Merge pull request #15 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'

Project.toml

@@ -5,9 +5,7 @@ version = "0.1.0"
 
 [deps]
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
-NetCDF = "30363a11-5582-574a-97bb-aa9a979735b9"
 OMAS = "91cfaa06-6526-4804-8666-b540b3feef2f"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"

README.md

@@ -1,40 +1,21 @@
 # SOLPS2IMAS.jl
 
-Utility for loading data from existing SOLPS runs, including custom data in b2time.nc, from native SOLPS output format into IMAS
+![Format Check](https://github.com/ProjectTorreyPines/SOLPS2IMAS.jl/actions/workflows/format_check.yml/badge.svg)
 
-## OMAS structure notes
-
-(using xx for indices that do not matter)
-
-1. edge_profiles.ggd store data of quantities; edge_profiles.grid_ggd store data about the grid geometry
-2. For both ggd and grid_ggd, different slices are different slices in time. That is, what we were calling grid_number is actually time iteration number/index (say it). ggd[it].time and grid_ggd[it].time will store the time array value.
-3. grid_ggd[it]
-   1. grid_ggd[it].space[xx].identifier.index needs to be selected based on grid type (1 for linear, 2 for cylinder, 4 for single null etc.)
-   2. grid_ggd[it].grid_subset[xx] are various subsets like nodes, edges, cells etc. each with required index value at  grid_ggd[it].grid_subset[xx].index
-   3. grid_ggd[it].grid_subset[xx] properties are automatically generated for nodes, edges or cells but are required to be given for other kinds of subsets (like boundaries)
-4. ggd[it]
-   1. ggd[it].electrons.<quantity>[xx].grid_subset_index needs to be mentioned to indicate whether the quantity is at a node, edge, or cell.
-   2. ggd[it].electrons.<quantity>[xx].values store the actual value.
-   4. ggd[it].electrons.<quantity>[xx].coefficients store interpolation function coefficients
-   5. For multi-specie data, ggd[it].ions[xx].<quantity>[xx].values is used. For each species, ggd[it].ions[xx].element[:] is used to describe Z and charge state.
-
-## To-do:
-
-- [ ] Read atleast all electron properties.
-- [ ] Final function should accept one state/time file and one geometry file to return a OMAS.dd object.
-- [ ] Add support for boundary properties.
-- [ ] Add support for multi-species data.
-- [ ] Test using new [h5i2imas functionality](https://github.com/ProjectTorreyPines/OMAS.jl/commit/904562b4040c857260d832747d1ba46a2bf614f6) added to OMAS.
-- [ ] Expand testing to some self-consistency test of read data.
+Utility for loading data from existing SOLPS runs, including custom data in b2time.nc,
+from native SOLPS output format into IMAS
 
 ## Running tests:
 
 Following code ensures it uses the enviroment described in ./Project.toml:
 
 ```
-(base) gupta@F-CJXNMY7L7 SOLPS2IMAS.jl % julia --project=./ ./test/runtests.jl 
-it's the omas function
-another fun function!!!!!11!!!!!
+(base) gupta@F-CJXNMY7L7 SOLPS2IMAS.jl % julia --proje
+ct=./ test/runtests.jl 
+solps2imas() time:   3.309287 seconds (9.92 M allocations: 666.357 MiB, 5.68% gc time, 71.71% compilation time)
+Test Summary: | Pass  Total  Time
+omasstuff     |    4      4  6.9s
+hello there
 Test Summary: | Pass  Total  Time
-omasstuff     |    3      3  2.5s
+utilities     |    3      3  0.0s
 ```

samples/.gitignore

@@ -0,0 +1,4 @@
+/b2fgmtry
+/b2fstate
+/b2time.nc
+/b2mn.dat

samples/README.md

@@ -0,0 +1,4 @@
+# samples
+
+* The sample files with _red suffix have been reduced to save space. Some fields have been deleted and some arrays have been decimated. These files are suitable for limited testing only.
+* The sample files shown here with .dvc extension are stored in nfs mount through iris or omega. Run `dvc pull` to get the data files downloaded. Note that this will only work from inside the fusion network. See [TestSamples](https://github.com/ProjectTorreyPines/TestSamples#readme) for more details.

samples/b2fgmtry.dvc

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