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ExpressCommands

Documentation for ExpressCommands.

See the Index for the complete list of documented functions and types.

The code is hosted on GitHub, with some continuous integration services to test its validity.

This repository is created and maintained by @singularitti. You are very welcome to contribute.

Please cite this package as:

Q. Zhang, C. Gu, J. Zhuang et al., express: extensible, high-level workflows for swifter ab initio materials modeling, Computer Physics Communications, 108515, doi: https://doi.org/10.1016/j.cpc.2022.108515.

The BibTeX format is:

@article{ZHANG2022108515,
  title    = {express: extensible, high-level workflows for swifter ab initio materials modeling},
  journal  = {Computer Physics Communications},
  pages    = {108515},
  year     = {2022},
  issn     = {0010-4655},
  doi      = {https://doi.org/10.1016/j.cpc.2022.108515},
  url      = {https://www.sciencedirect.com/science/article/pii/S001046552200234X},
  author   = {Qi Zhang and Chaoxuan Gu and Jingyi Zhuang and Renata M. Wentzcovitch},
  keywords = {automation, workflow, high-level, high-throughput, data lineage}
}

We also have an arXiv prepint.

Installation

The package can be installed with the Julia package manager. From the Julia REPL, type ] to enter the Pkg REPL mode and run:

pkg> add ExpressCommands

Or, equivalently, via the Pkg API:

