created QA.html for Quality Assurance in Julia

Author: svaksha

Algorithms.md

@@ -1,17 +1,17 @@
 __[ALGORITHMS and Data Structures](https://en.wikipedia.org/wiki/Category:Algorithms_and_data_structures) : Data Mining, Clustering, ...__
 
 + [ALGORITHMS](#algorithms)
-    + [Association Rule](#association-rule)
-    + [Checksum](#checksum)
-    + [Collaborative Filtering](#collaborative-filtering)
-    + [Graph Algorithms](#graph-algorithms)
-    + [Pattern Matching](#pattern-matching)
-    + [Quantum](#quantum)
-    + [Scheduling Algorithm](#scheduling-algorithm)
-    + [Sorting](#sorting)
-    + [Time](#time)
+   + [Association Rule](#association-rule)
+   + [Checksum](#checksum)
+   + [Collaborative Filtering](#collaborative-filtering)
+   + [Graph Algorithms](#graph-algorithms)
+   + [Pattern Matching](#pattern-matching)
+   + [Quantum](#quantum)
+   + [Scheduling Algorithm](#scheduling-algorithm)
+   + [Sorting](#sorting)
+   + [Time](#time)
 + [COMPUTATIONAL PROBLEMS](#computational-problems)
-    + [NP-complete](#np-complete)
+   + [NP-complete](#np-complete)
         + [SAT](#sat)
 
 ----

Biology.md

@@ -16,6 +16,7 @@
 + [PHARMACOLOGY](#pharmacology)
 + [Resources-Teaching](#resources-teaching)
 
+----
 ----
 
 + [COBRA.jl](https://github.com/opencobra/COBRA.jl) :: COnstraint-Based Reconstruction and Analysis, used to perform COBRA analyses such as Flux Balance Anlysis (FBA), Flux Variability Anlysis (FVA), or any of its associated variants such as `distributedFBA`.

Chemistry.md

@@ -1,4 +1,4 @@
-# Chemistry in Julia!
+# Chemistry.md
 
 + [§1. Chemical File Formats and Input Output](#1-chemical-file-formats-and-input-output)
 + [§2. Biochemistry](#2-Biochemistry)

DesktopApplications.md

@@ -12,7 +12,7 @@ The collective noun [application software](https://en.wikipedia.org/wiki/Applica
         + [Atom](#atom)
         + [Emacs](#emacs)
    + [Jupyter](#jupyter)
-   + [
+   + [Prettyprinting](#prettyprinting)
    + [WIDE](#wide) 
 
 ----

FileIO.md

@@ -1,7 +1,7 @@
 + [§1. Binary IO](#1-Binary-IO)
 + [§2. Data Formats](#2-Data-Formats)
-   + [Avro](#avro)
-   + [BSON](#bson)
+   + [§2.1. Avro](#2-1-Avro)
+   + [§2.2. BSON](#2-2-BSON)
    + [JSON](#json)
    + [ODS](#ods)
    + [PDF](#pdf)
@@ -23,16 +23,15 @@
 ----
 
 
-# §1. Binary IO. <span id="1-Binary-IO"><span>
+# §1. Binary IO <span id="1-Binary-IO"><span>
 + [FortranFiles.jl](https://github.com/traktofon/FortranFiles.jl) :: Read and write "unformatted" Fortran data, i.e. binary data interspersed with metadata about data records.
 + [HexEdit.jl](https://github.com/templarlabs/HexEdit.jl) :: Edit and display binary file data in hexadecimal format.
 + [LargeColumns.jl](https://github.com/tpapp/LargeColumns.jl) :: Handle large columns (vectors of equal length) with bits types in Julia using mmap - a thin wrapper for mmapped binary data, with a few sanity checks and convenience functions.
 + [StrPack.jl](https://github.com/pao/StrPack.jl) :: For encoding and decoding binary data streams and there is some [documentation](https://strpackjl.readthedocs.org/) at readthedocs.org.
 
 ----
 
-
-# §2. Data Formats. <span id="2-Data-Formats"><span>
+# §2. Data Formats <span id="2-Data-Formats"><span>
 **Libraries for Data serialization and (human readable) file formats.**
 + [AIDA.jl](https://github.com/jstrube/AIDA.jl) :: This package implements simple readers for legacy AIDA files.
 + [BEncode.jl](https://github.com/joshuamiller/BEncode.jl) :: A Julia library for BEncode metadata files used for encoding BitTorrent storage and transmission of loosely structured data.
@@ -66,10 +65,11 @@
 + [XPT.jl](https://github.com/lendle/XPT.jl) :: The XPT package reads SAS® software transport files and converts SAS software datasets to DataFrames.
 
