Swtich from HDF5 to NetCDF

.github/workflows/nightly.yaml

@@ -28,7 +28,7 @@ jobs:
  using Pkg
  Pkg.activate(".")
  Pkg.resolve()
- Pkg.activate("examples/fdp")
+ Pkg.activate("examples/SEIRS")
  Pkg.update()
  Pkg.resolve()
  shell: julia --color=yes {0} 
@@ -65,8 +65,8 @@ jobs:
  fair registry install
  fair registry start
  fair init --ci
- fair pull --debug examples/fdp/SEIRSconfig.yaml
- fair run --debug --dirty examples/fdp/SEIRSconfig.yaml
+ fair pull --debug examples/SEIRS/full_config.yaml
+ fair run --debug --dirty examples/SEIRS/full_config.yaml
  deactivate
  shell: bash
  env:

.github/workflows/testing.yaml

@@ -16,7 +16,6 @@ on:
 jobs:
  pipeline-tests:
  runs-on: ${{ matrix.os }}
- continue-on-error: ${{ matrix.experimental }}
  strategy:
  matrix:
  julia-version:
@@ -44,7 +43,7 @@ jobs:
  - name: Fix manifest for active Julia version
  run: |
  using Pkg
- Pkg.activate("examples/fdp")
+ Pkg.activate("examples/SEIRS")
  Pkg.resolve()
  shell: julia --color=yes {0} 
  - name: Set up python
@@ -118,8 +117,9 @@ jobs:
  fair registry install
  fair registry start
  fair init --ci
- fair pull --debug examples/fdp/SEIRSconfig.yaml
- fair run --debug --dirty examples/fdp/SEIRSconfig.yaml
+ fair pull --debug examples/SEIRS/full_config.yaml
+ fair run --debug --dirty examples/SEIRS/full_config.yaml
+ exit $?
  deactivate
  shell: bash
  env:

Project.toml

@@ -8,8 +8,6 @@ AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
-FTPClient = "01fcc997-4f28-56b8-8a06-30002c134abb"
-HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 NetCDF = "30363a11-5582-574a-97bb-aa9a979735b9"
@@ -26,8 +24,6 @@ YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 AxisArrays = "0.4"
 CSV = "0.8, 0.9, 0.10"
 DataFrames = "1"
-FTPClient = "1"
-HDF5 = "0.16, 0.17"
 HTTP = "0.9, 1"
 JSON = "0.21"
 NetCDF = "0.11"

docs/src/SEIRS.md

@@ -17,11 +17,11 @@ show(run(`fair init --ci`))
 
 ```@example
 print(pwd())
-read(`fair pull /home/runner/work/DataPipeline.jl/DataPipeline.jl/examples/fdp/SEIRSconfig.yaml`, String)
+read(`fair pull /home/runner/work/DataPipeline.jl/DataPipeline.jl/examples/SEIRS/full_config.yaml`, String)
 ```
 
 dsf
 
 ```@example
-show(run(`fair run /home/runner/work/DataPipeline.jl/DataPipeline.jl/examples/fdp/SEIRSconfig.yaml`))
+show(run(`fair run /home/runner/work/DataPipeline.jl/DataPipeline.jl/examples/SEIRS/full_config.yaml`))
 ```

examples/fdp/Manifest.toml → examples/SEIRS/Manifest.toml

@@ -93,9 +93,9 @@ version = "0.12.10"
 
 [[deps.Compat]]
 deps = ["Dates", "LinearAlgebra", "UUIDs"]
-git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957"
+git-tree-sha1 = "4e88377ae7ebeaf29a047aa1ee40826e0b708a5d"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.6.1"
+version = "4.7.0"
 
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -141,7 +141,7 @@ uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 version = "1.5.0"
 
 [[deps.DataPipeline]]
-deps = ["AxisArrays", "CSV", "DataFrames", "Dates", "FTPClient", "HDF5", "HTTP", "JSON", "NetCDF", "Plots", "PrettyTables", "SHA", "SQLite", "TOML", "URIs", "UnicodePlots", "YAML"]
+deps = ["AxisArrays", "CSV", "DataFrames", "Dates", "HTTP", "JSON", "NetCDF", "Plots", "PrettyTables", "SHA", "SQLite", "TOML", "URIs", "UnicodePlots", "YAML"]
 path = "../.."
 uuid = "9ced6f0a-eb77-43a8-bbd1-bbf3031b0d12"
 version = "0.53.2"
@@ -182,11 +182,17 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 version = "1.6.0"
 
+[[deps.ExceptionUnwrapping]]
+deps = ["Test"]
+git-tree-sha1 = "e90caa41f5a86296e014e148ee061bd6c3edec96"
+uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4"
+version = "0.1.9"
+
 [[deps.Expat_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d"
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "4558ab818dcceaab612d1bb8c19cee87eda2b83c"
 uuid = "2e619515-83b5-522b-bb60-26c02a35a201"
-version = "2.4.8+0"
+version = "2.5.0+0"
 