julia> import Pkg; Pkg.add("ExpressCommands")   Resolving package versions...
   Installed JpegTurbo_jll ──────────────── v2.1.2+0
   Installed x265_jll ───────────────────── v3.5.0+0
   Installed libfdk_aac_jll ─────────────── v2.0.2+0
   Installed Libmount_jll ───────────────── v2.35.0+0
   Installed GR_jll ─────────────────────── v0.71.1+0
   Installed LERC_jll ───────────────────── v3.0.0+1
   Installed Opus_jll ───────────────────── v1.3.2+0
   Installed LoggingExtras ──────────────── v1.0.0
   Installed MutableArithmetics ─────────── v1.1.0
   Installed Xorg_xkbcomp_jll ───────────── v1.4.2+4
   Installed Measures ───────────────────── v0.3.2
   Installed Grisu ──────────────────────── v1.0.2
   Installed InlineStrings ──────────────── v1.3.2
   Installed Xorg_xcb_util_wm_jll ───────── v0.4.1+1
   Installed Contour ────────────────────── v0.6.2
   Installed Xorg_xcb_util_image_jll ────── v0.4.0+1
   Installed RecipesPipeline ────────────── v0.6.11
   Installed PlotUtils ──────────────────── v1.3.1
   Installed Xorg_libpthread_stubs_jll ──── v0.1.0+3
   Installed OpenSSL ────────────────────── v1.3.2
   Installed ExpressCommands ────────────── v0.1.0
   Installed Cairo_jll ──────────────────── v1.16.1+1
   Installed Xorg_xcb_util_jll ──────────── v0.4.0+1
   Installed Fontconfig_jll ─────────────── v2.13.93+0
   Installed HTTP ───────────────────────── v1.5.5
   Installed Libgpg_error_jll ───────────── v1.42.0+0
   Installed Xorg_libXinerama_jll ───────── v1.1.4+4
   Installed Xorg_libxkbfile_jll ────────── v1.1.0+4
   Installed Xorg_libXau_jll ────────────── v1.0.9+4
   Installed Polynomials ────────────────── v2.0.25
   Installed DataFrames ─────────────────── v1.4.3
   Installed Configurations ─────────────── v0.16.6
   Installed FFMPEG ─────────────────────── v0.4.1
   Installed Showoff ────────────────────── v1.0.3
   Installed TikzGraphs ─────────────────── v1.1.0
   Installed ArnoldiMethod ──────────────── v0.1.0
   Installed Qt5Base_jll ────────────────── v5.15.3+2
   Installed Xorg_xcb_util_keysyms_jll ──── v0.4.0+1
   Installed xkbcommon_jll ──────────────── v1.4.1+0
   Installed Bzip2_jll ──────────────────── v1.0.8+0
   Installed Pipe ───────────────────────── v1.3.0
   Installed GR ─────────────────────────── v0.71.1
   Installed SimpleBufferStream ─────────── v1.1.0
   Installed HarfBuzz_jll ───────────────── v2.8.1+1
   Installed PlotThemes ─────────────────── v3.1.0
   Installed LZO_jll ────────────────────── v2.10.1+0
   Installed fzf_jll ────────────────────── v0.29.0+0
   Installed PackageCompiler ────────────── v1.6.0
   Installed Comonicon ──────────────────── v0.9.1
   Installed UnicodeFun ─────────────────── v0.4.1
   Installed FriBidi_jll ────────────────── v1.0.10+0
   Installed GLFW_jll ───────────────────── v3.3.8+0
   Installed x264_jll ───────────────────── v2021.5.5+0
   Installed MbedTLS ────────────────────── v1.1.7
   Installed Colors ─────────────────────── v0.12.8
   Installed FreeType2_jll ──────────────── v2.10.4+0
   Installed JLFzf ──────────────────────── v0.1.5
   Installed ExprTools ──────────────────── v0.1.8
   Installed AbInitioSoftwareBase ───────── v0.4.0
   Installed ColorSchemes ───────────────── v3.20.0
