Updates website to the v0.8.2 conventions of the kmerdb package.

.ruby-gemset

@@ -1 +1 @@
-forty
+kmerdbwebsite

.ruby-version

@@ -1 +1 @@
-ruby-2.4.2
+ruby-3.0.0

Gemfile

@@ -2,3 +2,5 @@ source "https://rubygems.org"
 gemspec
 
 gem "jekyll-toc", "~> 0.16.1"
+
+gem "webrick", "~> 1.8"

index.md

@@ -8,9 +8,9 @@ author: null
 show_tile: false
 ---
 
-The K-mer database (.kdb) is a file format and command-line utility (CLI) for accessing precomputed k-mers from sequencing data. .kdb views k-mer graph databases as a fundamental technology to look at biological sequence identities and abundances. K-mer methods have been noted as fast and are used in areas from NGS quality control to phylogenomic investigations.
+The K-mer database profile `kmerdb` is a file format (.kdb) and command-line utility (CLI) for creating k-mer count vector profiles from sequencing data. kmerdb views k-mers and their De Bruijn graphs as fundamental tools for biological sequence abundances and sequence similarities. K-mer methods have been noted as fast and are used in areas from NGS quality control to phylogenomic investigations.
 
-.kdb is based on the block GNU-zip file (bgzf) standard. Each .kdb file has a header or metadata section, much like .bam files. It is essentially a tab-delimited format with the last column unstructured for k-mer specific metadata. Input files and total k-mer counts are stored in the metadata block at the top of the file
+kmerdb is based on the block GNU-zip file (bgzf) standard. Each .kdb file has a metadata header section, much like .bam files. It is essentially a tab-delimited format with a YAML header. Input file checksums, unique and total k-mer counts, and nullomer counts are stored in the metadata block at the top of the file.
 
 Please visit the [Install](#/install) page for details on installation.
 

installation.md

@@ -20,15 +20,15 @@ image: assets/images/installation-symbol.png
 Install the latest version from PyPI
 
 ```bash
-pip install kdb
+pip install kmerdb
 ```
 
 Install locally for development
 
 ```bashn
-git clone [email protected]:MatthewRalston/kdb.git
-cd kdb
+git clone [email protected]:MatthewRalston/kmerdb.git
+cd kmerdb
 pip install -r requirements.txt
-pip install -e .
+pip install .
 ```
 

kdb_webite.gemspec → kmerdb_website.gemspec

@@ -1,17 +1,18 @@
 # coding: utf-8
 
 Gem::Specification.new do |spec|
-  spec.name          = "KDB_jekyll_theme_forty"
+  spec.name          = "kmerdb_jekyll_theme_forty"
   spec.version       = "1.2"
   spec.authors       = ["Matthew Ralston"]
-  spec.email         = ["mrals89@gmail.com"]
+  spec.email         = ["mralston.development@gmail.com"]
 
   spec.summary       = %q{A website for bioinformatics computation based on the forty theme by HTML5 UP.}
-  spec.homepage      = "https://github.com/MatthewRalston/kdb"
+  spec.homepage      = "https://github.com/MatthewRalston/kmerdb"
   spec.license       = "Apache"
 
   spec.files         = `git ls-files -z`.split("\x0").select { |f| f.match(%r{^(assets|_layouts|_includes|_sass|LICENSE|README)}i) }
 
-  spec.add_development_dependency "jekyll", "~> 4.0"
-  spec.add_development_dependency "bundler", "~> 2.1"
+  spec.add_development_dependency "jekyll", "~> 4.2"
+  spec.add_development_dependency "bundler", "~> 2.5"
+  spec.add_development_dependency "webrick", "~> 1.8"
 end