Merge pull request #81 from CliMA/emilyg

commits for new module Processor and Partitioner
CliMA · Sep 8, 2023 · 846c745 · 846c745
2 parents 42d9d33 + abf9fe1
commit 846c745
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diff --git a/.github/workflows/Julia-1.6.yml → .github/workflows/Julia-1.7.yml b/.github/workflows/Julia-1.6.yml → .github/workflows/Julia-1.7.yml
@@ -1,4 +1,4 @@
-name: Julia-1.6
+name: Julia-1.7
 on:
   push:
     branches:
@@ -16,7 +16,7 @@ jobs:
       - name: Set up Julia
         uses: julia-actions/setup-julia@v1
         with:
-          version: "1.6"
+          version: "1.7"
       - name: Install Dependencies
         run: julia --project -e 'ENV["PYTHON"]=""; using Pkg; Pkg.instantiate();'
       - name: Run Tests

diff --git a/.gitignore b/.gitignore
@@ -5,10 +5,18 @@ docs/src/generated/*
 docs/src/paper*
 
 *.gif
+*.txt
 *.html
 *.jpg
-*.nc
-*.nc4
 *.pdf
 *.png
 *.tar.gz
+*.nc*
+*.json
+*.csv
+
+test/demo_*.jl
+test/testcase_creation*
+test/test_*.jl
+
+testcase_creation*
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,2 @@
+{
+}
diff --git a/Project.toml b/Project.toml
@@ -4,14 +4,21 @@ authors = ["Yujie Wang"]
 version = "0.2.10"
 
 [deps]
+ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
 Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
+JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
-NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
+NetcdfIO = "6a36f34d-89cf-423a-87c4-84549e82f670"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+PolygonInbounds = "e4521ec6-8c1d-418e-9da2-b3bc4ae105d6"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
@@ -22,7 +29,7 @@ Conda = "1.5.2"
 DocStringExtensions = "0.8.5, 0.9.0"
 HTTP = "0.9.14, 1.0.5"
 JSON = "0.21.2"
-NCDatasets = "0.12.14"
+NetcdfIO = "0.2.6"
 ProgressMeter = "1.7.1"
 PyCall = "1.92.3"
-julia = "1.6"
+julia = "1.7"
diff --git a/README.md b/README.md
@@ -10,8 +10,8 @@
 [st-img]: https://github.com/CliMA/GriddingMachine.jl/workflows/JuliaStable/badge.svg?branch=main
 [st-url]: https://github.com/CliMA/GriddingMachine.jl/actions?query=branch%3A"main"++workflow%3A"JuliaStable"
 
-[min-img]: https://github.com/CliMA/GriddingMachine.jl/workflows/Julia-1.6/badge.svg?branch=main
-[min-url]: https://github.com/CliMA/GriddingMachine.jl/actions?query=branch%3A"main"++workflow%3A"Julia-1.6"
+[min-img]: https://github.com/CliMA/GriddingMachine.jl/workflows/Julia-1.7/badge.svg?branch=main
+[min-url]: https://github.com/CliMA/GriddingMachine.jl/actions?query=branch%3A"main"++workflow%3A"Julia-1.7"
 
 [cov-img]: https://codecov.io/gh/CliMA/GriddingMachine.jl/branch/main/graph/badge.svg
 [cov-url]: https://codecov.io/gh/CliMA/GriddingMachine.jl
@@ -27,7 +27,7 @@ Please cite our paper(s) when you use GriddingMachine:
 
 
 ## About
-[`GriddingMachine.jl`][gm-url] includes a collection of global canopy propertie. To best utilize `Pkg.Artifacts` and FTP storage, [`GriddingMachine.jl`][gm-url] only supports julia 1.6 and above.
+[`GriddingMachine.jl`][gm-url] includes a collection of global canopy propertie. To best utilize `Pkg.Artifacts` and FTP storage, [`GriddingMachine.jl`][gm-url] only supports julia 1.7 and above.
 
 | Documentation           | CI Status             | Compatibility           | Code Coverage           |
 |:------------------------|:----------------------|:------------------------|:------------------------|

diff --git a/docs/src/API.md b/docs/src/API.md
@@ -37,24 +37,16 @@ Collector.wood_density_collection
 ### Query gridded datasets
 ```@docs
 Collector.query_collection
-Collector.query_collection(artname::String)
-Collector.query_collection(ds::Collector.GriddedCollection, version::String)
-Collector.query_collection(ds::Collector.GriddedCollection)
 ```
 
 ### Clean up collections
 ```@docs
 Collector.clean_collections!
-Collector.clean_collections!(selection::String)
-Collector.clean_collections!(selection::Vector{String})
-Collector.clean_collections!(selection::Collector.GriddedCollection)
 ```
 
 ### Sync collections
 ```@docs
 Collector.sync_collections!
-Collector.sync_collections!(gc::Collector.GriddedCollection)
-Collector.sync_collections!()
 ```
 
 

diff --git a/log_files/missing_files.log b/log_files/missing_files.log
@@ -0,0 +1,22 @@
+TROPO_SIF_2020-01-10_ungridded.nc
+TROPO_SIF_2020-01-11_ungridded.nc
+TROPO_SIF_2020-01-12_ungridded.nc
+TROPO_SIF_2020-01-13_ungridded.nc
+TROPO_SIF_2020-01-14_ungridded.nc
+TROPO_SIF_2020-01-15_ungridded.nc
+TROPO_SIF_2020-01-16_ungridded.nc
+TROPO_SIF_2020-01-17_ungridded.nc
+TROPO_SIF_2020-01-18_ungridded.nc
+TROPO_SIF_2020-01-19_ungridded.nc
+TROPO_SIF_2020-05-08_ungridded.nc
+TROPO_SIF_2020-05-09_ungridded.nc
+oco2_LtSIF_200104_B10206r_
+oco2_LtSIF_200105_B10206r_
+oco2_LtSIF_200106_B10206r_
+oco2_LtSIF_200107_B10206r_
+oco2_LtSIF_200122_B10206r_
+oco2_LtSIF_200123_B10206r_
+oco2_LtSIF_200124_B10206r_
+oco2_LtSIF_200125_B10206r_
+oco2_LtSIF_200126_B10206r_
+oco2_LtSIF_200127_B10206r_