From b09db0cb574c0125cd7cc6f0c903722ea8cf9def Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 30 Mar 2022 17:45:05 -0500 Subject: [PATCH] Add README Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- README.md | 163 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 163 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..d78ebd8 --- /dev/null +++ b/README.md @@ -0,0 +1,163 @@ +# JuliaPro Docker Image + +[![Unlicense](https://img.shields.io/github/license/MillironX/docker-JuliaPro)](https://github.com/MillironX/docker-JuliaPro/blob/master/LICENSE) +[![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/MillironX/docker-JuliaPro)](https://github.com/MillironX/docker-JuliaPro/tags) +[![Docker Pulls](https://img.shields.io/docker/pulls/millironx/juliapro)](https://hub.docker.com/r/millironx/juliapro) +[![Docker Repository on Quay](https://quay.io/repository/millironx/juliapro/status "Docker Repository on +Quay")](https://quay.io/repository/millironx/juliapro) + +Remember that clunky [Atom]-based [Julia] distribution that gave Julia LTS a UI +and debugger similar to [Matlab] and already included all the packages you could +possibly think to use? Remember [JuliaPro]? + +This is JuilaPro in a [Docker] image[^1]. + +## Usage + +The image is hosted on [Docker Hub], [Quay], and the [GitHub Container +Registry], and is compatible with [Docker], [Podman], and +[Singularity/Apptainer], and probably others. + +```bash +docker pull millironx/juliapro:latest +podman pull quay.io/millironx/juliapro:latest +singularity pull docker://ghcr.io/millironx/juliapro:latest +``` + +The packages are installed in a depot in `/usr/local/share/julia`, so keep this +in mind when overwriting the [`JULIA_DEPOT_PATH`] variable. For more information +on the rationale for this and examples, see + +- nf-core tools discussion: +- Alex Peltzer's blog: + +## Included Packages + +The following packages were included in JuliaPro as of April 26, 2020 according +to [the Wayback Machine]. A checkmark indicates the package was included in this +image, clear boxes indicate that it couldn't be included. I've included several +other packages that I consider essential today at the bottom of the list. + +### General Programming + +- [x] [DataStructures](https://github.com/JuliaLang/DataStructures.jl) +- [x] [LightGraphs](https://github.com/JuliaGraphs/LightGraphs.jl) +- [ ] ~~[Atom](https://github.com/JunoLab/Atom.jl)~~ (Interop meaningless in + container) +- [x] [JuliaWebAPI](https://github.com/JuliaWeb/JuliaWebAPI.jl) +- [ ] ~~[IJulia](https://github.com/JuliaLang/IJulia.jl)~~ (Soft dependency on + Python, which isn't included in the container) +- [x] [Nettle](https://github.com/staticfloat/Nettle.jl) +- [x] [DSP](https://github.com/JuliaDSP/DSP.jl) +- [x] [NearestNeighbors](https://github.com/KristofferC/NearestNeighbors.jl) +- [x] [Parameters](https://github.com/mauro3/Parameters.jl) +- [x] [ParserCombinator](https://github.com/andrewcooke/ParserCombinator.jl) +- [x] [Libz](https://github.com/BioJulia/Libz.jl) +- [x] [BenchmarkTools](https://github.com/JuliaCI/BenchmarkTools.jl) +- [x] ~~[Rebugger](https://github.com/timholy/Rebugger.jl)~~ (Errors on + precompilation) +- [x] [Debugger](https://github.com/JuliaDebug/Debugger.jl) + +### General Math + +- [x] [Calculus](https://github.com/johnmyleswhite/Calculus.jl) +- [x] [DataFrames](https://github.com/JuliaStats/DataFrames.jl) +- [x] [StatsBase](https://github.com/JuliaStats/StatsBase.jl) +- [x] [Distributions](https://github.com/JuliaStats/Distributions.jl) +- [x] [HypothesisTests](https://github.com/JuliaStats/HypothesisTests.jl) +- [x] [GLM](https://github.com/JuliaStats/GLM.jl) +- [x] [OnlineStats](https://github.com/joshday/OnlineStats.jl) +- [x] [DifferentialEquations](https://github.com/JuliaDiffEq/DifferentialEquations.jl) +- [ ] ~~[SymPy](https://github.com/JuliaPy/SymPy.jl)~~ (No Python in container) +- [x] [KernelDensity](https://github.com/JuliaStats/KernelDensity.jl) +- [x] [Zygote](https://github.com/FluxML/Zygote.jl) + +### Optimization + +- [x] [Optim](https://github.com/JuliaOpt/Optim.jl) +- [x] [Roots](https://github.com/JuliaMath/Roots.jl) + +### Databases + +- [x] [JDBC](https://github.com/JuliaDB/JDBC.jl) + +### Building UIs and Visualization + +- [ ] ~~[PyPlot](https://github.com/JuliaPy/PyPlot.jl)~~ (No Python in container) +- [x] [Interact](https://github.com/JuliaGizmos/Interact.jl) +- [x] [LaTeXStrings](https://github.com/stevengj/LaTeXStrings.jl) +- [x] [Formatting](https://github.com/JuliaIO/Formatting.jl) +- [x] [Images](https://github.com/JuliaImages/Images.jl) +- [x] [Plots](https://github.com/JuliaPlots/Plots.jl) +- [x] [GR](https://github.com/jheinen/GR.jl) +- [x] [UnicodePlots](https://github.com/Evizero/UnicodePlots.jl) +- [x] [ImageMagick](https://github.com/JuliaIO/ImageMagick.jl) +- [x] [StatsPlots](https://github.com/JuliaPlots/StatsPlots.jl) +- [x] [PGFPlots](https://github.com/JuliaTeX/PGFPlots.jl) + +### Deep Learning and Machine Learning + +- [x] [Knet](https://github.com/denizyuret/Knet.jl) +- [x] [Clustering](https://github.com/JuliaStats/Clustering.jl) +- [x] [DecisionTree](https://github.com/bensadeghi/DecisionTree.jl) +- [x] [MLBase](https://github.com/JuliaStats/MLBase.jl) +- [x] [Flux](https://github.com/FluxML/Flux.jl) +- [ ] ~~[TensorFlow](https://github.com/malmaud/TensorFlow.jl)~~ (Dependency + conflict with Flux: opted for Flux over TensorFlow) +- [x] [Metalhead](https://github.com/FluxML/Metalhead.jl) +- [ ] ~~[ScikitLearn](https://github.com/cstjean/ScikitLearn.jl)~~ (No Python in + container) + +### Interoperability with Other Languages + +All interoperability has been lost due to not including the other languages in +this image. + +- [ ] ~~[RCall (Interoperability with R)](https://github.com/JuliaInterop/RCall.jl)~~ +- [ ] ~~[JavaCall (Java)](https://github.com/JuliaInterop/JavaCall.jl)~~ +- [ ] ~~[PyCall (Python)](https://github.com/JuliaPy/PyCall.jl)~~ +- [ ] ~~[Conda (Python dependencies)](https://github.com/JuliaPy/Conda.jl)~~ +- [ ] ~~[JuliaInXL (Microsoft Excel)](https://github.com/JuliaComputing/JuliaInXL)~~ + +### File and Data Formats + +- [x] [JSON](https://github.com/JuliaIO/JSON.jl) +- [x] [JLD2](https://github.com/JuliaIO/JLD2.jl) +- [x] [CSV](https://github.com/JuliaData/CSV.jl) +- [x] [LightXML](https://github.com/JuliaIO/LightXML.jl) +- [x] [StaticArrays](https://github.com/JuliaArrays/StaticArrays.jl) +- [x] [ProtoBuf](https://github.com/JuliaIO/ProtoBuf.jl) +- [ ] ~~[CuArrays](https://github.com/JuliaGPU/CuArrays.jl)~~ (Package + deprecated and depends on GPU hardware) + +### Economics and Finance + +- [x] [QuantEcon](https://github.com/QuantEcon/QuantEcon.jl) +- [x] [BusinessDays](https://github.com/JuliaFinance/BusinessDays.jl) +- [ ] ~~[Bloomberg](https://github.com/milktrader/Bloomberg.jl)~~ (Empty package + -- maybe proprietary?) +- [ ] ~~[Blpapi (Bloomberg connector)](https://juliacomputing.com/docs/blpapi-manual.pdf)~~ (Package unavailable) +- [ ] ~~[Miletus](https://github.com/JuliaComputing/Miletus.jl)~~ (Package old + enough to require more downgrades than I'm comfortable with) + +### My Own Additions + +- [x] [EzXML](https://github.com/JuliaIO/EzXML.jl) +- [x] [JSON3](https://github.com/quinnj/JSON3.jl) +- [x] [YAML](https://github.com/JuliaData/YAML.jl) +- [x] [NLsolve](https://github.com/JuliaNLSolvers/NLsolve.jl) + +[^1]: This image doesn't include Juno, just the curated packages. + +[`JULIA_DEPOT_PATH`]: https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH +[atom]: https://atom.io +[docker hub]: https://hub.docker.com +[docker]: https://www.docker.com +[github container registry]: https://ghcr.io +[julia]: https://julialang.org +[juliapro]: https://web.archive.org/web/2/https://juliacomputing.com/products/juliapro +[matlab]: https://www.mathworks.com/matlab +[podman]: https://podman.io +[quay]: https://quay.io +[singularity/apptainer]: https://apptainer.org +[the wayback machine]: https://web.archive.org/web/20200426173353/https://juliacomputing.com/products/juliapro#curated-pkgs