domluna/JuliaFormatter.jl

Chemistry.md

@@ -3,17 +3,17 @@
 + [§1. Chemical File Formats and Input Output](#1-chemical-file-formats-and-input-output)
 + [§2. Biochemistry](#2-Biochemistry)
 + [§3. Chemoinformatics](#3-Chemoinformatics)
-+ [Chemometrics](#chemometrics)
-+ [General Resources](#general-resources)
++ [§4. Chemometrics](#4-chemometrics)
++ [§5. General Resources](#5-general-resources)
 + [§6. Physical Chemistry](#6-Physical-Chemistry)
   + [§6.1. Reaction Kinetics](#6-1-Reaction-Kinetics)
   + [§6.2. Thermochemistry](#6-2-thermochemistry)
-+ [Simulation Methods](#simulation-methods)
-+ [Solid State Chemistry and Materials Science](#solid-state-chemistry-and-materials-science)
-+ [Uncategorized](#uncategorized) 
++ [§7. Simulation Methods](#7-simulation-methods)
+  + [§7.1. Solid State Chemistry and Materials Science](#7-1-solid-state-chemistry-and-materials-science)
++ [§8. Uncategorized](#8-uncategorized) 
 
 ----
-
+----
 
 # §1. Chemical File Formats and Input Output <span id="1-chemical-file-formats-and-input-output"><span>
 
@@ -33,11 +33,11 @@
 + [Synchrony.jl](https://github.com/simonster/Synchrony.jl) :: Coherence/phase-locking statistics in Julia.
 
 
-# §4. Chemometrics
+# §4. Chemometrics <span id="4-Chemometrics"><span>
 + [ChemometricsTools.jl](https://github.com/caseykneale/ChemometricsTools.jl) :: A collection of tools to perform fundamental and advanced Chemometric analysis and machine learning in Julia.
 + [Qlab.jl](https://github.com/blakejohnson/Qlab.jl) :: is a data manipulation and analysis tool based on the Savitzky–Golay filter - a digital filter that can be applied to a set of digital data points for the purpose of smoothing the data to increase the signal-to-noise ratio without greatly distorting the signal. Savitzky and Golay's paper is one of the most widely cited papers in the Analytical Chemistry journal.
 
-# §5. General Resources
+# §5. General Resources <span id="5-General-Resources"><span>
 + [PeriodicTable.jl](https://github.com/JuliaPhysics/PeriodicTable.jl) :: Well its the periodic table - in Julia!
 + [PhysicalConstants.jl](https://github.com/JuliaPhysics/PhysicalConstants.jl) :: A package containing curated physical constants.
 + [Videos for JuliaQuantum](https://www.youtube.com/channel/UCXeOiWjj3rcYUQqfgelTDWQ) technical talks and meetups.
@@ -56,7 +56,7 @@
 + [Psychro.jl](https://github.com/pjabardo/Psychro.jl) :: Thermodynamics properties of wet air and gasses.
 
 
-# §7. Simulation Methods
+# §7. Simulation Methods <span id="#7-Simulation-Methods"><span>
 Overview of Julia packages for simulation methods related to chemistry and
 [Molecular Modelling](https://en.wikipedia.org/wiki/Category:Molecular_modelling),
 such as [Molecular dynamics](https://en.wikipedia.org/wiki/Molecular_dynamics),
@@ -77,15 +77,15 @@ such as [Molecular dynamics](https://en.wikipedia.org/wiki/Molecular_dynamics),
 + [QSimulator.jl](https://github.com/BBN-Q/QSimulator.jl) :: Unitary and Lindbladian evolution of quantum states in Julia.
 + [QuantumLab.jl](https://github.com/vonDonnerstein/QuantumLab.jl) :: A workbench for Quantum Chemistry and Quantum Physics in Julia.
 
