From 58395efe68cc3de84fd16b1668b5f1c351315caf Mon Sep 17 00:00:00 2001 From: SVAKSHA Date: Thu, 28 Oct 2021 16:24:20 +0200 Subject: [PATCH] domluna/JuliaFormatter.jl --- Chemistry.md | 22 +++++++++++----------- DesktopApplications.md | 8 +++++++- Probability-Statistics.md | 2 +- Programming-Paradigms.md | 1 - Utilities.md | 2 +- db.csv | 36 ++++++++++++++++++------------------ 6 files changed, 38 insertions(+), 33 deletions(-) diff --git a/Chemistry.md b/Chemistry.md index 78efa27d7a..35607f3ca0 100755 --- a/Chemistry.md +++ b/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 @@ -33,11 +33,11 @@ + [Synchrony.jl](https://github.com/simonster/Synchrony.jl) :: Coherence/phase-locking statistics in Julia. -# §4. Chemometrics +# §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. + [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 + [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 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), @@ -77,7 +77,7 @@ 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 + [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. @@ -85,7 +85,7 @@ such as [Molecular dynamics](https://en.wikipedia.org/wiki/Molecular_dynamics), ---- -# §8. Uncategorized +# §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 + [Dimers.jl](https://github.com/sswatson/Dimers.jl) :: Oligomers with two structurally similar monomers. See, http://en.wikipedia.org/wiki/Category:Dimers_%28chemistry%29 diff --git a/DesktopApplications.md b/DesktopApplications.md index de5af42398..d9f1f1ee19 100755 --- a/DesktopApplications.md +++ b/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. diff --git a/Probability-Statistics.md b/Probability-Statistics.md index 17b4daa7f2..71050566e9 100755 --- a/Probability-Statistics.md +++ b/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) diff --git a/Programming-Paradigms.md b/Programming-Paradigms.md index 6f599464c6..37a998efb7 100755 --- a/Programming-Paradigms.md +++ b/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) diff --git a/Utilities.md b/Utilities.md index b414ec5128..083f508332 100755 --- a/Utilities.md +++ b/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. diff --git a/db.csv b/db.csv index 3e586ea3d9..80d89c34cb 100755 --- a/db.csv +++ b/db.csv @@ -430,28 +430,28 @@ Chemistry,"§2.Biochemistry",BioSymbols.jl,http Chemistry,"§3.Chemoinformatics",MolecularGraph.jl,https://github.com/mojaie/MolecularGraph.jl,a graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia. Chemistry,"§3.Chemoinformatics",OpenSMILES.jl,https://github.com/caseykneale/OpenSMILES.jl,OpenSMILES string representations to LightGraphs.jl format. Chemistry,"§3.Chemoinformatics",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",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,"§6.1.ReactionKinetics",ChemicalKinetics.jl,https://github.com/papamarkou/ChemicalKinetics.jl, DiffEq related functionality for defining biological models. Chemistry,"§6.2.Thermochemistry",CoolProp.jl,https://github.com/CoolProp/CoolProp.jl,CoolProp wrapper for Julia Chemistry,"§6.2.Thermochemistry",Lavoisier.jl,https://github.com/longemen3000/lavoisier,Thermodynamics models of gasseus compounds. Chemistry,"§6.2.Thermochemistry",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",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,"§7.1.[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,"§7.1.[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,"§7.1.[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" 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.