Merge pull request #16 from ProjectTorreyPines/dev

Releasing v0.1.0

.JuliaFormatter.toml

@@ -0,0 +1,27 @@
+align_assignment = true
+align_conditional = true
+align_matrix = true
+align_pair_arrow = true
+align_struct_field = true
+always_for_in = true
+always_use_return = true
+annotate_untyped_fields_with_any = false
+conditional_to_if = true
+for_in_replacement = "∈"
+format_docstrings = true
+import_to_using = true
+indent = 4
+indent_submodule = true
+join_lines_based_on_source = true
+long_to_short_function_def = true
+margin = 88
+normalize_line_endings = "unix"
+pipe_to_function_call = true
+remove_extra_newlines = true
+separate_kwargs_with_semicolon = true
+surround_whereop_typeparameters = true
+trailing_comma = true
+whitespace_in_kwargs = false
+whitespace_ops_in_indices = false
+whitespace_typedefs = true
+yas_style_nesting = true

.dvc/.gitignore

@@ -0,0 +1,3 @@
+/config.local
+/tmp
+/cache

.dvcignore

@@ -0,0 +1,3 @@
+# Add patterns of files dvc should ignore, which could improve
+# the performance. Learn more at
+# https://dvc.org/doc/user-guide/dvcignore

.github/workflows/format_check.yml

@@ -0,0 +1,36 @@
+name: Format Check
+
+on:
+  push:
+    branches: ["master", "dev", "format"]
+  pull_request:
+    branches: ["master", "dev"]
+jobs:
+  check:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1.9.3]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v1
+      - name: Install JuliaFormatter and format
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

.gitignore

@@ -0,0 +1,5 @@
+# File generated by Pkg, the package manager, based on a corresponding Project.toml
+# It records a fixed state of all packages used by the project. As such, it should not be
+# committed for packages, but should be committed for applications that require a static
+# environment.
+Manifest.toml

Project.toml

@@ -0,0 +1,14 @@
+name = "GGDUtils"
+uuid = "b7b5e640-9b39-4803-84eb-376048795def"
+authors = ["Anchal Gupta <[email protected]>"]
+version = "0.1.0"
+
+[deps]
+ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
+NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
+OMAS = "91cfaa06-6526-4804-8666-b540b3feef2f"
+RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
+SOLPS2IMAS = "09becab6-0636-4c23-a92a-2b3723265c31"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

README.md

@@ -1,2 +1,5 @@
 # GGDUtils
+
+![Format Check](https://github.com/ProjectTorreyPines/GGDUtils.jl/actions/workflows/format_check.yml/badge.svg)
+
 Package holding utilities for Generalized Grid Description (GGD) objects in IMAS datastructure. Primary goals are interpolation and core profile extrapolation.

examples/Project.toml

@@ -0,0 +1,11 @@
+name = "GGDUtils_examples"
+authors = ["Anchal Gupta <[email protected]>"]
+version = "0.1.0"
+
+[deps]
+GGDUtils = "b7b5e640-9b39-4803-84eb-376048795def"
+GR = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
+LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
+OMAS = "91cfaa06-6526-4804-8666-b540b3feef2f"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+SOLPS2IMAS = "09becab6-0636-4c23-a92a-2b3723265c31"