 
-## [Avro](https://en.wikipedia.org/wiki/Apache_Avro]
-+ [Avro.jl](https://github.com/JuliaData/Avro.jl) ::  Julia implementation of the Apache Avro data standard. It provides convenient APIs for reading/writing data directly in the avro format, or as schema-included object container files.
+## §2.1. [Avro](https://en.wikipedia.org/wiki/Apache_Avro] <span id="2-1-Avro"><span>
+
++ [Avro.jl](https://github.com/JuliaData/Avro.jl) :: Julia implementation of the Apache Avro data standard. It provides convenient APIs for reading/writing data directly in the avro format, or as schema-included object container files.
 
-## BSON
+## §2.2. BSON <span id="2-2-BSON"><span>
 + [BSON.jl](https://github.com/MikeInnes/BSON.jl) :: A Julia package for working with the Binary JSON serialisation format, that can be used as a general store for Julia data structures.
 + [BSONify.jl](https://github.com/OliverColeman/BSONify.jl) :: Convert just about any data structure - including primitive types, arbitrary composite types defined by other modules or your own data structures, nested and recursive data structures, complicated parametrised types, and even type unions - to clean and simple BSON and back again. Save and load to/from files or a MongoDB.
 

Optimization.md

@@ -1,32 +1,32 @@
+# Optimization.md
 __[Mathematical Optimization](https://en.wikipedia.org/wiki/Category:Mathematical_optimization) packages in Julia!__
 
-
-+ [FRAMEWORKS](#frameworks)
-+ [Linear Programming-Optimization](#linear-programming-optimization)
-+ [Nonlinear Programming](#nonlinear-programming)
-+ [UNCLASSIFIED](#unclassified)
++ [§1. FRAMEWORKS](#1-FRAMEWORKS)
++ [§2. Linear Programming-Optimization](#2-Linear-Programming-Optimization)
++ [§3. Nonlinear Programming](#3-Nonlinear-Programming)
++ [§4. UNCLASSIFIED](#4-UNCLASSIFIED)
 
+----
 ----
 
-# FRAMEWORKS
+# §1. FRAMEWORKS <span id="1-FRAMEWORKS"><span>
 + [JuMP.jl](https://github.com/jump-dev/JuMP.jl) :: A modeling language for Mathematical Optimization (linear, mixed-integer, conic, semidefinite, nonlinear).
 
 
 ----
 
-# [Linear Programming-Optimization](https://en.wikipedia.org/wiki/Linear_programming)
+# §2. [Linear Programming-Optimization](https://en.wikipedia.org/wiki/Linear_programming) <span id="2-Linear-Programming-Optimization"><span>
 + [Clp.jl](https://github.com/jump-dev/Clp.jl) :: Interface to the Coin-OR Linear Programming solver (CLP)
 + [Gurobi.jl](https://github.com/jump-dev/Gurobi.jl) :: is a Julia interface for the Gurobi Optimizer, a [commercial optimization solver for a variety of mathematical programming problems](https://en.wikipedia.org/wiki/Gurobi), including linear programming (LP), quadratic programming (QP), quadratically constrained programming (QCP), mixed integer linear programming (MILP), mixed-integer quadratic programming (MIQP), and mixed-integer quadratically constrained programming (MIQCP).
 + [jlSimplex](https://github.com/mlubin/jlSimplex) :: Proof-of-concept implementation of the (dual) simplex algorithm for linear programming in Julia.
 + [NLTester](https://github.com/IainNZ/NLTester) :: Code for benchmarks comparing AMPL, Julia, and YALMIP (MATLAB) for nonlinear modeling.
 + [PiecewiseLinearOpt.jl](https://github.com/joehuchette/PiecewiseLinearOpt.jl) :: Optimizing over piecewise linear functions.
 + [Tulip.jl](https://github.com/ds4dm/Tulip.jl) :: is an open-source interior-point solver for linear optimization, written in pure Julia. It implements the homogeneous primal-dual interior-point algorithm with multiple centrality corrections, and therefore handles unbounded and infeasible problems.
 