-## [Solid State Chemistry](https://en.wikipedia.org/wiki/Solid-state_chemistry) and Materials Science
+## §7.1. [Solid State Chemistry](https://en.wikipedia.org/wiki/Solid-state_chemistry) and Materials Science <span id="#7-1-Solid-State-Chemistry-and Materials Science"><span>
 + [ClassicalLaminateTheory.jl](https://github.com/goedman/ClassicalLaminateTheory.jl) :: Laminate model functions used in EDX course __AA432x Composite Materials Overview for Engineers__ by K.Y.Lin.
 + [HydrocarbonNets.jl](https://github.com/Ismael-VC/HydrocarbonNets.jl) :: Artificial Hydrocarbon Networks (AHNs) in Julia.
 + [Lattices.jl](https://github.com/JuliaPhysics/Lattices.jl) :: A Lattice Library for Julia.
 
 
 ----
 
-# §8. Uncategorized
+# §8. Uncategorized <span id="#8-Uncategorized"><span>
 
 + [Cliffords.jl](https://github.com/BBN-Q/Cliffords.jl) :: This library allows for efficient calculation of Clifford circuits by tracking the evolution of X and Z generators (the so-called tableau representation). Ref: http://en.wikipedia.org/wiki/Clifford_algebra
 + [Dimers.jl](https://github.com/sswatson/Dimers.jl) :: Oligomers with two structurally similar monomers. See, http://en.wikipedia.org/wiki/Category:Dimers_%28chemistry%29

DesktopApplications.md

@@ -12,10 +12,11 @@ The collective noun [application software](https://en.wikipedia.org/wiki/Applica
         + [Atom](#atom)
         + [Emacs](#emacs)
    + [Jupyter](#jupyter)
+   + [
    + [WIDE](#wide) 
 
 ----
-
+----
 
 # [DEBUGGER](https://en.wikipedia.org/wiki/Category:Debuggers)
 + [ASTInterpreter2.jl](https://github.com/Keno/ASTInterpreter2.jl) :: Re-write of ASTInterpreter for julia v0.6+.
@@ -154,6 +155,11 @@ __Generic Syntax Highlighter__
 + How to create a [Custom IJulia Widget](http://nbviewer.ipython.org/urls/gist.githubusercontent.com/avrahamruderman/116845471f0d79942aff/raw/fb1f659e635f4585ebb449aa2519deffd15aba31/writing-custom-ijulia-widgets.ipynb)
 + [Run Jupyterhub on a Supercomputer](http://zonca.github.io/2015/04/jupyterhub-hpc.html).
 
+
+### [Prettyprinting](https://en.wikipedia.org/wiki/Prettyprint)
+* [https://github.com/domluna/JuliaFormatter.jl](https://github.com/domluna/JuliaFormatter.jl) :: A code formatter for Julia. 
+
+
 ### [WIDE](https://en.wikipedia.org/wiki/Web_integrated_development_environment)
 + [JuliaBox](https://juliabox.com/) :: Jupyter/IJulia sandboxed by Docker containers that allows you to run Julia on the browser. Here is the [source code](https://github.com/JuliaLang/JuliaBox), [installation instructions](https://github.com/JuliaLang/JuliaBox/blob/master/docs/INSTALL.MD), a [collection of example notebooks](https://github.com/shashi/IJuliaNotebooks).
    + [JuliaBoxUtils.jl](https://github.com/tanmaykm/JuliaBoxUtils.jl) :: JuliaBox utility methods.

Probability-Statistics.md

@@ -3,7 +3,7 @@
    + [§1.2. STOCHASTICS](#1-2-stochastics)
         + [§1.2.1. Bayesian](#1-2-1-Bayesian)
         + [§1.2.2. Gaussian](#1-2-2-Gaussian)
-        + [§1.2.3. Markovian)(#1-2-3-Markovian)
+        + [§1.2.3. Markovian](#1-2-3-Markovian)
 + [STATISTICS](#statistics)
    + [REGRESSION](#regression)
    + [DENSITIES](#densities)

Programming-Paradigms.md

@@ -132,7 +132,6 @@ Programming Paradigms: __Packages and resources that support various programming
 + [OCCA.jl](https://github.com/ReidAtcheson/OCCA.jl) :: Julia interface into [OCCA2](https://github.com/tcew/OCCA2) by @tcew, an extensible multi-threading programming API written in C++.
 + [TiledIteration.jl](https://github.com/JuliaArrays/TiledIteration.jl) :: Julia package to facilitate writing mulithreaded, multidimensional, cache-efficient code.
 