examples/plotting.ipynb

@@ -0,0 +1,171 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Plotting examples using GGDUtils\n",
+    " \n",
+    " For running this notebook, you need to install package IJulia in your home environment (that is messy, but that is the only way I know right now). So in your terminal:\n",
+    " ```\n",
+    " % julia\n",
+    " julia > ]\n",
+    " (@v1.9 pkg) pkg> add IJulia\n",
+    " ```\n",
+    "\n",
+    " After this, Julia kernel would appear in your jupyter notebooks as an option. This also works for julia notebooks directly opened on VSCode. Select the Julia kernel to run this notebook."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "using Pkg\n",
+    "Pkg.activate(\"./\")\n",
+    "Pkg.add(url=\"[email protected]:ProjectTorreyPines/OMAS.jl.git\")\n",
+    "Pkg.add(url=\"[email protected]:ProjectTorreyPines/SOLPS2IMAS.jl.git\", rev=\"dev\")\n",
+    "Pkg.add(path=\"../\")\n",
+    "Pkg.add(PackageSpec(name=\"GR\", version=\"0.72.9\"))\n",
+    "Pkg.pin(\"GR\")\n",
+    "Pkg.add(\"Plots\")\n",
+    "Pkg.add(\"LaTeXStrings\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "using SOLPS2IMAS\n",
+    "using GGDUtils\n",
+    "using Plots\n",
+    "using LaTeXStrings"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "b2gmtry = \"../samples/b2fgmtry\"\n",
+    "b2output = \"../samples/b2time_red.nc\"\n",
+    "gsdesc = \"../samples/gridspacedesc.yml\"\n",
+    "b2mn = \"../samples/b2mn.dat\"\n",
+    "dd = solps2imas(b2gmtry, b2output, gsdesc, b2mn)\n",
+    "grid_ggd = dd.edge_profiles.grid_ggd[1]\n",
+    "space = grid_ggd.space[1]\n",
+    "dd.edge_profiles.ggd[1].electrons.density[5].grid_subset_index = 5  # This is a bug in SOLPS2IMAS to be fixed"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Plotting grid and subsets"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Choose backend\n",
+    "gr()           # Fast and can save pdf\n",
+    "# plotlyjs()   # Use for interactive plot, can only save png\n",
+    "\n",
+    "plot(space) # Simply plot the grid described in space, all common arguments to plot can be given here\n",
+    "\n",
+    "# You can overlay any subset by giving a second argument\n",
+    "# Labels \n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 6), markercolor=:chocolate1)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 7), linecolor=:red, linewidth=2)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 8), linecolor=:darkred, linewidth=2)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 9), linecolor=:limegreen, linewidth=2)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 10), linecolor=:darkgreen, linewidth=2)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 11), linecolor=:cyan, linewidth=2)\n",
+    "# plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 12), linecolor=:teal, linewidth=1)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 13), linecolor=:royalblue1, linewidth=2)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 14), linecolor=:navyblue, linewidth=2)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 15), linecolor=:fuchsia, linewidth=2, linestyle=:dash)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 16), linecolor=:purple4, linewidth=2, linestyle=:dash)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 101), markershape=:rect, markercolor=:royalblue1)\n",
+    "# plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 102), markershape=:rect, markercolor=:maroon)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 103), markershape=:diamond, markercolor=:fuchsia)\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 104), markershape=:diamond, markercolor=:purple4)\n",
+    "\n",
+    "# Legend is supressed unless asked for specifically\n",
+    "plot!(legend=true)\n",
+    "# Default labels are subset.identifier.name but can be changed by providing a label argument"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Plotting 2D quantities as heatmaps"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Choose backend\n",
+    "gr()           # Fast and can save pdf\n",
+    "# plotlyjs()   # Use for interactive plot, can only save png\n",
+    "\n",
+    "plot(dd.edge_profiles.grid_ggd, dd.edge_profiles.ggd[1].electrons.density[5], colorbar_title=\"Electrons density / \" * L\"m^{-3}\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### You can overlap any grid on top of a quantity"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Choose backend\n",
+    "gr()           # Fast and can save pdf\n",
+    "# plotlyjs()   # Use for interactive plot, can only save png\n",
+    "\n",
+    "plot(dd.edge_profiles.grid_ggd, dd.edge_profiles.ggd[1].electrons.density[5]) # Note default label in colorbar\n",
+    "plot!(space, SOLPS2IMAS.get_grid_subset_with_index(grid_ggd, 16), linecolor=:red, linewidth=2, linestyle=:solid, label=\"Separatix\", legend=true)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Julia 1.9.2",
+   "language": "julia",
+   "name": "julia-1.9"
+  },
+  "language_info": {
+   "file_extension": ".jl",
+   "mimetype": "application/julia",
+   "name": "julia",
+   "version": "1.9.2"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

samples/.gitignore

@@ -0,0 +1,4 @@
+/edge_profiles.h5
+/b2time.nc
+/b2mn.dat
+/b2fgmtry

samples/b2fgmtry.dvc

@@ -0,0 +1,12 @@
+md5: bcf05d7d7b6d91ef1025c0dc018c4bbf
+frozen: true
+deps:
+- path: ITER_Lore_2296_00000/baserun/b2fgmtry
+  repo:
+    url: [email protected]:ProjectTorreyPines/SOLPSTestSamples.git
+    rev_lock: df499f1275428ec06175c48dc4af6ecbd5ec6117
+outs:
+- md5: 6589953daeef49b21744d159af970cbb
+  size: 2908856
+  hash: md5
+  path: b2fgmtry

samples/b2mn.dat.dvc

@@ -0,0 +1,12 @@
+md5: c0c920771883f03bc0abe98425b38d5e
+frozen: true
+deps:
+- path: ITER_Lore_2296_00000/run_time_dep_EIRENE_jdl_to_ss_cont_sine2_2d_output/b2mn.dat
+  repo:
+    url: [email protected]:ProjectTorreyPines/SOLPSTestSamples.git
+    rev_lock: df499f1275428ec06175c48dc4af6ecbd5ec6117
+outs:
+- md5: 1af9d167996ea1a420f49e0d89c98e6d
+  size: 13925
+  hash: md5
+  path: b2mn.dat

samples/b2time.nc.dvc

@@ -0,0 +1,13 @@
+md5: b94876ee58c5d62734d4ee32c28bb0da
+frozen: true
+deps:
+- path: 
+    ITER_Lore_2296_00000/run_time_dep_EIRENE_jdl_to_ss_cont_sine2_2d_output/b2time.nc
+  repo:
+    url: [email protected]:ProjectTorreyPines/SOLPSTestSamples.git
+    rev_lock: df499f1275428ec06175c48dc4af6ecbd5ec6117
+outs:
+- md5: 778b3bb62b82f493c785373d872f6a1f
+  size: 13630424
+  hash: md5
+  path: b2time.nc

samples/edge_profiles.h5.dvc

@@ -0,0 +1,12 @@
+md5: 583339f63b0b4d2aa3f7f7a659a5b07c
+frozen: true
+deps:
+- path: ITER_Lore_2296_00000/IMAS/edge_profiles.h5
+  repo:
+    url: [email protected]:ProjectTorreyPines/SOLPSTestSamples.git
+    rev_lock: df499f1275428ec06175c48dc4af6ecbd5ec6117
+outs:
+- md5: c3d60ce69e9d3a9b9ec621e9276858e0
+  size: 168176600
+  hash: md5
+  path: edge_profiles.h5