-
-
 ----
 
-# [Nonlinear Programming](https://en.wikipedia.org/wiki/Nonlinear_programming)
+# §3. [Nonlinear Programming](https://en.wikipedia.org/wiki/Nonlinear_programming) <span id="3-Nonlinear-Programming"><span>
+ 
 + [BARON.jl](https://github.com/joehuchette/BARON.jl) :: A wrapper for the BARON mixed-integer nonlinear programming solver.
 + [ConicNonlinearBridge.jl](https://github.com/mlubin/ConicNonlinearBridge.jl) :: Wrapper to solve conic optimization problems with derivative-based nonlinear solvers.
 + [Convex.jl](https://github.com/jump-dev/Convex.jl) :: A Julia library for mathematical programming that makes it easy to formulate and fast to solve nonlinear convex optimization problems.
@@ -42,7 +42,8 @@ __[Mathematical Optimization](https://en.wikipedia.org/wiki/Category:Mathematica
 
 ----
 
-# UNCLASSIFIED
+# §4. UNCLASSIFIED <span id="4-UNCLASSIFIED"><span>
+
 + [AmplNLReader.jl](https://github.com/JuliaSmoothOptimizers/AmplNLReader.jl) :: A Julia Interface to AMPL.
 + [AmplNLWriter.jl](https://github.com/jump-dev/AmplNLWriter.jl) :: Julia interface to AMPL-enabled solvers
 + [AutomotiveDrivingModels.jl](https://github.com/tawheeler/AutomotiveDrivingModels.jl) :: For car encounter models.

Programming-Paradigms.md

@@ -21,6 +21,7 @@ Programming Paradigms: __Packages and resources that support various programming
    + [Turnaround Time](#turnaround-time)
 + [Style Guidelines](#style-guidelines)
 
+----
 ----
 
 # [Automata](https://en.wikipedia.org/wiki/Category:Automata_(computation))

QA.md

@@ -0,0 +1,17 @@
+# QA.md
+[Quality Assurance](https://en.wikipedia.org/wiki/Quality_assurance) in Julia!
+
++ [§1. Data QA](#1-Data-QA) 
++ [§2. Package QA](§2-Package-QA]
+
+----
+----
+
+# §1. Data QA <span id="1-Data-QA"><span>
++ [ReferenceTests.jl](https://github.com/JuliaTesting/ReferenceTests.jl) :: QA package for comparing data against reference files.
+
+----
+
+# §2. Package QA <span id="2-Package-QA"><span>
++ [Aqua.jl(https://github.com/JuliaTesting/Aqua.jl) :: Automate Quality Assurance for Julia packages.
+

README.md

@@ -35,6 +35,7 @@
 + [Physics](https://github.com/svaksha/Julia.jl/blob/master/Physics.md) :: Julia software related to Physics.
 + [Programming Paradigms](https://github.com/svaksha/Julia.jl/blob/master/Programming-Paradigms.md) :: Programming Paradigms and language concepts that are used in the type system, data types, etc..
 + [Publications](https://github.com/svaksha/Julia.jl/blob/master/Publications.md) :: Research Papers (journal and conference publications).
++ [QA](https://github.com/svaksha/Julia.jl/blob/master/QA.md) :: Quality Assurance in Julia.
 + [Resources](https://github.com/svaksha/Julia.jl/blob/master/Resources.md) :: List of community resources, development links, including events, (un)conferences, forums/ meetup groups, NEWS, blogs, cookbooks, cheatsheets, IJulia NoteBooks, and other useful resources.
 + [Server](https://github.com/svaksha/Julia.jl/blob/master/Server.md) :: HTTP/Web, Networking, and other server-side utils...
 + [Space Science](https://github.com/svaksha/Julia.jl/blob/master/Space-Science.md) :: Astronomy, Imaging, Planetary and [space science](https://en.wikipedia.org/wiki/Outline_of_space_science) related packages.
@@ -50,9 +51,6 @@
 
 + COPYRIGHT © 2012-Now [SVAKSHA](http://svaksha.com/pages/Bio), herewith dual-licensed for the data (ODbL-v1.0+) and the software (AGPLv3+), respectively.
 
-   + [§2.1. ODbL and AGPLv3](#2-1-ODbL-and-AGPLv3)
-
-
 ## §2.1. AGPLv3 and ODbL <span id="2-1-AGPLv3-and-ODbL"><span>
 This repo uses multiple licences for data and code, viz. [ODbL](https://opendatacommons.org/licenses/odbl/1-0/) and [AGPLv3](http://www.gnu.org/licenses/agpl-3.0.html)
 

Utilities.md

@@ -3,17 +3,19 @@
 [Utility software](https://en.wikipedia.org/wiki/Utility_software) for storage, disk and OS utils to help analyze, configure, optimize or maintain a computer, viz. middleware, utility software, Shells and other handy utilities
 