-
 ----
 
 # [Metaprogramming](https://en.wikipedia.org/wiki/Metaprogramming)

Utilities.md

@@ -22,7 +22,7 @@
 + [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 
 + [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.

db.csv

@@ -430,28 +430,28 @@ Chemistry,"§2.Biochemistry<spanid=""2-Biochemistry""><span>",BioSymbols.jl,http
 Chemistry,"§3.Chemoinformatics<spanid=""3-Chemoinformatics""><span>",MolecularGraph.jl,https://github.com/mojaie/MolecularGraph.jl,a graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia.
 Chemistry,"§3.Chemoinformatics<spanid=""3-Chemoinformatics""><span>",OpenSMILES.jl,https://github.com/caseykneale/OpenSMILES.jl,OpenSMILES string representations to LightGraphs.jl format.
 Chemistry,"§3.Chemoinformatics<spanid=""3-Chemoinformatics""><span>",Synchrony.jl,https://github.com/simonster/Synchrony.jl,Coherence/phase-locking statistics in Julia.
-Chemistry,§4.Chemometrics,ChemometricsTools.jl,https://github.com/caseykneale/ChemometricsTools.jl,A collection of tools to perform fundamental and advanced Chemometric analysis and machine learning in Julia.
-Chemistry,§4.Chemometrics,Qlab.jl,https://github.com/blakejohnson/Qlab.jl,is a data manipulation and analysis tool based on the Savitzky–Golay filter - a digital filter that can be applied to a set of digital data points for the purpose of smoothing the data to increase the signal-to-noise ratio without greatly distorting the signal. Savitzky and Golay's paper is one of the most widely cited papers in the Analytical Chemistry journal.
-Chemistry,§5.GeneralResources,PeriodicTable.jl,https://github.com/JuliaPhysics/PeriodicTable.jl,Well its the periodic table - in Julia!
-Chemistry,§5.GeneralResources,PhysicalConstants.jl,https://github.com/JuliaPhysics/PhysicalConstants.jl,A package containing curated physical constants.
-Chemistry,§5.GeneralResources,Videos for JuliaQuantum,https://www.youtube.com/channel/UCXeOiWjj3rcYUQqfgelTDWQ) technical talks and meetups,
+Chemistry,"§4.Chemometrics<spanid=""4-Chemometrics""><span>",ChemometricsTools.jl,https://github.com/caseykneale/ChemometricsTools.jl,A collection of tools to perform fundamental and advanced Chemometric analysis and machine learning in Julia.
+Chemistry,"§4.Chemometrics<spanid=""4-Chemometrics""><span>",Qlab.jl,https://github.com/blakejohnson/Qlab.jl,is a data manipulation and analysis tool based on the Savitzky–Golay filter - a digital filter that can be applied to a set of digital data points for the purpose of smoothing the data to increase the signal-to-noise ratio without greatly distorting the signal. Savitzky and Golay's paper is one of the most widely cited papers in the Analytical Chemistry journal.
+Chemistry,"§5.GeneralResources<spanid=""5-General-Resources""><span>",PeriodicTable.jl,https://github.com/JuliaPhysics/PeriodicTable.jl,Well its the periodic table - in Julia!
+Chemistry,"§5.GeneralResources<spanid=""5-General-Resources""><span>",PhysicalConstants.jl,https://github.com/JuliaPhysics/PhysicalConstants.jl,A package containing curated physical constants.
+Chemistry,"§5.GeneralResources<spanid=""5-General-Resources""><span>",Videos for JuliaQuantum,https://www.youtube.com/channel/UCXeOiWjj3rcYUQqfgelTDWQ) technical talks and meetups,