 [[deps.FFMPEG]]
 deps = ["FFMPEG_jll"]
@@ -200,12 +206,6 @@ git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd"
 uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
 version = "4.4.2+2"
 
-[[deps.FTPClient]]
-deps = ["LibCURL", "URIParser"]
-git-tree-sha1 = "fcdcac297167852b23bae6d7bb3bf82a726ff70c"
-uuid = "01fcc997-4f28-56b8-8a06-30002c134abb"
-version = "1.2.1"
-
 [[deps.FilePathsBase]]
 deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"]
 git-tree-sha1 = "e27c4ebe80e8699540f2d6c805cc12203b614f12"
@@ -290,23 +290,17 @@ git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
 uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe"
 version = "1.0.2"
 
-[[deps.HDF5]]
-deps = ["Compat", "HDF5_jll", "Libdl", "Mmap", "Random", "Requires", "UUIDs"]
-git-tree-sha1 = "c73fdc3d9da7700691848b78c61841274076932a"
-uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
-version = "0.16.15"
-
 [[deps.HDF5_jll]]
 deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"]
 git-tree-sha1 = "4cc2bb72df6ff40b055295fdef6d92955f9dede8"
 uuid = "0234f1f7-429e-5d53-9886-15a909be8d59"
 version = "1.12.2+2"
 
 [[deps.HTTP]]
-deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
-git-tree-sha1 = "5e77dbf117412d4f164a464d610ee6050cc75272"
+deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
+git-tree-sha1 = "2613d054b0e18a3dea99ca1594e9a3960e025da4"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "1.9.6"
+version = "1.9.7"
 
 [[deps.HarfBuzz_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"]
@@ -629,9 +623,9 @@ version = "10.40.0+0"
 
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
-git-tree-sha1 = "5a6ab2f64388fd1175effdf73fe5933ef1e0bac0"
+git-tree-sha1 = "4b2e829ee66d4218e0cef22c0a64ee37cf258c29"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.7.0"
+version = "2.7.1"
 
 [[deps.Pipe]]
 git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d"
@@ -806,9 +800,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[deps.SpecialFunctions]]
 deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
-git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880"
+git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "2.2.0"
+version = "2.3.0"
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"]
@@ -886,12 +880,6 @@ git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.9.13"
 
-[[deps.URIParser]]
-deps = ["Unicode"]
-git-tree-sha1 = "53a9f49546b8d2dd2e688d216421d050c9a31d0d"
-uuid = "30578b45-9adc-5946-b283-645ec420af67"
-version = "0.4.1"
-
 [[deps.URIs]]
 git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a"
 uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
@@ -912,9 +900,9 @@ version = "0.4.1"
 
 [[deps.UnicodePlots]]
 deps = ["ColorSchemes", "ColorTypes", "Contour", "Crayons", "Dates", "LinearAlgebra", "MarchingCubes", "NaNMath", "PrecompileTools", "Printf", "Requires", "SparseArrays", "StaticArrays", "StatsBase"]
-git-tree-sha1 = "66b7b2f49e6be1ffaf6c36ea88ac38616122e5f1"
+git-tree-sha1 = "b96de03092fe4b18ac7e4786bee55578d4b75ae8"
 uuid = "b8865327-cd53-5732-bb35-84acbb429228"
-version = "3.5.4"
+version = "3.6.0"
 
 [[deps.Unitful]]
 deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"]

examples/fdp/SEIRSconfig.yaml → examples/SEIRS/full_config.yaml

@@ -2,8 +2,8 @@ run_metadata:
  default_input_namespace: testing
  description: SEIRS Model julia
  script: |
- julia --project=examples/fdp -e "using Pkg; Pkg.instantiate()"
- julia --project=examples/fdp examples/fdp/seirs_sim.jl
+ julia --project=examples/SEIRS -e "using Pkg; Pkg.instantiate()"
+ julia --project=examples/SEIRS examples/SEIRS/seirs_sim.jl
 
 register:
 - namespace: PSU

examples/SEIRS/register_config.yaml

@@ -0,0 +1,20 @@
+run_metadata:
+ default_input_namespace: testing
+ description: SEIRS Model julia registration
+
+register:
+- namespace: PSU
+ full_name: Pennsylvania State University
+ website: https://ror.org/04p491231
+
+- external_object: SEIRS_model/parameters
+ namespace_name: PSU
+ root: https://raw.githubusercontent.com/
+ path: FAIRDataPipeline/rSimpleModel/main/inst/extdata/static_params_SEIRS.csv
+ title: Static parameters of the model
+ description: Static parameters of the model
+ identifier: https://doi.org/10.1038/s41592-020-0856-2
+ file_type: csv
+ release_date: 2020-06-01T12:00
+ version: "1.0.0"
+ primary: False