   Installed CodecZlib ──────────────────── v0.7.0
   Installed Xorg_libxcb_jll ────────────── v1.13.0+3
   Installed libpng_jll ─────────────────── v1.6.38+0
   Installed libaom_jll ─────────────────── v3.4.0+0
   Installed MPICH_jll ──────────────────── v3.4.3+1
   Installed SimpleWorkflows ────────────── v0.8.1
   Installed Xorg_libXext_jll ───────────── v1.3.4+4
   Installed MatchCore ──────────────────── v0.1.1
   Installed TensorCore ─────────────────── v0.1.1
   Installed Plots ──────────────────────── v1.36.6
   Installed Zstd_jll ───────────────────── v1.5.2+0
   Installed ColorTypes ─────────────────── v0.11.4
   Installed Expat_jll ──────────────────── v2.4.8+0
   Installed Poppler_jll ────────────────── v21.9.0+0
   Installed Intervals ──────────────────── v1.8.0
   Installed Express ────────────────────── v0.2.3
   Installed TimeZones ──────────────────── v1.9.0
   Installed Libtiff_jll ────────────────── v4.4.0+0
   Installed Libffi_jll ─────────────────── v3.2.2+1
   Installed Xorg_libXrender_jll ────────── v0.9.10+4
   Installed Ogg_jll ────────────────────── v1.3.5+1
   Installed ColorVectorSpace ───────────── v0.9.9
   Installed ExproniconLite ─────────────── v0.6.13
   Installed PrettyTables ───────────────── v2.2.1
   Installed XSLT_jll ───────────────────── v1.1.34+0
   Installed Xorg_libXcursor_jll ────────── v1.2.0+4
   Installed Xorg_libXi_jll ─────────────── v1.7.10+4
   Installed Wayland_protocols_jll ──────── v1.25.0+0
   Installed Libuuid_jll ────────────────── v2.36.0+0
   Installed LittleCMS_jll ──────────────── v2.12.0+0
   Installed Xorg_xcb_util_renderutil_jll ─ v0.3.9+1
   Installed Graphite2_jll ──────────────── v1.3.14+0
   Installed Gettext_jll ────────────────── v0.21.0+0
   Installed libass_jll ─────────────────── v0.15.1+0
   Installed TikzPictures ───────────────── v3.2.0
   Installed Pixman_jll ─────────────────── v0.40.1+0
   Installed Latexify ───────────────────── v0.15.17
   Installed LightGraphs ────────────────── v1.3.5
   Installed Wayland_jll ────────────────── v1.19.0+0
   Installed Xorg_xtrans_jll ────────────── v1.4.0+3
   Installed OpenSSL_jll ────────────────── v1.1.19+0
   Installed Mocking ────────────────────── v0.7.5
   Installed OpenJpeg_jll ───────────────── v2.4.0+0
   Installed Libgcrypt_jll ──────────────── v1.8.7+0
   Installed FFMPEG_jll ─────────────────── v4.4.2+2
   Installed BitFlags ───────────────────── v0.1.7
   Installed Xorg_xkeyboard_config_jll ──── v2.27.0+4
   Installed Xorg_libXrandr_jll ─────────── v1.5.2+4
   Installed Xorg_libXfixes_jll ─────────── v5.0.3+4
   Installed LAME_jll ───────────────────── v3.100.1+0
   Installed FixedPointNumbers ──────────── v0.8.4
   Installed IniFile ────────────────────── v0.5.1
   Installed LaTeXStrings ───────────────── v1.3.0
   Installed Glib_jll ───────────────────── v2.74.0+1
   Installed EquationsOfStateOfSolids ───── v0.2.2
   Installed libvorbis_jll ──────────────── v1.3.7+1
   Installed Xorg_libX11_jll ────────────── v1.6.9+4
   Installed Xorg_libXdmcp_jll ──────────── v1.1.3+4
   Installed Libglvnd_jll ───────────────── v1.6.0+0
   Installed Unzip ──────────────────────── v0.2.0
   Installed StringManipulation ─────────── v0.3.0
    Updating `~/work/ExpressCommands.jl/ExpressCommands.jl/docs/build/developers/Project.toml`
⌃ [0fa58581] + ExpressCommands v0.1.0
    Updating `~/work/ExpressCommands.jl/ExpressCommands.jl/docs/build/developers/Manifest.toml`
⌅ [df5135bc] + AbInitioSoftwareBase v0.4.0
⌅ [ec485272] + ArnoldiMethod v0.1.0
  [30b0a656] + ArrayInterfaceCore v0.1.26
  [d1d4a3ce] + BitFlags v0.1.7
  [49dc2e85] + Calculus v0.5.1
  [d360d2e6] + ChainRulesCore v1.15.6
  [9e997f8a] + ChangesOfVariables v0.1.4
  [944b1d66] + CodecZlib v0.7.0
  [35d6a980] + ColorSchemes v3.20.0
  [3da002f7] + ColorTypes v0.11.4
  [c3611d14] + ColorVectorSpace v0.9.9
  [5ae59095] + Colors v0.12.8
  [38540f10] + CommonSolve v0.2.3
  [bbf7d656] + CommonSubexpressions v0.3.0
⌅ [863f3e99] + Comonicon v0.9.1
  [8f4d0f93] + Conda v1.7.0
⌅ [5218b696] + Configurations v0.16.6
  [187b0558] + ConstructionBase v1.4.1
  [d38c429a] + Contour v0.6.2
  [9a962f9c] + DataAPI v1.13.0
  [a93c6f00] + DataFrames v1.4.3
  [e2d170a0] + DataValueInterfaces v1.0.0
  [b429d917] + DensityInterface v0.4.0
  [163ba53b] + DiffResults v1.1.0
  [b552c78f] + DiffRules v1.12.2
  [31c24e10] + Distributions v0.25.79
  [ffbed154] + DocStringExtensions v0.9.2
  [fa6b7ba4] + DualNumbers v0.6.8
  [8d49d7c9] + EquationOfStateRecipes v0.1.3
  [0438fec6] + EquationsOfState v4.0.0
⌅ [1eaa2786] + EquationsOfStateOfSolids v0.2.2
  [e2ba6199] + ExprTools v0.1.8
⌅ [b12df14e] + Express v0.2.3
⌃ [0fa58581] + ExpressCommands v0.1.0
⌅ [55351af7] + ExproniconLite v0.6.13
  [c87230d0] + FFMPEG v0.4.1
  [1a297f60] + FillArrays v0.13.5
  [6a86dc24] + FiniteDiff v2.17.0
  [53c48c17] + FixedPointNumbers v0.8.4
  [59287772] + Formatting v0.4.2
  [f6369f11] + ForwardDiff v0.10.33
  [28b8d3ca] + GR v0.71.1
  [42e2da0e] + Grisu v1.0.2
  [cd3eb016] + HTTP v1.5.5
  [34004b35] + HypergeometricFunctions v0.3.11
  [b5f81e59] + IOCapture v0.2.2
  [d25df0c9] + Inflate v0.1.3
  [83e8ac13] + IniFile v0.5.1
  [842dd82b] + InlineStrings v1.3.2
  [d8418881] + Intervals v1.8.0
  [3587e190] + InverseFunctions v0.1.8
  [41ab1584] + InvertedIndices v1.2.0
  [92d709cd] + IrrationalConstants v0.1.1
  [ceb4388c] + IsURL v0.2.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [1019f520] + JLFzf v0.1.5
  [692b3bcd] + JLLWrappers v1.4.1
  [b964fa9f] + LaTeXStrings v1.3.0
  [23fbe1c1] + Latexify v0.15.17
  [093fc24a] + LightGraphs v1.3.5
  [2ab3a3ac] + LogExpFunctions v0.3.19
  [e6f89c97] + LoggingExtras v1.0.0
⌅ [2fda8390] + LsqFit v0.12.1
  [1914dd2f] + MacroTools v0.5.10
  [5dd3f0b1] + MatchCore v0.1.1
  [739be429] + MbedTLS v1.1.7
  [442fdcdd] + Measures v0.3.2
  [e1d29d7a] + Missings v1.0.2
  [78c3b35d] + Mocking v0.7.5
  [d8a4904e] + MutableArithmetics v1.1.0
  [d41bc354] + NLSolversBase v7.8.3
  [77ba4419] + NaNMath v1.0.1
  [4d8831e6] + OpenSSL v1.3.2
  [87e2bd06] + OptimBase v2.0.2
  [90014a1f] + PDMats v0.11.16
⌅ [9b87118b] + PackageCompiler v1.6.0
  [b98c9c47] + Pipe v1.3.0
  [ccf2f8ad] + PlotThemes v3.1.0
  [995b91a9] + PlotUtils v1.3.1
  [91a5bcdd] + Plots v1.36.6
  [3a141323] + PolynomialRoots v1.0.0
⌅ [f27b6e38] + Polynomials v2.0.25
  [2dfb63ee] + PooledArrays v1.4.2
  [21216c6a] + Preferences v1.3.0
  [8162dcfd] + PrettyPrint v0.2.0
  [08abe8d2] + PrettyTables v2.2.1
  [438e738f] + PyCall v1.94.1