 Chemistry,"§6.1.ReactionKinetics<spanid=""#6-1-Reaction-Kinetics""><span>",ChemicalKinetics.jl,https://github.com/papamarkou/ChemicalKinetics.jl, DiffEq related functionality for defining biological models.
 Chemistry,"§6.2.Thermochemistry<spanid=""#6-2-Thermochemistry""><span>",CoolProp.jl,https://github.com/CoolProp/CoolProp.jl,CoolProp wrapper for Julia
 Chemistry,"§6.2.Thermochemistry<spanid=""#6-2-Thermochemistry""><span>",Lavoisier.jl,https://github.com/longemen3000/lavoisier,Thermodynamics models of gasseus compounds.
 Chemistry,"§6.2.Thermochemistry<spanid=""#6-2-Thermochemistry""><span>",Psychro.jl,https://github.com/pjabardo/Psychro.jl,Thermodynamics properties of wet air and gasses.
-Chemistry,§7.SimulationMethods,JuliaMolSim,https://github.com/JuliaMolSim,Github organization for molecular simulation in Julia
-Chemistry,§7.SimulationMethods,Brownian.jl,https://github.com/UniversityofWarwick/Brownian.jl,Simulation of Brownian-Based Stochastic Processes.
-Chemistry,§7.SimulationMethods,Elsa.jl,https://github.com/pablosanjose/Elsa.jl,Simulation of tight-binding models on arbitrary lattices.
-Chemistry,§7.SimulationMethods,Fermi.jl,https://github.com/FermiQC/Fermi.jl,Development plataform and production level implementations of wave function methods.
-Chemistry,§7.SimulationMethods,Molly.jl,https://github.com/jgreener64/Molly.jl,Molecular dynamics in Julia.
-Chemistry,§7.SimulationMethods,pyquante2,https://github.com/rpmuller/pyquante2/,"PyQuante is a Quantum Chemistry suite written in Python, with Julia support for HF and methods for integrals."
-Chemistry,§7.SimulationMethods,QSimulator.jl,https://github.com/BBN-Q/QSimulator.jl,Unitary and Lindbladian evolution of quantum states in Julia.
-Chemistry,§7.SimulationMethods,QuantumLab.jl,https://github.com/vonDonnerstein/QuantumLab.jl,A workbench for Quantum Chemistry and Quantum Physics in Julia.
-Chemistry,[SolidStateChemistry](https://en.wikipedia.org/wiki/Solid-state_chemistry)andMaterialsScience,ClassicalLaminateTheory.jl,https://github.com/goedman/ClassicalLaminateTheory.jl,Laminate model functions used in EDX course __AA432x Composite Materials Overview for Engineers__ by K.Y.Lin.
-Chemistry,[SolidStateChemistry](https://en.wikipedia.org/wiki/Solid-state_chemistry)andMaterialsScience,HydrocarbonNets.jl,https://github.com/Ismael-VC/HydrocarbonNets.jl,Artificial Hydrocarbon Networks (AHNs) in Julia.
-Chemistry,[SolidStateChemistry](https://en.wikipedia.org/wiki/Solid-state_chemistry)andMaterialsScience,Lattices.jl,https://github.com/JuliaPhysics/Lattices.jl,A Lattice Library for Julia.
-Chemistry,§8.Uncategorized,Cliffords.jl,https://github.com/BBN-Q/Cliffords.jl,This library allows for efficient calculation of Clifford circuits by tracking the evolution of X and Z generators (the so-called tableau representation). Ref: http://en.wikipedia.org/wiki/Clifford_algebra
-Chemistry,§8.Uncategorized,Dimers.jl,https://github.com/sswatson/Dimers.jl,"Oligomers with two structurally similar monomers. See, http://en.wikipedia.org/wiki/Category:Dimers_%28chemistry%29"
+Chemistry,"§7.SimulationMethods<spanid=""#7-Simulation-Methods""><span>",JuliaMolSim,https://github.com/JuliaMolSim,Github organization for molecular simulation in Julia
