Timeline for "General quality assurance of biomedical applications inside Debian" - from May 23, 2016 to August 23, 2016.
The task is to do Quality Assurance on any Debian Med packages by verifying runtime tests and autopkgtests as well as checking for lintian issues, hardening options and code review.
Following table contains minimal possible timeline:
| Week | Packages sheduled |
|---|---|
| May 23 - May 29 | Dssp, Profbval,(+Tm-align) |
| May 30 - June 5 | Pdb2pqr, R-cran-bio3d |
| #!/usr/bin/env julia | |
| # this file contains little bit of magic: | |
| # I thought that function returning Expr formed by other expression and set of key/value pairs might be useful for my evil purposes. | |
| # should work with julia 0.4 | |
| # I called it `withenv`, just like function from standard lib, | |
| # because it does almost the same thing (variable substitution) - except it doesn't compute Expr in any way. | |
| function withenv(expr :: Expr, kv :: Pair...) | |
| v = [ | |
| begin | |
| if isa(arg, Symbol) && (ind = findfirst(kvpair -> kvpair.first == arg, kv)) > 0 && arg == kv[ind].first |
| sealed trait BombLike { | |
| def power : Int | |
| def name : String | |
| } | |
| case class Bomb(power : Int, name : String) extends BombLike { | |
| println("Explosion!") | |
| } | |
| case object Clock extends BombLike { |
| # from file MASS/R/add.R | |
| # dropterm method redefined | |
| addterm2 <- | |
| function(object, ...) UseMethod("addterm2") | |
| addterm2.default <- | |
| function(object, scope, scale = 0, test = c("none"), | |
| k = 2, sorted = FALSE, trace = FALSE, ...) | |
| { | |
| if(missing(scope) || is.null(scope)) stop("no terms in scope") |
| ```{r} | |
| library(knitr) | |
| library(lattice) | |
| library(MASS) | |
| library(latticeExtra) | |
| library(rgl) | |
| library(hash) | |
| ``` | |
| ```{r} |
| type Profile{T} | |
| raw_data :: Array{Char, 2} | |
| data :: Array{Dict{Char, T}, 1} | |
| size :: Int64 | |
| Profile(raw :: Array{Char, 2}) = get_pr(raw) | |
| Profile(str :: String) = Profile{T}( reshape([ letter for letter in str ], length(str), 1) ) | |
| function get_pr(raw::Array{Char, 2}) | |
| raw_data = copy(raw) |
| \documentclass[a4paper]{article} | |
| \usepackage{graphicx} % needs this to use resizebox command | |
| \begin{document} | |
| %\resizebox*{\textheight}{!} { | |
| \scalebox{0.6}{ | |
| \begin{tabular}{c*{6}{c}} | |
| \hline | |
| $P_\alpha$ & $P_\beta$ & $P_\gamma$ & $f_i$ & $f_{i+1}$ & $f_{i+2}$ & $f_{i+3}$ \\ | |
| \hline |
| #!~/bin/ruby | |
| # ruby 1.9.3 | |
| # ----------- | |
| # MAIN CODE | |
| # ----------- | |
| puts "Print permutation elements:" | |
| a = [0] + gets.split.map{|x| x.to_f } # assume that input values are float | |
| n = a.size - 1 |
| require 'ruby_decorators' | |
| require './ruby_class_decorators.rb' | |
| # http://stackoverflow.com/questions/4191214/callback-for-classes-defined-inside-a-module | |
| # | |
| class SingletonMachine < RubyClassDecorator | |
| def call(this, *args, &block) | |
| this.class_eval do | |
| def self.new(*arg) | |
| @@instance ||= super(*arg) |
| require 'ruby_decorators' | |
| class TimeMachine < RubyDecorator | |
| def call(this, *args, &blk) | |
| start_time = Process.times | |
| puts "#{'%.4f' % (start_time.stime + start_time.utime)}ms #{this.name}" | |
| this.call(*args, &blk) | |
| end_time = Process.times | |
| puts " +#{ '%.9f' % (end_time.stime + end_time.utime - start_time.utime - start_time.stime).abs }ms" | |
| end |