation available?

Also, you say it will work with an OGE/SGE type scheduler. What about PBS?

Thanks much! We find this software very useful, and I'm excited to try out version 0.3+ (we'd been using pyani 0.2.7).

pyani Version:

Other than what we've already discussed, I'd like to work on some things listed below. I tend to enjoy micromanaging things, so please let me know if I'm stepping on your toes or if you desire something different. In the end I just want to help out.

Add Labels

I discovered zenhub a long time ago, but I recently started using it more. Especially for bigger projects. I've also started u

As @layamene so effectively put it in her review (#46), most tables are effectively "hidden." Tables should be more discoverable.

FishBase has too many tables. We need:

• Clear, consise & searchable documentation of all endpoints / implemented tables
• an endpoint to search across tables to find which one has a particular field,
• Merge more tables in advance:
  • Tables with

We had the following comment on a review:

For example, bodiversity data sets often contain mutliple columns denoting the taxon (order, family, genus, etc) because often questions for those data require aggregating at different levels. One of the problems with this is that as a result the taxon information in the dataset is highly denormalized, with corresponding problems as a result. How woul

Document the essential current webservices and their usage in order to assess consequences of deprecation. Decide whether the existing list matching and 4D4life services need to be migrated.

Overview

Everything in lib/utilities is intended to be Rails agnostic (though many use some feature like .blank?. These libraries are execellent targets for extraction and simplification of our code base.

Extraction target

• https://github.com/SpeciesFileGroup/taxonworks/blob/development/lib/utilities/dates.rb and corresponding specs

Re-integration

Refactoring should be s