iroki 0.0.29 → 0.0.30

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data/README.md

@@ -11,6 +11,18 @@
 Command line app and library code for Iroki, a phylogenetic tree
 customization program.
 
+## Citation ##
+
+Iroki is research software. If you use Iroki, please cite the Iroki preprint:
+
+```
+Moore RM, Harrison AO, McAllister SM, Marine R, Chan C, Wommack KE. 2017. Iroki: automatic customization for phylogenetic trees. doi: https://doi.org/10.1101/106138
+```
+
+## Documentation ##
+
+For in depth docs and examples, please see the [Iroki wiki](https://github.com/mooreryan/iroki/wiki) page.
+
 ## Installation ##
 
 ### Running with Docker ###

data/lib/iroki/biom.rb

@@ -16,8 +16,9 @@
 # You should have received a copy of the GNU General Public License
 # along with Iroki.  If not, see <http://www.gnu.org/licenses/>.
 
-def count_or_rel_abund? str
-  str.match /\A[01]?.?[0-9]+\Z/
+def valid_numerical_val? str
+  # looks something like sci notation
+  str.match(/[-+]?[0-9]?\.?[0-9]?[eE]?[-+]?[0-9]+/)
 end
 
 module Iroki
@@ -39,9 +40,9 @@ module Iroki
                    "Line #{idx+1} has no sample"
 
           the_counts.flatten.each do |count|
-            abort_unless count_or_rel_abund?(count),
-                         "The value '#{count}' in the biom file " +
-                         "was not a count or relative abundance"
+            abort_unless valid_numerical_val?(count),
+                         "The value '#{count}' in the " +
+                         "biom file might not be valid"
           end
 
           if lineno.zero?

data/lib/iroki/version.rb

@@ -18,8 +18,8 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.29"
-  COPYRIGHT = "2015 - 2016 Ryan Moore"
+  VERSION = "0.0.30"
+  COPYRIGHT = "2015 - 2017 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/iroki"
   LICENSE   = "GPLv3"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: iroki
 version: !ruby/object:Gem::Version
-  version: 0.0.29
+  version: 0.0.30
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-10-13 00:00:00.000000000 Z
+date: 2017-03-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler