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@kongdd
kongdd committed Feb 10, 2025
1 parent 280839a commit 9f36943
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2 changes: 0 additions & 2 deletions Project.toml
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Expand Up @@ -6,11 +6,9 @@ version = "0.1.0"
[deps]
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

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14 changes: 12 additions & 2 deletions notebooks/Duffing oscillator with EnKF.ipynb
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Expand Up @@ -2,17 +2,27 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"using EnKF\n",
"using Distributions\n",
"using LinearAlgebra\n",
"using ProgressMeter\n",
"using OrdinaryDiffEq"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"using Pkg;\n",
"Pkg.activate(\"..\")\n",
"using EnKF"
]
},
{
"cell_type": "code",
"execution_count": null,
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141 changes: 128 additions & 13 deletions notebooks/Linear system with EnKF.ipynb
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@@ -1,15 +1,137 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"\u001b[32m\u001b[1m Activating\u001b[22m\u001b[39m project at `d:\\GitHub\\jl-pkgs\\EnKF.jl`\n",
"\u001b[91m\u001b[1mERROR: \u001b[22m\u001b[39mLoadError: ArgumentError: Package Distributions [31c24e10-a181-5473-b8eb-7969acd0382f] is required but does not seem to be installed:\n",
" - Run `Pkg.instantiate()` to install all recorded dependencies.\n",
"\n",
"Stacktrace:\n",
" [1] \u001b[0m\u001b[1m_require\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mpkg\u001b[39m::\u001b[0mBase.PkgId, \u001b[90menv\u001b[39m::\u001b[0mString\u001b[0m\u001b[1m)\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90mBase\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4mloading.jl:2515\u001b[24m\u001b[39m\n",
" [2] \u001b[0m\u001b[1m__require_prelocked\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90muuidkey\u001b[39m::\u001b[0mBase.PkgId, \u001b[90menv\u001b[39m::\u001b[0mString\u001b[0m\u001b[1m)\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90mBase\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4mloading.jl:2388\u001b[24m\u001b[39m\n",
" [3] \u001b[0m\u001b[1m#invoke_in_world#3\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4messentials.jl:1089\u001b[24m\u001b[39m\u001b[90m [inlined]\u001b[39m\n",
" [4] \u001b[0m\u001b[1minvoke_in_world\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4messentials.jl:1086\u001b[24m\u001b[39m\u001b[90m [inlined]\u001b[39m\n",
" [5] \u001b[0m\u001b[1m_require_prelocked\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90muuidkey\u001b[39m::\u001b[0mBase.PkgId, \u001b[90menv\u001b[39m::\u001b[0mString\u001b[0m\u001b[1m)\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90mBase\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4mloading.jl:2375\u001b[24m\u001b[39m\n",
" [6] \u001b[0m\u001b[1mmacro expansion\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4mloading.jl:2314\u001b[24m\u001b[39m\u001b[90m [inlined]\u001b[39m\n",
" [7] \u001b[0m\u001b[1mmacro expansion\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4mlock.jl:273\u001b[24m\u001b[39m\u001b[90m [inlined]\u001b[39m\n",
" [8] \u001b[0m\u001b[1m__require\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90minto\u001b[39m::\u001b[0mModule, \u001b[90mmod\u001b[39m::\u001b[0mSymbol\u001b[0m\u001b[1m)\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90mBase\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4mloading.jl:2271\u001b[24m\u001b[39m\n",
" [9] \u001b[0m\u001b[1m#invoke_in_world#3\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4messentials.jl:1089\u001b[24m\u001b[39m\u001b[90m [inlined]\u001b[39m\n",
" [10] \u001b[0m\u001b[1minvoke_in_world\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4messentials.jl:1086\u001b[24m\u001b[39m\u001b[90m [inlined]\u001b[39m\n",
" [11] \u001b[0m\u001b[1mrequire\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90minto\u001b[39m::\u001b[0mModule, \u001b[90mmod\u001b[39m::\u001b[0mSymbol\u001b[0m\u001b[1m)\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90mBase\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4mloading.jl:2260\u001b[24m\u001b[39m\n",
" [12] \u001b[0m\u001b[1minclude\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4mBase.jl:557\u001b[24m\u001b[39m\u001b[90m [inlined]\u001b[39m\n",
" [13] \u001b[0m\u001b[1minclude_package_for_output\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mpkg\u001b[39m::\u001b[0mBase.PkgId, \u001b[90minput\u001b[39m::\u001b[0mString, \u001b[90mdepot_path\u001b[39m::\u001b[0mVector\u001b[90m{String}\u001b[39m, \u001b[90mdl_load_path\u001b[39m::\u001b[0mVector\u001b[90m{String}\u001b[39m, \u001b[90mload_path\u001b[39m::\u001b[0mVector\u001b[90m{String}\u001b[39m, \u001b[90mconcrete_deps\u001b[39m::\u001b[0mVector\u001b[90m{Pair{Base.PkgId, UInt128}}\u001b[39m, \u001b[90msource\u001b[39m::\u001b[0mString\u001b[0m\u001b[1m)\u001b[22m\n",
"\u001b[90m @\u001b[39m \u001b[90mBase\u001b[39m \u001b[90m.\\\u001b[39m\u001b[90m\u001b[4mloading.jl:2881\u001b[24m\u001b[39m\n",
" [14] top-level scope\n",
"\u001b[90m @\u001b[39m \u001b[90m\u001b[4mstdin:6\u001b[24m\u001b[39m\n",
"in expression starting at d:\\GitHub\\jl-pkgs\\EnKF.jl\\src\\EnKF.jl:1\n",
"in expression starting at stdin:6\n"
]
},
{
"ename": "ErrorException",
"evalue": "Failed to precompile EnKF [685896a8-a41b-11e9-3419-3315e75b5d74] to \"C:\\\\Users\\\\kongdd\\\\.julia\\\\compiled\\\\v1.11\\\\EnKF\\\\jl_FB8.tmp\".",
"output_type": "error",
"traceback": [
"Failed to precompile EnKF [685896a8-a41b-11e9-3419-3315e75b5d74] to \"C:\\\\Users\\\\kongdd\\\\.julia\\\\compiled\\\\v1.11\\\\EnKF\\\\jl_FB8.tmp\".\n",
"\n",
"Stacktrace:\n",
" [1] error(s::String)\n",
" @ Base .\\error.jl:35\n",
" [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)\n",
" @ Base .\\loading.jl:3174\n",
" [3] (::Base.var\"#1110#1111\"{Base.PkgId})()\n",
" @ Base .\\loading.jl:2579\n",
" [4] mkpidlock(f::Base.var\"#1110#1111\"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})\n",
" @ FileWatching.Pidfile C:\\Users\\kongdd\\scoop\\apps\\julia\\current\\share\\julia\\stdlib\\v1.11\\FileWatching\\src\\pidfile.jl:95\n",
" [5] #mkpidlock#6\n",
" @ C:\\Users\\kongdd\\scoop\\apps\\julia\\current\\share\\julia\\stdlib\\v1.11\\FileWatching\\src\\pidfile.jl:90 [inlined]\n",
" [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})\n",
" @ FileWatching.Pidfile C:\\Users\\kongdd\\scoop\\apps\\julia\\current\\share\\julia\\stdlib\\v1.11\\FileWatching\\src\\pidfile.jl:116\n",
" [7] #invokelatest#2\n",
" @ .\\essentials.jl:1057 [inlined]\n",
" [8] invokelatest\n",
" @ .\\essentials.jl:1052 [inlined]\n",
" [9] maybe_cachefile_lock(f::Base.var\"#1110#1111\"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)\n",
" @ Base .\\loading.jl:3698\n",
" [10] maybe_cachefile_lock\n",
" @ .\\loading.jl:3695 [inlined]\n",
" [11] _require(pkg::Base.PkgId, env::String)\n",
" @ Base .\\loading.jl:2565\n",
" [12] __require_prelocked(uuidkey::Base.PkgId, env::String)\n",
" @ Base .\\loading.jl:2388\n",
" [13] #invoke_in_world#3\n",
" @ .\\essentials.jl:1089 [inlined]\n",
" [14] invoke_in_world\n",
" @ .\\essentials.jl:1086 [inlined]\n",
" [15] _require_prelocked(uuidkey::Base.PkgId, env::String)\n",
" @ Base .\\loading.jl:2375\n",
" [16] macro expansion\n",
" @ .\\loading.jl:2314 [inlined]\n",
" [17] macro expansion\n",
" @ .\\lock.jl:273 [inlined]\n",
" [18] __require(into::Module, mod::Symbol)\n",
" @ Base .\\loading.jl:2271\n",
" [19] #invoke_in_world#3\n",
" @ .\\essentials.jl:1089 [inlined]\n",
" [20] invoke_in_world\n",
" @ .\\essentials.jl:1086 [inlined]\n",
" [21] require(into::Module, mod::Symbol)\n",
" @ Base .\\loading.jl:2260\n",
" [22] eval\n",
" @ .\\boot.jl:430 [inlined]\n",
" [23] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)\n",
" @ Base .\\loading.jl:2734\n",
" [24] #invokelatest#2\n",
" @ .\\essentials.jl:1055 [inlined]\n",
" [25] invokelatest\n",
" @ .\\essentials.jl:1052 [inlined]\n",
" [26] (::VSCodeServer.var\"#217#218\"{VSCodeServer.NotebookRunCellArguments, String})()\n",
" @ VSCodeServer c:\\Users\\kongdd\\.vscode\\extensions\\julialang.language-julia-1.138.1\\scripts\\packages\\VSCodeServer\\src\\serve_notebook.jl:24\n",
" [27] withpath(f::VSCodeServer.var\"#217#218\"{VSCodeServer.NotebookRunCellArguments, String}, path::String)\n",
" @ VSCodeServer c:\\Users\\kongdd\\.vscode\\extensions\\julialang.language-julia-1.138.1\\scripts\\packages\\VSCodeServer\\src\\repl.jl:276\n",
" [28] notebook_runcell_request(conn::VSCodeServer.JSONRPC.JSONRPCEndpoint{Base.PipeEndpoint, Base.PipeEndpoint}, params::VSCodeServer.NotebookRunCellArguments)\n",
" @ VSCodeServer c:\\Users\\kongdd\\.vscode\\extensions\\julialang.language-julia-1.138.1\\scripts\\packages\\VSCodeServer\\src\\serve_notebook.jl:13\n",
" [29] dispatch_msg(x::VSCodeServer.JSONRPC.JSONRPCEndpoint{Base.PipeEndpoint, Base.PipeEndpoint}, dispatcher::VSCodeServer.JSONRPC.MsgDispatcher, msg::Dict{String, Any})\n",
" @ VSCodeServer.JSONRPC c:\\Users\\kongdd\\.vscode\\extensions\\julialang.language-julia-1.138.1\\scripts\\packages\\JSONRPC\\src\\typed.jl:67\n",
" [30] serve_notebook(pipename::String, debugger_pipename::String, outputchannel_logger::Base.CoreLogging.SimpleLogger; error_handler::var\"#5#10\"{String})\n",
" @ VSCodeServer c:\\Users\\kongdd\\.vscode\\extensions\\julialang.language-julia-1.138.1\\scripts\\packages\\VSCodeServer\\src\\serve_notebook.jl:147\n",
" [31] top-level scope\n",
" @ c:\\Users\\kongdd\\.vscode\\extensions\\julialang.language-julia-1.138.1\\scripts\\notebook\\notebook.jl:35"
]
}
],
"source": [
"using Pkg;\n",
"Pkg.activate(\"..\")\n",
"using EnKF"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"using Revise\n",
"using EnKF\n",
"using Distributions\n",
"using DocStringExtensions\n",
"using LinearAlgebra\n",
"using Plots\n",
"using ProgressMeter\n",
Expand Down Expand Up @@ -14193,13 +14315,6 @@
"source": [
"collect(T)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -14208,15 +14323,15 @@
"lastKernelId": null
},
"kernelspec": {
"display_name": "Julia 1.1.1",
"display_name": "Julia 1.11.3",
"language": "julia",
"name": "julia-1.1"
"name": "julia-1.11"
},
"language_info": {
"file_extension": ".jl",
"mimetype": "application/julia",
"name": "julia",
"version": "1.1.1"
"version": "1.11.3"
}
},
"nbformat": 4,
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7 changes: 4 additions & 3 deletions notebooks/Lorenz attractor with EnKF RTPS.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 513,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -17,8 +17,9 @@
}
],
"source": [
"using Pkg\n",
"Pkg.activate(\"/media/mat/HDD/EnKF/\")"
"using Pkg;\n",
"Pkg.activate(\"..\")\n",
"using EnKF"
]
},
{
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11 changes: 6 additions & 5 deletions notebooks/Lorenz attractor with EnKF.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -17,8 +17,9 @@
}
],
"source": [
"using Pkg\n",
"Pkg.activate(\"/media/mat/HDD/EnKF/\")"
"using Pkg;\n",
"Pkg.activate(\"..\")\n",
"using EnKF"
]
},
{
Expand Down Expand Up @@ -537,7 +538,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"\r\n",
"\u001b[32mProgress: 1%|▌ | ETA: 0:03:37\u001b[39m"
]
},
Expand Down Expand Up @@ -612,7 +613,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"\r\n",
"\u001b[32mProgress: 100%|█████████████████████████████████████████| Time: 0:00:02\u001b[39m\n"
]
},
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7 changes: 4 additions & 3 deletions notebooks/Lorenz95 with EnKF.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -17,8 +17,9 @@
}
],
"source": [
"using Pkg\n",
"Pkg.activate(\"/media/mat/HDD/EnKF/\")"
"using Pkg;\n",
"Pkg.activate(\"..\")\n",
"using EnKF"
]
},
{
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7 changes: 4 additions & 3 deletions notebooks/Propagator using DifferentialEquations.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -17,8 +17,9 @@
}
],
"source": [
"using Pkg\n",
"Pkg.activate(\"/media/mat/HDD/EnKF/\")"
"using Pkg;\n",
"Pkg.activate(\"..\")\n",
"using EnKF"
]
},
{
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7 changes: 4 additions & 3 deletions notebooks/Vortex Blob Clustering-AOA20 (Pulsed)-EnKF Modular.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -17,8 +17,9 @@
}
],
"source": [
"using Pkg\n",
"Pkg.activate(\"/media/mat/HDD/EnKF/\")"
"using Pkg;\n",
"Pkg.activate(\"..\")\n",
"using EnKF"
]
},
{
Expand Down
10 changes: 5 additions & 5 deletions notebooks/Vortex Blob Clustering-AOA20 (Pulsed)-EnKF clean.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -14,13 +14,14 @@
}
],
"source": [
"using Pkg\n",
"Pkg.activate(\"/media/mat/HDD/EnKF/\")"
"using Pkg;\n",
"Pkg.activate(\"..\");\n",
"using EnKF"
]
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -42,7 +43,6 @@
"using Revise\n",
"using EnKF\n",
"using Distributions\n",
"using DocStringExtensions\n",
"using RecursiveArrayTools"
]
},
Expand Down
7 changes: 4 additions & 3 deletions notebooks/Vortex Blob Clustering-AOA20 (Pulsed)-EnKF short.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -17,8 +17,9 @@
}
],
"source": [
"using Pkg\n",
"Pkg.activate(\"/media/mat/HDD/EnKF/\")"
"using Pkg;\n",
"Pkg.activate(\"..\")\n",
"using EnKF"
]
},
{
Expand Down
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