 
-+ [UTILS](#utils)
-   + [File Compression](#file-compression)
-   + [Microsoft Windows](#microsoft-windows)
-   + [Terminal](#terminal)
-+ [Communication](#communication)
-   + [SMS](#sms)
-   + [VOIP](#voip)
++ [§1. UTILS](#1-UTILS)
+   + [§1.1. File Compression](#1-1-File-Compression)
+   + [§1.2. Microsoft Windows](#1-2-Microsoft-Windows)
+   + [§1.3. Terminal](#1-3-Terminal)
++ [§2. Communication](#2-Communication)
+   + [§2.1. IRC](#2-1-IRC) 
+   + [§2.2. SMS](#2-2-SMS)
+   + [§2.3. VOIP](#2-3-VOIP)
 
 ----
+----
 
-# UTILS
+# §1. UTILS <span id="1-UTILS"><span>
 + [Events.jl](https://github.com/SimonDanisch/Events.jl) :: Simple Event system.
 + [FilePaths.jl](https://github.com/Rory-Finnegan/FilePaths.jl) ::  A type based approach to working with filesystem paths in julia.
 + [Graze.jl](https://github.com/iamed2/Graze.jl) :: A feed reader. 
@@ -22,8 +24,7 @@
 + [SO.jl](https://github.com/dlfivefifty/SO.jl) :: Personal macros for Julia.
 + [Utils.jl](https://github.com/SimonDanisch/Utils.jl) :: Some utility functions by @SimonDanisch.
 
-https://github.com/domluna/JuliaFormatter.jl
-## File Compression 
+## §1.1. File Compression <span id="1-1-File-Compression"><span>
 + [Blosc.jl](https://github.com/stevengj/Blosc.jl) :: The Blosc Module provides fast lossless compression for the Julia language by interfacing the Blosc Library, currently limited to 32-bit buffer sizes.
 + [gzip.jl](https://github.com/jvns/gzip.jl) :: GunZip in Julia.
 + [GZip.jl](https://github.com/JuliaLang/GZip.jl) :: A Julia interface for gzip functions in zlib.
@@ -34,8 +35,7 @@ https://github.com/domluna/JuliaFormatter.jl
    + DOCS :: https://zipfilejl.readthedocs.org/en/latest/
 + [Zlib.jl](https://github.com/dcjones/Zlib.jl) :: Zlib bindings for Julia.
 
-
-## Microsoft Windows
+## §1.2. Microsoft Windows <span id="1-2-Microsoft-Windows"><span>
 + [COMCall.jl](https://github.com/ihnorton/COMCall.jl) :: COM Interface for Julia. Ref :: [COM Class Objects and CLSIDs](http://msdn.microsoft.com/en-us/library/windows/desktop/ms678406%28v=vs.85%29.aspx)
 + [IniFile.jl](https://github.com/JuliaLang/IniFile.jl) :: Reading and writing Windows-style INI files.
 + [IUP.jl](https://github.com/joa-quim/IUP.jl) :: Julia interface to IUP windowing toolkit.
@@ -48,7 +48,8 @@ https://github.com/domluna/JuliaFormatter.jl
 + [XCB.jl](https://github.com/JuliaGL/XCB.jl) :: XCB windowing library wrapper.
 
 
-## Terminal
+## §1.3. Terminal <span id="1-3-Terminal"><span>
+
 + [AnsiColor.jl](https://github.com/Aerlinger/AnsiColor.jl) :: Support for ANSI colored strings in Julia. Supported in REPL/Shell environment for both Unix and Mac.
 + [ArgParse.jl](https://github.com/carlobaldassi/ArgParse.jl) :: Package for parsing command-line arguments to Julia programs.
 + [CLI.jl](https://github.com/Roger-luo/CLI.jl) :: A library for automatically generating command line interfaces from absolutely Julia object, inspired by `python-fire`.
@@ -75,15 +76,15 @@ https://github.com/domluna/JuliaFormatter.jl
 
 ----
 
-# Communication
+# §2. Communication <span id="2-Communication"><span>
 
-## IRC
+## §2.1. IRC <span id="2-1-IRC"><span>
 + [DandelionSlack.jl](https://github.com/dandeliondeathray/DandelionSlack.jl) :: Slack API in Julia.
 + [Slackbot.jl](https://github.com/jiahao/Slackbot.jl) :: A Julia REPL that interacts with Slack.com's webhook integration.
 
-## SMS
+## §2.2. SMS <span id="2-2-SMS"><span>
 + [Twilert.jl](https://github.com/glesica/Twilert.jl) :: A small SMS alert library for Julia.
 
-## VOIP
+## §2.2. VOIP <span id="2-2-VOIP"><span>
 + [Discord.jl](https://github.com/PurgePJ/Discord.jl) :: Julia Discord wrapper.
 + [Toxcore.jl](https://github.com/SimonDanisch/Toxcore.jl) :: A Julia wrapper for [Tox](http://en.wikipedia.org/wiki/Tox_%28software%29).