+Chemistry,"§7.SimulationMethods<spanid=""#7-Simulation-Methods""><span>",Brownian.jl,https://github.com/UniversityofWarwick/Brownian.jl,Simulation of Brownian-Based Stochastic Processes.
+Chemistry,"§7.SimulationMethods<spanid=""#7-Simulation-Methods""><span>",Elsa.jl,https://github.com/pablosanjose/Elsa.jl,Simulation of tight-binding models on arbitrary lattices.
+Chemistry,"§7.SimulationMethods<spanid=""#7-Simulation-Methods""><span>",Fermi.jl,https://github.com/FermiQC/Fermi.jl,Development plataform and production level implementations of wave function methods.
+Chemistry,"§7.SimulationMethods<spanid=""#7-Simulation-Methods""><span>",Molly.jl,https://github.com/jgreener64/Molly.jl,Molecular dynamics in Julia.
+Chemistry,"§7.SimulationMethods<spanid=""#7-Simulation-Methods""><span>",pyquante2,https://github.com/rpmuller/pyquante2/,"PyQuante is a Quantum Chemistry suite written in Python, with Julia support for HF and methods for integrals."
+Chemistry,"§7.SimulationMethods<spanid=""#7-Simulation-Methods""><span>",QSimulator.jl,https://github.com/BBN-Q/QSimulator.jl,Unitary and Lindbladian evolution of quantum states in Julia.
+Chemistry,"§7.SimulationMethods<spanid=""#7-Simulation-Methods""><span>",QuantumLab.jl,https://github.com/vonDonnerstein/QuantumLab.jl,A workbench for Quantum Chemistry and Quantum Physics in Julia.
+Chemistry,"§7.1.[SolidStateChemistry](https://en.wikipedia.org/wiki/Solid-state_chemistry)andMaterialsScience<spanid=""#7-1-Solid-State-Chemistry-andMaterialsScience""><span>",ClassicalLaminateTheory.jl,https://github.com/goedman/ClassicalLaminateTheory.jl,Laminate model functions used in EDX course __AA432x Composite Materials Overview for Engineers__ by K.Y.Lin.
+Chemistry,"§7.1.[SolidStateChemistry](https://en.wikipedia.org/wiki/Solid-state_chemistry)andMaterialsScience<spanid=""#7-1-Solid-State-Chemistry-andMaterialsScience""><span>",HydrocarbonNets.jl,https://github.com/Ismael-VC/HydrocarbonNets.jl,Artificial Hydrocarbon Networks (AHNs) in Julia.
+Chemistry,"§7.1.[SolidStateChemistry](https://en.wikipedia.org/wiki/Solid-state_chemistry)andMaterialsScience<spanid=""#7-1-Solid-State-Chemistry-andMaterialsScience""><span>",Lattices.jl,https://github.com/JuliaPhysics/Lattices.jl,A Lattice Library for Julia.
+Chemistry,"§8.Uncategorized<spanid=""#8-Uncategorized""><span>",Cliffords.jl,https://github.com/BBN-Q/Cliffords.jl,This library allows for efficient calculation of Clifford circuits by tracking the evolution of X and Z generators (the so-called tableau representation). Ref: http://en.wikipedia.org/wiki/Clifford_algebra
+Chemistry,"§8.Uncategorized<spanid=""#8-Uncategorized""><span>",Dimers.jl,https://github.com/sswatson/Dimers.jl,"Oligomers with two structurally similar monomers. See, http://en.wikipedia.org/wiki/Category:Dimers_%28chemistry%29"
 DataScience,SOFTWARE,CommonCrawl.jl,https://github.com/tanmaykm/CommonCrawl.jl,Interface to common crawl dataset on Amazon S3.
 DataScience,SOFTWARE,Faker.jl,https://github.com/codeneomatrix/Faker.jl,A package that generates fake data.
 DataScience,SOFTWARE,FaceDatasets.jl,https://github.com/dfdx/FaceDatasets.jl,A package for easy access to face-related datasets.