  [5a1273f0] + PyQHA v0.1.1
  [1fd47b50] + QuadGK v2.6.0
  [3cdcf5f2] + RecipesBase v1.3.1
  [01d81517] + RecipesPipeline v0.6.11
  [189a3867] + Reexport v1.2.2
  [05181044] + RelocatableFolders v1.0.0
  [ae029012] + Requires v1.3.0
  [79098fc4] + Rmath v0.7.0
⌅ [f2b01f46] + Roots v1.2.0
  [6c6a2e73] + Scratch v1.1.1
  [efcf1570] + Setfield v1.1.1
  [992d4aef] + Showoff v1.0.3
  [777ac1f9] + SimpleBufferStream v1.1.0
  [699a6c99] + SimpleTraits v0.9.4
⌅ [6a97d125] + SimpleWorkflows v0.8.1
  [a2af1166] + SortingAlgorithms v1.1.0
  [276daf66] + SpecialFunctions v2.1.7
  [90137ffa] + StaticArrays v1.5.11
  [1e83bf80] + StaticArraysCore v1.4.0
  [82ae8749] + StatsAPI v1.5.0
  [2913bbd2] + StatsBase v0.33.21
  [4c63d2b9] + StatsFuns v1.0.1
  [69024149] + StringEncodings v0.3.5
  [892a3eda] + StringManipulation v0.3.0
  [4093c41a] + StructHelpers v0.1.5
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.10.0
  [62fd8b95] + TensorCore v0.1.1
⌃ [b4f28e30] + TikzGraphs v1.1.0
⌃ [37f6aa50] + TikzPictures v3.2.0
  [f269a46b] + TimeZones v1.9.0
  [3bb67fe8] + TranscodingStreams v0.9.9
  [3a884ed6] + UnPack v1.0.2
  [1cfade01] + UnicodeFun v0.4.1
  [1986cc42] + Unitful v1.12.1
  [a7773ee8] + UnitfulAtomic v1.0.0
  [41fe7b60] + Unzip v0.2.0
  [81def892] + VersionParsing v1.3.0
  [ddb6d928] + YAML v0.4.8
  [6e34b625] + Bzip2_jll v1.0.8+0
  [83423d85] + Cairo_jll v1.16.1+1
  [2e619515] + Expat_jll v2.4.8+0
  [b22a6f82] + FFMPEG_jll v4.4.2+2
  [a3f928ae] + Fontconfig_jll v2.13.93+0
  [d7e528f0] + FreeType2_jll v2.10.4+0
  [559328eb] + FriBidi_jll v1.0.10+0
  [0656b61e] + GLFW_jll v3.3.8+0
  [d2c73de3] + GR_jll v0.71.1+0
  [78b55507] + Gettext_jll v0.21.0+0
  [7746bdde] + Glib_jll v2.74.0+1
  [3b182d85] + Graphite2_jll v1.3.14+0
  [2e76f6c2] + HarfBuzz_jll v2.8.1+1
  [aacddb02] + JpegTurbo_jll v2.1.2+0
  [c1c5ebd0] + LAME_jll v3.100.1+0
  [88015f11] + LERC_jll v3.0.0+1
  [dd4b983a] + LZO_jll v2.10.1+0
⌅ [e9f186c6] + Libffi_jll v3.2.2+1
  [d4300ac3] + Libgcrypt_jll v1.8.7+0
  [7e76a0d4] + Libglvnd_jll v1.6.0+0
  [7add5ba3] + Libgpg_error_jll v1.42.0+0
  [94ce4f54] + Libiconv_jll v1.16.1+1
  [4b2f31a3] + Libmount_jll v2.35.0+0
  [89763e89] + Libtiff_jll v4.4.0+0
  [38a345b3] + Libuuid_jll v2.36.0+0
  [d3a379c0] + LittleCMS_jll v2.12.0+0
⌅ [7cb0a576] + MPICH_jll v3.4.3+1
  [e7412a2a] + Ogg_jll v1.3.5+1
  [643b3616] + OpenJpeg_jll v2.4.0+0
  [458c3c95] + OpenSSL_jll v1.1.19+0
  [efe28fd5] + OpenSpecFun_jll v0.5.5+0
  [91d4177d] + Opus_jll v1.3.2+0
  [30392449] + Pixman_jll v0.40.1+0
  [9c32591e] + Poppler_jll v21.9.0+0
  [ea2cea3b] + Qt5Base_jll v5.15.3+2
  [f50d1b31] + Rmath_jll v0.3.0+0
  [a2964d1f] + Wayland_jll v1.19.0+0
  [2381bf8a] + Wayland_protocols_jll v1.25.0+0
  [02c8fc9c] + XML2_jll v2.9.14+0
  [aed1982a] + XSLT_jll v1.1.34+0
  [4f6342f7] + Xorg_libX11_jll v1.6.9+4
  [0c0b7dd1] + Xorg_libXau_jll v1.0.9+4
  [935fb764] + Xorg_libXcursor_jll v1.2.0+4
  [a3789734] + Xorg_libXdmcp_jll v1.1.3+4
  [1082639a] + Xorg_libXext_jll v1.3.4+4
  [d091e8ba] + Xorg_libXfixes_jll v5.0.3+4
  [a51aa0fd] + Xorg_libXi_jll v1.7.10+4
  [d1454406] + Xorg_libXinerama_jll v1.1.4+4
  [ec84b674] + Xorg_libXrandr_jll v1.5.2+4
  [ea2f1a96] + Xorg_libXrender_jll v0.9.10+4
  [14d82f49] + Xorg_libpthread_stubs_jll v0.1.0+3
  [c7cfdc94] + Xorg_libxcb_jll v1.13.0+3
  [cc61e674] + Xorg_libxkbfile_jll v1.1.0+4
  [12413925] + Xorg_xcb_util_image_jll v0.4.0+1
  [2def613f] + Xorg_xcb_util_jll v0.4.0+1
  [975044d2] + Xorg_xcb_util_keysyms_jll v0.4.0+1
  [0d47668e] + Xorg_xcb_util_renderutil_jll v0.3.9+1
  [c22f9ab0] + Xorg_xcb_util_wm_jll v0.4.1+1
  [35661453] + Xorg_xkbcomp_jll v1.4.2+4
  [33bec58e] + Xorg_xkeyboard_config_jll v2.27.0+4
  [c5fb5394] + Xorg_xtrans_jll v1.4.0+3
  [3161d3a3] + Zstd_jll v1.5.2+0
⌅ [214eeab7] + fzf_jll v0.29.0+0
  [a4ae2306] + libaom_jll v3.4.0+0
  [0ac62f75] + libass_jll v0.15.1+0
  [f638f0a6] + libfdk_aac_jll v2.0.2+0
  [b53b4c65] + libpng_jll v1.6.38+0
  [f27f6e37] + libvorbis_jll v1.3.7+1
  [1270edf5] + x264_jll v2021.5.5+0
  [dfaa095f] + x265_jll v3.5.0+0
  [d8fb68d0] + xkbcommon_jll v1.4.1+0
  [8bf52ea8] + CRC32c
  [8bb1440f] + DelimitedFiles
  [8ba89e20] + Distributed
  [9fa8497b] + Future
  [4af54fe1] + LazyArtifacts
  [1a1011a3] + SharedArrays
  [2f01184e] + SparseArrays
  [10745b16] + Statistics
  [4607b0f0] + SuiteSparse
  [8dfed614] + Test
  [05823500] + OpenLibm_jll v0.8.1+0
  [efcefdf7] + PCRE2_jll v10.40.0+0
        Info Packages marked with ⌃ and ⌅ have new versions available, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
    Building TimeZones ──────→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/d634a3641062c040fc8a7e2a3ea17661cc159688/build.log`
    Building ExpressCommands → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/0f2cf8d948a47b63d5b232ee81970f7a7fa9f3a6/build.log`
Precompiling project...
  ✓ IniFile
  ✓ Contour
  ✓ SimpleBufferStream
  ✓ Grisu
  ✓ CodecZlib
  ✓ BitFlags
  ✓ LoggingExtras
  ✓ MbedTLS
  ✓ Showoff
  ✓ Latexify
  ✓ OpenSSL
  ✓ HTTP
  ✓ GR
  ✓ Plots
  ✓ ExpressCommands
  15 dependencies successfully precompiled in 124 seconds. 203 already precompiled.
  1 dependency precompiled but a different version is currently loaded. Restart julia to access the new version

Command Line Interface

Add ~/.julia/bin to your PATH to enable command line interface. Or run ExpressCommands.comonicon_install_path() to install everything automatically.

Sometimes, you won't trigger the package build of Julia. You can install the command line interface manually via ExpressCommands.comonicon_install().

Completions

If you are using ZSH, you can enable the auto-completion by ExpressCommands.comonicon_install_path(). Or add the FPATH to your .zshrc

export FPATH="$HOME/.julia/completions:$FPATH"

if you do not have oh-my-zsh installed, you need to add

autoload -Uz compinit && compinit

to your .zshrc as well.

Documentation

  • STABLE — documentation of the most recently tagged version.
  • DEV — documentation of the in-development version.

Project status

The package is tested against, and being developed for, Julia 1.6 and above on Linux, macOS, and Windows.

Questions and contributions

Usage questions can be posted on our discussion page.

Contributions are very welcome, as are feature requests and suggestions. Please open an issue if you encounter any problems. The contributing page has a few guidelines that should be followed when opening pull requests and contributing code.

Manual outline

Library outline

Index